1899 is a key year regarding this question. I believe that when you look at all of the anecdotal evidence, that you come away with a clear impression that the New Haven Railroad envisioned, at the very least, a South Shore and Metro-West (today's parlance) electric rapid transit system and domination. 1899 was the year that construction began on BERY's Main Line Elevated which would extend southerly in Boston in a very similiar route as the New Haven's inherited Boston-Providence Main Line, going as far as Roxbury, and then practically using the same alignment from then on to Roslindale. 1899 was also the year that an enclosed subterrainean loop was included into the construction at South Station. Legend has it that engineers attempted to use this loop with steam equipment, realizing that the contained fumes made it impossible to do so. When you look at the other structures and facilities designed by the New Haven, do you see indications of similiar poor decisions ? Coincidentally, a subterrainean two track platform-fed installation was included into the construction at their Back Bay Station. This one specifically was labelled on diagrams for the building as "suburban (electric)" tracks which had an island platform, which like the South Stations "loop", were never used. The stated reason for this failure was that the Back Bay Suburban Electric tracks had difficult access by passengers at the upstairs waiting room. The New Haven went on to widen the Main Line, equipping it as a four-track mainline. It publicly announced plans to run commuter trains on the outer tracks with high-speed trains on the inner ones. Fences would divide the two modes. Rapid Transit scaled trolleys were installed on the Pemberton-Nantasket Branch, utilizing an experimental third-rail system in 1895. As has been suggested, I believe that this attempt to dominate was done privately and behind closed doors. Probably a few green backs may possibly have been involved in a commute of their own from one pocket to another. I believe that this is why that one-hundred years later, that there is no official record of the movements made to this end. Also as has been suggested, I believe that forces in Boston told the New Haven that they were not welcome (in so many words) to overtake BERy. It is this reason, I believe, that find that the New Haven to Boston leg of the Main Line was not electrified under NH. Either the NH didn't feel that the cost of electrifying this segment wasn't worth the expense without the increased revenue that additional suburban service would afford or they just plain were snubbing Greater Boston for it's refusal to submit as so many other areas had. The necessity of maintaining dual equipment and continually having to break through trains at New Haven, Ct., must have surpassed the cost of electrifying this segment. While researching the New Haven's founder J.P.Morgan, I found this interesting sideline regarding J.P. (he preferred to be called "Piepont") Morgan from Wikipedia - "Morgan suffered a rare business defeat in 1902 when he attempted to enter the London Underground field. The notorious transit magnate Charles Tyson Yerkes thwarted Morgan's effort to obtain parliamentary authority to build an underground road that would have competed with "Tube" lines controlled by Yerkes. Morgan called Yerkes' coup "the greatest rascality and conspiracy I ever heard of.""
I think that perhaps you can make an argument that any one or even two of these irregularities may be a coincidence, but I think when looked at as a whole, that there can be little doubt.
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