海洋生態環境是一個開放且動態的系統且提供生態系統服務給全人類使用。為了維持海洋生態系統的永續性，1992年聯合國環境及發展會議 (United Nations Conference on Environment and Development, UNCED) 中提出大型海洋生態系統 (Large Marine Ecosystems, LMEs) 的概念並開始推動執行。在目前區畫的64個LMEs已含蓋全球95%的魚類及其他海洋生物，但全球的魚類資源卻有高達70%處於過度捕撈 (overexploited) 之危機中。海洋生態系統管理 (Marine ecosystem management, MEM) 係為一具全面性、整合性及系統性的海洋資源管理系統，且其強調各面向的同時考量，包含了生態、經濟、社會、法令與政治等面向。然海洋生態系統的複雜性 (complexity) 與不確定性 (uncertainty) 提升了執行MEM的難度，甚已成為目前執行MEM的重大挑戰。因此，本研究將試圖應用科學管理 (scientific management) 的概念來解決目前MEM所面臨的四大挑戰。
海洋保護區 (marine reserve)雖已被視為能提升魚群豐度的重要管理機制，但於現有的保護區中似乎不易明確的獲得證實。根據相關的海洋保護區規劃研究顯示，海洋保護區在設計規劃時較缺乏數理上的理論基礎，以及相關數理模式的實用性不高等弱項。因此，本研究將以魚群的反應-擴散形式去建構一個具實用性的數學通式，用以預估保護區的範圍大小。為了確認在保護區內的魚群量，本研究應用機率理論與統計抽樣理論重新建構一個常態基礎 (normal-based) 的方程去推算保護區的半徑大小。本研究進一步將常態基礎方程應用於不同的保護區個案中進行推論與比較，顯示此方程應可視為一具實用性的工具來解決海洋保護區規劃時的複雜性與不確定性。就管理程序的挑戰而論，本研究針對權益關係人 (stakeholder) 的觀點去勾勒出在執行海洋空間規劃 (Marine Spatial Planning, MSP) 其間的重要管理面向。其主要的目的在於試圖透過管理面向的分析，歸納出一個重要管理元素，以期能協助未來MEM的推動。就海洋資源管理的衝突解決而言，本研究應用整合性參與的多準則決策分析法來解決權益關係人間的衝突爭端。由研究結果顯示政府當局與權益關係人的相互重要性，並進一步建議政府當局在保護區規劃之初應充分的善用其公權力的行使，而權益關係人則應積極的參與並進行知識的交流。台灣已經制定出多項漁業政策以處理複雜的漁業問題，但在政策的推動上卻日益艱辛，引發的衝突亦日益高漲。為試圖處理目前漁業保育政策推動不易的困境，本研究應用合作賽局的方法去計算各權益關係人的最佳報酬，並進一步運用結盟 (coalition) 的方式去分析各權益關係人在不同漁業政策中的結盟報酬，以提供作為意見相左時的解決方案。最後，本研究更試圖去建構一個新的MEM方針，以作為未來執行MEM的參考依據。

Marine ecological environment is an open and dynamic system that offers ecosystem service for human. In 1992, United Nations Conference on Environment and Development (UNCED) launched Large Marine Ecosystems (LMEs) to maintain sustainable marine ecosystem, however, there are 95% of the global fishes and other marine living resource come from 64 LMEs but 70% of global fish stocks are overexploited. Marine ecosystem management is an entire, integrated and systematical marine resource management system which is emphasized that the considering of the ecological, economic, social, legitimate, and political aspects simultaneously. Complexity and uncertainty increased the difficulty to manage marine ecosystems, and resulted in four challenges to hinder the implementation of Marine ecosystem management; therefore, this study attempts to apply the concept of scientific management to deal with four challenges.
Marine reserve could be conducive to increasing fish abundance; however, these results do not show the adequacy of the fish stock size within the reserve. According to the planning of marine reserve, we have known that the design of reserve size lacks a theoretical foundation of mathematic and practicability. This study based on the reaction-diffusion of fish stocks to rebuild a practicable general equation for the estimating of reserve boundary. In order to explain the amount of fish stocks within the reserves, this study provides a new concept, that was applied the Probability Theory and Statistical Sampling to build a normal-based equation to determine reserve radius. The estimated radius could be regarded as a practicable tool to resolve a complexity and uncertainty marine reserve planning. With regard to the challenge of management proceeding, this study focuses on stakeholder perspective to demonstrate what type of management dimension should be emphasized during the implementation of marine spatial planning (MSP). The primary purpose of this article attempted to induce a critical element to assist in executing the marine ecosystems management in the future. In terms of conflict resolution of marine resource management, this study used the integrated participatory multicriteria decision method to result in the reasons of stakeholders’ conflict, and further argued that the governmental authorities should fully implement their power in the initial stages, and stakeholders should actively participate and share their knowledge. Taiwan has made different fishery policy to handle complex fishery problem, however, the implementation of fishery policy become more difficult currently due to the competition of limited fishery resources. In order to resolve the dilemma, this study attempts to apply cooperative games to gain an optimal payoff between stakeholders and policies, and further to adopt the coalition approach to analyze the cooperative relationship of stakeholders for different fishery policy. Finally, this study attempted to construct a new approach for efficient implementation of marine ecosystems management form the dealing with four challenges.

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