A modular approach to Integrated Assessment modeling

In this paper, we present a new approach to model coupling that probably forms the methodological basis of a new generation of Integrated Assessment models. This approach respects the knowledge and expertise that is embodied in existing models and encourages their gradual evolution. Modularity is the guiding principle. Our approach is distinguished by the way modules are coupled which is based on an interplay of a job control module, a numerical coupling module, and a couple of stand-alone functional modules. The numerical coupling module - the core component - serves to treat the feedbacks between the functional modules. A first implemented example that couples an economic and a climate module by means of a two-phase meta-optimization is presented here. The algorithm and mathematical structure behind are discussed as well as important features such as convergence behavior and reliability.     

Collaborative study to improve the quality control of rare earth element determinations in environmental matrices

In order to control the quality of rare earth determinations in environmental matrices, the Standards, Measurements and Testing Programme (formerly Community Bureau of Reference, BCR) of the European Commission has started a project, the final aim of which is to certify four types of matrices (tuna muscle, mussel tissue, aquatic plant and estuarine sediment) for their contents of a range of rare earth elements (Sc, Y and the lanthanides: La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb and Lu). The elements U and Th were added to the study. The first part of this project consisted of an interlaboratory study which aimed to test the feasibility of preparation of environmental reference materials and to detect and remove most of the pitfalls observed in rare earth determinations. This paper presents the preparation of the four matrices for the intercomparison study and for the candidate reference material. The main results are presented of the interlaboratory study that was carried out prior to the certification campaign. This collaborative trial is the first attempt ever carried out at this scale to evaluate the state-of-the-art of rare earth determinations in the environment. Its impact on the improvement of chemical measurements will have positive effects on the comparability of data necessary for environmental monitoring.     

Optimizing the removal of small fish passage barriers

Removing small artificial barriers that hinder upstream migrations of fish is a major problem in riparian habitat restoration. Because of budgetary limitations, it is necessary to prioritize barrier removal and repair decisions. These have usually been based on scoring and ranking procedures, which, although simple to use, can be very inefficient in terms of increasing the amount of accessible instream habitat. We develop a novel decision-making approach, based on integer programming techniques, which optimizes repair and removal decisions. Results show based on real datasets of barrier culverts located in Washington State that scoring and ranking is over 25% below the optimum on average and a full 100% below in the worst case, producing no net habitat gain whatsoever. This is compared to a dynamic programming method that was able to find optimal solutions in less than a second, even for problems with up to several hundred variables, and a heuristic method, which found solutions with less than a 1% average optimality gap in even less time.     

Application of a checklist for quality assistance in environmental modelling to an energy model

Large, complex energy models present considerable challenges to develop and test. Uncertainty assessments of such models provide only partial guidance on the quality of the results. We have developed a model quality assistance checklist to aid in this purpose. The model checklist provides diagnostic output in the form of a set of pitfalls for the model application. The checklist is applied here to an energy model for the problem of assessing energy use and greenhouse gas emissions. Use of the checklist suggests that results on this issue are contingent on a number of assumptions that are highly value-laden. When these assumptions are held fixed, the model is deemed capable of producing moderately robust results of relevance to climate policy over the longer term. Checklist responses also indicate that a number of details critical to policy choices or outcomes on this issue are not captured in the model, and model results should therefore be supplemented with alternative analyses.     

Characterization of microbial communities from coastal waters using microarrays

Molecular methods, including DNA probes, were used to identify and enumerate pathogenic Vibrio species in the Chesapeake Bay; our data indicated that Vibrio vulnificus exhibits seasonal fluctuations in number. Our work included a characterization of total microbial communities from the Bay; development of microarrays that identify and quantify the diversity of those communities; and observation of temporal changes in those communities. To identify members of the microbial community, we amplified the 16S rDNA gene from community DNA isolated from a biofilm sample collected from the Chesapeake Bay in February, 2000. The resultant 75 sequences were 95% or more similar to 7 species including two recently described Shewanella species, baltica and frigidimarina, that have not been previously isolated from the Chesapeake. When the genera of bacteria from biofilm after culturing are compared to those detected by subcloning amplified 16S fragments from community DNA, the cultured sample exhibited a strong bias. In oysters collected in February, the most common bacteria were previously unknown. Based on our 16S findings, we are developing microarrays to detect these and other microbial species in these estuarine communities. The microarrays will detect each species using four distinct loci, with the multiple loci serving as an internal control. The accuracy of the microarray will be measured using sentinel species such as Aeromonas species, Escherichia coli, and Vibrio vulnificus. Using microarrays, it should be possible to determine the annual fluctuations of bacterial species (culturable and non-culturable, pathogenic and non-pathogenic). The data may be applied to understanding patterns of environmental change; assessing the health of the Bay; and evaluating the risk of human illness associated with exposure to and ingestion of water and shellfish.     

A Metamodeling Approach for Integrated Assessment of Air Quality Policies

A method is proposed to build integrated models (also called Metamodels) aimed at quantifying the economic efficiency of air quality policies. This Metamodeling approach is based on the coupling of two complementary models, that operate at different scales in space and time, and which represent the economic and the physical and chemical processes, respectively. The joint consideration of the physico-chemical and techno-economic structure of the pollution control problems permits a comprehensive evaluation of air pollution abatement strategies. The motivating pollution control problems include urban-regional air quality management through efficient energy and traffic control policies. A pilot study, exploiting data collected in the Geneva canton (Switzerland), is used to demonstrate the potential of the approach.     

The modern theory of biological evolution: an expanded synthesis

In 1858, two naturalists, Charles Darwin and Alfred Russel Wallace, independently proposed natural selection as the basic mechanism responsible for the origin of new phenotypic variants and, ultimately, new species. A large body of evidence for this hypothesis was published in Darwins Origin of Species one year later, the appearance of which provoked other leading scientists like August Weismann to adopt and amplify Darwins perspective. Weismanns neo-Darwinian theory of evolution was further elaborated, most notably in a series of books by Theodosius Dobzhansky, Ernst Mayr, Julian Huxley and others. In this article we first summarize the history of life on Earth and provide recent evidence demonstrating that Darwins dilemma (the apparent missing Precambrian record of life) has been resolved. Next, the historical development and structure of the modern synthesis is described within the context of the following topics: paleobiology and rates of evolution, mass extinctions and species selection, macroevolution and punctuated equilibrium, sexual reproduction and recombination, sexual selection and altruism, endosymbiosis and eukaryotic cell evolution, evolutionary developmental biology, phenotypic plasticity, epigenetic inheritance and molecular evolution, experimental bacterial evolution, and computer simulations (in silico evolution of digital organisms). In addition, we discuss the expansion of the modern synthesis, embracing all branches of scientific disciplines. It is concluded that the basic tenets of the synthetic theory have survived, but in modified form. These sub-theories require continued elaboration, particularly in light of molecular biology, to answer open-ended questions concerning the mechanisms of evolution in all five kingdoms of life.Dedicated to Prof. Dr. Dr. hc mult. Ernst Mayr on the occasion of his 100th birthdayThis revised version was published online in March 2004, with corrections to the caption of Figure 6.     

Overestimates of black carbon in soils and sediments

Several recent reports suggest that black carbon (BC), which broadly encompasses charcoal, soot, and other forms of pyrogenic carbon, may constitute a significant proportion of the refractory carbon in soil and sedimentary organic matter. BC is a sink for biospheric and atmospheric carbon dioxide, and is intimately tied to the biogeochemical cycling of both carbon and oxygen through its role in organic matter cycling. Additionally, BC may represent a large fraction of the missing carbon sink in global carbon accounting. Here, we demonstrate that documented measurements of BC may be the result of methodological artifacts, which inadvertently overestimate the amount of BC. We found that a widely used thermal oxidative method can create a residue that falls under the operational definition of BC in samples that are relatively BC-free. Moreover, during this procedure, labile organic matter constituents are condensed into pyrogenic carbon, implying that the labile components are present in lesser quantities. These methodological deficiencies are promoting overestimates in the amount of refractory carbon in soil and sedimentary organic matter and may endorse inaccuracies in the rates of carbon fluxes, the mean residence times of terrestrial carbon, and organic matter burial rates in oceanic environments.     

Prenatal diagnosis of inborn errors in peroxisomal β-oxidation

In recent years, an increasing number of inherited diseases in man have been recognized in which there is an impairment in the peroxisomal β-oxidation of very-long-chain fatty acids. In general, these disorders are associated with severe neurological and physical abnormalities and death within the first years of life. In this paper we describe our experience with regard to the prenatal diagnosis of a number of different inborn errors of peroxisomal β-oxidation. Eleven pregnancies at risk were monitored by measuring very-long-chain fatty acid levels as well as very-long-chain fatty acid β-oxidation in cultured chorionic villous fibroblasts and/or amniotic fluid cells. Five affected fetuses were identified. It is concluded that prenatal diagnosis in this group of diseases can be done reliably using cultured chorionic villous fibroblasts or amniotic fluid cells.