With powerful friends, it resisted an effort in the 1990s to move the museum out of the park and successfully fought for a new parking garage and against creating more car-free spaces in the park.
The academy is a living, dynamic institution, much like the building's signature living roof and subject to the same kinds of hard choices in coming years about whether to emphasize scientific purity or pursue more pragmatic pathways.
After touring the museum, I did a telephone interview with Paul Kephart, CEO of Rana Creek, which designed the roof and wanted to simulate a local ecosystem of flora and fauna that went through natural life cycles, including periods of death and decay.
"Selling the idea to the academy and the board was one of the most challenging aspects of the project," Kephart said.
He explained that the idea is to maintain the roof using an irrigation system for the first couple years, until it establishes itself, then remove the irrigation and stop actively tending the space, letting nature take over, even if that means weeds.
"I think that's a good thing," he said. "The roof should be allowed the opportunity for nature to express itself and be less controlled and more adaptive to climate and environment.... I always saw the roof as an experimental design."
Yet it's also an integral part of the building's design and aesthetics, and the academy has not yet decided how much of the roof will be allowed to go natural and how much will be managed. Kephart said it has amazing research possibilities because "nature will have the most influence on how the roof will behave."
Similar choices were at play in other parts of the museum, such as the Steinhart Aquarium, which was designed by the New York City firm Thinc.
"The whole idea underlying the aquarium is, this is an institution that studies the natural world," Thinc president Tom Hennes told me at the academy. While the new aquarium is larger than its predecessor, a few of its more ambitious plans such as an open ocean exhibit and twice as many dive stations as the current five were scaled back.
"Any exhibit starts with a huge dream," Hennes said. "Then you whittle it down to size."