NEW YORK - The human remains of the day shelter in the shade of a white tent near the East River's edge.
Here, set off by wilted bouquets, are the unanswered questions of the World Trade Center dead, stored in the 16 refrigerated trailer trucks parked on this shaded sliver of vacant pavement.
Each question is an anonymous flake of human bone or fleck of flesh picked from the rubble and preserved in a scientific limbo. There are 14,994 of them. This is death divorced from identity - body parts without names to claim them; names without remains that can be mourned.
These human fragments are the dark heart of an unconventional murder mystery that will take years to solve. There is no question who committed the Sept. 11 attack or why terrorists may have acted as they did; little question now of the 2,797 names of those who died. The only answer authorities still seek - at a cost of $58 million since last fall - is how to settle those names on these unidentified remains. Only half the dead have been identified so far.
The search has brought investigators to the edge of what science can discern of death.
By necessity, forensic specialists led by Dr. Robert Shaler, head of forensic biology at the New York Chief Medical Examiner's Office, are virtually reinventing the science of identification.
Their pursuit of identity has turned the busiest morgue in the United States into a laboratory at the forefront of human gene research. They are forging the new tools of 21st century forensic medicine.
They are creating better ways of handling DNA, perfecting new genetic testing techniques, and developing computer programs to analyze genetic variations. The new techniques one day may help diagnose inherited traits across the entire human population.
'New territory'
"We are moving into new territory," Shaler, 59, said. "I feel as nervous as I did the first day of the attack."
In its scale and scientific demands, the federally financed World Trade Center investigation is unique in the annals of crime and forensic medicine, experts said.
In an effort that rivals the Human Genome Project, Shaler has marshaled a national network that includes the New York State Police, the FBI, six biotechnology companies, a score of DNA consultants, computer software developers and an advisory committee of 30 forensic experts that has met every eight weeks to thrash out technical issues.
So crushed, burned, waterlogged and corroded are these remains that they defy conventional identification techniques, forensic specialists quickly discovered.
Consequently, almost half of the identifications made so far have been solely on the basis of genetic testing - 682 of the 1,411 named - and DNA analysis helped in the identification of 343.
Of the unidentified remains, there is not enough undamaged DNA to build a normal genetic profile.
Even now, no one can even tell how many people these refrigerated tissues encompass. No one knows how many people vaporized in the fiery crashes and collapsing towers.
The fires took three months to extinguish. Crews sifted 1.6 million tons of debris for nine months to exhume the remains.
Death crushed some people so fiercely that only genetic analysis has been able to tell their intermingled cells apart.
The forensic experts so far have matched 4,930 body pieces to 1,411 of the victims, and given over many of them for burial or cremation.
"If this had occurred in 1980, or even 1990, the forensic work would have to stop now, with only half the people identified after heroic, intensive work," said noted forensic anthropologist Clyde Snow, who helped pioneer modern identification techniques.
600 more identities
By pushing the state of the forensic art, Shaler is hoping to identify remains of at least 600 more victims.
In recent weeks, the forensic experts have invented more refined testing techniques to extract usable DNA. They are retesting every one of the thousands of unclaimed pieces of bone, flesh, hair and clotted blood samples.
Conventional genetic testing - the mainstay of the effort so far - is reaching its limits. Shaler is resorting to experimental genetic techniques never before used on such a scale.
Since June, DNA experts at Celera Genomics in Rockville, Md., have processed 19,000 DNA specimens from victims and relatives, examining the genetic material contained in the thousands of mitochondria in every cell. The DNA in these cellular power plants is inherited directly from each person's mother. It is much smaller than DNA found in the nucleus of a cell, but is much tougher and more likely to survive intact in damaged tissue.
This month, forensic experts at Orchid Cellmark Inc. in Germantown, Md., expect to begin tests that look for single variations in the 3 billion characters of the human genome. These differences - called single nucleotide polymorphisms - are part of the reason every individual is unique. So far, scientists have mapped 1.4 million of these molecular variations in humankind.
Of the 2,797 dead, only 287 whole bodies were found. Only 185 people could be identified solely from their teeth; 70 from their fingerprints alone.
To identify the fragments, the medical examiner's technicians would have to look deep into the heart of the human cell.
Only one-tenth of a single percent of DNA differs from one person to the next.
Scientists can use these variable regions to generate a DNA profile of an individual, using samples from blood, bone, hair and other body tissues. In conventional genetic testing, a series of chemical probes will bind to the DNA sample in a distinctive pattern for an individual.
That in turn can be compared to DNA from the victim's personal effects or with relatives.
Robotic gene sequencers and supercomputer bioinformatics systems would have to do what family and loved ones could not.
"We take snippets of tissue - less than a cubic centimeter," Shaler said. "It is not much, but there are tons of cells in there. You just need to find 100 good cells."
It is technology whose time had come.
By last year, 120 DNA crime laboratories were involved in more than 16,000 cases and were analyzing more than 265,000 convicted offender samples. In New York alone, genetic testing is being used to re-evaluate evidence in 17,000 unsolved rapes.
As a new tool of mass identification, genetic testing helped investigators identify all 230 of the victims of TWA Flight 800, which crashed in the ocean off Long Island in 1996. It helped establish the identities of the murdered from the mass graves of Bosnia and Guatemala. It reunited families with remains of long-missing soldiers killed in Korea and Vietnam.
In the process, genetic testing also altered public expectations about the anonymity of death. With so much scientific knowledge to be had from the code of life, a nameless death seemed an affront.
Just as genetic testing altered the forensic science of identification, however, the demands of the World Trade Center dead would in turn change the technology of genetic testing.
As a laboratory technique, modern genetics depends on highly automated machinery that can perform the mindless, repetitive chemical work of gene-sequencing at high speed, running as many as 800,000 genotypes a day.
Scientists around the world dump more than 100 million bases each week into a public data repository. It takes arrays of supercomputers to make sense of the raw genetic sequences, by identifying the patterns of DNA code that indicate genes or the presence of identifying markers.
Although New York City has the largest forensic DNA lab in the country, the demands of the World Trade Center investigation instantly swamped its resources.
The medical examiner quickly drafted the New York State Police forensic DNA laboratory in Albany, and two of the world's largest genetic sequencing companies: Myriad Genetic Laboratories Inc. in Salt Lake City, and Celera Genomics, which was the first private company to sequence the human genome. A third company, Applied Biosystems Inc. in Foster City, Calif., provided equipment and expertise.
Two of the most experienced private forensic DNA identity laboratories, Orchid Cellmark and the Bode Technology Group in Springfield, Va., also joined the investigation.
Laboratory Corporation of America, which has 900 DNA centers around the country, and the New York State police collected almost 7,000 razor blades, combs, toothbrushes, lipsticks and other items that had belonged to victims, which could be tested for DNA and compared to remains. From relatives, they also collected more than 6,800 DNA swab samples to be compared with victims' genetic profiles.
Soon, couriers were crisscrossing the country carrying sealed pouches full of bar-coded vials of DNA.
But no one had ever tried to use these high-speed laboratory DNA extractors and gene sequencers to handle so many tissue samples so badly damaged.
Nor were research laboratories accustomed to the unforgiving demands of forensic identification or the legal niceties of handling evidence.
Too much for robots
From the outset, it was more than the robots and the prepackaged biochemical kits could handle.
Shaler's technicians processed the first 3,000 sets of remains by hand, extracting the DNA themselves.
The chemical extraction solutions had to be customized by trial and error, the timing adjusted and procedures revamped. As the weeks went on, every one of the processing methods was customized to handle these unusual human cells, said Brian Ward, president of operations at Myriad.
Scientists were retrained. Laboratories were rebuilt and secure evidence rooms constructed to hold the DNA. The reliability of new procedures was tested again and again, then certified by the New York Department of Health.
At Celera, the new labs were ready by November but it took until June to develop computer programs that could analyze all the data the high-speed sequencers spit out.
"There has never been a laboratory using high-speed robotics to process such a large number of mitochondrial samples, not the FBI, not the Defense Department, not anywhere," said Rhonda Roby, forensic manager for Applied Biosystems.
20,000 samples
Almost 20,000 DNA samples were sent to Myriad for analysis on its 12 high-speed sequencing robots.
More than 13,000 bone samples were shipped out for testing and analysis to the Bode laboratory. So were DNA extracts from 4,000 remains and 3,000 DNA samples gathered from family members or personal effects.
As the weeks turned into months, however, only half the remains yielded useful DNA. Almost one-fourth showed no DNA at all.
Shaler soon realized they would have to test all the unclaimed remains again, in the hope that they had learned enough from the year to coax a name from even these damaged cells.
In the DNA identification room, Shaler squinted at the matrix of the dead scrolling across the computer monitor.
Each numbered cluster of items detailed a set of body pieces, personal effects and DNA from families of victims that all have a genetic sequence in common.
Shaler clicked on a case number with the computer mouse.
The microprocessors whirred, then flagged one collection of remains with a yellow tag.
"This looks like a potential mix-up," Shaler said.
Retesting revealed that two people - a man and a woman - had died in the same spot, their remains intermingled in the crush of tons of falling Trade Center rubble. The tissues were recovered by rescue workers and collected in a single 50-milliliter test tube. Muscle clung to bone.
"People died together," Shaler said. "We have a lot of that."
Down the hall, three industrial freezers were stocked with vials of World Trade Center DNA. Nearby, a walk-in chiller held a room full of bones gleaned from the rubble. Red plastic containers holding personal effects of disaster victims were stacked six deep to the ceiling.
On Shaler's computer display, it was all reduced to symbols: life code and computer code.
In this molecular search and rescue effort, they are aided by a sophisticated computer matching program developed during the course of the investigation by an Ann Arbor, Mich., company called Gene Codes Forensics. The program can cross-match thousands of gene sequences at a keystroke.
"DNA is the sexy part but the real underpinning of all this is computer software," Shaler said. "Without this, it would be impossible."
Shaler moved the computer cursor down the ranks of the dead.
He clicked on a case number.
The screen blossomed into a matrix of genetic sequences from 63 body parts, matched against the DNA extracted from the bristles of a toothbrush brought in by a victim's family.
"They all match this one person," Shaler said. "And we have the identification."
Even so, the computer's conclusion must be independently confirmed by a second set of genetic tests, then laboriously cross-checked against all the family records and personal effects on file, to make sure that no one puts the right name to the wrong body.
"Even if you were 99 perfect, you would have still misidentified 28 people," said Mike Hennessey, project leader for the World Trade Center identification system.
Robert Lee Hotz is a reporter for the Los Angeles Times, a Tribune Publishing newspaper.