Fish barrier vs. carp DNA: What to believe?

Author: Dan Egan, Milwaukee Journal Sentinel

Photo by Gary Porter

A towboat pushes barges upriver in July past the U.S. Army Corps of Engineers' electric fish barrier on the Chicago Sanitary and Ship Canal in Romeoville, Ill. The effectiveness of the barrier in stopping Asian carp is a key point of controversy between Illinois and its neighboring states.

This piece is the third of the three-part series "Deep Trouble - A High-Tech Hunt for Asian Carp," by Dan Egan, reporter for the Milwaukee Journal Sentinel. 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. Read the original article online.

More than $100 million has been spent in a battle to keep Asian carp from invading the Great Lakes. It is a fight the federal government insists it is winning, due largely to its electric barrier system on the Chicago Sanitary and Ship Canal. But is the evidence that these fish-shocking machines work any more reliable than the DNA evidence indicating Asian carp may have already breached them?


Anyone who has looked into the soupy river and canal waters flowing through Chicago knows that even with a diver's mask and halogen light you'd be lucky to spot a sunken barge, let alone a fish that might be, depending on its age, no bigger than your thumb.

But that's what a University of Notre Dame team of researchers believed it had essentially done in fall 2009 when 32 water samples taken from the Chicago Sanitary and Ship Canal above an electrical fish barrier tested positive for Asian carp DNA.

Because the canal is engineered to flow away from Lake Michigan, Notre Dame biologist David Lodge reckoned it meant at least some Asian carp had somehow gotten past the U.S. Army Corps of Engineers' barrier.

DNA, like everything else, doesn't float upstream.

Environmental groups and politicians from neighboring Great Lakes states pounced at the news that indicated this last line of defense, located just 35 miles downstream from Lake Michigan, had somehow failed. They demanded the Army Corps shut two navigation locks near downtown Chicago to form makeshift dams to block the carp's final advance into Lake Michigan, a move that Illinois barge operators said would have disastrous consequences not only for their businesses but for the industries they serve, as well as the recreational and tour boat industry in Chicago.

Army Corps Maj. Gen. John Peabody wasn't about to recommend lock closure, which he argued wouldn't necessarily stop the fish because the structures are aged and leaky - and they would have to be opened if big rains hit to avoid devastating floods in Chicago.

Peabody clearly felt he was already doing enough.

He'd recently doubled the voltage at the barrier and, just days before he learned that Asian carp DNA had been found beyond it, his agency backed a plan to poison the canal. The kill was ordered because the barrier needed to be briefly shut down for maintenance. Even though no actual Asian carp had been found within 15 miles of it - about 50 miles from Lake Michigan - and even though a weaker adjacent backup electric barrier would continue running during the shutdown, Peabody and everybody else in the carp fight wanted the canal sterilized, just in case.

So on Dec. 3, 2009, hundreds of government employees from across the Great Lakes region were dispatched to destroy every fish in a 6-mile stretch of canal. Reporters descended, lured by the prospect of witnessing thousands of invasive fish popping to the surface. But as afternoon stretched into dusk, there was still no word of any Asian carp floating in the whole chemical mess.

Finally, at 7 p.m., Illinois Department of Natural Resources assistant director John Rogner summoned reporters to the canal's edge. They had found what they were looking for - a single, 22-inch bighead Asian carp.

While it was unsettling news for the Great Lakes that Asian carp had indeed arrived in the waters just below the barrier, a wave of relief washed over Lodge as word reached the Notre Dame team. The sight of that one fish, he thought, at least validated his science.

The feeling would be fleeting. Carcass mop-up would continue on the canal for three more days, but yield no more Asian carp.

DNA process scrutinized

The trust that Peabody had put in Lodge's DNA tool was being tested.

On Dec. 15, 2009, less than two weeks after the poisoning, a team of federal scientists arrived in South Bend to inspect Lodge's lab. They scrutinized how water samples were stored, how they were filtered and what steps were taken to ensure Asian carp DNA hadn't somehow contaminated any of the equipment, which could result in false positive results.

The Notre Dame team felt a bit like its spouse had hired a private investigator to catch it cheating. The investigators found no such evidence. In fact, they came away impressed, writing in their official report that Lodge's process is "sufficiently reliable and robust in reporting a pattern of detection that should be considered actionable in a management context."

The Notre Dame team took that to mean that if you've got DNA, you've got strong evidence that the fish are there, and you could justify taking action to kill those fish and block others from making the same trip.

Still, Peabody wasn't ready to believe that a positive sample necessarily meant the presence of fish. The general worried the DNA might have gotten past the barrier some other way. Perhaps bilge water from barges. Or bird excrement. Or carp flopping onto the deck of a barge passing through the barrier. Or even the toilet flush of a person who had eaten Asian carp for dinner.

Peabody always knew he was taking a chance adopting a novel, untested technology in a high-stakes fight, but he felt compelled to find out where the fish were so he could make the smartest decision about how high to operate the barrier voltage. That was all he ever wanted from Lodge's DNA sampling. He never expected DNA to surface beyond the barrier, but he was taken aback by the fuss it caused when it did. The general had been in combat; it's clear he knows the value of keeping cool in battle.

"We got a few hits above the barrier, and some people were flat-panicked by that," he said.

In the wake of those finds, a coalition of Great Lakes states turned to the U.S. Supreme Court to force the Army Corps, the State of Illinois and the Chicago sewerage district to take more drastic actions to stop the carp. The states wanted the locks closed, though they acknowledged the locks would have to be opened on an emergency basis if big rains hit to avoid flooding in Chicago.

Ironically, these were four of the five purple states - Minnesota, Wisconsin, Michigan, Ohio - that President Barack Obama had wooed with his zero-tolerance pledge for new Great Lakes invasions in 2008. Now the states were battling the Obama administration over what they saw as its lack of commitment to protect the Great Lakes from the next invader.

The justices declined to take up the matter. The states pressed on, and several months later, along with Pennsylvania, they filed a new federal lawsuit in a lower court, a case still being argued.

Once lawyers got involved, the marriage between Peabody and the Notre Dame team hit the rocks.

"Everybody got into this expecting we wouldn't have any positive samples above the barrier," said Lindsay Chadderton, an invasive species expert from the Nature Conservancy who helped the Lodge team develop and deploy the DNA testing.

"The reality is if we had only found positives below the electric barrier . . . none of this controversy would have happened. The minute we started finding positives above the barrier, that is when the blame game started. That is when the litigation started with the lock closure, and that is when things started to get testy."

Most biologists acknowledge a small number of fish breaching the barrier does not mean a self-sustaining population in the Great Lakes has arrived, or that one is inevitable. For an invasion to be successful, first the fish have to be sexually mature, then they have to find appropriate spawning areas, then they have to find each other, and then their offspring have to figure out how to survive to adulthood and find their own mates. Then the next generation has to have similar success, and so on.

For Peabody, this meant it wasn't time to retreat and move the fight nearer to the Lake Michigan shoreline; it was time to stand his ground at the electric barrier about 35 miles downstream.

Meanwhile, Lodge's team continued testing the waters beyond the barrier throughout the spring of 2010, and it kept getting more positive DNA hits. These positive samples were far more alarming than the earliest ones taken below the barrier because they suggested the general's last line of defense was marginal, if not Maginot.

In late May 2010, six months after the first canal poisoning, the federal government and state of Illinois conducted another river poisoning just six miles from the Lake Michigan shoreline.

The second poisoning claimed another 100,000 pounds of fish representing about 40 species. Not one was an Asian carp. Peabody and the rest of the federal team walked away more confident that the barrier was holding back the fish, and less confident that Lodge's DNA samples meant fish were in the area.

Lodge was floored. He never expected the netting expeditions and even the poisonings to yield many, if any, Asian carp because of the size of the waterway and the idea that there were probably only a small number of fish at the leading edge of the invasion. He had, in fact, warned the federal government not to conduct the second poisoning because the most recent sampling in the days before the barrels of poison were dumped showed no DNA evidence of Asian carp in the area.

Still, Lodge had seen enough positive samples in enough places above the electric barrier throughout early 2010 to be convinced a Lake Michigan invasion was "imminent" if the government didn't put in place a more impenetrable barrier in the Chicago canal system. Peabody and state officials needed to see actual fish - and not just a lab report - before they would be convinced an invasion was under way.

One bighead carp

Finally, on June 23, 2010 - a month after the second river poisoning and about a year after the Army Corps first hired Notre Dame to help it find the leading edge of the invasion, the Illinois Department of Natural Resources announced that a 20-pound adult bighead carp had been caught beyond the barrier - just six miles from the Lake Michigan shoreline.

"We set out on a fact-finding mission and we have found what we were looking for," proclaimed Rogner.

Lodge once again felt a grim sort of vindication, but the find, of course, also indicated that the general's electric barrier might not be stopping the fish as he had hoped.

Yet there were other plausible explanations for that fish getting beyond the barrier. It could have ridden into the canal in floodwaters from the Des Plaines River - a Mississippi tributary - that in places runs within a few hundred yards of the Chicago canal. That gap in the defense was plugged in late 2010 with a $13 million concrete and chain-link barrier.

Asian carp have in recent years also been found in some Chicago ponds unconnected to Lake Michigan, the likely result of catfish plantings that were contaminated with Asian carp. Maybe similar batches of "catfish" were at some point planted in the Chicago canal systems, though there is no record of this. Some Asian carp also may have made it past the barrier when some maintenance work was done on it in the fall of 2008.

There is also the possibility that the barrier might chronically leak fish. But any idea that the rogue fish simply swam through the electrified water appeared to be doused when Rogner issued another news release several weeks later that said his agency believed the fish spent its early life in waters downstream of the barrier and then put forward a story that it might have been lifted around the barrier by human hands.

To figure out how the fish made its way so close to Lake Michigan, Rogner's staff sent the carcass to an Illinois lab to analyze its ear bones. These bones can sometimes tell researchers where a fish once lived, because different water bodies can leave different chemical signatures on the bone. But an independent reviewer of the lab analysis warned that no definitive conclusion could be reached about this particular bighead's life history.

Even so, Rogner said in a news release that the bone analysis "does suggest to us that the fish . . . may have been put there by humans, perhaps as a ritual cultural release or through bait bucket transfer." If that were true, that would diminish the concerns that the barrier wasn't working.

The problem: Beyond the peer reviewer's caution not to use this fish's ear bones to infer anything about its life history, ear bones don't contain any information about how a fish moved from one water body to another.

As for the story about a human planting it, rumors of "cultural releases" of Asian carp by people of Asian ancestry have swirled around Chicago for years, and the practice of releasing animals into the wild has indeed been historically documented. But when an Illinois Department of Natural Resources spokesman was pressed for any evidence of this actually happening with bighead carp in Chicago, the best he could muster was a link to a Wikipedia article. It stated that animal releases were a common practice during the Ming Dynasty in China.

The Ming Dynasty ended in 1644.

Peabody and Lodge eventually stopped communicating.


Lodge and Peabody finally ended up in a downtown Chicago federal courtroom in early September 2010. They were both called as witnesses in the federal lawsuit brought by the neighboring states. In addition to lock closures, the states sued to force the Army Corps to expedite a study of what it would take to reconstruct the natural barrier between the Great Lakes and Mississippi basin that the Chicago canal system destroyed more than a century ago. That is a project that could force billions of dollars' worth of changes in the way Chicago manages its sewage, moves it barges and recreational boats, and deals with floodwaters, because it could mean damming and re-reversing the Chicago River so that it once again flows into Lake Michigan.

When Peabody took the stand, he looked mildly agitated.

"Never in my worst nightmares or wildest imagination did I think that a fish would so dominate my time and attention, because you don't think of the Corps of Engineers doing that," he would say later in an interview. "You think of us as managing water resource infrastructure and building things and fighting floods and doing that kind of stuff."

Peabody expressed his doubts that positive DNA samples meant the presence of live fish, and he had a fish expert ally in the courtroom in Charlie Wooley, the deputy regional director of the U.S. Fish and Wildlife Service.

Wooley testified that the Army Corps and its sister federal agencies had gone to extraordinary lengths to try to follow up on the positive DNA samples with evidence of actual fish. They hunted for the fish with nets, electro-shockers and barrels of poison. And all they had to show for it was a single bighead above the barrier, and a single bighead in the waters just below the barrier - the fish killed in the first poisoning.

"The traditional methods allow us to go out and sample large areas very effectively, very efficiently in a relatively short period of time," Wooley testified. "They are tried and true."

Lodge countered that in his testimony by citing a study that showed traditional sampling tools are effective at capturing only 1% of a fish population on a large, open river system. That means if small numbers of Asian carp lurked among tens of thousands of fish, odds are they would never turn up in a net or float to the surface if shocked. Asian carp also have a tendency to sink when poisoned.

All this, Lodge continues to argue to this day, is precisely what makes DNA surveillance so powerful. But it's only as powerful as the trust you put it in it.

"Continuing to try to use the traditional tools to detect the presence of rare or of very sparse populations is like saying: You know, even though we've got an MRI machine, I'm going to try and detect your cancer with a physical exam," he said later in an interview. "I don't really understand what this MRI machine is doing, so I'm not going to believe it. I'm going to poke you with my fingers and figure out whether you've got cancer or not."

Lodge was shaking as he ate from a bag of M&M's during a break after his testimony. He looked as if he had been the one on trial.

The judge sided with the Army Corps and refused to issue an emergency order to shut the locks, though the case remains ongoing.

Lodge said later that the DNA controversy took a "very high" toll on him personally - but he doesn't regret jumping into it.

"From the perspective of a scientist wanting (his) science to contribute to helping solve society's problems? There is no choice. I'd have to do it again," he said. "It's made a difference. It's too early to say whether it's made the ultimate difference. Are we going successfully prevent the invasion of the Great Lakes? I don't know. But we uncovered a situation of an imminent invasion that was not recognized."

Evidence of carp spreads

Lodge's team finally published a peer-reviewed paper validating the science behind environmental DNA sampling in January 2011. A second Army Corps-funded external review of the process released in fall 2011 further validated it - with the caveat that it can't reveal how the DNA got in the river in the first place.

Lodge always acknowledged this weakness, and he also believes that some of the positive DNA samples found above the barrier likely did get in the water by means other than a live fish.

But, he and his colleague Chadderton argue, the DNA has turned up in too many places and too many times - in areas where barges can't travel, upstream of sewage treatment plant outflows, in cold months when many birds that might move DNA aren't feeding in Chicago waterways - for there to be any question about whether some live fish have made it past the barrier. They liken the evidence to that in a murder investigation.

"If it was a single fingerprint on the murder weapon and in the house where the crime occurred, you might ask the question: Well, maybe not? But the reality is, we've got fingerprints all over the crime scene," said Chadderton. "They're on the body. They're on the knife. . . . They're smeared all over the place and they're on the handle of the door into house. It's just like, come on people . . . the reality is the body of the evidence says we're dealing with live fish!"

The genetic fingerprints keep showing up. The Army Corps, which has taken over testing the canal for DNA, has so far this year found more than 30 positive detections above the barrier as part of its regular $650,000 monitoring program.

But the agency is spending at least as much trying to figure out what a positive result means.

It has investigated whether DNA in a river can be traced back to fertilizer made from Asian carp carcasses (it can't). Research has moved on to sampling bird feces and feathers to determine whether either can be a carrier of carp DNA. Army Corps crews could also be found in early June in Chicago's Chinatown pouring melted ice that had been chilling dead carp into city gutters to see if DNA can ride through a sewer and out into the canal system (it can, though that surprised nobody, Lodge included).

Another study is trying to determine how long DNA persists in open water - the Army Corps provided photo evidence of a case this spring in which a silver carp, which famously jump, was found on the deck of a barge above the barrier. If a dead fish such as this got kicked into the water, it might be a source for positive DNA samples.

"Are a lot of hits due to a whole bunch of fish, or is just a single carcass sitting on the bottom of the river, releasing DNA all day long?" Army Corps researcher Richard Lance asked earlier this year.

Lance's staff in Vicksburg, Miss., now processes the DNA samples shipped in regularly from Chicago that arrive in Styrofoam boxes. Because of the lawsuit between the Army Corps and the Great Lakes states, the samples require chain of custody documentation worthy of a urine sample taken from a big league slugger.

Pressed as to whether he believes the positive DNA hits are triggered by live fish swimming in the canal system, Lance demurred.

"We don't go there," he said. "We're not trying to pooh-pooh the idea, we're just trying to look at what else we need to understand to make sense of the positive hits."

Peabody sounds like a man who wants to have faith in environmental DNA, or eDNA, but that would require ignoring his common sense - or senses.

"As time goes on, our inability to confirm eDNA evidence with live fish, it's caused me to question eDNA quite frankly, and its viability," he said.

"I hate to sound like a doubting Thomas, because I'm a Catholic . . . but this is not one of those things that I can take on faith purely," he added.

Asian carp expert Duane Chapman said nobody should be surprised all the intense fishing expeditions in the past two years have proved fruitless, particularly if there are only a small number of Asian carp beyond the barrier system.

"These fish are extremely difficult to catch, compared to our native fish," said Chapman, a biologist for the U.S. Geological Survey.

Chapman once marshaled four boats and chased three radio-tagged Asian carp for two days on a Missouri River tributary using electroshocking gear and commercial fishing nets. The radio tags were emitting a signal that told the crew the precise location of the fish, which had been trapped between two sets of nets stretching the entire width and depth of the river. But the water evidently was too deep for the electroshockers to force the fish to surface, and the carp proved cagey enough to avoid getting snarled in the nets.

"They know what nets are," said Chapman, "and they avoid them."

Doubts about the barrier persist

Thom Cmar, an attorney with the Natural Resources Defense Council, says the message coming from the Obama administration for the past year is essentially this: Don't trust the DNA results, but do trust us when we tell you the barrier is working.

"The barrier is still just a giant science experiment, and most of the tests to validate it have been done in contraptions that are glorified bathtubs," Cmar said. "They act like the barrier is the one thing they're sure of and they have spent lots of time publicly questioning eDNA when, in fact, eDNA has survived peer review, and - at least at this point - their barrier science hasn't."

Army Corps officials point to a number of lab studies they have done with electricity and fish, as well as an ongoing field study that shows about 180 radio-tagged fish put in the canal have never swum through the barrier. They say external reviews of their barrier studies are planned, but can't say when they will be completed. They also point to the fact that to date they have found only one Asian carp beyond the barrier. Illinois officials are equally convinced the barrier is doing its job.

"We cannot discount the possibility that there might be a few Asian carp above the barrier, but if they are there, they are in very, very low numbers," Rogner said in an interview this summer. "That would suggest to me that if the barrier is not 100% effective, it's pretty darn close to it."

But there is ample evidence to suggest the barrier system hasn't provided the security many hoped it would.

It wasn't turned up to a voltage strong enough to repel fish 5.4 inches or smaller until fall 2011, and several weeks later it had to be turned down briefly because the higher voltage was somehow interfering with a nearby railroad signal. Army Corps officials say the higher voltage is just a precaution because they say small fish have not been found any closer than 100 miles downstream.

The complete barrier system, which is now two adjacent barriers running simultaneously with a third barrier on standby, mysteriously shut down for 13 minutes in early May because of a power surge. Evidence also suggests that metal barges might mute some of the electric shock as they move through the barrier, providing a safe "bubble" for carp swimming below. The Army Corps is hoping field tests will determine how big of a threat this might pose.

Other proposals to stop invaders

No longer advocating for emergency lock closures and instead pushing for a stouter, more permanent line of defense, Cmar's group released a $100,000 study in 2010 that showed dams could be placed in the Chicago waterways to block the fish yet allow the city to continue to send its wastewater downstream. The group said such a system could be designed and built within two years. It acknowledges its plan could have severe consequences for the barges and recreational boats that ply the Chicago waterways but argues those problems can be addressed later. The present threat to the lakes, Cmar contends, demands dramatic action now.

"Most of the effort over the last two years from the Obama administration has been to fight a public relations battle to defend what they've done, rather than really rolling up their sleeves and advancing a real solution to the problem," he said.

Cmar's group isn't the only one exploring more dramatic action. The Great Lakes Commission and a group that represents the region's mayors - including Chicago's and Milwaukee's - funded a $2 million study released this year that concluded the Army Corps could indeed plug the canal to block the carp, though its authors acknowledged it probably would take a decade to engineer and construct.

That study puts forward a solution that would stop invasive species while at the same time "maintain or enhance" Chicago's water quality as well as its stormwater and navigation systems at a maximum cost of $4.27 billion. The study noted that the cost of the original canal system, in 2010 dollars, was $11 billion.

Peabody is dubious any permanent separation of the watersheds is coming soon - if ever.

"I'm not saying it can't be done," he said. "But I think if it were to be done it would have to be done over an enormous period of time at great expense and as a practical matter, given where the country is fiscally right now - funding it, it would take a court order, I suppose. But even judges are going to have to get fiscally realistic at some point."

The political pressure to plug the canal isn't going to go away anytime soon. In June, Congress ordered the Army Corps to fast-track its study on how to permanently separate the Mississippi from the Great Lakes and have it completed in 2013, rather than its slated date of 2015.

Even Chicago Mayor Rahm Emanuel is thinking about a permanent fix, saying he welcomed the ideas advanced in the Great Lakes Commission study.

"I am very interested in solutions that improve flood control, transportation and water quality in the Chicago River while protecting the Great Lakes," he said when the study was released in January. "We are eager to work with leaders around the region to plan solutions that work for Chicago and also stop invasive species."

A black box

Despite some federal officials continuing to question the utility of environmental DNA, its use is spreading. European researchers have deployed it in species surveys of entire lakes. It's being used to detect rare salamanders in the western United States. The U.S. Fish and Wildlife Service is building a dedicated DNA laboratory in La Crosse to process samples from water bodies across the region.

"We're not the only ones singing this song," Lodge said.

And Chicago isn't the only place where environmental DNA is likely to spark controversy. Indeed, the Chicago story already appears to be playing out in Minnesota. DNA samples taken on the upper Mississippi River in late 2011 revealed a flurry of silver carp hits. There has been a clamor to close navigation locks near Minneapolis to keep the fish from spreading into the Mississippi headwaters, into the heart of the Land of 10,000 Lakes.

University of Minnesota biologist and invasive species expert Peter Sorensen started using environmental DNA in 2011 with open eyes. He is a man of science, but he has had a hard time reconciling what the DNA samples are telling him with what he is - or isn't - seeing in the river.

The DNA tests tell him up to 40% of water samples in some areas are positive for silver carp. His eyes are telling him there are no fish. He's not saying it's a flawed tool; it's just so . . . frustrating.

"It's a black box," he said last winter. "It just spits out a yes or a no."

Joel Brammeier of the conservation group Alliance for the Great Lakes sees it as something else - a siren warning that the enemy is at the door. But rather than trying to slam shut that door by permanently plugging the Chicago canal, Brammeier says the government has decided, essentially, to take a wait-and-see approach.

"DNA is an early warning that gives you a chance to assemble the troops and start to build a permanent solution, and so far we aren't taking advantage of it," he said.

The federal and Illinois government workers involved in the fight assert they have the problem under control. They tout the fact that more than $150 million has been allocated in recent years to do things such as research the effectiveness of the electric barriers and hunt for the fish with commercial fishing nets, scuba divers and sonar. They are trying to develop Asian carp-specific poisons and they are netting the fish in areas downstream of the barriers - the idea being that harvesting in heavily infested areas will reduce the species' need to migrate north toward Lake Michigan. They are trying to develop pheromones to corral the fish. They plan to build another electric barrier on the Chicago canal.

"Those are all good things that have to be done," Brammeier said. "But we could have broken ground on a permanent solution by now."

So what will happen if more than Asian carp molecules start turning up in Lake Michigan waters in the coming months or even years?

Will the tens of millions of Americans living in the Great Lakes basin believe the Obama administration lived up to its "zero tolerance" pledge?

Or will they trust their eyes?


About this story

This story draws from research compiled since 2006. It involved more than 100 interviews and is informed by thousands of pages of documents, including court filings, scientific research papers and archival materials.