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Neofunctionalism is a theory of regional integration, building on the work of Ernst B. Haas, a German-born American political scientist and also Leon Lindberg, an American political scientist. The explicit purpose of the neofunctionalists was to utilize the pioneering European experience of integration to generate hypotheses for testing in other contexts. Jean Monnet's approach to European integration, which aimed at integrating individual sectors in hopes of achieving spill-over effects to further the process of integration, is said to have followed the neofunctional school's tack. Haas later declared the theory of neofunctionalism obsolete, a statement he revoked in his final book, after the process of European integration started stalling in the 1960s, when Charles de Gaulle's "empty chair" politics paralyzed the institutions of the European Coal and Steel Community, European Economic Community, and European Atomic Energy Community. The theory was updated and further specified namely by Wayne Sandholtz, Alec Stone Sweet, and their collaborators in the 1990s and in 2000s (references below). The main contributions of these authors was an employment of empiricism.
Neofunctionalism describes and explains the process of regional integration with reference to how three causal factors interact with one another: (a) growing economic interdependence between nations, (b) organizational capacity to resolve disputes and build international legal regimes, and (c) supranational market rules that replace national regulatory regimes.
Early Neofunctionalist theory assumed a decline in importance of nationalism and the nation-state; it predicted that, gradually, elected officials, interest groups, and large commercial interests within states would see it in their interests to pursue welfarist objectives best satisfied by the political and market integration at a higher, supranational level. Haas theorized three mechanisms that he thought would drive the integration forward: positive spillover, the transfer of domestic allegiances and technocratic automaticity.
Neofunctionalism was modified and updated in two important books that helped to revive the study of European integration: European Integration and Supranational Governance (1998), and The Institutionalization of Europe (2001). Wayne Sandholtz and Alec Stone Sweet describe and assess the evolution of Neofunctionalist theory and empirical research in their 2009 paper, Neo-functionalism and Supranational Governance.
Intergovernmentalism is an alternative theory of political integration, where power in international organizations is possessed by the member-states and decisions are made by unanimity. Independent appointees of the governments or elected representatives have solely advisory or implementational functions. Intergovernmentalism is used by most international organizations today. An alternative method of decision-making in international organizations is supranationalism.
Intergovernmentalism is also a theory on European integration which rejects the Neofunctionalist mechanisms of integration. The theory, initially proposed by Stanley Hoffmann and refined by Andrew Moravcsik suggests that governments control the level and speed of European integration. Any increase in power at supranational level, he argues, results from a direct decision by governments. He believed that integration, driven by national governments, was often based on the domestic political and economic issues of the day. The theory rejects the concept of the spill over effect that neofunctionalism proposes. He also rejects the idea that supranational organisations are on an equal level (in terms of political influence) as national governments.
Neofunctionalists have attacked Intergovernmentalism on theoretical grounds, and on the basis of empirical evidence which they claim show that Intergovernmentalism is incapable of explaining the dynamics and overall trajectory of European integration.  Today, approaches with affinities to Neofunctionalism dominate the study of European integration, and especially research on the European Union's legal system, and there is little research in the Intergovernmentalist vein currently being produced.
In the last decades Haas' theory has been revived by several authors, who describe the neofunctionalist theoretical legacy left by him as able to speak directly to current EU studies and comparative regionalism, if it is seen as a dynamic theory that corresponds to established social scientiﬁc norms with disciplinary openness.