Yet in June 2005, a panel of scientists appointed by the Environmental Protection Agency determined that the air was still too dirty.
The evidence was more subtle, but according to the latest studies, tiny particles - similar to those that had fallen on Donora - could shorten lifespans even at the invisible everyday levels found in much of the United States. No matter where the mix of particles came from - trucks, buses, power plants - their small size meant they could penetrate deep into the lungs.
The panel recommended tougher rules to limit long-term exposure, a move that EPA's own scientists said could prevent thousands of premature deaths annually.
EPA Administrator Stephen L. Johnson rejected their advice.
His decision took the panel by surprise, but before long, it would fit into a familiar pattern.
Over the next three years, leading environmental scientists would denounce Johnson for substituting politics for science on key pollution issues - from not regulating greenhouse gases blamed for global warming to delaying the assessment of toxic chemicals.
But it was in a succession of decisions on air quality that Johnson's uneven application of science had perhaps the most severe impacts on human health.
In the case of particles, a key element of Johnson's scientific justification was characterized by a top expert as "silly."
When considering restrictions on ozone, the chief component of smog, Johnson flatly rejected the recommendations of the nation's top 23 experts.
For a new rule on airborne lead pollution, Johnson attempted to cripple the very panel created by Congress to advise him on all three decisions.
In all three cases, it took a court order to get the EPA to make a decision.
And in all three cases, according to documents and interviews, Johnson chose to take a more industry-friendly course after pressure from the White House.
"What good is a scientific committee if you're just going to march to the White House and ask the president?" asked toxicologist Rogene Henderson, who was appointed by Johnson and chaired the panel during all three agency decisions.
Johnson, a career EPA scientist before taking the top spot in 2005, noted that the law gives him the final call on matters of science policy, and he said criticisms of him were unfair. While science is one of the "foundational principles" of a regulatory decision, he said, it's not the only one.
"For those who like the decision," Johnson said, "it's a great decision, and those who don't, you know, there's the 'you-caved-in.' "
The chorus of "you-caved-ins" has grown among scientists and other critics who say that Johnson has allowed the White House Office of Management and Budget (OMB) to unduly influence him - and that he weighs economic concerns more heavily than public safety.
Johnson himself asked Congress this year to rewrite the Clean Air Act to allow him to take into account economic impacts when setting air pollution standards.
But he vigorously denies that his rulings were in any way dictated by the White House.
"Every one of my decisions has been my decision. If they were not my decisions, I would not be here," he said.
George Gray, EPA science adviser and assistant administrator for research, said his boss skillfully navigates the difficult task of incorporating sound science with effective public policy.
"He has a real challenge reminding people that science doesn't provide answers. It provides input and you have to use that in some kind of a broader process to inform decisions that you need to make."
That process has been corrupted, says U.S. Sen. Barbara Boxer, a California Democrat who chairs the Senate committee with EPA oversight.
"Almost every time he acts," Boxer said, "it's against his scientists."
The danger of a short-term spike in pollution particles was illustrated by the 1948 deaths in Donora, and even more alarmingly four years later, when a smoky "fog" killed thousands in London.
Scientists at the time had only crude ways to measure this emerging threat, known as particulate matter. And in the ensuing decades, as some experts began to explore the possibility that such microscopic particles were harmful over the long term, many had their doubts.
"A lot of people were very skeptical," said Henderson, the toxicologist. "It's not intuitive."
In 1993, a Harvard study of more than 8,000 people in six cities began to convince the skeptics. Then came papers in 1995 and 2002, using data from several hundred thousand people, collected by the American Cancer Society.
The clearest culprit seemed to be "fine" particles - those measuring roughly 1/40 the thickness of a sheet of office paper.
For every 10-microgram increase of fine particles per cubic meter of air, according to the 2002 study, there was an 8 percent increase in heart attacks and other cardiopulmonary deaths. It was a modest but statistically significant impact, and there was evidence of harm even in relatively clean cities.
The findings held up even when other risk factors were taken into account: smoking, diet, occupation, exposure to other kinds of pollution.
The six-city study, meanwhile, found that the dangers from fine particles were even greater. And new experiments suggested just how these unseen invaders might be doing their damage.
Studies on animals, for example, indicated that long-term inhalation of such particles causes inflammation, which in turn can lead to plaque buildup in the arteries.
Still unclear was whether particles emitted by certain sources were more harmful than others - say, cement dust vs. diesel soot - but collectively there was evidence of harm.
The EPA was slow to act - so slow that in 2003 the American Lung Association and others sued it to speed the review.
As the law mandates, the agency weighed the evidence with the help of an in-depth review by a panel of independent scientists: the Clean Air Scientific Advisory Committee.
Armed with the science panel's advice and detailed research by EPA staff, the administrator is charged with setting standards that are "requisite to protect the public health" with an "adequate margin of safety."
The latest studies were not without uncertainty; the biggest one, for example, did not have information on whether smokers continued to smoke throughout the 16-year period.
But for the science panel, the evidence was clear enough.
Its conclusion, in 2005, was that the daily limit for fine particles should be lowered sharply from 65 micrograms per cubic meter of air to 35 micrograms or below. That is, pollution readings in a given county would not be allowed to spike above 35 for more than a few days a year.
Average yearly limits, the science panel felt, should be lowered from 15 micrograms per cubic meter to 14 or 13.
For every decline of a single microgram in average levels, deaths would fall roughly 1 percent, the evidence indicated. That could translate into preventing thousands of premature deaths.
But it would require significant pollution controls: from putting costly scrubbers on coal-burning power plants to mandatory cutbacks on engine idling of diesel trucks.
In recent years, Philadelphia's fine-particle measurements have averaged about 15 micrograms per cubic meter of air - on the cusp of meeting the standards. New York tends to be slightly higher, and Los Angeles is the nation's worst, at times above 20.
Fine particles have been a special concern in Camden's Waterfront South neighborhood, where the problem is aggravated by a cement plant, other industry, and the steady rumbling of about 700 diesel trucks per day.
Henderson, the science panel chair, had been studying air pollution since 1967, publishing 240 articles. She had no doubt the rules needed to be tougher.
"Setting it at 15 didn't give any margin of safety," she said.
All seven of the panel's charter members agreed, as did most of the additional 15 scientists who were brought in for their expertise.
The only two to dissent were both former chairmen of the panel: George Wolff, a scientist at General Motors Corp., and Roger O. McClellan, a toxicologist with extensive experience both at an industry-funded group and at an independent research institute.
McClellan said he did not think it was the role of scientists to recommend specific numbers, as the law gives that power to the administrator.
"I think we start getting on pretty thin ice when scientists start saying what is going to be an adequate margin of safety," he said.
In September 2006, Johnson announced his decision. He cut the daily limit from 65 micrograms to 35 - a dramatic reduction that fell within the range recommended by the scientists and his own staff.
The annual average standard, on the other hand, Johnson left unchanged at 15 - despite recent studies suggesting that this everyday background pollution killed even more people than occasional spikes.
His explanation, published in the Federal Register, was curious:
The big studies found evidence of premature deaths well below the existing 15-microgram pollution limit. But on average, the pollution level for the dozens of cities studied was about 18 micrograms. Since the existing standard was 15 micrograms, well below 18, Johnson decided it was already tough enough.
The evidence of harm, he wrote, was strongest at the long-term average - around 18 - because that's where most of the data were.
Yet a review of the data offers little support for Johnson's claim.
Roughly speaking, the data form a straight line on a graph: the cleaner the air during the years studied, the fewer people died.
And statistically speaking, that evidence is just as reliable at 13 or 14 as it is at the higher, average level that guided Johnson - as measured by the width of what are called confidence intervals.
C. Arden Pope, who co-authored both the big studies the panel relied on, was puzzled by Johnson's focus on the average.
He said it was a bit like looking at a group of people, a few of whom smoke two packs a day while most don't smoke at all. Under Johnson's logic, Pope said, it would be like concluding that it is safe to smoke the "average" amount, say, 10 cigarettes a day.
"It's silly," said Pope, a professor of economics at Brigham Young University.
Yet Pope said he sympathized with the administrator, because improving air quality to conform with the Clean Air Act's "adequate margin of safety" is likely to be unrealistic.
"You've got the empirical evidence that looks like almost any pollution will hurt you," Pope said.
How clean is clean enough? While lawyers may debate the meaning of "adequate," Johnson's own staff assembled some numbers: how many lives would be saved in each case.
Such estimates are tricky, because no one knows how low you can go and still achieve additional health impacts. Experts consulted by the agency said Johnson's rule would prevent anywhere from 1,200 to 13,000 premature deaths each year, whereas tightening the annual standard by just one microgram would prevent somewhere between 2,200 and 24,000.
Jason Burnett, a former EPA official involved in the rule-making process, said Johnson's decision to leave the standard alone was in keeping with the signals coming from the White House.
"They didn't want to tighten it, even though the vast majority of the evidence and the scientific advice we were receiving was to tighten it," said Burnett, who left the agency in part because he disagreed with the fine-particle rule.
When pressed, he declined to reveal details of when and how the pressure was applied.
But several months before Johnson issued his decision, the White House OMB wrote him to express skepticism about the big studies upon which the science panel based its advice. In an April 2006 letter, the OMB's Donald R. Arbuckle, a senior official, urged further analysis and "a more complete characterization of the uncertainty."
The new rule on particles has now been challenged in federal court by the American Lung Association, with a decision expected early next year. If the rule stands, the incoming Obama administration still could elect to revisit and toughen the standards, but the process could take years.
Through a spokeswoman, the EPA declined to comment on Johnson's reasoning for leaving the annual pollution limit unchanged, citing the litigation. Under Bush, the agency did move to reduce particle pollution from buses and construction equipment. But legally speaking, the annual pollution limit is the driving force for cleanup efforts by the individual states, and by leaving it alone, Johnson left little impetus for change.
For Henderson, what Johnson did was worse than a missed opportunity. Johnson's rule, she felt, did not provide the margin of safety required by the Clean Air Act.
"His decision contrasts with what the law clearly says," she said.
Like a sunburn
In her lab in Albuquerque, N.M., Henderson was disappointed after the 2006 decision.
Now, her panel faced two more major air-pollution reviews: ozone and lead. She hoped things would get better.
They got a lot worse.
Scientists know that ground-level ozone, the chief component of smog, kills thousands of people a year. Even small changes in ozone concentrations, just 10 parts per billion over the short term, can cause death rates to climb by 0.5 percent, particularly among the elderly.
In Philadelphia alone, the EPA estimates, dozens die each year.
The noxious gas is formed by a chemical reaction when organic compounds and nitrogen oxides are exposed to sunlight. Those pollutants come from cars, power plants and oil refineries, among other sources.
It also aggravates asthma and inflames the lungs - "like a sunburn on the skin," the EPA says - and on those days when levels are high, officials warn the vulnerable to stay indoors. When levels spike, so do hospital emergency room visits.
The Clean Air Act requires the EPA to review ozone limits every five years, but the agency had not examined them since 1997, when it was set at 80 parts per billion. Ozone levels in the air are measured by about 1,200 ultraviolet monitors positioned across the United States.
In March 2003, the American Lung Association and a cadre of environmental and public-health groups sued the EPA to force a review, and a judge ordered EPA to complete one by March 12, 2008.
The law required Johnson to set two standards, a primary standard to protect human health and a secondary standard that would protect crops, plants and ecosystems.
The science panel and EPA spent almost four years assessing the risk from ozone. They all agreed that the current standard of 80 parts per billion was too high.
But what level of ozone was safe?
The panel combed through 1,700 new scientific studies to see if they could determine how much ozone, mixed into the everyday cocktail of pollution, made people sick.
These types of studies can establish relationships between pollutants and health problems, but it is easier to pinpoint a specific culprit in a controlled laboratory study.
For that, the panel turned to William C. Adams, an exercise physiologist at the University of California at Davis. Adams had conducted two studies in which healthy adults directly inhaled a controlled amount of ozone at doses near the level that was being considered for the new safety standard.
Both studies were paid for by the American Petroleum Institute.
The studies showed a statistically significant effect when subjects inhaled ozone at the current level set by the EPA, 80 parts per billion. But some adults also showed a decrease in lung function when they inhaled ozone at 60 parts per billion.
If healthy young adults found it harder to breathe with ozone at 60 parts per billion, the panel reasoned, then clearly more vulnerable populations were at risk at that level.
Adams later said he thought the panel placed too much weight on some of his findings, but the experts considered his arguments and disagreed.
In October 2006, the panel recommended that Johnson set the primary level between 60 and 70 parts per billion.
It also said Johnson should set a separate secondary standard, designed to address ozone's effects on a plant's ability to produce and store food. This secondary standard would limit cumulative ozone levels during daylight hours over three months. The panel recommended that the total not be higher than 15 "parts per million-hours" - an environmental measure akin to man-hours.
By February 2008, Johnson had reached a conclusion. In a draft to the OMB, he said the evidence for making a change to both the primary and secondary standards was "compelling."
He set the primary standard at 75 parts per billion, higher than the recommendation. He set the secondary limit for protecting plants at 21 parts per million-hours - also considerably higher.
But the OMB would have to sign off on the rulings.
On March 6, one week before the court-ordered ozone deadline, Susan Dudley, head of the OMB Office of Information and Regulatory Affairs, wrote to Johnson to say that the science did not justify a new secondary standard - one that would be expensive to put in place.
"EPA has not considered or evaluated the effects of adopting a standard on economic values, personal comfort and well-being, as specifically enumerated in the Act," Dudley wrote.
In a footnote, she noted that the EPA was obligated to consider any benefits of ozone.
The next day, EPA Deputy Administrator Marcus Peacock sent a memo to Dudley saying EPA was unaware of any beneficial effects of ozone. Further, the science supported the tougher rule and the agency was barred under the Clean Air Act from considering cost when setting standards.
Dudley sought to block the rule anyway.
With the EPA and OMB in a deadlock, Johnson turned to the White House.
Johnson has refused to discuss what happened next, but a document prepared for his meeting with the White House on March 11 called the intended lowering of the secondary standard the most scientifically defensible.
The EPA staff pointed out that in addition to the science panel, the National Academy of Sciences, the U.S. Department of Agriculture, and the National Park Service recognized the need for a separate secondary standard.
"The president has concluded that . . . added protection should be afforded to public welfare by strengthening the secondary ozone standard and setting it to be identical to the new primary standard," wrote OMB's Dudley.
Dudley's letter sparked a flurry of activity as EPA staffers were told to edit the final rule to reflect the White House's last-minute changes.
Johnson defended himself, saying the panel had gone too far; its recommendation was based on a "mixture of scientific and policy considerations." He did not have confidence, he added, in his own agency's scientific analysis. Adams, he noted, had his own reservations.
EPA staff members were appalled, calling the move "pure politics" in e-mails made public during a congressional investigation into Johnson's handling of the ozone standard. One questioned why a final version of the rule included a sentence about parks and forests, "since we're not really protecting any of them properly."
Another manager wrote: "I know how incredibly frustrated and disgusted we all are at the moment."
The last-minute shuffle also inflamed the science advisory panel.
"That's no way to set a standard, by fiat behind closed doors," Henderson said. "They have no shame."
Burnett, the former senior EPA aide who worked on the ozone decision with Johnson, said it was difficult to get the White House to understand the gravity of its decision.
"There were people at the White House who openly said they didn't believe smog causes health problems," he said. "How do you discuss policy with people like that?"
Panel members thought Johnson failed on both ozone rules.
In a letter to Johnson sent April 7, the panel wrote that it did "not endorse the new primary ozone standard as being sufficiently protective of public health," especially the most vulnerable, and that it failed "to satisfy the explicit stipulations of the Clean Air Act."
"It's outrageous," said John Balmes, a physician who studies ozone and served on the panel.
"When you have a committee of 23 people from a variety of disciplines unanimously agreeing on the science," Balmes said, "and he says separately that there is too much uncertainty to follow the recommendations of the panel, a kind phrase would be 'B.S.' This is not a committee of wild-eyed radicals."
About the same time Henderson and the panel were considering ozone, they were also reviewing airborne lead.
It was one pollutant everyone could agree was bad.
Since the 1970s, evidence had been piling up that airborne lead spewed from smelting plants, leaded gasoline and other sources impaired cognitive functioning in children.
The EPA had not changed the standard since 1978.
The agency's rationale was that it had already eliminated much of the danger of airborne lead when, in 1996, it banned leaded gasoline after a 25-year phase-out program.
But some dangers remained.
It was a fact well known to the Missouri town of Herculaneum, where a smelting plant had been in operation for more than 100 years. One study in 2001 showed that within a half-mile of the facility, 53 percent of children under 6 had high lead levels in their blood.
On some of the town's streets, the lead dust along roadways was so prevalent that officials warned pregnant women and children under 6 to stay away.
The plant, run by the Doe Run company, had violated emissions laws, and in 2002 part of the town was shuttered because it was too contaminated.
The company said it has worked hard to reduce lead emissions by investing in new cleaner technologies. "It's our community, too," said Kent Martin, a spokesman for Doe Run. "That's why these standards needed to be upgraded."
In 2004, an environmental coalition sued EPA to compel a review of the standard.
To make their recommendation about where the new standards should be set, the panel would rely on the EPA "staff paper," a review of the more than 6,000 studies that had been conducted on lead and its effects over the last few decades.
The staff paper is an essential part of any ambient air quality review, but Henderson and the panel noticed that the paper was not among the key documents the EPA provided.
Henderson asked for the paper, but was told that the agency had decided to change how air-pollution reviews would be conducted.
It was all laid out in a Dec. 7, 2006, memorandum from Peacock, the deputy administrator, to Gray, the EPA science adviser.
Now, the EPA would give the panel a "policy assessment" reflecting the agency's views. The policy assessment would be short on science and long on policy options, giving the administrator a wide berth in setting standards.
"It was done to give the administrator a way to control the process," said panel member Bruce Lanphear, a toxicologist and lead expert. Lanphear said he was so disgusted by what he saw as the undermining of the panel's role that he later moved to Canada.
The policy assessment would be published in the Federal Register, and the EPA science panel would have to stand in line and comment on it just like the general public.
Thus, reduced to the role of an outside critic, Henderson's panel would no longer shape and strengthen the EPA staff's scientific findings.
In justifying the move, Peacock said the process would help improve efficiency, while ensuring that the best science from a broad field of experts would be considered.
The panel was outraged. They were, after all, a creation of Congress, chartered under the Clean Air Act to serve as an objective scientific body in advising the EPA administrator.
They demanded the paper.
Then they got a stroke of luck.
The lead review had been prompted by a federal lawsuit, which meant the EPA would need permission from the presiding judge to alter the process.
The coalition objected to the changes, and were joined by the State of Missouri.
"Certainly, in this case, after a draft Staff Paper has already been completed, it seems as if the agency is trying to hide the ball, not bring it into the light," Missouri Attorney General Jeremiah W. Nixon wrote in a brief he filed in the case.
"Missouri believes EPA's new procedure is deeply flawed and actually undermines the interests it purports to serve."
The court ruled that the EPA would have to turn over the staff paper, as well as the policy assessment.
That allowed a unique opportunity to compare the two and measure what effect the new process would have on future reviews.
The results were alarming.
"If it had not been so serious, it would have been laughable," Henderson said. All 23 scientists on the lead review panel expressed concern over the regressive nature of the assessment.
The panel wrote Johnson in January to say the agency's revised process "represented a remarkable weakening of the scientific foundation of the . . . review process."
For example, the policy assessment said Johnson should view as acceptable blood-lead levels in children considered so toxic by the Centers for Disease Control and Prevention that they require treatment. The panel in a letter to Johnson in January called such a starting point "particularly troubling."
Jonathan Samet, chair of the epidemiology department at Johns Hopkins University, wrote that the policy assessment was "an unacceptable result of a process that should be evidence-based but has clearly gone off course and lost its links to a substantial body of evidence."
The assessment also suggested removing lead from regulation altogether, an option that had been considered and dismissed as "scientifically indefensible."
It took the EPA nearly nine months to reply. When it did, the agency said that while the policy assessment was not as informative as it could have been, it was moving forward with the changes.
So the agency's next move took the panel by surprise.
After more than two years of heated exchanges with the panel, and ruling against it in two prior air-pollution decisions, Johnson followed the scientists' advice.
He drastically cut the amount of lead allowed in the air to 1/10 the existing level - from 1.5 micrograms per cubic meter of air to 0.15.
Henderson, whose tenure on the board ended this fall, praised Johnson's ruling, calling it a tough new standard.
Yet in the days after his ruling, Johnson's legacy was tarnished again after it was revealed that, under pressure from the White House, there would be certain exemptions to the new lead rule:
Two hundred of the 350 plants - those that emit between a half-ton and one ton of lead a year - would go unmonitored.
Johnson is fond of saying that he set the toughest air-quality standards to date.
Henderson and other members concede that they are tougher, but not as strong as the science demands.
After 40 years studying the damage caused by air pollution, Henderson knows as well as anyone that science is fraught with uncertainty, and that answers are not always clear-cut. But when human health is at stake, she feels, there is one certainty: Science has an obligation to protect the public as best it knows how. The law requires it.
"When I came on, I thought we could establish the best possible standards to protect public health," she said. "In the end, I found that he was totally loyal to his boss. That was disappointing to me."
Contact staff writer John Sullivan at 215-854-2473 or email@example.com.