In Maine’s largest city, the waterfront has seen some hard times. The fish processing plants are gone, the fishing industry is a shadow of its former self, and the Portland Fish Exchange recently leased out part of its refrigerated hall because it just doesn’t need the space. The container port was closed for much of last year (it lives or dies on the health of Old Town’s paper mill) and the new Ocean Gateway Terminal, built under bogus economic assumptions, just lost its only customer, The CAT, a high-speed ferry that can’t make ends meet in the new world of expensive oil.

But one institution is still growing on the western waterfront, one that has demonstrated some impressive, federal-level political savvy.

The Gulf of Maine Research Institute (formerly the Gulf of Maine Aquarium) recently announced two acquisitions. Both are orphans of one sort or another of the United States government, which had been a neglectful (and in one case, abusive) parent.

The first is the Gulf of Maine Ocean Observing System, better known as GoMoos, which GMRI absorbed at the end of the year.

GoMoos-a network of offshore buoys collecting real time oceanographic data-has many fans. The U.S. Coast Guard uses its wave and current data to better calculate where distressed mariners will be by the time the rescue chopper hits their position. Scientists use salinity and temperature records to better predict the movements of lobster larvae or the likely size of the upcoming shrimp catch. It used to provide salmon farmers an early warning when lethally cold water was en route to the pens.

It also was a model for the national network of ocean observing systems endorsed by both the Bush administrations’ U.S. Commission on the Oceans and the independent Pew Oceans Commission, a system capable of collecting the sort of data vital to properly managing marine ecosystems in future. One study reckoned overall economic benefits at $33 million a year in rescued property, improved fisheries management, and oil spills that didn’t happen.

But the federal government let it die on the vine, unwilling or unable to come up with the paltry $2 million a year needed to keep it running properly. Much of the paltry funds Congress was willing to devote to ocean observing were diverted to help build new systems on the West Coast, forcing GoMoos to permanently retire four of eleven buoys last year.

Most of what’s left of the buoy system is under the care of the University of Maine, but it hasn’t been clear how the data processing team-the people who make and maintain all the whiz-bang applications that turn the data into forms useful to scientists, surfers, fishermen, and kayakers-was to survive. That GoMoos team has now found a home inside GMRI.

Don Perkins, GMRI’s president, says the merger doesn’t solve the funding problem, but puts the organization on a better footing to find new partners and revenue streams. “By attaching to us, GoMoos gets a larger institutional platform,” he says. “We’re really sophisticated when it comes to strategy and management, and because they are surrounded by marine scientists, educators, and conflict facilitators, it’s like working inside a giant stakeholder focus group.”

“We’re going to help GoMoos take a broader looks at the kind of problems they could be addressing and where the new markets lie,” he adds. Possibilities: providing know-how to other entities focused on collecting data and making it useful to various kinds of users, including those well inland.

As the GoMoos deal was closing in early November, GMRI scored another victory: a $1.5 million gift from the people of Maine, approved at the polls as part of a transportation ballot measure. When added to the $400,000 Maine taxpayers gave the institution under the 2005 transportation bond, the $700,000 they allocated via the 2007 bond, and another $717,000 from the federal Department of Energy, GMRI now has enough money to make good on a deal to take custody of another federal orphan, Portland’s old Naval Reserve Pier.

The pier, located behind the GMRI building and next to the Portland Fish Pier, was owned by the Coast Guard, which tied up its 110-foot cutters there for decades. Unfortunately, as the pier aged, the Coast Guard wasn’t able to secure the $4 million needed to repair it.

“We have a finite budget each year for shore recapitalization,” like pier repairs, explains Coast Guard Capt. Michael Carosotto, commanding officer at the Civil Engineering Unit in Warwick, R.I. “There are a lot of competing demands and you have to prioritize your work based on what has the most mission impact, the biggest bang for your buck.”

Although it was soon to be condemned, the Portland pier didn’t compete well on the national stage, largely because of the presence of the Coast Guard base just across the water in South Portland. “It had to compete with similar pier replacement projects in places in the country that had no other [ship mooring] options at all,” Carosotto says.

Enter GMRI, which conjured up the following 2002 deal with the help of senators Olympia Snowe and Susan Collins and Maine’s past and present Congresspeople. The Coast Guard would give the 4.13 acre property to GMRI if it came up with the repair money by the end of 2009. The research center is obligated to lease docking space back to the Coast Guard, rent free, for 30 years.

Take a step back to enjoy the irony: for lack of federal assets, a U.S government property is turned over to another institution, which repairs it with federal and state assets. (The property on which the GMRI building was built was secured in a similar deal with the U.S. Navy.)

While the process may seem bewildering to those who don’t spend much time inside the Beltway, the result appears to be a good thing all the way around. The Coast Guard gets the use of their pier back, relieving crowding over in South Portland. GMRI gets a deepwater dock to attract oceanographic researchers and space to build up to 250,000 square feet of new research park development.

“The state will have put in $2.4 million for the bulkhead, but the property has the capacity for something like $100 to $120 million of facility construction and employment accommodating on the order of 1000 people on the site,” says Perkins, who argues it will be a significant return on the public’s investment.

GMRI’s original dream of building an aquarium on the site has been dispensed with in favor of what Perkins describes as “an intellectual capital park”: four to five buildings housing innovative fish processors, marine biotechnology researchers, offshore wind energy firms, and fisheries researchers.

“Portland has the potential to emerge as one of the nation’s marine science cities,” he says. “Over the next decade, I think we’ll see a lot happening here.”

If so, the public’s investment in GMRI will have proved a smart one.

Colin Woodard is an award-winning journalist and author of The Lobster Coast: Rebels, Rusticators, and the Struggle for a Forgotten Frontier.