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They just accept that there is a risk involved when taking freight and amtrak at speeds between 60 and 70 mph over rough stretches of track. It makes enough money that they don't care about the freight, and amtrak makes so little money that they don't care to fix anything just for passenger rail. It's sad, because good rail service is way better than plane travel. Especially over short distances like the northeast corridor, it would be cheaper, more comfortable, and quicker than flight when accounting for TSA times and wait times.
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