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New water samples reveal that Asian carp DNA has been found in Lake Michigan near the city of Chicago, the first indication that the giant leaping fish, which can upend entire ecosystems, has made it up the Chicago Sanitary and Ship Canal and into the world's largest freshwater system.

The Journal Sentinel learned of the apparent breach just minutes before the U.S. Supreme Court announced it had declined a request from a coalition of Great Lakes states to force the U.S. Army Corps of Engineers to slam shut two lakeside navigation locks in a drastic attempt to protect the Great Lakes and their $7 billion annual fishery.

Biologists fighting to halt the invasion are not conceding defeat; they say there is still no indication the lake is home to a breeding population of silver or bighead carp. In fact, biologists have yet to land a single fish above an electric fish barrier on the Chicago Sanitary and Ship Canal, about 20 miles downstream from Lake Michigan.

But the news was another distressing development in what conservationists and politicians alike have characterized as a slow-motion ecological disaster decades in the making.

The water samples, taken Dec. 8, showed the presence of carp DNA in Calumet Harbor near the Chicago shoreline as well as in the Calumet River just above the O'Brien lock, one of the structures the State of Michigan last month asked the Supreme Court to order shuttered. The hope was to buy some time in the fight to beat back the fish that have been migrating north from Arkansas since the 1970s.

The Army Corps said Tuesday it is scrambling to figure out how to best protect the lakes, but the locks were built for navigation, and that is how the Corps must prioritize management of them.

Asked if he had the authority to order the gates shut, Maj. General John Peabody replied: "The short answer is no."

Peabody said he could recommend to the secretary of the U.S. Army a change in the way the locks are operated, but before he makes any such decision he needs to assess the effectiveness of relying on the aged, leaky locks to halt or even slow the migration. He also has to assess the impacts such a move could have on Chicago in terms of flooding and waterborne commerce.

Peabody figures it will be weeks before he knows enough to make a decision.

The State of Michigan was hoping the Supreme Court would make that decision for the Corps, but the court declined in a statement released Tuesday morning. It did not offer a reason why.

The barge industry that uses the locks to move millions of tons of cargo annually was relieved by the news.

"We are gratified that the U.S. Supreme Court has taken action to prevent disastrous consequences to Midwest consumers and to the hardworking Americans employed in the towing industry and in all the industries and companies that rely on the essential commodities shipped by barge," said Thomas Allegretti, president of the American Waterways Operators.

The Supreme Court, however, did not rule on a separate request from the State of Michigan to reopen an ongoing case over the Chicago Sanitary and Ship Canal, which provides an artificial link between the Mississippi River basin and Lake Michigan.

"They just denied the motion for preliminary injunction to shut the locks, they're completely silent on the petition to reopen the case," said Noah Hall, a Wayne State University law professor who has followed the case closely.

In that portion of the case, the State of Michigan, backed by Wisconsin, New York, Ohio and Minnesota, is hoping the court will reopen a decades-old lawsuit over the operation of the Chicago canal. Their goal is to force the Corps and Chicago to permanently re-engineer the canal system to once again separate Lake Michigan from the Mississippi.

The canal, which opened in 1900, was built to flush Chicago sewage toward the Gulf of Mexico.

Briefs in the petition to reopen the case are due Feb. 19.

Breach not a surprise

Peabody says it is "bothersome" that no actual fish have been found at a time he's being pressured to dramatically change the way water flows through Chicago, but he is not discounting the tests' validity.

"It's not a dead-certain lock, but we've got to take it seriously," he said.

Others, however, believe the presence of DNA in lake waters is essentially as good as finding a fish.

The U.S. Environmental Protection Agency, for example, dispatched a team to the laboratories at the University of Notre Dame where the DNA tests are being conducted, and concluded that the tests are a reliable means of detecting the presence of a fish.

The technology can sniff out even the tiniest trace of fish DNA, and scientists say it indicates a fish has been in the area within the past two days.

The material likely comes from a carp's digestive tract, and while there are other possible explanations for the material to be found in a body of water - contaminated ballast discharges from a barge, for example - the scientists behind the technology say that is highly unlikely.

What the tests do not reveal, however, are how many fish may be in an area, or the size or age of the fish.

News of the apparent carp advance did not come as a surprise to Phil Moy, a University of Wisconsin Sea Grant biologist who has co-chaired the panel that helped the Army Corps construct a system of electric fish barriers on the canal.

"The fish have probably been up there around the locks for a year," Moy said.

The reason: He said the Army Corps turned off the power to the first-generation barrier system in October 2008 for about a week's worth of maintenance, and he believes the fish likely slipped through at that time.

That first barrier was not built to operate at level strong enough to repel juvenile fish, which need a bigger jolt.

A second, stronger barrier was turned on in April, but it was not cranked up to a level strong enough to deter small fish until August because of the dangers it posed to barge operators and recreational boaters traveling the canal.

Biologists have said all is not lost if a small population of fish make it into Lake Michigan, because it can be very difficult for a breeding population to get established.

"If a few fish get into the Great Lakes, it's not game over," Duane Chapman, a U.S. Geological Survey researcher who has made a career out of studying the fish on the heavily infested Missouri River, said last month.

The fish can grow to 50 pounds and consume up to 20% of their weight in plankton per day - food upon which every other species in a water system either directly or indirectly depends.

Chapman said they do indeed pose a dire threat to fishing and recreational boating on the world's largest freshwater system.

But he said what matters now is how many get into the lake.

First, the invading fish have to find each other. Then they have to find a place to spawn. A handful of adult fish were found in Lake Erie several years ago, but because no juveniles were found biologists determined the lake is not home to a breeding population.

The worry now is what the carp could do to Lake Michigan's $7 billion commercial and recreational fishery, as well as the recreational boating industry.

It is a worry that did not disappear with the Supreme Court ruling.

Wisconsin Gov. Jim Doyle and Michigan Gov. Jennifer Granholm said Tuesday they are asking the Obama administration, which opposed Michigan's request to shut the locks, to convene a summit between Great Lakes leaders and senior White House staff to address the threat.