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Humans have been altering the marine environment for millennia. Up till now, five critical environmental issues have affected the oceans: over-fishing, chemical pollution and eutrophication, habitat destruction, invasion of exotic species and global climate change. However, one of the major threats the oceans may face in the twenty-first century is radioactive pollution over the second half of the twentieth century.

Marine biodiversity is threatened by human impact. Though few marine species are regarded as being extinct due to Man, many species are critically endangered (e.g. the monk seal Monachus monachus), endangered (e.g. the Mediterranean giant limpet Patella ferruginea) or vulnerable, i.e. dwindling rapidly, although not threatened with extinction in the immediate future (e.g. the large mollusk Pinna nobilis). There are also threats to ecosystems (ecodiversity), such as, in the Mediterranean, the Lithophyllum byssoides rim and the seagrass Posidonia oceanica meadow. Marine Protected Areas (MPAs) were initially established to protect biodiversity via the removal of human exploitation and occupation. However, since the 1970s, the notion of MPA has moved on to a more general concept of nature conservation, then to a more dynamic one of nature management, within the framework of sustainable development. Today, the aims of MPAs are therefore sixfold: nature conservation, public education, reference areas for scientific research, tourism, export of fish eggs, larvae and adults to adjacent areas and finally management of the various uses of the sea (e.g. commercial fishing, recreational fishing, pleasure boating and tourism) in such a way that they do not conflict with each other or with conservation aims. Mediterranean MPAs, especially the Port-Cros National Park, illustrate the fact that they are rather characterized by the management of human activities than by a set of prohibitions and that there is no negative interaction between biodiversity conservation and artisanal fishing (i.e. small-scale commercial fishing), at least in the way it is done (i.e. with additional constraints to general regulations: mesh size, prohibition of trawling and longlining, etc.). Consequently, MPAs are generally of benefit to the economy (e.g. commercial fishing and tourism industry), not only within MPAs but also in adjacent areas. They therefore constitute a powerful tool for integrated coastal management.

There is a clear relationship between nutrient enrichment and the eventual deterioration of coastal water quality (eutrophication). Eutrophication occurs when the rate of nutrient supply exceeds its transformation or removal rate and excess nutrients stimulate excess biological production. This imbalance may be corrected to varying degrees by enhancing certain natural biological/ecological attributes (ecosystem services), such as the removal of particles by means of filter feeding animals. This topic is addressed by means of a case study — aquaculture in coastal waters. We begin by examining the impacts related to the release of nutrient-rich effluents from a commercial fish farm in the oligotrophic Gulf of Aqaba. This is followed by description of 3 approaches that have been tested as means to capture and remove aquaculture effluents, as an example of how we may enhance the sustainability or reduce the environmental impacts of commercial activities. These approaches include placement of detritus feeding grey-mullets in benthic enclosures on the organically enriched seafloor below commercial fish cages, mooring artificial reefs as benthic biofilters next to fish farms and deployment of pelagic biofilters in the water column, adjacent to fish cages.

During the decade since the 1992 United Nations Conference on Environment and Development, considerable movement has been made by international organizations engaged in ocean affairs to move nations toward adopting ecosystem-based assessment and management strategies. The 191 nations, including 82 heads of state, participating in the 2002 World Summit on Sustainable Development in Johannesburg agreed to a plan of implementation (POI) that encourages nations to apply the ecosystem approach to marine resource assessment and management practices by 2010, and maintain or restore fish stocks to levels that can produce maximum sustainable yield levels by 2015. To achieve these targets will require an improved understanding and assessment of the effects of physical, biological and human forcing causing changes in biomass yields of large marine ecosystems (LMEs). An international financial mechanism, the Global Environment Facility (GEF), is assisting developing countries in meeting the Summit targets by supporting LME assessment and management projects. Of the 29 LMEs for which published case study information is available for analyses of principal forces driving changes in biomass yields, fishing effort was the primary forcing mechanism in 14 LMEs; climate forcing was the principal factor in 13 LMEs, eutrophication in one case and the data were inconclusive in another. Fishing effort was a secondary driver of change in biomass yields in the LMEs driven by climate forcing. Mitigating actions for reducing fishing effort to promote recovery of lost biomass yield is proving successful in one case study. Actions for improving forecasts of oceanographic conditions affecting fish stocks are underway in four GEF supported LME projects (e.g. Humboldt Current, Canary Current, Guinea Current, Benguela Current); measures to assess and manage excessive fishing effort are planned for 8 LME projects, eutrophication reduction and control in another, and 6 LMEs with relatively stable decadal biomass yields appear suitable for mandating precautionary total allowable catch (TAC) levels. The GEF-LME projects include countries that contributed to 45% of global marine biomass yields in 1999.

Decision-making in environmental projects can be complex and seemingly intractable, principally due to the inherent existence of tradeoffs between sociopolitical, environmental, and economic factors. One tool that has been used to support environmental decision-making is comparative risk assessment (CRA). Central to CRA is the construction of a two-dimensional decision matrix that contains project alternatives' scores on various criteria. The projects are then evaluated by either qualitatively comparing the projects' scores on the different criteria or by somehow quantitatively aggregating the criterion scores for each project and comparing the aggregate scores. Although CRA is laudable in its attempts to evaluate projects using multiple criteria, it has at least one significant drawback. That drawback is the unclear or unsupported way in which it combines performance on criteria to arrive at an optimal project alternative. In the case of qualitative comparison of project scores using CRA, it can be unclear why an alternative is chosen if it performs better only on some criteria compared to another alternative. Quantitative CRAs are often unsupported in how they determine the relative importance of each criterion in determining an aggregate score for each alternative.

The demand for new sophisticated methods for ensuring sustainable development of exploited ecosystems is increasing worldwide. Today, the natural resources, including water, air, soil, flora and fauna, etc., are significantly affected by disastrous pollution from industrial, agricultural, municipal, and other anthropogenic sources. Without careful global management and coordination of international anti-pollution efforts, the world's oceans are threatened with catastrophic changes; under an unprecedented high rate of natural resource degradation due to pollution and overexploitation, the whole marine ecosystems may lose its integrity and collapse. These worrying situations call for efficient approaches that may help biologists detect, analyze, assess and solve the problems that occur in ecosystems in general and marine ecosystems in particular. Solving these problems involves activities that should be implemented and managed. We consider this aspect in this paper.

In order to understand, manage, and regulate the environmental impacts of marine aquaculture (or any other form of ecosystem utilisation) we need to be able to predict its effects. Prediction is based on modelling, and reliable models of how activities like aquaculture affect the marine environment are essential if such activities are to develop in a way that is environmentally friendly and compatible with other uses of marine ecosystems. Modelling must be supplemented with sophisticated and comprehensive data management, and the results of model runs must be presented to stakeholders in a clear and transparent format.

While this paper focuses on modelling the environmental impacts of marine aquaculture, most of the issues are relevant to many aspects of management of marine ecosystems, and the material is presented with this generality in mind.

Ecosystem modelling has become a very important way to study marine ecosystems processes. A valuable tool for model development is the use of the software package , which enables the construction of foodwebs and their simulation over time and space according to different scenarios. An important part of the process of ecosystem modelling is to compare results from the model with those from observations, followed by an analysis of the remaining sources of error. However, few of the currently developed models have gone so far as to examine the uncertainty in analyses. Thus, it would be useful to address this problem, to clearly define the type of uncertainty that may be encountered in ecosystem modelling, and the means by which it may handled. Sensitivity analyses represent one solution by which one might address uncertainty in . This approach functions by examining the sensitive elements as revealed in model results with differing scenarios of model-building and construction. In addition, other tools can also be used to perform uncertainty analysis routines. Examples are the and tools, all of which are included the software package. Furthermore, it is possible to combine these approaches with other modelling techniques in order to get an even stronger analysis of uncertainty. The purpose of this paper is to examine the strengths and weaknesses of these different approaches in addressing uncertainty.

This paper considers a pollution and control game which uses a queuing framework. This framework allows to account for pollution events, environmental pollution quality and the application of controls to maintain a desirable quality of the environment. A number of examples are used to highlight the approach and demonstrate both its theoretical and practical usefulness.

Algorithmic undecidability of the problem of determining computational complexity of models describing various ecosystems has been proved from a formal language theory point of view