NEW YORK, N.Y. -- 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
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
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
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 U.S. into a laboratory at the forefront of human gene
research. They are forging the new tools of 21st century
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
"We are moving into new territory," Shaler 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 say.
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 rest, 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
Death crushed some people so fiercely that only genetic
analysis has been able to tell their intermingled cells
Death made a jigsaw of others. More than 180 pieces of
one victim have been identified so far. The slayers and the
slain mingle, flesh and bone, in an autopsy test tube.
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 Clyde Snow, a
forensic anthropologist who helped pioneer modern
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
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.
Forensic experts are contemplating more exotic methods
that might allow them to rebuild shattered fragments of DNA
the way a cosmetic surgeon can rebuild a face.
Even for those professionally hardened to death, the work
is emotionally exhausting.
It is not uncommon to find forensic technicians weeping
at their computer terminals. Several have asked for
transfers. One lab expert quit under the strain earlier this
year. A second broke down emotionally and was
There is no room for error. Perfection is the acceptable
Even so, they must anticipate failure.
Morgue technicians already are drying these tissues, like
petals of rare flowers, to preserve them for a day when more
advanced technology may allow the identification of the most
"If somebody wants to look at this 20 years from now,
they will be able to scrutinize it," Shaler said. "Somebody,
someday will challenge what we have done."
When the first hijacked airliner hit the World Trade
Center, Shaler was holding his regular Tuesday morning staff
meeting to plan the workload for the 90 forensic experts
under his direction.
Shaler, 59, has unblinking blue eyes shielded by
frameless glasses. A closely trimmed white beard softens his
expression. He is light on his feet as he sidesteps the
cardboard boxes of unfinished cases that crowd his office
In more ways than one, Shaler is married to his work. His
wife, whom he met at a medical examiners conference, is a
forensic scientist for the New Jersey State Police.
After almost 14 years in the medical examiner's office,
he is no stranger to the confusion that fogs the
circumstances of violent death.
The city's Office of the Chief Medical Examiner, led by
Dr. Charles Hirsch, is the country's busiest, handling
25,000 deaths a year, including 3,300 homicides and sexual
assaults. Hirsch recruited Shaler to found the forensic
As conflicting reports filtered back to the medical
examiner's office on Sept. 11, a seven-member emergency
morgue team mobilized and headed downtown, in accordance
with the city's long-standing plans for any air
It was no surprise when they left without asking anyone
from the forensic DNA team to go with them. They were never
included in disaster drills.
Within hours, the sobering scale of the World Trade
Center disaster emerged. Early reports placed the dead at
6,700 or more. Morgue experts were braced to handle as many
as a million body parts. The numbers of the missing and
murdered continued to fluctuate for months.
In all, they would find 19,924 body parts.
For nine months, human remains recovered from the Trade
Center site or culled from rubble trucked to the Fresh Kills
landfill on Staten Island were delivered to the open-air bay
by the side entrance of the medical examiner's office. Even
now, tissue still turns up. The most recent fragment was
delivered from the World Trade Center area Monday.
There, under a canopy on a cul-de-sac blockaded by six
metal barricades and under police guard, Shaler and his
staff took possession of the dead.
As the only full-time forensic anthropologist on the
medical examiner's staff, Amy Zelson Mundorff was the first
to examine remains when they came through the door, the last
one to sign them out when they finally were identified.
Pathologists, dental experts and fingerprint analysts
searched each new set of remains for identifying marks or
features that might help distinguish it from the other
dead--a distinctive tattoo, a pattern of freckles, a healed
bone fracture, a birthmark, a wedding ring.
Each piece was cataloged, tagged with a bar code and
"We would go through the bags and sort out the cases,"
Mundorff said. "Anything that was not attached to something
else got its own case number. We would take the time, if we
could, to put the pieces back together, if we could make it
into one case."
She kept at it 12 hours a day, six days a week.
For many emergency workers, the difference between the
quick and the dead at the World Trade Center was
On that Tuesday morning, Mundorff had rushed to the World
Trade Center shortly after the first aircraft crashed into
the building, as part of the disaster team dispatched to
assess the scene.
Pressing forward with other emergency workers, she was
caught in the tumbling outwash of debris from the fall of
the south tower. Slammed against a wall, she suffered a
concussion and broken ribs. Rubble and broken glass slashed
her legs. One of her co-workers fractured his skull.
For the first month, she looked at sets of remains
through two blackened eyes.
"We were too close," she said. "When I look at the cases
on the table, I feel lucky."
As Mundorff and her colleagues sorted through bag after
bag, it became clear that the mainstays of forensic
identification-- detailed skeletal analysis, dental X-rays
and comparison with existing medical records--were all but
There rarely was enough bone to make a recognizable
skeleton; no faces that could be reconstructed; few teeth to
be matched to dental records; even fewer whole fingers to
"So many of our traditional anthropological techniques
are obsolete in a mass disaster like this," Mundorff said.
"It is frustrating. We have to take what we know and apply
it in a different way."
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.
By contrast, remains of the 44 people who died in the
crash of United Airlines Flight 93 near Shanksville, Pa.,
were all quickly identified, aided by accurate passenger
All but five of the 189 people who died at the Pentagon
have been identified. Forensic experts were able to take
advantage of military identification tags and extensive
government medical files.
Remains of nine hijackers from those two crash sites also
have been identified.
But the victims of the World Trade Center attack included
office workers and visitors from 60 countries, shredded now
beyond all recognition.
To identify the fragments, the medical examiner's
technicians would have to look deep into the heart of the
Properly treated, the nucleus of a cell can yield the
long, twisted thread of DNA that forms the unique molecular
signature for every individual. Stretched to its full
length, that strand of DNA is almost 6 feet long. It weighs
barely a billionth of a gram.
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 that of relatives.
Robotic gene sequencers and supercomputer bioinformatics
systems would have to do what family and loved ones could
"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
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
samples from convicted offenders. In New York alone, genetic
testing is being used to reevaluate evidence in 17,000
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 resurrect 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.
Even America's Unknown Soldier was no longer unknown.
In 1998, the remains of an unidentified American
serviceman from the Vietnam War, buried beneath the Tomb of
the Unknowns in Arlington National Cemetery, was removed
from his public tomb, identified through genetic testing and
returned to his family.
The crypt has since remained vacant.
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
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 Corp. 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.
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
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.
"The bones are the hardest to do," said Tom Bode, general
manager of Bode Technology Group. "Most of them have been
subjected to 2,000 degrees Fahrenheit for weeks on end."
The pressure of so many dead pushed the company's workers
and technology to new extremes.
When Alaska Airlines Flight 261 crashed two years ago off
the Ventura County coast, it took the Bode laboratory three
months to process DNA from 860 bones recovered from the
ocean, then considered a record pace.
By comparison, the lab processed 2,000 bone fragments
from the World Trade Center dead in one week last October.
Working around the clock, they continued to process 1,000
new samples a week for the rest of the fall.
As the weeks turned into months, however, only half the
remains yielded useful DNA. Almost one-fourth showed no DNA
Shaler soon realized that technicians 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
In the DNA identification room, Shaler squinted at the
matrix of the dead scrolling across the computer
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
The microprocessors brooded briefly, 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
Down the hall, three industrial freezers were stocked
with vials of World Trade Center DNA. Nearby, a walk-in
chiller held a roomful 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
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
"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.
The heart of the system is the program developed by Gene
Code Forensics. With 96,000 lines of code, the software
links every item in the investigation, information once
scattered through 22 different databases and countless file
cabinets at laboratories in five states. With it, Shaler and
his forensic team can simultaneously sort in seconds
information from three different types of DNA tests on
almost 20,000 partial human remains and compare it to more
than 3,000 DNA samples gleaned from cheek swabs of victims'
kin and genetic material taken from almost 8,000 personal
Other computer programs allow morgue analysts to
cross-check family relationships and calculate the
statistical probabilities of a match between genetic samples
and family groups.
In some cases, Shaler and his team have been able to use
the computer programs to meld partial fragments of DNA from
different but related samples, to create virtual genetic
profiles for comparison purposes.
The company delivered the first version of the program,
called the Mass Fatality Identification System, in
It made 55 conclusive identifications its first day. Now
the team revises it every week to handle the changing
demands of the investigation.
"This requires a level of quality assurance beyond
anything we have ever done, because of the consequences of a
mistake and the emotional pressure," said Howard Cash, the
president of Gene Code Forensics. "Nothing can ever be
Every Friday morning, Cash flies from Michigan to New
York, hand- carrying the latest update of the software.
When he walks through the lobby of the medical examiner's
office, he passes a child's note taped to the wall, written
in red crayon on white construction paper: "I hope you find
The dead transform the landscape they occupy, even as a
In this way, a cornfield becomes a battlefield monument.
A stretch of invasion beach becomes a place in the
So too this sloping asphalt slab where the homeless dead
are parked has--without planning or public ceremony--become
There is no plaque.
There is the smell of the dead, the steady hum of cooling
fans and the roar of the rush-hour traffic on FDR Drive
beyond the barbed- wire fence.
By the morgue tent, three unpainted plywood walls have
been erected to give visiting families an easel to write
their thoughts of love and remembrance. An architect is at
work on drawings for a temporary mausoleum.
Along the walls, mourners taped up a photograph of the
wife, the husband, the father, the mother, the son, the
daughter, the friend whose remains have yet to be identified
Every Friday afternoon, Charles Flood, an Episcopal
chaplain from Philadelphia, lights a single candle by the
morgue tent and holds a prayer service. He reads aloud the
23rd Psalm, should any among the living be there to
"This DNA process is all wrapped up in feelings of
wanting to conquer death," Flood said. "It is very American.
It is a way of saying we will prevail: This dust shall have
a name again."
Some families cannot bring themselves to come. A few
cannot stay away.
There is a woman who comes every day and leaves one fresh
flower. A couple from New Jersey paid their first visit not
so many evenings ago.
Their son is here. They know the trailer where his
remains are stored. More of him may yet be identified. They
agonized over how much longer to wait before holding his
They left his picture by the trailer.