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Commuter railroad service on the [[San Francisco Peninsula]] was inaugurated in 1863 as the [[San Francisco and San Jose Rail Road]] and purchased by [[Southern Pacific]] in 1890. In the early 1950s, Southern Pacific began introducing diesel locomotives on the route.<ref>{{citeweb|url=http://www.caltrain.com/about/Caltrain150/Milestones/Early_Milestones.html|title=Early Milestones|publisher=Caltrain|accessdate=March 29, 2017}}</ref> However, by 1977, Southern Pacific began facing rapidly declining ridership and petitioned the state Public Utilities Commission to allow them discontinue the commute operation. From 1980 until 1992, the [[California Department of Transportation]] (Caltrans) and the three service counties, [[San Francisco]], [[San Mateo County, California|San Mateo]], and [[Santa Clara County, California|Santa Clara]], subsidized Southern Pacific operations on the railway until the local Peninsula Joint Powers Board acquired the right-of-way in 1991.<ref>{{citeweb|url=http://www.caltrain.com/about/Caltrain150/Milestones.html|title=Historic Milestones|publisher=Caltrain|accessdate=March 29, 2017}}</ref> One year later, Caltrans released the first feasibility study over the possibility of electrifying the railroad between San Francisco and San Jose.<ref name="first proposal">{{citeweb|url=http://bayrailalliance.org/files/library/Caltrans_feasibility_study_of_electrification.pdf|title=Feasibility Study for Electrifying the Caltrain/PCS Railroad|publisher=[[California Department of Transportation]]|date=October 1992|accessdate=March 29, 2017}}</ref>
Due to funding shortages, the project was postponed for the next two decades. In 2004, Caltrain introduced a [[Caltrain Express|express service]] that reduced travel time along the railroad. Within a year, ridership increased by 12%<ref>{{cite news |url=http://www.sfgate.com/bayarea/article/BART-S-PENINSULA-LINE-FALLS-SHORT-OF-HOPES-2658527.php |title=BART's Peninsula Line Falls Short of Hopes / Competition from cheaper baby Bullet trains could be hurting ridership on extension |author=Murphy, Dave |date=30 June 2005 |newspaper=San Francisco Chronicle |accessdate=25 March 2017}}</ref> and doubled by 2012.<ref name="2016ridership">{{citeweb|url=http://www.caltrain.com/Assets/__Agendas+and+Minutes/JPB/Board+of+Directors/Presentations/2016/2016-05-05+Annual+Counts.pdf|title=2016 Annual Passenger Counts|page=3|date=May 5, 2016|accessdate=March 29, 2017}}</ref>
In February 2015, shortly after the project received environmental clearance from [[California]], the town of [[Atherton, California|Atherton]], which lies on the tracks, sued Caltrain, alleging that the agency's environmental impact review was inadequate and that its collaboration with the CHSRA should be further vetted. On September 2016, [[Contra Costa County Superior Court]] Judge [[Barry Goode]] sided with Caltrain, ruling that the electrification project does not hinge on the high-speed rail project's success, and is thus independent from the latter.<ref>{{citeweb|url=http://www.smdailyjournal.com/articles/lnews/2016-09-27/judge-gives-caltrain-electrification-green-light-atherton-loses-lawsuit-claims-local-project-was-too-closely-tied-to-high-speed-rail/1776425168923.html|title=Judge gives Caltrain electrification green light: Atherton loses lawsuit, claims local project was too closely tied to high-speed rail|publisher=''The Daily Journal''|date=September 27, 2016|author=Weigel, Samantha|accessdate=March 29, 2017}}</ref> [[File:Elaine Chao large.jpg|thumb|left|Secretary of Transportation [[Elaine Chao]] deferred expected federal funding for the electrification project just before construction was about to commence.]]
By February 2017, the electrification project had secured $1.3 billion in state, local, and regional funding, with the remaining funding gap to be closed by a $647 million grant from the [[Federal Transit Administration]]’s (FTA) Core Capacity program.<ref>{{citeweb|url=http://www.caltrain.com/about/MediaRelations/news/Caltrain_Statement__Electrification_Must_Move_Forward.html|title=Caltrain Statement: Electrification Must Move Forward|publisher=Caltrain|date=February 8, 2017|accessdate=March 29, 2017}}</ref> The grant had undergone a two-year review process under the [[Obama Administration]] and received a "medium-high" rating from the FTA, and was waiting the new [[Trump Administration]]-appointed Secretary of Transportation [[Elaine Chao]]'s signature after a thirty-day review period.<ref name="contractextension">{{citeweb|url=http://www.mercurynews.com/2017/02/28/caltrain-agreement-with-contractors-to-extend-deadline-keeps-electrification-project-alive/|title=Caltrain: Agreement with contractors to extend deadline keeps electrification project alive|publisher=''[[San Jose Mercury News]]''|author=Green, Jason|date=February 28, 2017|accessdate=March 29, 2017}}</ref> However, during the review period, the fourteen [[Republican Party (United States)|Republican party]] [[United States House of Representatives|U.S. House]] representatives from California sent a letter to Secretary Chao, urging her to deny funding due to the project's ties with high-speed rail, which they opposed. They called the high-speed rail project a "boondoggle" and the Caltrain grant as a "waste of taxpayer dollars".<ref name="grant">{{citeweb|url=https://www.nytimes.com/2017/03/06/us/trump-and-republicans-block-caltrain-grant.html|title=In Silicon Valley, Caltrain Upgrade Is Imperiled as Trump Withholds Funds|publisher=''[[The New York Times]]''|date=March 6, 2017|accessdate=March 29, 2017}}</ref>
Secretary Chao heeded their arguments, and deferred the grant in a letter to Caltrain which stated that the FTA needed "additional time to complete review of this significant commitment of Federal resources".<ref name="contractextension"/> Caltrain had expected Secretary Chao to approve the grant by March 1, which is normally a ''[[pro forma]]'' step done after the thirty-day comment period for a highly-rated project, and had already awarded construction contracts.<ref name="contractextension"/><ref name="SV">{{citeweb|url=http://www.eastbaytimes.com/2017/03/24/trump-chao-get-an-earful-on-caltrain-funds/|title=Trump, Chao get an earful on Caltrain funds from Silicon Valley leaders|publisher=''East Bay Times''|author=Richards, Gary|date=March 24, 2017|accessdate=March 29, 2017}}</ref> [[Balfour Beatty Construction]] and [[Stadler Rail]] had already begun preparations to upgrade the existing tracks and build electrical trainsets, respectively. In response, Caltrain negotiated an emergency four-month extension at the cost of $20 million.<ref name="contractextension"/>
In response to the grant deferral, various local officials traveled to [[Washington D.C.]] in order to lobby federal officials to release the money. San Jose Mayor [[Sam Liccardo]] met with Department of Transportation officials, urging them to upgrade a system that "was built under the presidency of [[Abraham Lincoln]]". Additionally, more than 120 Silicon Valley business leaders sent a letter to Secretary Chao, asking her to explain "the last-minute attempt to derail two decades of work".<ref name="SV"/> On March 21, 2017, California Governor [[Jerry Brown]] met with Secretary Chao and House Majority Leader [[Kevin McCarthy]], author of House Republican letter to Chao, urging them to reconsider the funding deferral, saying afterward that he was "cautiously optimistic" that the money would be released.<ref>{{citeweb|url=http://www.sacbee.com/news/politics-government/capitol-alert/article139943463.html|title=Jerry Brown meets with Republicans, ‘cautiously optimistic’ about Caltrain approval|publisher=''[[Sacramento Bee]]''|date=March 21, 2017|accessdate=March 29, 2017}}</ref>
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