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http://newsinsider.cjb.net/editorials/ancient_evils_2.html Daily source for under-reported news and analysis 26 August 2002 Ancient Evils Anthrax, Greed, and Deceit (Part II of II) By Cheryl Seal 26 August 2002 PART TWO Bioterrorism isn't a new concept -the US 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". 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 (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 polymoprhism (SNP) -a transcription error involving just one nucleotide in a given sequence of nucleotides -i.e., 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 tatoo in a society of tatooless 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 US, 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. What the public has NOT been told (unless they access alternative web news, BBC and other non- mainstream or non-US 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 NYT revealed 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 US 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 Department 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 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 US 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. Scarier 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 (Unkown News Oct 15) 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. 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. But this kind of thing goes on and on 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 US 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 polymmorphisms 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. It has only "broken" as a story in the mainstream media in the US 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). Also, early breakthroughs in identifying differences in the attack isolates were reported as early as. January 2002. The big point is, it has now been nearly five months since the 60 genetic markers were identified. Another long delay. Why? 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 and so probably won't ultimately be found to be the mailer. 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. 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 is the abstract I did of the June 14 article by Tim Read's team that appeared in 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 US 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 the Federation of American Scientists. Allegations about the investigation on the BBC. Examination of general ethical issues around the investigation. Good commentary on the overall case. Explosive detailed summary of the BioPort, Cipro cases by Dr. Leonard Horowitz. Copyright � 2002 by the News Insider and Cheryl Seal Copyright notice The use of the editorials published on this site is free, as long as News Insider is notified and referred to as the source of the information cited. We believe in the free sharing of information, but we do not encourage plagiarism. If our editorials are of use to you, please contact us to let us know. Thank you for your cooperation. Copyright � the News Insider 2000-2002. 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