Impact of climate change on insect pests of trees

There are many interactions and it is exetremely difficult to predict the impact of climate change on insect pests in the future, but we may expect an increase of certain primary pests as well as secondary pests and invasive specie

Introducing a Pictographic Language for Envisioning a Rich Variety of Enactive Systems with Different Degrees of Complexity

Notwithstanding the considerable amount of progress that has been made in recent years, the parallel fields of cognitive science and cognitive systems lack a unifying methodology for describing, understanding, simulating and implementing advanced cognitive behaviours. Growing interest in ’enactivism’ - as pioneered by the Chilean biologists Humberto Maturana and Francisco Varela - may lead to new perspectives in these areas, but a common framework for expressing many of the key concepts is still missing. This paper attempts to lay a tentative foundation in that direction by extending Maturana and Varela’s pictographic depictions of autopoietic unities to create a rich visual language for envisioning a wide range of enactive systems - natural or artificial - with different degrees of complexity. It is shown how such a diagrammatic taxonomy can help in the comprehension of important relationships between a variety of complex concepts from a pan-theoretic perspective. In conclusion, it is claimed that visual language is not only valuable for teaching and learning, but also offers important insights into the design and implementation of future advanced robotic systems

Accommodating Ontologies to Biological Reality—Top-Level Categories of Cumulative-Constitutively Organized Material Entities

BACKGROUND: The Basic Formal Ontology (BFO) is a top-level formal foundational ontology for the biomedical domain. It has been developed with the purpose to serve as an ontologically consistent template for top-level categories of application oriented and domain reference ontologies within the Open Biological and Biomedical Ontologies Foundry (OBO). BFO is important for enabling OBO ontologies to facilitate in reliably communicating and managing data and metadata within and across biomedical databases. Following its intended single inheritance policy, BFO's three top-level categories of material entity (i.e. ‘object’, ‘fiat object part’, ‘object aggregate’) must be exhaustive and mutually disjoint. We have shown elsewhere that for accommodating all types of constitutively organized material entities, BFO must be extended by additional categories of material entity. METHODOLOGY/PRINCIPAL FINDINGS: Unfortunately, most biomedical material entities are cumulative-constitutively organized. We show that even the extended BFO does not exhaustively cover cumulative-constitutively organized material entities. We provide examples from biology and everyday life that demonstrate the necessity for ‘portion of matter’ as another material building block. This implies the necessity for further extending BFO by ‘portion of matter’ as well as three additional categories that possess portions of matter as aggregate components. These extensions are necessary if the basic assumption that all parts that share the same granularity level exhaustively sum to the whole should also apply to cumulative-constitutively organized material entities. By suggesting a notion of granular representation we provide a way to maintain the single inheritance principle when dealing with cumulative-constitutively organized material entities. CONCLUSIONS/SIGNIFICANCE: We suggest to extend BFO to incorporate additional categories of material entity and to rearrange its top-level material entity taxonomy. With these additions and the notion of granular representation, BFO would exhaustively cover all top-level types of material entities that application oriented ontologies may use as templates, while still maintaining the single inheritance principle

Spatio-structural granularity of biological material entities

<p>Abstract</p> <p>Background</p> <p>With the continuously increasing demands on knowledge- and data-management that databases have to meet, ontologies and the theories of granularity they use become more and more important. Unfortunately, currently used theories and schemes of granularity unnecessarily limit the performance of ontologies due to two shortcomings: (i) they do not allow the integration of multiple granularity perspectives into one granularity framework; (ii) they are not applicable to cumulative-constitutively organized material entities, which cover most of the biomedical material entities.</p> <p>Results</p> <p>The above mentioned shortcomings are responsible for the major inconsistencies in currently used spatio-structural granularity schemes. By using the Basic Formal Ontology (BFO) as a top-level ontology and Keet's general theory of granularity, a granularity framework is presented that is applicable to cumulative-constitutively organized material entities. It provides a scheme for granulating complex material entities into their constitutive and regional parts by integrating various compositional and spatial granularity perspectives. Within a scale dependent resolution perspective, it even allows distinguishing different types of representations of the same material entity. Within other scale dependent perspectives, which are based on specific types of measurements (e.g. weight, volume, etc.), the possibility of organizing instances of material entities independent of their parthood relations and only according to increasing measures is provided as well. All granularity perspectives are connected to one another through overcrossing granularity levels, together forming an integrated whole that uses the <it>compositional object perspective </it>as an integrating backbone. This granularity framework allows to consistently assign structural granularity values to all different types of material entities.</p> <p>Conclusions</p> <p>The here presented framework provides a spatio-structural granularity framework for all domain reference ontologies that model cumulative-constitutively organized material entities. With its multi-perspectives approach it allows querying an ontology stored in a database at one's own desired different levels of detail: The contents of a database can be organized according to diverse granularity perspectives, which in their turn provide different <it>views </it>on its content (i.e. data, knowledge), each organized into different levels of detail.</p

Top-Level Categories of Constitutively Organized Material Entities - Suggestions for a Formal Top-Level Ontology

Application oriented ontologies are important for reliably communicating and managing data in databases. Unfortunately, they often differ in the definitions they use and thus do not live up to their potential. This problem can be reduced when using a standardized and ontologically consistent template for the top-level categories from a top-level formal foundational ontology. This would support ontological consistency within application oriented ontologies and compatibility between them. The Basic Formal Ontology (BFO) is such a foundational ontology for the biomedical domain that has been developed following the single inheritance policy. It provides the top-level template within the Open Biological and Biomedical Ontologies Foundry. If it wants to live up to its expected role, its three top-level categories of material entity (i.e., 'object', 'fiat object part', 'object aggregate') must be exhaustive, i.e. every concrete material entity must instantiate exactly one of them.By systematically evaluating all possible basic configurations of material building blocks we show that BFO's top-level categories of material entity are not exhaustive. We provide examples from biology and everyday life that demonstrate the necessity for two additional categories: 'fiat object part aggregate' and 'object with fiat object part aggregate'. By distinguishing topological coherence, topological adherence, and metric proximity we furthermore provide a differentiation of clusters and groups as two distinct subcategories for each of the three categories of material entity aggregates, resulting in six additional subcategories of material entity.We suggest extending BFO to incorporate two additional categories of material entity as well as two subcategories for each of the three categories of material entity aggregates. With these additions, BFO would exhaustively cover all top-level types of material entity that application oriented ontologies may use as templates. Our result, however, depends on the premise that all material entities are organized according to a constitutive granularity

Ecological quality of the soil

This report describes the meaning of ecological quality of soil and two ways to quantify such quality. A high number of processes takes place in the soil. These processes are important for mankind (ecosystem services) as they contribute to, e.g., food production, the quality and type of nature and the production of clean groundwater (for the drinking water production). The role of soil organisms is important in these processes. For a sustainable use of the soil it is important to use and manage the soil organisms in a way that these processes are secured for the future. Also a change in soil use must always be possible. To facilitate a sustainability policy for the soil a biological indicator for soil quality (BISQ) is being developed, which is designed for application on a national scale. Therefore ecological data are collected on species diversity, species abundance and activity of soil organisms. For environmental policy making a system must be developed to characterise the ecological quality of soil as 'good' or 'bad', or in a sense of 'desired' and 'undesired'. Two ways to derive quality criteria for soil based on interpretation of the collected data are described. The mechanistic or functional method: In this method the wanted combination of ecosystem services on a certain place is determined and subsequently the optimal biodiversity within such an ecosystem is deduced by statistic interpretation of soil ecological data that have been collected. The statistic method: In this method for a certain combination of land-use and soil type data are collected from a group of reference locations that have been classified on beforehand as 'good'. Based on these data, a statistically derived optimal composition of an ecosystem type is given, with the label 'good quality'. In the application of the indicator, in both approaches it is possible to formulate how far a present local quality satisfies the desired state. Because of the complexity of the subject it is proposed to use both approaches independently in further development according to the 'multiple lines of evidence' principle. Ideally both approaches will lead to corresponding results. Finally the further development of the indicator for application on both international and local scale is discussed.In dit rapport wordt beschreven wat ecologische kwaliteit van bodem is, en op welke wijze deze gekwantificeerd kan worden. In bodem vinden een groot aantal processen plaats, die van belang zijn voor de mens (nutsfuncties), omdat ze bijdragen aan bijvoorbeeld de voedselvoorziening, het type en de kwaliteit van de natuur en de levering van schoon grondwater (voor de productie van drinkwater). Bodemorganismen spelen een belangrijke rol in die processen. Bij een duurzaam gebruik van de bodem is het van belang, om de bodemorganismen zodanig te gebruiken en te beheren, dat deze processen ook voor de toekomst gewaarborgd zijn. Hierbij moet ook de mogelijkheid beschikbaar blijven om het bodemgebruik te veranderen. Ter onderbouwing van het duurzaamheidsbeleid van de bodem wordt gewerkt aan de ontwikkeling van een bodembiologische indicator (BoBI) voor gebruik op nationale schaal. Daarvoor worden ecologische gegevens over de soortdiversiteit, het aantal organismen per soort en de activiteit van de organismen verzameld. Ten behoeve van het beleid moet een karakteriseringsysteem van de bodem worden ontwikkeld in de termen van 'goed' en 'slecht'. In dit rapport worden twee benaderingen beschreven om tot dergelijke kwaliteitscriteria te komen op basis van de tot dusver verzamelde data. 1) De mechanistische of functionele methode. Hierbij wordt nagegaan welke combinatie van nutsfuncties op een bepaalde plek gewenst is en vervolgens wordt de samenstelling van het daarbij behorende 'goede' bodemecosysteem beschreven met behulp van statistische interpretatie van de verzamelde bodemecologische data. 2) De statistische methode. Bij deze methode wordt voor een bepaalde combinatie van grondsoort en bodemgebruik bodemecologische data van een groep van geografische referenties verzameld en op basis daarvan wordt dan aangegeven wat de optimale samenstelling van het bodemecosysteem type is. Bij de toepassing van de indicator zou dan, in beide benaderingen, moeten worden aangegeven, in hoeverre de huidige kwaliteit voldoet aan de criteria van de gewenste kwaliteit. Vanwege de complexiteit van de materie wordt voorgesteld beide benaderingen onafhankelijk van elkaar te ontwikkelen volgens het principe van multiple lines of evidence. Idealiter zullen beide benaderingen uiteindelijk tot een overeenkomend resultaat leiden. Tenslotte wordt een verdere ontwikkeling van de indicator voor toepassing op internationale en lokale schaal besproken

Ecological quality of the soil

In dit rapport wordt beschreven wat ecologische kwaliteit van bodem is, en op welke wijze deze gekwantificeerd kan worden. In bodem vinden een groot aantal processen plaats, die van belang zijn voor de mens (nutsfuncties), omdat ze bijdragen aan bijvoorbeeld de voedselvoorziening, het type en de kwaliteit van de natuur en de levering van schoon grondwater (voor de productie van drinkwater). Bodemorganismen spelen een belangrijke rol in die processen. Bij een duurzaam gebruik van de bodem is het van belang, om de bodemorganismen zodanig te gebruiken en te beheren, dat deze processen ook voor de toekomst gewaarborgd zijn. Hierbij moet ook de mogelijkheid beschikbaar blijven om het bodemgebruik te veranderen. Ter onderbouwing van het duurzaamheidsbeleid van de bodem wordt gewerkt aan de ontwikkeling van een bodembiologische indicator (BoBI) voor gebruik op nationale schaal. Daarvoor worden ecologische gegevens over de soortdiversiteit, het aantal organismen per soort en de activiteit van de organismen verzameld. Ten behoeve van het beleid moet een karakteriseringsysteem van de bodem worden ontwikkeld in de termen van 'goed' en 'slecht'. In dit rapport worden twee benaderingen beschreven om tot dergelijke kwaliteitscriteria te komen op basis van de tot dusver verzamelde data. 1) De mechanistische of functionele methode. Hierbij wordt nagegaan welke combinatie van nutsfuncties op een bepaalde plek gewenst is en vervolgens wordt de samenstelling van het daarbij behorende 'goede' bodemecosysteem beschreven met behulp van statistische interpretatie van de verzamelde bodemecologische data. 2) De statistische methode. Bij deze methode wordt voor een bepaalde combinatie van grondsoort en bodemgebruik bodemecologische data van een groep van geografische referenties verzameld en op basis daarvan wordt dan aangegeven wat de optimale samenstelling van het bodemecosysteem type is. Bij de toepassing van de indicator zou dan, in beide benaderingen, moeten worden aangegeven, in hoeverre de huidige kwaliteit voldoet aan de criteria van de gewenste kwaliteit. Vanwege de complexiteit van de materie wordt voorgesteld beide benaderingen onafhankelijk van elkaar te ontwikkelen volgens het principe van multiple lines of evidence. Idealiter zullen beide benaderingen uiteindelijk tot een overeenkomend resultaat leiden. Tenslotte wordt een verdere ontwikkeling van de indicator voor toepassing op internationale en lokale schaal besproken.This report describes the meaning of ecological quality of soil and two ways to quantify such quality. A high number of processes takes place in the soil. These processes are important for mankind (ecosystem services) as they contribute to, e.g., food production, the quality and type of nature and the production of clean groundwater (for the drinking water production). The role of soil organisms is important in these processes. For a sustainable use of the soil it is important to use and manage the soil organisms in a way that these processes are secured for the future. Also a change in soil use must always be possible. To facilitate a sustainability policy for the soil a biological indicator for soil quality (BISQ) is being developed, which is designed for application on a national scale. Therefore ecological data are collected on species diversity, species abundance and activity of soil organisms. For environmental policy making a system must be developed to characterise the ecological quality of soil as 'good' or 'bad', or in a sense of 'desired' and 'undesired'. Two ways to derive quality criteria for soil based on interpretation of the collected data are described. The mechanistic or functional method: In this method the wanted combination of ecosystem services on a certain place is determined and subsequently the optimal biodiversity within such an ecosystem is deduced by statistic interpretation of soil ecological data that have been collected. The statistic method: In this method for a certain combination of land-use and soil type data are collected from a group of reference locations that have been classified on beforehand as 'good'. Based on these data, a statistically derived optimal composition of an ecosystem type is given, with the label 'good quality'. In the application of the indicator, in both approaches it is possible to formulate how far a present local quality satisfies the desired state. Because of the complexity of the subject it is proposed to use both approaches independently in further development according to the 'multiple lines of evidence' principle. Ideally both approaches will lead to corresponding results. Finally the further development of the indicator for application on both international and local scale is discussed.VROM-DGM-BW

Ecologische kwaliteit van de bodem

In dit rapport wordt beschreven wat ecologische kwaliteit van bodem is, en op welke wijze deze gekwantificeerd kan worden. In bodem vinden een groot aantal processen plaats, die van belang zijn voor de mens (nutsfuncties), omdat ze bijdragen aan bijvoorbeeld de voedselvoorziening, het type en de kwaliteit van de natuur en de levering van schoon grondwater (voor de productie van drinkwater). Bodemorganismen spelen een belangrijke rol in die processen. Bij een duurzaam gebruik van de bodem ishetvan belang, om de bodemorganismen zodanig te gebruiken en te beheren, dat deze processen ook voor de toekomst gewaarborgd zijn. Hierbij moet ook de mogelijkheid beschikbaar blijven om het bodemgebruik te veranderen. Ter onderbouwing van het duurzaamheidsbeleid van de bodem wordt gewerkt aan de ontwikkeling van een bodembiologische indicator (BoBI) voor gebruik op nationale schaal. Daarvoor worden ecologische gegevens over de soortdiversiteit, het aantal organismen per soort en deactiviteitvan de organismen verzamel