Governance options for science–policy interfaces on biodiversity and ecosystem services: comparing a network versus a platform approach

Science–policy-interfaces (SPIs) are expected to go beyond the linear model of scientific policy advice through creating spaces for exchange and dialogue between ‘policy’ and ‘knowledge’. Given that most environmental issues require inter- and transdisciplinary approaches, SPIs must take into account a variety of knowledge types, views and interests of scientists, policymakers and other decision makers. Moreover, acceptance and durability of SPIs depend largely on their perceived legitimacy and the credibility of their knowledge-gathering processes, providing additional challenges for their internal organisation. As the interplay between different knowledge types and decision making is far from neutral, a reflexive approach is required in the design of an SPI so that it is capable of learning from past experiences. The aim of this article is to discuss which governance arrangements could best support the development of an effective and legitimate SPI for European biodiversity politics. We analyse different options for facilitating the implementation of a ‘Network of Knowledge’ approach. This approach has been developed to improve the interface between diverse knowledge-holder communities and decision making processes for biodiversity and ecosystem services—a field where multi-scalar and multi-dimensional problems arise. In this article, we develop and discuss two stylized extreme governance models as our starting point: an `informal network model´, which almost entirely depends on the dedication of individuals, versus a more formalized `platform model´, predominantly based on the needs and interests of the organisations involved. We discuss the pros and cons of each of these models in reaching their objectives and in developing sound governing processes for a ‘Network of Knowledge’. From this discussion, we derive a recommended design for the reflexive governance of such a network in the context of the European Union and finish by discussing some more general lessons learnt.     

Social networks and the development of social skills in cowbirds

The complex interrelationships among individuals within social environments can exert selection pressures on social skills: those behaviours and cognitive processes that allow animals to manipulate and out-reproduce others. Social complexity can also have a developmental effect on social skills by providing individuals with opportunities to hone their skills by dealing with the challenges posed in within-group interactions. We examined how social skills develop in captive, adult male brown-headed cowbirds (Molothrus ater) that were exposed to differing levels of 'social complexity' across a 2-year experiment. After each year, subjects housed in groups with dynamic social structure (where many individuals entered and exited the groups during the year) outcompeted birds who had been housed in static groups. Exposure to dynamic structure subsequently led to substantial changes to the social networks of the home conditions during the breeding season. Static groups were characterized by a predictable relationship between singing and reproductive success that was stable across years. In dynamic conditions, however, males showed significant variability in their dominance status, their courting and even in their mating success. Reproductive success of males varied dramatically across years and was responsive to social learning in adulthood, and socially dynamic environments 'trained' individuals to be better competitors, even at an age when the development of many traits important for breeding (like song quality) had ended.     

Use of single-protoplast isolates in the study of the mating phenomena of <Emphasis Type="Italic">Rhizoctonia solani</Emphasis> (<Emphasis Type="Italic">Thanatephorus cucumeris</Emphasis>) AG-1 IC and IA

This study evaluates the effectiveness of using single-protoplast isolates (SPIs) to study the mating phenomena of Rhizoctonia solani AG-1 IC and IA. SPIs obtained from three field isolates (F-1, Rh28, and RO2) of AG-1 IC were paired with representative single-basidiospore isolate (SBI)-M1/-M2 testers, each from their own field isolates, or paired in all possible combinations. Tufts were formed between SPIs and SBI-M1/-M2 testers and between SPIs-M1 and -M2. The separation ratios of SPIs-M1 and -M2 were approximately 1:1, which were similar to the results obtained with SBIs. SPIs obtained from three isolates (GNSD, R59, and Tr8) of AG-1 IA, which failed to form basidiospores, were paired in all possible combinations. Although no tufts formed among SPIs from Tr8 and R59, tufts did form between SPIs from GNSD. SPIs from GNSD were separated into homokaryotic (-M1 or -M2) and heterokaryotic isolates, and the separation ratio of -M1 and -M2 was also around 1:1. Amplified fragment length polymorphism (AFLP) phenotypes of the tuft isolates formed between GNSD SPIs-M1 and -M2 suggested that these tuft isolates were all heterokaryotic. These results indicate that all three isolates of AG-1 IC and one isolate GNSD of AG-1 IA are heterokaryotic, and that the other two isolates of Tr8 and R59 of AG-1 IA are homokaryotic. Single-protoplast isolates are effective for studies of the mating phenomena of isolates belonging to different AGs of R. solani that could not form a perfect stage.     

Beyond Just Research: Experiences from Southern Africa in Developing Social Learning Partnerships for Resource Conservation Initiatives

There is a well-acknowledged communication or knowledge gap between scientists and decision-makers. Many scientists who take on the challenge of narrowing this gap operate on the understanding that their role is to communicate their findings in a one-way flow of information: from science to decision-makers. However, to be effective scientists must engage in an ongoing social learning process with decision-makers, and regard themselves as facilitators, and also as one among many stakeholders who have valid and important ecological knowledge. The developing world poses some particular challenges in this regard, specifically in terms of the large number of local level subsistence resources users who are important de facto decision-makers. We examine four natural resource management case studies from South Africa that differ in spatial scale and complexity, ranging from a single village to a whole biome. We distil seven lessons to help guide development of social learning processes and organizations in similar situations relating to natural resource planning and management. The lessons pertain to: maintaining 'key individuals' within social learning processes; the role of researchers; the formulation of research questions that social learning processes require adaptive long-term funding and capacity support; that local resource users are key decision-makers in developing countries; some perspectives on knowledge; and the need to measure research success.     

Multi-Level Semiosis: a Paradigm of Emergent Innovation

In this introductory article to the special issue on Multi-level semiosis we attempt to stage the background for qualifying the notion of “multi-levelness” when considering communication processes and semiosis in all life forms, i.e. from the cellular to the organismic level. While structures are organized hierarchically, communication processes require a kind of processual organization that may be better described as being heterarchical. Theoretically, the challenge arises in the temporal domain, that is, in the developmental and evolutionary dimension of dynamic semiotic processes. We discuss the importance of this fundamental difference in order to explain how levels, domains and orders of magnitude, on the one hand, and synchronic and diachronic processes, on the other, contribute to the overall organization of every living being. To account for such multi-level organization, semiotic freedom is assumed to be a scalar property that endows living systems at different levels and domains with the capacity to ponder selectively the overall structural coherence and functional compatibility of their heterarchical processing, which is increasingly less conditioned by the underlying molecular determinism.     

Interactive instruction of cellular physiology for remote learning.

The biomedical sciences are a rapidly changing discipline that have adapted to innovative technological advances. Despite these many advances, we face two major challenges: a) the number of experts in the field is vastly outnumbered by the number of students, many of whom are separated geographically or temporally and b) the teaching methods used to instruct students and learners have not changed. Today's students have adapted to technology--they use the web as a source of information and communicate via email and chat rooms. Teaching in the biomedical sciences should adopt these new information technologies (IT), but has thus far failed to capitalize on technological opportunity. Creating a "digital textbook" of the traditional learning material is not sufficient for dynamic processes such as cellular physiology. This paper describes innovative teaching techniques that incorporate familiar IT and high-quality interactive learning content with user-centric instruction design models. The Virtual Labs Project from Stanford University has created effective interactive online teaching modules in physiology (simPHYSIO) and delivered them over broadband networks to their undergraduate and medical students. Evaluation results of the modules are given as a measure of success of such innovative teaching method. This learning media strategically merges IT innovations with pedagogy to produce user-driven animations of processes and engaging interactive simulations.     

Assessing the contributions of multiple interacting traits to plant reproductive success: environmental dependence

The reproductive success of sibling cocklebur plants (Compositae: Xanthium strumarium) was monitored after growth at different levels of availability of water and nutrient resources. Variation in reproductive success among individual plants was related to physiological, structural, and phenological characteristics. Reproductive success increased with increased availability of resources, but the relative contribution of particular traits to reproductive success varied with resource availability. Allocation of biomass to different vegetative tissues, time to seedling emergence, degree of branching, transpiration rates, water use efficiency, the rate of decline in height growth after seedling emergence and final plant size all varied significantly with resource availability. However, the changes in each of these phenotypic traits across three garden environments did not always correlate with reproductive success. The shifts across environments in the apparent importance of somatic traits for reproductive success were attributed to plastic changes in the traits but also to changes in the phenotypic correlations of the traits with reproductive success.     

Dynamic changes in display architecture and function across environments revealed by a systems approach to animal communication*

Animal communication is often structurally complex and dynamic, with signaler and receiver behavior varying in response to multiple environmental factors. To date, studies assessing signal dynamics have mostly focused on the relationships between select signaling traits and receiver responses in a single environment. We use the wolf spider Schizocosa floridana to explore the relationships between courtship display form and function across two social contexts (female presence vs absence) and two light environments (light vs dark). We use traditional analytical methods to determine predictors of copulation success (i.e., signal function) and examine these predictors in a structural context by overlaying them on signal phenotype networks (Wilkins et al. 2015). This allows us to explore system design principles (degeneracy, redundancy, pluripotentiality), providing insight into hypotheses regarding complex signal evolution. We found that both social context and light environment affect courtship structure, although the predictors of mating success remain similar across light environments, suggesting system degeneracy. Contrastingly, the same display traits may serve different functions across social environments, suggesting pluripotentiality. Ultimately, our network approach uncovers a complexity in display structure and function that is missed by functional analyses alone, highlighting the importance of systems‐based methodologies for understanding the dynamic nature of complex signals.     

Smart process development: Application of machine-learning and integrated process modeling for inclusion body purification processes

The development of a biopharmaceutical production process usually occurs sequentially, and tedious optimization of each individual unit operation is very time-consuming. Here, the conditions established as optimal for one-step serve as input for the following step. Yet, this strategy does not consider potential interactions between a priori distant process steps and therefore cannot guarantee for optimal overall process performance. To overcome these limitations, we established a smart approach to develop and utilize integrated process models using machine learning techniques and genetic algorithms. We evaluated the application of the data-driven models to explore potential efficiency increases and compared them to a conventional development approach for one of our development products. First, we developed a data-driven integrated process model using gradient boosting machines and Gaussian processes as machine learning techniques and a genetic algorithm as recommendation engine for two downstream unit operations, namely solubilization and refolding. Through projection of the results into our large-scale facility, we predicted a twofold increase in productivity. Second, we extended the model to a three-step model by including the capture chromatography. Here, depending on the selected baseline-process chosen for comparison, we obtained between 50% and 100% increase in productivity. These data show the successful application of machine learning techniques and optimization algorithms for downstream process development. Finally, our results highlight the importance of considering integrated process models for the whole process chain, including all unit operations.     

Lipid mimetics: A versatile toolbox for lipid biology and beyond

Being the principal component of biological membranes lipids are essential building blocks of life. Given their huge biological importance, the investigation of lipids, their properties, interactions and metabolic pathways is of prime importance for the fundamental understanding of living cells and organisms as well as the emergence of diseases. Different strategies have been applied to investigate lipid-mediated biological processes, one of them being the use of lipid mimetics. They structurally resemble their natural counterparts but are equipped with functionality that can be used to probe or manipulate lipid-mediated biological processes and biomembranes. Lipid mimetics therefore constitute an indispensable toolbox for lipid biology and membrane research but also beyond for potential applications in medicine or synthetic biology. Herein, we highlight recent advances in the development and application of lipid-mimicking compounds.     

Basics of voice dysfunction--etiology and prevention of voice damage

Voice is one of the most important means of communication and as such should be taken care of. The etiology of voice disorders is diverse. Due to the development of the society we live in, way of life, environmental factors, and exposure to pharmacological agents as well as demands we make towards our voice, there is a substantial growth in the number of people with voice disorders. We tasked ourselves to find out if it is possible to enlighten people on the importance of voice, to motivate them to take care of it, to notice the changes in its quality and eventually ask for help. We assessed in which measure do we understand the importance of a healthy voice, and do we know which is the most important factor that adds to its decline. For a long number of years voice therapists and other experts in the voice disorder field have been discussing the optimal voice impostation as well as vocal exercises and methods behind voice recovery. They have all come to the same conclusion that phonation is dependant on the sort of the voice disorder and the patient motivation. We wanted to go one step further and investigate, dependence of voice quality and the damage etiology (organic - functional), which are the predominant causes, what are the factors that account for the damage and how the disorder motivates the patient and therefore influences the rehabilitation success rate.     

Fitness costs of worker specialization for ant societies

Division of labour is of fundamental importance for the success of societies, yet little is known about how individual specialization affects the fitness of the group as a whole. While specialized workers may be more efficient in the tasks they perform than generalists, they may also lack the flexibility to respond to rapid shifts in task needs. Such rigidity could impose fitness costs when societies face dynamic and unpredictable events, such as an attack by socially parasitic slavemakers. Here, we experimentally assess the colony-level fitness consequences of behavioural specialization in Temnothorax longispinosus ants that are attacked by the slavemaker ant T. americanus. We manipulated the social organization of 102 T. longispinosus colonies, based on the behavioural responses of all 3842 workers. We find that strict specialization is disadvantageous for a colony''s annual reproduction and growth during slave raids. These fitness costs may favour generalist strategies in dynamic environments, as we also demonstrate that societies exposed to slavemakers in the field show a lower degree of specialization than those originating from slavemaker-free populations. Our findings provide an explanation for the ubiquity of generalists and highlight their importance for the flexibility and functional robustness of entire societies.     

Chokepoints in Mechanical Coupling Associated with Allosteric Proteins: The Pyruvate Kinase Example

Although the critical role of allostery in controlling enzymatic processes is well appreciated, there is a current dearth in our understanding of its underlying mechanisms, including communication between binding sites. One potential key aspect of intersite communication is the mechanical coupling between residues in a protein. Here, we introduce a graph-based computational approach to investigate the mechanical coupling between distant parts of a protein, highlighting effective pathways via which protein motion can transfer energy between sites. In this method, each residue is treated as a node on a weighted, undirected graph, in which the edges are defined by locally correlated motions of those residues and weighted by the strength of the correlation. The method was validated against experimental data on allosteric regulation in the human liver pyruvate kinase as obtained from full-protein alanine-scanning mutagenesis (systematic mutation) studies, as well as computational data on two G-protein-coupled receptors. The method provides semiquantitative information on the regulatory importance of specific structural elements. It is shown that these elements are key for the mechanical coupling between distant parts of the protein by providing effective pathways for energy transfer. It is also shown that, although there are a multitude of energy transfer pathways between distant parts of a protein, these pathways share a few common nodes that represent effective “chokepoints” for the communication.     

Climate change and nesting behaviour in vertebrates: a review of the ecological threats and potential for adaptive responses

Nest building is a taxonomically widespread and diverse trait that allows animals to alter local environments to create optimal conditions for offspring development. However, there is growing evidence that climate change is adversely affecting nest‐building in animals directly, for example via sea‐level rises that flood nests, reduced availability of building materials, and suboptimal sex allocation in species exhibiting temperature‐dependent sex determination. Climate change is also affecting nesting species indirectly, via range shifts into suboptimal nesting areas, reduced quality of nest‐building environments, and changes in interactions with nest predators and parasites. The ability of animals to adapt to sustained and rapid environmental change is crucial for the long‐term persistence of many species. Many animals are known to be capable of adjusting nesting behaviour adaptively across environmental gradients and in line with seasonal changes, and this existing plasticity potentially facilitates adaptation to anthropogenic climate change. However, whilst alterations in nesting phenology, site selection and design may facilitate short‐term adaptations, the ability of nest‐building animals to adapt over longer timescales is likely to be influenced by the heritable basis of such behaviour. We urgently need to understand how the behaviour and ecology of nest‐building in animals is affected by climate change, and particularly how altered patterns of nesting behaviour affect individual fitness and population persistence. We begin our review by summarising how predictable variation in environmental conditions influences nest‐building animals, before highlighting the ecological threats facing nest‐building animals experiencing anthropogenic climate change and examining the potential for changes in nest location and/or design to provide adaptive short‐ and long‐term responses to changing environmental conditions. We end by identifying areas that we believe warrant the most urgent attention for further research.     

Learning rules for optimal selection in a varying environment: mate choice revisited

The quality of a chosen partner can be one of the most significantfactors affecting an animal's long-term reproductive success.We investigate optimal mate choice rules in an environment wherethere is both local variation in the quality of potential mateswithin each local mating pool and spatial (or temporal) variationin the average quality of the pools themselves. In such a situation,a robust rule that works well across a variety of environmentswill confer a significant reproductive advantage. We formulatea full Bayesian model for updating information in such a varyingenvironment and derive the form of the rule that maximizes expectedreward in a spatially varying environment. We compare the theoreticalperformance of our optimal learning rule against both fixedthreshold rules and simpler near-optimal learning rules andshow that learning is most advantageous when both the localand environmental variances are large. We consider how optimalsimple learning rules might evolve and compare their evolutionwith that of fixed threshold rules using genetic algorithmsas minimal models of the relevant genetics. Our analysis pointsup the variety of ways in which a near-optimal rule can be expressed.Finally, we describe how our results extend to the case of temporallyvarying environments.     

Equipment ontology for modular reconfigurable assembly systems

Evolvable and Reconfigurable Assembly Systems (RAS) enable enterprises to rapidly respond to changes in today’s increasingly volatile and dynamic global markets. One of the key success factors for the effective use of RAS is methods and tools that can rapidly configure and reconfigure assembly systems driven by changing requirements. The focus of this paper is the development of a suitable equipment model to support the effective design of reconfigurable assembly systems. The work has been motivated by the need to provide solutions for increasing product customisation and volume changes over the product life-cycle that directly impact on the final product assembly. The paper proposes a comprehensive equipment ontology to enable effective decision-making during the design and evaluation of new RAS configurations. The proposed ontology is based on the function-behaviour-structure paradigm, and is formalised to facilitate its application in distributed web-enabled decision-making environments. The equipment configuration and reconfiguration approach and prototype decision-making environment are illustrated using system design examples.     

Selection on laying date is connected to breeding density in the pied flycatcher

Timing of reproduction and clutch size are important determinants of breeding success, especially in seasonal environments. Several recent bird population studies have shown changes in breeding time and in natural selection on it. These changes have often been linked with climate change, but few studies have investigated how the traits or natural selection are actually connected with climatic factors. Furthermore, the effect of population density on selection has been rarely considered, despite the potential importance of density in demographic processes. We studied variation in natural selection on laying date and on clutch size in relation to measures of spring phenology and population density in a long-term study of pied flycatchers in SW Finland. The phenological stage of the environment at mean egg-laying did not affect the direction of selection on either laying date or on clutch size. There was, however, stronger selection for earlier laying date when the breeding density of the population was high, suggesting that early breeding is not necessarily beneficial as such, but that its importance is emphasized when high population density increases competition. In addition, early breeding was favoured when the pre-breeding period was cool, which may indicate an increased advantage for the fittest individuals in harsher conditions. In the middle of the twentieth century, there was selection for large clutch size, which subsequently ceased, along with an overall decrease in recruit production. Our results indicate that attention should be paid to demographic factors such as breeding density when studying natural selection and temporal changes in it.     

Job co-allocation strategies for multiple high performance computing clusters

To more effectively use a network of high performance computing clusters, allocating multi-process jobs across multiple connected clusters becomes an attractive possibility. This allocation process entails dividing the processes of a job among several clusters, which we refer to as co-allocation. Co-allocation offers the possibility of more efficient use of computer resources, reduced turn-around time and computations using numbers of processes larger than processes on any single cluster. In order to realize these possibilities, effective co-allocation, ultimately, depends on the inter-cluster communication cost. In this paper, we introduce a scalable co-allocation strategy called the Maximum Bandwidth Adjacent cluster Set (MBAS) strategy. The strategy makes use of two thresholds to control allocation: one to control the limit on bandwidth on usable inter-cluster communication links and another to control how jobs are split. A simulator that can simulate the dynamic behavior of jobs running across multiple clusters was developed and used to examine the performance of the MBAS co-allocation strategy. Our results indicate that by adjusting the thresholds for link level control and chunk size control in splitting jobs, the MBAS co-allocation strategy can significantly improve both user satisfaction and system utilization.