Deep Trouble: In hunt for Asian carp, scientists find DNA, controversy

University of Notre Dame's David Lodge (left) helped create a genetic-based technique to track elusive Asian carp. Here he watches as Joel Corush, a research technician, filters a sample of water for telltale traces of DNA. Gary Porter

This report was originally published on Aug. 21, 2012. It is a part of the series "Deep Trouble."

A fish pond in Missouri reveals just how stealthy Asian carp can be.

Maybe an acre in size, the pond had been stocked with catfish, bass and bluegills. The owner was pumping it full of fish food, yet the fish appeared to be starving. So in early 2010 the owner called in a consultant.

"They came out with electrofishing gear, caught some fish and looked at them," said Duane Chapman, one of the country's leading Asian carp experts and a biologist with the U.S. Geological Survey. "The fish were emaciated and he didn't know why. He said, 'There's something wrong here. We need to start over again.' They brought in rotenone and completely killed the pond."

Over the next week, the rotting carcasses of about 300 bighead carp surfaced. The smallest were 20 pounds. The big ones were a border collie-sized 35 pounds. Poisoned Asian carp, Chapman explained, are different from many fish species in that they typically don't surface unless the water is warm enough for gases to build up in their bellies, a process that can take a week.

"It was quite amazing there could be that much poundage in one small pond," Chapman said.

It turned out that a decade earlier the previous property owner had stocked the pond with bighead. They had flourished right under the nose of the new owner, who had smelled trouble - but couldn't see a thing.

David Lodge is one of the country's leading invasive species experts and in recent years has earned a reputation as a scientist who isn't content to see his work go dusty on library shelves. The bespectacled 54-year-old with a younger man's shock of black hair still has a bit of a Southern drawl from his boyhood in Alabama, yet he enunciates his words in such a precise manner it is easy to picture him as the budding naturalist he remembers being as a child.

"I was one of those kids who just was fascinated with nature from the get-go," he said in his office at the University of Notre Dame's Innovation Park, a gleaming new campus building where fingerprint scans open locked doors. "I spent all my idle moments turning over rocks in streams and swimming, snorkeling, fishing, catching frogs and snakes and turtles and whatever else I could catch . . . I spent my free time inside reading field guides. That's not your average teenager activity. But I was more happy doing that than playing baseball."

Lodge thought about studying history when he got to college, "But in the end I think it was pretty clear to others, even if it wasn't always clear to me, that I just loved biology."

That love carried him to Oxford University as a Rhodes Scholar. He went on to serve as chairman of President Bill Clinton's Invasive Species Advisory Council and to create Notre Dame's Environmental Change Initiative, a team of university researchers that tries to inform public policy decisions on hot-button environmental issues such as invasive species and climate change.

Crossing the line from pure academic research into public policy is not something he did lightly, because at the beginning of his career it wasn't considered acceptable.

"When you wrote proposals to get research to support your work, you didn't couch them in terms of what problems you were going to solve in the world," he said. "You couched them in terms of intellectual excitement and new ideas."

But that line has blurred in recent years, and today Lodge's work is often at the center of some of the region's prickliest ecological and political debates. He's done research to predict which species are most likely to invade the Great Lakes if ships are allowed to continue discharging contaminated ballast water; he's tried to put a price tag on the annual cost of invasive species to the Great Lakes (an estimated $200 million); he's done work predicting which freshwater fish species are most likely to go extinct because of climate change.

Straddling the worlds of politics and science has never been a comfortable exercise for Lodge. Messengers, after all, don't just get blamed for delivering grim news. Sometimes they get vilified. But Lodge always figured the stress of publicly defending his work in the media and to policy-makers was the price he paid for doing science that mattered.

By summer 2009, with Asian carp advancing toward the Great Lakes and federal officials desperate to find someone who could show them exactly where the "leading edge" of the invasion was, that price was about to explode.

Lodge's skills as an ecologist and his willingness to wade into sticky issues made him and his colleagues a logical choice a few years back when a think tank funded by most of the Great Lakes states gave his lab a grant to develop a genetic-based test to identify invasive species hitchhiking into the lakes in the ballast tanks of overseas freighters.

Law enforcement investigators have been using DNA analysis for more than two decades to put bad guys behind bars. These genetic fingerprints can be harvested from almost anything the human body sheds - flecks of skin, strings of saliva, drops of semen, chips of toenails.

From that material, scientists can isolate and identify the molecules that are an individual's DNA, the famous double helix. Each minuscule twisting ladder is made up of billions of rungs built from four types of chemicals, called nucleotides. DNA is such a powerful forensic tool because the order of these billions of rungs, each made up of two interlocking nucleotides, is unique for each individual. Scientists zero in on relatively short sequences of nucleotides on a piece of human DNA to see if the genetic material harvested from a crime scene is a match for DNA taken from a suspect.

But this genetic fingerprinting process also works on the species level; all silver carp, for example, share an identical sequence of nucleotides at various places in their DNA.

It wasn't a big leap for the Notre Dame team to realize that its idea to deploy DNA testing to detect species in ballast tanks might also work in the U.S. Army Corps of Engineers' blind hunt to find the fish in the turbid flows of the Chicago Sanitary and Ship Canal. This kind of analysis had already been done on a smaller scale by an Italian researcher who used DNA to find American bullfrogs in European ponds.

It works because fish and other aquatic life constantly shed cells in things such as mucus, urine and feces. Those cells tend to stay suspended in water, and that means every fish leaves in its wake a genetic trail. That trail can be traced by filtering all the DNA from all the different species that have left behind a piece of themselves in a water sample.

Once that pile of DNA is isolated, lab technicians put it in a test tube and add to it some precisely engineered genetic markers - called primers - that are designed to attach only to the DNA of the targeted species. A concoction with free-floating nucleotides is also added to the mix and then the sample is heated. The heat unravels the DNA helixes of all the species filtered from the original water sample.

If any of the targeted species' DNA is present, the primers glom on to each separated helix as the sample cools. That starts a zipper-like reaction in which an enzyme that is added to the sample binds the free-floating nucleotides to each strand of original DNA. Suddenly one piece of DNA has been turned into two. The process is repeated dozens of times so that even a single piece of DNA can be replicated beyond a billion, to the point the target DNA can actually be seen as a glow under an ultraviolet light when yet another chemical is added.

One piece of DNA wouldn't be enough to identify a species in a sample, nor would 100,000. But once you get a billion or beyond, a visible glow emerges.

Now your eyes can see fish in a manner no one ever could.

It all worked beautifully in the Notre Dame lab, but Lodge's team knew there was a big difference between isolating DNA floating in aquariums and sifting it from a free-flowing river. By early 2009, Lodge's staff was ready to try.

At a January meeting in downtown Chicago among researchers guiding operation of the Army Corps' electric fish barrier, located on the Chicago canal about 35 miles downstream from Lake Michigan, one of Lodge's assistants pulled an Army Corps biologist into a quiet corner. He told her he believed they had cracked the problem of filtering and identifying Asian carp DNA from open water. And he thought it could be applied on the Chicago canal. She took the idea to her bosses and got the go-ahead.

Andy Mahon, an ecologist and genetics expert at Central Michigan University who was working in Lodge's lab at the time, remembers the miserable morning in spring 2009 when he and a colleague gave their new tool a whirl on the muddy, spring-swollen Illinois River. They figured if DNA didn't turn up in a place known to be thick with Asian carp, there was no sense trying to detect it where there might be only a handful of the fish.

The two spent the morning freezing their hands filling 2-liter plastic bottles, but the excitement they had felt just weeks earlier in the lab tumbled away with the caramel-colored river. How could they possibly find, in all this water, mere molecules of fish? Mahon headed back to South Bend with his spirit as chilled as the bones in his fingers.

"Neither of us had any thoughts that this process, for us, was going to work," Mahon said.

Mahon was alone in his lab testing the samples a few days later when he saw the telltale glow. He dashed down the hallway looking for Lodge and the others.

"Shocked," is how he described their collective reaction.

The team decided to move the testing slowly up the river, toward areas where carp numbers were known to be lower.

"We had developed the tool and tested it the best way we could - in the lab, and in the field in a preliminary way," Lodge said. "But to build our own confidence and build the confidence of anybody else, we wanted to start in places where everybody agreed there were fish. So the general strategy was to start south and work our way north (toward the barrier), because the whole idea was to identify where the leading edge of the invasion front was."

When Maj. Gen. John Peabody, the head of the Army Corps' Great Lakes region at the time, got word of what they were up to, he requested a face-to-face meeting with the Notre Dame scientists.

In the summer of 2009, Peabody and his staff showed up at Rosie's Family Restaurant just down the road from the electric fish barrier in a gritty corner of southwest suburban Chicago. The general and staff arrived in combat dress - camouflaged pants tucked into high-laced boots - to grill one of Lodge's colleagues on what the Notre Dame team was trying to do.

Peabody planted himself at the head of a table with the Notre Dame scientist at his side (Lodge had a class to teach), and the general's staff scattered around, some standing, some sitting at the table.

A map was unfolded. Sugar packets were used to represent things such as fish, barriers and boats. It was at times an awkward summit between military men who were demanding crystal-clear, yes-no, answers and a scientist who makes his living in the fuzzy place at the edge of human knowledge.

Lodge's crew knew all along it was wading into murky waters. For one thing, the specific technique it developed to hunt for Asian carp in rivers hadn't at that point been published in a scientific journal, which meant it had not been independently validated by other scientists.

What's more, DNA analysis can indicate nothing about numbers of fish, their precise location (DNA drifts on the current), exactly how long the genetic material has been in the river or even how it might have gotten there. But Peabody was determined to find out if the fish were pressing his new barrier. Because of worries of electricity arcing between barges, the barrier at that time was only operating at one-quarter of its designed strength. If the general could demonstrate that the fish had arrived, that could justify turning up the voltage. Peabody heard enough that day to be convinced DNA was the best tool he had to find the fish.

The Notre Dame team continued northward in its testing - and continued to turn up evidence of the fish.

In December 2012, reporter Dan Egan took an in-depth look at efforts to separate the Great Lakes and Mississippi River basins.

In September 2009, it reported Asian carp DNA about 10 miles farther upriver than the fish had ever been seen. If the DNA evidence was correct, Asian carp had passed through the last navigation lock before the electric barrier.

Navigation locks are hydrologic lifts that allow boats to bypass a dam. Though a lock is not designed specifically to stop fish, it is a tricky obstacle because a fish has to accompany a boat into the lock chamber and exit with it once the boat is lifted and the lock gates are opened. Think of a cockroach using an elevator to migrate from the basement of a building to a top floor - a lot of things have to go right for that to happen. Then a mate has to make the trip. Then they have to find each other, as well as a safe and appropriate place to lay their eggs.

The general might not have been happy with fresh intelligence that at least one fish had apparently breached the last lock before the electric barrier. But at least this new tool seemed to work precisely the way he had hoped. Like a pair of night-vision goggles, it had illuminated a previously invisible enemy, and that gave him a chance to fight back.

As the positive DNA results crept upriver, Peabody doubled the barrier voltage to two volts per inch - still only half of its designed strength, but a surge that would help repel the smaller Asian carp that require a bigger a jolt than larger fish.

The Notre Dame team pressed on with its sampling. Lodge didn't plan to stop until he got to an area of the river where all sampling showed no trace of DNA. "The whole point," he said, "is to go to where we got all zeros, and of course, everybody, including us, was hoping all zeros happened below the barrier."

What Lodge now refers to as "the difficulties" began as the samples started regularly showing evidence of carp in places where the fish had previously been undetectable; when they opened everyone's eyes to the immediacy of the ecological threat facing the Great Lakes.

On Nov. 18, 2009, at 7:48 a.m. Lodge sent an email notifying Army Corps officials that water samples beyond the barrier tested positive for Asian carp. It wasn't a memo Lodge wanted to write, and he said he was left with a distinct feeling when it was time to hit the send button.

"It made me feel a little sick."

This story draws from research compiled since 2006. It involved more than 100 interviews and is based on a review of thousands of pages of documents, including court filings, government reports, scientific research papers and archival materials.