posted on August 16, 2002 12:26:20 AM new
Bioterrorism isn't a new concept — the U.S. practiced a state-sponsored version
of the black art when government agents knowingly handed out
smallpox-infested blankets to cold, hungry Native Americans back in the 1800s.
But bioterrorists are becoming progressively more sophisticated. So, fortunately,
are the scientist sleuths who match wits with them. In fact, a whole new branch
of biology has opened up that is devoted to tracking down microscopic killers.
Microbial forensics is devoted to tracing the source of a pathogen using a
sophisticated system of molecular markers — the high-tech bio version of
fingerprinting. An excellent overview, tied into the current anthrax situation, can
be found in BioSino: "Microbial Forensics: Cross-examining Pathogens."
http://www.biosino.org/ bioinformatics/ 20020621-2.htm. The infamous
HIV-spreading dentist in Florida (why do so many nasty things of late emanate
from Florida?) was caught dead to rights by microbial forensics...although, alas,
Dr. Evil was dead before they could read him his rights. Microbial forensic
biologists also identified the anthrax strain that had been obtained by the Aum
Shinrikyo cult in Japan, which, back in the mid-90s tried, unsuccessfully to
release a variety of pathogens on the public http://www.cdc.gov/ ncidod/ EID/
vol5no4/ olson.htm (the cultists used a veterinary strain of the pathogen).
The fact of the matter is, thanks to the availability of advanced techniques for
screening the genetic material of these bugs (call it their fingerprint) and the
ever-growing data base of genetic info ("fingerprints on file", tracing microbes
with great precision is becoming progressively easier — easier on an almost
weekly basis, in fact, as researchers race to fill in the gaps in the "fingerprint
files" (technically known as genetic sequence banks).
Which brings us to the current case in question: the 2001 anthrax attacks. There
are more than a few researchers out there, including Dr. Barbara Rosenberg of
the Federation of American Scientists, who think that something in the
government's investigation stinks....and it ain't anthrax-laced cow poop.
Before you can appreciate just HOW truly rotten the government's failure to
make an arrest yet smells, you may need a crash course .....we'll call it
Microbial Forensics 101
To understand the importance of genetic markers used by forensic biologists to
track microbial killers, it helps to understand how the genome (an individual's
genetic blueprint) is constructed.
Sort of humbling to realize it, but the fundamental stuff from which we are
genetically constructed consists of three things you can find in some form laying
around the kitchen or potting shed: sugar (in the form of deoxyribose),
phosphate, and nitrogen (in the form of four different bases)
These three building blocks come together in various combos to create the next
step up: nucleotides. There are two types of nucleotides: adenosine phosphates
(which plays a huge role in metabolic activity) and nucleic acids, which are what
we are concerned about here. There are two forms of nucleic acid nucleotides:
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
DNA nucleotides form long, complex chains. Two of these chains are joined
together like the long rails of a ladder by hydrogen bonds, which form the
ladder's "rungs". Give the ladder a twist and voila — DNA's double helix.
About three billion DNA nucleotides go into the human genome — one copy of
which can be found in each cell in the body. A gene is simply the specific series
of DNA nucleotides (a section of links in the chain) required to spell out the
directions for building one protein. An allele is a gene or gene sequence
corresponding to a specific trait (the allele for hair color, for example). RNA acts
as a "courier," delivering a copy of the DNA blueprint to the sites in the cell
where the required proteins are built to spec.
Proteins are made from amino acids, which are strung together, then folded up
in a specific way unique to each protein. Amino acids are constructed from thin
air (harhar — pardon the chemical joke): hydrogen, carbon, oxygen, and
nitrogen in 20 possible configurations. Examples of proteins include enzymes,
hormones, hemoglobin, muscle fiber, hair, cartilage, and, (drum roll) bacterial
toxins like the ones released by the anthrax bug — all formed from different
combinations of just 20 amino acids.
Sometimes, when the genome reproduces itself, some of the nucleotides end up
getting copied in the wrong order....a typo in the book of life, so to speak.
These typos are officially called polymorphisms (as in "many forms".
Polymorphisms are of great interest to forensic biologists because they can be
used as a "genetic fingerprint" to track the origin of a specific genome.
Three types of polymorphisms are widely used as genetic markers by forensic
biologists, including the guys hot on the scent of the 2001 killer:
Single-nucleotide polymorphism (SNP) — a transcription error involving just
one nucleotide in a given sequence of nucleotides — ie., a "single-letter typo"
Variable number tandem repeats (VNTRs), which are multiple copies of the
same nucleotides sequences at a specific site on a chromosome (specific sites on
the chromosome are called loci, or locus singularly)
Indels :nucelotide sequences that have been either inserted (ie., added) or
deleted from the DNA
Once incorporated into the genome, these polymorphisms can persist for many
generations — some even for thousands of years, which makes them very
useful for tracing the historic origins of species. It also makes them very useful
in tracing pathogens. A strain may exhibit no new polymorphisms for many
bacteria lifetimes (which ain't all that long). When polymorphisms do occur,
they serve as an identifying mark of the population of pathogens in which they
occur. Sort of like finding a bunch of people with the same tattoo in a society of
tattooless clones.
Enter Anthrax
What makes Bacillus anthracis both maddening and promising as target of a
criminal investigation is its "clone-like" nature. Until recently, researchers believe
it was the most genetically stable and unvarying of all bacteria — a veritable
cookie-cutter bug, with each strain having its own unchanging cookie cutter. In
1999 researcher Tim Read of the non-profit Genomics Research Institute
succeeded in sequencing what is known as the Ames strain of B. anthracis. The
source of this "subclone" was a 14-month-old, 700-pound Beefmaster heifer
that died on a ranch in Jim Hogg County, Texas. in 1981. The Ames strain was
used in defensive biological weapons research at Fort Detrick in Maryland and
several other labs in the U.S., Europe (including France, Sweden, and the
United Kingdom) and Russia — and those are just the ones we are told about.
We seem to have spread the stuff about like a fast food franchise...MacAnthrax.
http://www.the-scientist.com/ yr2000/ apr/ lewis_p1_000417.html
What the public has NOT been told (unless they access alternative web news,
BBC and other non-mainstream or non-U.S. news), is that the military has, in
recent years, routinely hired private contractor companies to undertake classified
bio-defense projects. So competitive and self-interested are these contractors,
whose reps hover around the D.C. pork palace, that they are referred to as
"beltway bandits." In the WEEK before 9/11, The New York Times carried an
AP story revealing that a contractor called Battelle was carrying out a secret
project that had as its goal, the creation of genetically altered anthrax. The CIA
is also involved in secret biowarfare schemes — also through beltway bandits.
However, because of the very secretiveness of these enterprises, it would be
impossible to say how many projects have been undertaken and how many are
still actively being pushed forward.
However, this week, Donald "Pharmaceutical Flimflam Artist Turned King of
the Pentagon" Rumsfeld announced in a press conference that he was hot to trot
to shunt more "defense contracts" to the private sector (i.e., the administration's
buddies). Of course, this is the same man who, as CEO of Searle "called in his
markers" in Washington (his own words!) to insure that aspartame was
approved by the FDA — despite the fact that the safety of the substance was so
seriously questioned it was the subject of a federal investigation. The U.S.
Assistant Attorney General who was supposed to be representing the public, one
William Conlon, let the case collapse...and was hired soon afterward by Searle,
no doubt at double his original pay. Couple Rumsfeld's total lack of scruples
with the scruple voids of Cheney, Bush, Tom White, et al and you can see the
ethical standards the Bush crew is working from....as in NONE. But they
continue to have a vulture's field day. A recent Bush administration report, in
fact, has called for a whopping 30,000 Dept. of Defense jobs to be considered
for "outsourcing." Outsourcing, of course, is a euphemistic term that means
"firing people with benefits and contracting out work to your friends." Want a
contract to build laser weapons that will blind people on the ground (a project
farmed out to Lockheed, see http://www.newscientist.com/ news/ news.jsp? id=
ns99992585) or to create mutant anthrax? Just belly up to the pork barrel.
Nothing is sacred to the pork peddlers Best of all for the peddlers and their
"clients," outsourced work is subject to little or no public oversight, which is
why the final bills routinely include items like $5,000-apiece metal screws. This
week alone, Halliburton, not exactly known for its honest practices, received
part of a $725 MILLION contract for work at the U.S. nuclear weapons lab at
Los Alamos. Don't know about you, but I feel pretty damn uncomfortable
letting any outfit with Cheney's imprint on it anywhere near anything nuclear.
More scary by far is the prospect that the corporations colluding with the
government are also colluding with each other, spreading the greasy largesse as
far as it can be spread. I broke the story last year (Unknown News, Oct 15,
2001) about how the government had named Cipro as the "only approved
treatment" for anthrax just as Bayer's patent on its cash cow Prozac was due to
run out — just weeks before the anthrax attacks. Is it too much of a stretch to
imagine that a person or persons unknown working for a beltway bandit engaged
in an anthrax biodefense project might arrange an attack as a way to send Bayer
stock soaring through the ceiling in a very short time? Look at all the corporate
outrages that have come to light in the past several months....It wouldn't surprise
me if they were just the cleanest tip of a very dirty iceberg. I find it more than a
bit suspicious that many folks in the administration, including, it is alleged, Bush
and Aschroft, started taking Cipro BEFORE the attacks.
But the "official story" according to the Bush circus
is that the investigation has narrowed the
investigation down to Fort Detrick, at least as a first
source (Ft. Detrick anthrax was shuffled all over the
globe). This week (Aug 11) a big show was made of
hustling suspects connected to the Detrick,
especially a guy who looked particularly big mean
and swarthy...but who was a virologist, not an
anthrax researcher. It smells strongly of
smokescreen.
On a side note — the latest super-hyped West Nile virus scare comes just a few
months after Duke University released a study showing that DEET can cause
brain damage. So what is the government and media pushing as the solutions to
the West Nile threat (which will affect about 1/10,000 the number of people
felled by the next round of flu)? DEET, of course. Gotta move that product.
http://www.dukehealth.org/ news/ article.asp? unid=
FDBA084D3CE3DB8B85256BAC006E6369. But this kind of thing goes on and
on...http://democrats.com/ view.cfm? id= 4410
In any case, some scientists are extremely skeptical of how the alleged anthrax
investigation is being handled. Dr. Barbara Rosenberg of the Federation of
American Scientists said that in 1998 a secret report was filed on a study by
Battelle Memorial Institute investigating how anthrax might be sent through the
mail.. Rosenberg has suggested that someone connected to that study may have
been involved in the 2001 attacks. Rosenberg, who has risked her career to
speak out, has also accused the FBI of intentionally dragging out the anthrax
investigation through a variety of ploys, including failing to subpoena anthrax
samples from U.S. labs in a timely manner. In fact, she has suggested that the
FBI knows who perpetrated the attacks and is simply refusing to arrest him/her.
Of course, the CIA, Bush administration and FBI had completely refuted
Rosenberg's claims. But Rosenberg is not alone in her suspicions. Among her
supporters is Milton Leitenberg of the Center for International and Security
Studies, Dr. Leonard Horowiotz and many others.
I also have a hunch that a frustrated Tim Read went public with his recent
findings on the polymorphisms in the Florida anthrax isolate as a way to get the
real story out — a sort of "coded message." Any person conversant with
forensic genomics (as you, gentle reader, now are) who sees his results will ask:
"Why they hell hasn't the FBI been allowed to moved faster on this stuff?!"
Another fact not mentioned in the mainstream reports is that the Ames strain
genome sequence had been available for nearly two years when the attacks
occurred. In fact, the latest "amazing breakthrough" by Read and his fellow
forensic biologists actually occurred in MARCH, 2002 (see
http://www.nature.com/ nsu/ 020506/ 020506-9.html). It has only "broken" as a
story in the mainstream media in the U.S. in recent weeks.(Read's report
appeared in the American counterpart of "Nature" in mid-June and in May as a
"preview" report at his institute's website http://www.tigr.org/ new/
press_release_5-09-02.shtml).Also, early breakthroughs in identifying differences
in the attack isolates were reported as early as January 2002
http://www.reporter-news.com/ 1998/ 2001/ anthrax/ diff0123.html
But, the big point is, it has now been nearly five months since the 60 genetic
markers were identified. Another long delay. Why? http://www.guardian.co.uk/
anthrax/ story/ 0,1520,719367,00.html But then, why did it take several months
before forensic researchers had the lab samples they needed to work with in the
first place? A researcher at the Northern Arizona University who asked the same
question last winter was instructed not to talk to the press — he couldn't even let
anyone know he was officially working on the investigation.
But the "official story" according to the Bush circus is that the investigation has
narrowed the investigation down to Fort Detrick, at least as a first source (Ft.
Detrick anthrax was shuffled all over the globe). This week (Aug 11) a big show
was made of hustling suspects connected to the Detrick, especially a guy who
looked particularly big mean and swarthy...but who was a virologist, not an
anthrax researcher. It smells strongly of smokescreen.
Bottom line ... and here comes the "punchline" finish! — a few years back,
working with just fragments of the genome of West Nile virus from a victim in
New York, researchers were able to rapidly and conclusively link the NY isolate
(within just a few months) TO A DEAD GOOSE IN ISRAEL, determine that
the strain was a wild pathogen (not a lab strain) and to formulate detailed
hypotheses as to how the pathogen made its way to New York.
http://www.the-scientist.com/ yr2000/ apr/ lewis_p1_000417.html Now,
considering that the anthrax team is working with not one but two or three
complete anthrax strain genomes, with another 1,200 isolates "on file" and are
using the most advanced genomic screening techniques available (as I said,
advances are now occurring on an all but weekly basis — 1999 is now "the old
days".....we are supposed to believe that, had those controlling the investigation
been truly serious about nailing the culprit, that they could not have done so by
now?
I don't buy it. Not for a New York...or Florida... second.
Supplmentary material
Here's my abstract of the article by Tim Read's team that appeared in the June
14 issue of Science:
To determine who is responsible for the deadly anthrax attacks which occurred
in the autumn of 2001 in the United States, researchers have been conducting
extensive genetic analyses of the bacteria which infected the victims. Bacillus
anthracis exhibits very little genetic variation over time and across strains, with
99% of the nucleotide sequences found in the genes of different isolates
matching. As a result, any variations that can be detected can, potentially, be
used to trace a specific strain to its source.
At present, the most accurate way to identify the strain of different isolates
(populations of bacteria recovered from given sites) is by detecting
variable-number tandem repeat (VNTR) markers. VNTR analysis revealed that
the strain used in the attacks came from the same original source: a dead cow in
Texas in 1981. Designated the Ames strain, this strain was used in defensive
biological weapons research at Fort Detrick in Maryland and several other labs in
the U.S. and Europe. Now, thanks to the availability of the nearly complete
genome sequence of B. anthracis at the Institute for Genomic Research in
Rockville. Maryland, researchers have been able to compare the genome of the
isolates involved in the bioterrorism attack and the genomes of previously
sequenced B. anthracis virulence plasmids, the chromosome (bacteria have a
single chromosome) of the Porton strain, a strain derived from the 1981 isolate
and sent to the United Kingdom from Fort Detrick, and two unrelated strains (a
1925 cow isolate and a 1997 goat isolate). Three types of genetic markers were
screened: VNTRs, indels (nucleotide sequences that have either been deleted or
inserted into the DNA), and single-nucelotide polymorphisms (variations in the
placement of single nucleotides). The analysis reveals 60 new difference
markers, including indels, VNTRs, and single-nucleotide polymorphisms that
were unique to the isolate obtained from the Florida victim.
Links to stories about the anthrax investigation
Listing of anthrax investigation articles from federation of American Scientists:
http://www.fas.org/ bwc/ news.htm
Allegations about investigation in BBC: http://news.bbc.co.uk/ 1/ hi/ audiovideo/
programmes/ newsnight/ archive/ 1873368.stm
Examination of general ethical issues around investigation: http://www.the-scientist.com/ yr2002/ jan/ prof3_020121.html
Explosive detailed summary of the BioPort, Cipro cases by Dr. Leonard Horowitz:
http://www.tetrahedron.org/ articles/ anthrax/ anthrax_espionage.html
.....we are supposed to believe that, had those controlling the investigation