Whenever Martin and his buddy Terry Wickett get sick of all the politics and compromises at the McGurk Institute, they like to fantasize about building a lab out in the Vermont wilderness and working on science experiments with total freedom. As Terry says,
"Some day I'm going to figure out a way of making a lab here pay […] and I'll put up a couple more buildings on the flat by the lake, and have one absolutely independent place for science." (37.1.29)
Terry, you see, already owns the property in Vermont, and all he needs is one good excuse to cut ties with McGurk.
By the end of the book, Terry and Martin both make good on their dreams and head out to their Vermont shack. There's no hot water and the shack is usually cold. As Martin says, "It's kind of a mis'able return to monasteries […] except that we're not trying to solve anything for anybody but our own fool selves" (40.3.6).
You can hear some of the humor in this line, because even though Martin doesn't like the cold, he's more than happy to make this sacrifice in order to do his work the way he wants to do it. And that's exactly what the shack comes to symbolize by the end of the book—total freedom to pursue his personal interests.