New York Times, At Limits of Science, 9/11 ID Effort Comes to End,

April 3, 2005, New York Times, At Limits of Science, 9/11 ID Effort Comes to End, By Eric Lipton,

Again and again, the standard DNA tests came up negative on a three-inch-by-two-inch piece of muscle recovered from the World Trade Center site, and just a year after the 2001 attacks, forensics experts were stymied. Yet now, the scrap has been linked to a firefighter from Midtown Manhattan, allowing his death to be confirmed and giving his wife and two children some sense of finality.

Solving brutally difficult cases like that one required an investment of two extra years and millions of dollars by the medical examiner's office in New York, which sought out and used DNA identification technologies that had never been tried.

That labor - which is coming to a close, at least for now - is why families of victims of the 2001 attacks are gathering in New York today for an interfaith service where they plan to thank the chief medical examiner, Dr. Charles S. Hirsch, and his staff.

But as it turns out, the identification of the firefighter is one of relatively few that resulted from this extra effort to push beyond the limits of traditional DNA testing.

So far, 58 percent of the victims of the trade center attack - 1,592 - have been identified. But only about 111 were positively identified during what staff members at the medical examiner's office agree was an excruciatingly difficult and at times frustrating two years when it tried the new testing methods.

"We were looking at thousands of different bits of information and continually going down dead ends, and often not coming up with the answers we needed," said Dr. Robert C. Shaler, the office's forensic biologist, who led the effort.

Given the extraordinary violence of the towers' collapse and the relentless fires that burned for months afterward at ground zero, nearly everyone involved - from city officials to the families to the scientists laboring over only the tiniest scraps of remains - considers the identification effort a major achievement.

Because of the trial and exposure they received in New York, the new techniques are already in use in other places around the world, including Thailand, as part of the effort to identify tsunami victims, and Texas, for a missing-persons project.

But the work in New York has also served to demonstrate just how hard it is, however intense the determination or high-profile the job, to ignore scientific barriers and apply brand-new technologies.

"Our attitude was, if we need the technology we are going to make it happen," said Thomas Brondolo, deputy commissioner in the medical examiner's office. "That same kind of attitude is what got them to clean up ground zero so quickly. But when you get to the science side, it gets much more difficult. I don't think any of us appreciated at the time what we were up against."

What they faced was more than a dozen refrigerated tractor-trailers filled with human remains that had been pounded or burned into bits far too tiny or degraded to yield to standard DNA tests and more traditional means of identification, like dental records or fingerprints.

The medical examiner pinned his hopes mainly on two new technologies that had been under development for a few years but never used in forensic investigations.

One, known as mini short tandem repeats, or mini S.T.R.'s, was developed by John Butler, a research chemist at the National Institute of Standards and Technology in Gaithersburg, Md. The other, called single nucleotide polymorphism analysis, or SNP's, was created by Orchid BioSciences, of Princeton, N.J.

Both methods require far smaller intact pieces of DNA than the so-called S.T.R., the standard process used globally for everything from crime investigations to paternity tests, as well as the first round of DNA tests conducted on most of the 19,915 body parts collected from the trade center site. (There were 2,749 victims, according to the medical examiner's count.)

When the city began to try the two new approaches in 2002, about 1,000 of the dead had been officially identified. Dr. Shaler predicted that within a year or so he might have another 1,000 new identifications.

"It was a guess, a pure guess from hope," he recalled in an interview on Thursday.

Then reality set in.

From each collected bit of remains, three rectangular plates of DNA samples - each with 96 eyedrop-size wells in them - had been preserved at the medical examiner's office and then frozen at minus 80 degrees Fahrenheit. But frequently, when the staff sent the microscopic samples out for standard testing, the results came back incomplete.

Dr. Shaler and his staff could not say for sure whether this was because the DNA had been damaged by the effects of the attack, or simply because there was not enough genetic material remaining after previous tests.

Fearing that the inconsistencies might lead to errors, the State Health Department would not certify the SNP's procedure. But Dr. Shaler pushed on, sending his own staff to Orchid offices in Texas to inspect their protocols and approve the test.

"There was nothing wrong with the data that would lead us to believe we would get mismatches," he said. "And that was what matters."

As the testing continued, many other samples came back with matches that pointed to an identity, like that of the Manhattan firefighter, Thomas J. McCann, 46. But these matches were often not certain enough to warrant informing the family.

In Mr. McCann's case, as of July 2003 the staff knew that the muscle fragment was his, based on a match with DNA from his toothbrush that would occur only once for about 4,600 men. But the standard the city had agreed upon, in consultation with experts nationwide, was once in at least a trillion. (Even with this high threshold, in about five cases the city made a faulty identification and had to reclaim a part from a family.)

These calculations would have been impossible without a computer software program developed for the identification effort by a Michigan company, Gene Codes Corporation. The program assembled all the data from the different tests, recalculating the percentage of certainty each time a new result came in.

In many cases, remains that were newly identified turned out to have come from victims who had already been confirmed dead based on another body part. Other times, the percentage of certainty for a new identification would rise, but not enough.

Dr. Shaler began to wonder if the specific DNA locations that had been selected for the new tests were the best ones. Certain areas of the genome are more vulnerable to degradation as a result of fire, or even enzymes that are created as a cell dies.

Dr. Butler, the research chemist from the National Institute, and Mark D. Stolorow, an executive at Orchid, said the primary reason they were convinced they did not get a greater number of new identifications was that the DNA samples were in bad shape. "The extent of the destruction of the DNA was just worse than any of us anticipated," Mr. Stolorow said.

So each successful identification - including three that were made late last month - represented a major victory for the medical examiner's staff assigned to the World Trade Center identification unit, which dropped from about 70 in 2001 to 16 last year, to only 2 today.

"All this endless testing we were doing, all this hard work, all this pressure and stress, after all that, it did feel good," said Elaine Mar, the unit's supervisor. "But it was a long time coming."

For the firefighter, Mr. McCann, it was an SNP's test, more than two years after the small bit of muscle had been recovered, that finally produced the needed degree of certainty. "I wanted something," said his widow, Anne Marie, who had been waiting anxiously for some remnant she could memorialize. "I absolutely applaud them."

Ms. Mar and Erik Bieschke, the other remaining full-time staff member, are busy cataloging their work and pushing to close a few final cases, perhaps with positive identifications. But within the next week or so, the medical examiner will send a letter to families telling them that the push has come to at least a temporary stop. Families that had left identified pieces with the medical examiner - waiting until perhaps more might be found - will be encouraged to claim them.

But after three and a half years of work costing a total of $80 million, there is already talk about a new contract, to try out yet another new technology, although it will take at least three years just to test it. For now, the city will accept that it has hit the limits of science.

"We have done everything we can do, so I feel good about that," Dr. Shaler said. "We have done more than anyone would have done in our shoes. I am proud of the fact we have gone as far as we have."

Copyright 2005 The New York Times Company