Jami Cash, daughter of dead coal miner Michael Elswick, attends a vigil following the Upper Big Branch Memorial Service in Whitesville, W.Va. (Jeff Gentner/AP)

The owner of a rogue coal mine in West Virginia — where sparking machinery and built-up gases led to an explosion that killed 29 men last year — has agreed to pay a record $209 million penalty and make historic changes to protect miners from harm, federal prosecutors said Tuesday.

The settlement with Virginia-based Alpha Natural Resources, which bought the parent company of the mine, Massey Energy, is more than 40 times the size of any previous fine for a coal disaster. It came 20 months after the blast at the Upper Big Branch mine, the worst U.S. mining disaster in 40 years.

Also Tuesday, a new government report detailed the world inside the mine on April 5, 2010 — where modern men went underground to face problems out of the 19th century. Miners worked amid pockets of neck-high water and buildups of explosive methane and coal dust. Their bosses kept two sets of safety logs, a real one and a fake one to show government inspectors.

“If basic safety measures had been in place,” said the report, from the federal Mine Safety and Health Administration, there would have been no loss of life.”

The settlement requires Alpha to pay $1.5 million each to the families of 29 dead and two injured miners.

It also requires the company to spend at least $80 million on measures intended to prevent another disaster: better air monitors inside mines and new devices to provide oxygen for suffocating men.

“You can’t trade lives for money,” was the message to the coal industry as a whole, said Davitt McAteer, a mine-safety expert who led the state of West Virginia’s inquiry into the disaster. “You have to make it hurt enough, and try to make them pay attention.”

McAteer said that the Upper Big Branch disaster was a reminder of how little had changed in mining since the days of canaries and dynamite. The Upper Big Branch miners were killed by the same unsolved safety problems that caused the country’s worst mining disaster, at Monongah, W.Va., in 1907.

“It was coal dust. It was ventilation” problems, McAteer said. “Same [stuff], 104 years later.”

Tuesday’s agreement will end the threat of federal prosecution for Alpha as a company. Its penalties also include $48 million, to be placed in a trust for mine safety research, and $34.8 million to pay off Massey’s outstanding fines for safety violations.

“What I hope they get from it is that they can’t just write a check and make an investigation go away,” U.S. Attorney R. Booth Goodwin II said in a telephone interview Tuesday night. “They have to have a commitment to incorporating . . . real, tangible safety measures.”

The agreement would still allow Massey executives and managers to be charged as individuals. So far, only one has been prosecuted — mine security chief Hughie Elbert Stover, who was convicted last month of lying to investigators and trying to destroy mine records.

Miners’ families can still pursue lawsuits against Alpha. But prosecutors said that, if a future judge awards them more than $1.5 million, Alpha can subtract that amount from their settlement.

The chief executive of Alpha Natural Resources, Kevin Crutchfield, said in a written statement that, “we’re particularly pleased that a substantial portion of the settlement is going towards furthering miner safety, which has always been Alpha’s guiding principle.”

Despite the record size of the penalty, some mine-safety experts said they worried it would not be enough to make serious changes. Alpha owns more than 80 coal mines, which means the money for safety upgrades would be just $1 million per site.

“Although it sounds dramatic, it may not effect meaningful improvements” because the equipment is so expensive, said Judy Rivlin, associate general counsel with the United Mine Workers of America.

Mine safety experts also said the settlement addresses the physical safety issues but does little to fix a corporate culture that often seeks to skirt safety rules.

“Doing more research to determine how a mine blows up doesn’t get at the real problem,” said Celeste Monforton, a former federal mine-safety official. “What do you do to address the organizational pressure on the ground every day to place [coal] production over safety?”

The new federal report, which ran more than 1,000 pages, described an operation where rampant safety problems were hidden from federal inspectors.

The mine’s ventilation system — in which giant fans push in fresh air and vent flammable gases — was not working properly. Flammable coal dust was allowed to build up despite requirements that it be covered with inert rock dust.

The government said that the mine’s operators kept these problems out of the books shown to inspectors. When inspectors arrived, officials stayed a step ahead, warning miners underground to either clean up or shut down.

Massey officials intimidated their employees, according to the report: When one miner stopped to address a safety concern, he was told “if you don’t start running coal up there, I’m going to bring the whole crew outside and get rid of every one of you.”

That miner, Dean Jones, died with 28 others when a spark from a faulty machine set off a pocket of methane. That explosion set off another — and much larger — one in the coal dust. The government said flames whipped for miles through the mine’s tunnels, followed by suffocating gases called “afterdamp.”

In the small river-valley town of Rock View, W.Va., the mother of one lost miner said she was glad to see more money going to safety measures. Linda Clark said she still talks to the picture of her son, Robert Clark, that she keeps on a dresser. She said his son, now 5, asks about his father: “Ma-maw, tell me a story about me and my daddy,” he often asks.

Despite the record fine, however, Clark said she doesn’t feel that the mine’s executives understand the gravity of their mistakes.

“God in the heaven above, forgive me,” Linda Clark said on Tuesday. “I hope when they go to bed at night, that they see every one of those men’s faces in their dreams.”