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But what about the connections between Rochester and Buffalo, Buffalo and Niagara Region, and Niagara and the GTA?
How many Canadians cross the border to work in Buffalo? How many people on the Canadian side would closely associate with people on the other side? What frequent transportation links are there between Niagara and Buffalo? Certainly there is some interaction across the border but it is insignificant compared to the interaction across the boundaries of Burlington and Oakville.
How much of a connection does Boston have with Washington? Or Hamilton with Oshawa for that matter?
Boston and Washington have frequent corridor services by Amtrak and special corridor flights between their airports. The cluster is well connected inside itself with no defined work boundaries. Hamilton and Oshawa are also connected by GO Transit's network and continual built up area. Someone living in Burlington is quite likely to work in Hamilton or Oakville, Someone in Oakville is quite likely to work in Toronto, Mississauga, or Burlington, etc. There is no boundary between these places which creates a barrier to work and social patterns.
Before the wall fell in Berlin, East and West Berlin were different cities. They were together geographically but far apart socially. Economic hubs and innovation come from working together and that is more of a social measure than a geographic one.