The connectionist framework for gene regulation

I show that gene regulation networks are qualitatively consistent and therefore sufficiently similar to linearly seperable connectionist networks to warrant that the connectionist framework be applied to gene regulation. On this view, natural selection designs gene regulation networks to overcome the difficulty of development. I offer some general lessons about their evolvability that can be learned by examining the generic features of connectionist networks.

Individual variability of behavioural responses by Wandering Albatrosses (Diomedea exulans) to human disturbance

Sub-Antarctic Marion Island has had a permanent research station for 50 years and the islands Wandering Albatrosses have been intensively studied for 20 years. The reactions of breeding birds to approaches by a human on foot were recorded. Three response variables were calculated: intensity of vocal reaction (IVR), intensity of non-vocal reaction (INR) and overall response index (ORI). At 5 m from the nest, twice as many birds stood and/or vocalised as at 15 m. Nearest neighbour distance, age and gender did not explain individual variability of responses. Study colony birds had higher IVR scores than non-study colony birds; birds at colonies closest to the station had the highest ORI scores. A better breeding record was associated with lower IVR and ORI scores, but a causative relationship remains to be demonstrated. A minimum viewing distance of 25 m is recommended for breeding Wandering Albatrosses.

---

Advertising and the Predation Loop: A Biosemiotic Model

The basic premise of biosemiotics as a discipline is that there are elementary processes linking signifying strategies in all forms of animate life. Correspondingly, the discoveries of biosemiotics should, in principle, be capable of revealing new insights about human signification. In the present article, I show that this is in fact the case by constructing a biosemiotic model that links advertising strategies with corresponding structures in animal predation. The methodological framework for this model is the catastrophe theory of René Thom. The end result is a revised understanding of an ostensibly cultural phenomenon that demonstrates its continuity with signalling processes conventionally associated with the natural world.

Modeling brain dynamics using computational neurogenetic approach

The paper introduces a novel computational approach to brain dynamics modeling that integrates dynamic gene–protein regulatory networks with a neural network model. Interaction of genes and proteins in neurons affects the dynamics of the whole neural network. Through tuning the gene–protein interaction network and the initial gene/protein expression values, different states of the neural network dynamics can be achieved. A generic computational neurogenetic model is introduced that implements this approach. It is illustrated by means of a simple neurogenetic model of a spiking neural network of the generation of local field potential. Our approach allows for investigation of how deleted or mutated genes can alter the dynamics of a model neural network. We conclude with the proposal how to extend this approach to model cognitive neurodynamics.

Hierarchical analysis of piecewise affine models of gene regulatory networks

A key point in the analysis of dynamical models of biological systems is to handle systems of relatively high dimensions. In the present paper we propose a method to hierarchically organize a certain type of piecewise affine (PWA) differential systems. This specific class of systems has been extensively studied for the past few years, as it provides a good framework to model gene regulatory networks. The method, shown on several examples, allows a qualitative analysis of the asymptotic behavior of a PWA system, decomposing it into several smaller subsystems. This technique, based on the well-known strongly connected components decomposition, is not new. However, its adaptation to the non-smooth PWA differential equations turns out to be quite relevant because of the strong discrete structure underlying these equations. Its biological relevance is shown on a 7-dimensional PWA system modeling the gene network responsible for the carbon starvation response in Escherichia coli.

---

Leitlinien zur molekulargenetischen Diagnostik: Fragiles-X und Fragiles-X assoziiertes Tremor/Ataxie Syndrom

Ohne Zusammenfassung

---

Formation of Oil/Water Emulsions due to Electrochemical Instability at the Liquid/Liquid Interface

This study is dedicated to the development of manufacturing principles of food emulsions for food functionalization and formulation. In the experiments presented, the emulsions are generated using the effects of electrochemical instability and surface tension decrease at a polarized liquid/liquid interface. Polarization of the oil/liquid interface is studied in various aqueous systems including electrolytes and water-based solutions of cationic, anionic, zwitterionic, and nonionic surfactants. The physical features of the obtained emulsions, such as hydrodynamic flow patterns, droplet size distribution, and emulsion organization, are described. The efficacy of different electrode configurations is also evaluated. The theoretical model of the liquid/liquid interface polarization and experimental data obtained from various emulsification regimes are presented.

Hennigian Phylogenetic Systematics and the ‘Groundplan’ vs. ‘Post-Groundplan’ Approaches: A Reply to Kukalová-Peck

The recent contribution by Jarmila Kukalová-Peck on Hennigian phylogenetics and hexapod limb evolution is critically evaluated.

Beyond Population and Environment: Household Demographic Life Cycles and Land Use Allocation Among Small Farms in the Amazon

Most research featuring demographic factors in environmental change has focused on processes operating at the level of national or global populations. This paper focuses on household-level demographic life cycles among colonists in the Amazon, and evaluates the impacts on land use allocation. The analysis goes beyond prior research by including a broader suite of demographic variables, and by simultaneously assessing their impacts on multiple land uses with different economic and ecological implications. We estimate a system of structural equations that accounts for endogeneity among land uses, and the findings indicate stronger demographic effects than previous work. These findings bear implications for modeling land use, and the place of demography in environmental research.

Objects limit human comprehension

This paper demonstrates that the human visual system, the primary sensory conduit for primates, processes ambient energy in a way that obligatorily constructs the objects that we ineluctably perceive. And since our perceptual apparatus processes information only in terms of objects (along with the properties and movements of objects), we are limited in our ability to comprehend ‘what is’ when we move beyond our ordinary world of midsize objects—as, for example, when we address the micro microworld of quantum physics.

Adaptationism and the adaptive landscape

Debates over adaptationism can be clarified and partially resolved by careful consideration of the ‘grain’ at which evolutionary processes are described. The framework of ‘adaptive landscapes’ can be used to illustrate and facilitate this investigation. We argue that natural selection may have special status at an intermediate grain of analysis of evolutionary processes. The cases of sickle-cell disease and genomic imprinting are used as case studies.

Best practices for improved governance of coral reef marine protected areas

Coral reef marine protected areas (MPA) are widely distributed around the globe for social and ecological reasons. Relatively few of these MPAs are well managed. This review examines the governance of coral reef MPAs and the means to improve coral reef MPA management. It highlights common governance challenges, such as confused goals, conflict, and unrealistic attempts to scale up beyond institutional capacity. Recommendations, based on field experience and empirical evidence from around the world, are made for best practices at various stages of MPA implementation.

Towards dynamical system models of language-related brain potentials

Event-related brain potentials (ERP) are important neural correlates of cognitive processes. In the domain of language processing, the N400 and P600 reflect lexical-semantic integration and syntactic processing problems, respectively. We suggest an interpretation of these markers in terms of dynamical system theory and present two nonlinear dynamical models for syntactic computations where different processing strategies correspond to functionally different regions in the system’s phase space.

Teaching Evolution with Historical Narratives

This paper focuses on evolution as a unifying theme in biology education. Our aim is to argue that the different topics taught in secondary school biology classes should be enriched with and linked together by means of accounts of the history of life. We named this approach a “natural history perspective” on biology education. An essential aspect of the natural history perspective is the claim that evolutionary history forms the context for the development of an understanding of evolutionary processes. While there are some indications that a natural history perspective can function as a context for understanding micro-evolutionary processes, more research is called for.

The work of wetland credit markets: two cases in entrepreneurial wetland banking

Wetland banking has been discussed in the policy literature mainly at a high level of abstraction, using economic models or generic examples to illustrate the concepts and tensions within wetland banking. This article illustrates two cases of wetland bank creation in-depth using the methodology of the extended case study, following the process from the initiation of interest in forming a bank through to the approval of credits for sale. The close attention to actual cases serves to move discussion beyond the goodness of models or the supposed rationality of economic actors, towards a consideration of actual market participants in complex situations. Successful wetland credit producers must negotiate a number of different economic, political, interpersonal, and ecological forces which impact their project from a number of different scales. While no optimal solution to this complexity is likely to be reached that is generalizable, the use of entrepreneurial wetland banking as a market-based policy may expand where skillful bankers and regulators together arrive at adequate solutions that are matched to the specificity of their contexts.

The Evolution of Complex Organs

The origin of complex biological structures has long been a subject of interest and debate. Two centuries ago, natural explanations for their occurrence were considered inconceivable. However, 150 years of scientific investigation have yielded a conceptual framework, abundant data, and a range of analytical tools capable of addressing this question. This article reviews the various direct and indirect evolutionary processes that contribute to the origins of complex organs. The evolution of eyes is used as a case study to illustrate these concepts, and several of the most common misconceptions about complex organ evolution are discussed.