CASE CLOSED … what really happened in the 2001 anthrax attacks?

* DOJ letter to NAS (9/15/08) regarding the proposed NAS review of the FBI’s anthrax science

Posted by DXer on September 20, 2009

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I have recently received a copy of a 3-page letter from the U.S. Department of Justice (DOJ) to the National Academy of Sciences (NAS) dated September 15, 2008, outlining the possible areas of investigation that NAS might undertake in a review of the science used by the FBI in its anthrax investigation. The letter appears in its entirety below.

  • The expectation of an independent panel and the list of topics certainly establishes a basis for the kind of solid review all of us want to see.
  • Of course, we can only hope that these sentiments and particularities made it into the eventual $880,000 contact between the FBI and the NAS, since that contract has not been made public.
  • There was certainly no mention in the August 2008 letter about sequestering FBI-submitted documents until the end of the NAS review, a condition which apparently did become part of the executed agreement.

I would like to draw attention to the following excerpt from p 3 of the letter …

DOJ to NAS - 9-15-08 p 3 of 3 - extract

Reading this excerpt in connection with the NAS/FBI decision to delay production of FBI-submitted documents until the conclusion of the NAS review raises some questions and observations …

  1. if the reason for withholding documents is because they are classified, that is of course proper
  2. but if that is the reason, why would the documents then become available under FOIA after the NAS review is completed?
  3. and why wouldn’t NAS simply say the documents to be withheld were classified?
  4. is it logical then to suppose that the withheld documents are not classified?


DOJ to NAS - 9-15-08 p1

DOJ to NAS - 9-15-08 p 2DOJ to NAS - 9-15-08 p 3 of 3

33 Responses to “* DOJ letter to NAS (9/15/08) regarding the proposed NAS review of the FBI’s anthrax science”

  1. DXer said

    A standard “Issue” GRE test takers are asked to discuss is:

    “It is a grave mistake to theorize before one has data.”

    The scientist from Sandia speaking today on weaponization wrote me to say that the FBI refused to give him the data relating to the Si and O in the first mailing to the media (as distinguished from the second mailing to the Senators). The level in the first mailing has been characterized as massive. I gave him what I represented to be the leaked data (and published on Lew’s blog) and JM was skeptical of the figures. That is all the more reason for the FBI to give him the data.

    The Microdroplet Cell Culture Technique I have linked contemplates, in a later step, removal of the silica from the surface through repeated centrifugation (although through a natural occurrence noted by Dr. Burans and Dr. Majidi, it is absorbed into the spore coat).

    Although I am not a scientist, isn’t it a grave mistake to theorize about the purpose of the Si and O in the first mailing without the data?

    And does it make sense to theorize about the purpose of the Si and O in the second mailing where the difference appears to just be additional centrifugation and/or sequential filtration?

    I think the FBI WMD Chief is correct in his assessment. The silica could have been in the culture medium.

    But I don’t think JM should be theorizing on the subject without the relevant data — which the FBI WMD Chief had seen but JM (when I heard from him) had not.

    I’m looking forward to the day Sandia is given the relevant data and comes around to be able to more expressly support the FBI WMD Chief’s conclusion.

    Then although it would serve no purpose, people with an interest in semantics can debate whether something that concentrates anthrax or biocidal agents or fertilizer or inhaled vaccines is properly understood to fit the term “weaponization.” Many processes are “dual purpose,” even when not intended.

  2. The questions raise what could be called the separability issue. Can the questions be answered independent of the specific facts or theory of the FBI/DOJ case?

    Question 4 on recoverability is an example. Does the answer depend on the specific piece of equipment, how it was handled, what size it is, what its internal geometry is, whether it has a complicated internal structure difficult to clean, doesn’t fit in a glove box, etc.

    If the answers to questions depend on the specific pieces of equipment or the specifics of the lab or the specifics of the events that happened, then answering them requires the NAS to go into the specifics of the FBI theory of Ivins as solely guilty.

    Could Ivins have cleaned the specific equipment in his lab in his glove box given his time given the state of that equipment and the records of the lab on that equipment and on Ivins.

    If the probability or other answer depends on the lab, equipment, information records on those, the people, and down to the suspect, then the NAS needs to say so and needs to indicate what the answers are for Ivins and other possibilities.

    • DXer said

      They mention a lyophilizer. Let’s consider the lyophilizer (a Speed-Vac) available to Dr. Ivins. The NAS panel seems inconvenienced by the fact that I did not notice anyone with any experience making aerosols or an anthrax simulant.

      The DARPA-funded work involving use of the lyophilizer by Dr. Ivins was the same lyophilizer involved in the DARPA-funded work done by Ann Arbor researchers. In thanking Dr. Ivins who in numerous patents for supplying the Ames, the researchers referenced his 1995 Vaccines article describing preparation of the spores (and the method included use of a lyophilizer). blogger Glen Greenwald explains:

      “The leaked ‘scientific’ evidence is no better. If anything, it’s worse. The Washington Post today reports — all based on anonymous leaks — that “key to the probe” is the fact that Ivins “borrowed from a bioweapons lab that fall freeze-drying equipment that allows scientists to quickly convert wet germ cultures into dry spores” and that “the drying device, known as a lyophilizer, could help investigators explain how he might have been able to send letters containing deadly anthrax spores to U.S. senators and news organizations.” The article further claims that “the device was not commonly used by researchers at the Army’s sprawling biodefense complex at Fort Detrick, Md.”

      But that appears to be completely false. Here is the abstract of a 1995 research report [ Vaccine Volume 13, Issue 18, 1995, Pages 1779-1784 ] , for which Ivins was the lead scientist, reporting on discoveries made as part of their research into anthrax vaccines.

      Throughout the period 2000-2008, the Ann Arbor researchers would explain: “B. anthracis spores, Ames and Vollum 1 B strains, were kindly supplied by Dr. Bruce Ivins (USAMRIID, Fort Detrick, Frederick, Md.), and prepared as previously described (Ivins et al., Vaccine 13:1779 [1995]).” That 1995 Vaccine article contemplated the routine use of a lyophilizer.

      Greenwald continues:

      “Clearly, Ivins’ legitimate work researching anthrax vaccines entailed the use of a lyophilizer. As the commenter notes, “If you google ‘lyophilize’ and ‘anthrax’, most of the pages returned are about anthrax vaccines, which is what Dr. Ivins was working on at Ft. Detrick.” Indeed, even the Post article — while breathlessly touting the profound importance of Ivins’ incriminating possession of a lyophilizer — says this:

      He did at least one project for the Defense Advanced Research Projects Agency that would have given him reason to use the drying equipment, according to a former colleague in his lab. [The DARPA-funded work that Ivins did is mentioned in numerous patents in which the Ann Arbor researchers thank Dr. Ivins for supplying Ames and note that the spores were prepared as described in Ivins, et al., Vaccine Volume 13, Issue 18, 1995, Pages 1779-1784 1 [FN. 1/ ]

      This morning I spoke with Dr. Luke D. Jasenosky of the Harvard School of Medicine’s Immune Disease Institute. Dr. Jasenosky said that it is “very common” for someone engaged in the vaccine research of the type Ivins did to use a lyophilizer, and that he “would actually be surprised if they weren’t using one.”

      The Post article goes to great lengths to stress how small and easily hidden this device is — to imply that Ivins could have weaponized the anthrax without being detected — but the FBI found out that Ivins had possession of a lyophilizer because of this:

      Ivins had to go through a formal process to check out the lyophilizer, creating a record on which authorities are now relying.

      So he didn’t exactly hide his acquisition and use of the device which, the FBI is now trying to suggest, he secretly used to convert wet spores into dry anthrax in order to perpetuate the anthrax attacks. Quite the opposite — he obtained the device in exactly the way that regulations required, knowing that there would be a clear and easy paper trail reflecting that he obtained this device — one which he obviously had legitimate reasons, on at least some occasions, to use in his work.”

      In an exclusive in early November 2008, the New York Post reported:

      “The lyophilizer, located in a hallway surrounded by four labs, did not have a protective hood. A hood is necessary to circulate and filter air and make it possible to use the lyophilizer to work with harmful bacteria without the bacteria becoming airborne. Co-workers say the hoodless lyophilizer would have spewed poisonous aerosols, infecting co-workers. But no colleagues of Ivins experienced any symptoms.

      Co-workers also point out that the machine would have to be fully decontaminated after use – a 24-hour process called paraformaldehyde decontamination that involves locking down the lab.

      Without a full decontamination, the machine would have contaminated other bacteria or liquids used on the machine at a later date. And if it had not been decontaminated, the FBI should have been able to find traces of the dry anthrax on the machine. Yet they swabbed Ivins’ machinery numerous times and were unable to find traces of dry anthrax spores in his lab, Kemp said.”

      There was someone at Merck who reported to the FBI an off-the-books contamination using paraformaldehyde and couldn’t rouse any apparent interest. There the area needed to be closed and everyone barred from entering the door by yellow police tape so as to avoid harm to the person. There was no such evidence of such decontamination done here.

      “Even if Ivins did have access to a freeze-drying machine and a protective hood, sources who worked closely with Ivins estimate it would take a minimum of 40 days of continuous work without detection to create the volume of spores used in the attacks.” “If he was working eight hours a day on spore prep every day, it would be noticed,” said Gerry Andrews, Ivins’ supervisor between 2000 and 2003. “It’s ridiculous.” Ivins’ lab – just 200 square feet – was in “highly trafficked areas, and Bruce had colleagues that worked with him every day,” Andrews said.

      Meanwhile, in September and October of 2001, Ivins was involved in 19 research projects, including working on the Department of Defense-funded anthrax vaccine that is now in clinical trials, anthrax vaccine testing on rabbits and monkeys, and an outside project with a government-contracted lab, the Battelle Memorial Institute in Ohio.”

      Dr. Gerard P. Andrews told the Baltimore Examiner “The only lyophylizer available was a speed vac,” he says. “That’s a low-volume instrument that you can’t even fit under a hood” used to contain pathogens. “The only opinions that I would place any confidence in would have to come from individuals who have made the stuff, in the same quantity of the letters,” said infectious disease specialist W. Russell Byrne. “And then I would ask them to go into B3 in building 1425, work there for a couple of weeks and reproduce what they say Bruce did. That’s the only way I could, in good conscience and in the spirit of objective scientific inquiry, believe them.”

      Dr. John Ezzell, the scientist referenced in Dr. Ivins’ email to Pat Fellows, tells me the aerosolized Ames he made for DARPA in 1996 had been irradiated (and testing confirmed that the irradiation had rendered the anthrax inactive). He worked for the FBI’s Hazardous Materials Resource Unit in 1996. The first order of business, then, is for the FBI to allow its scientist leading the first investigation into the attack anthrax made the dry powdered anthrax in 1996 and to see if the equipment and time he used was available to Dr. Ivins. Or at least lift the gag order to see what he did in making the aerosolized that matched the attack anthrax so closely according to what Dr. Ivins says he had heard from the person he named in an email to Patricia Fellows. I don’t even know that there is anyone on the NAS panel who has made an aerosol, let alone an anthrax simulant, a curious oversight. Now that at least one panel member has dropped, perhaps they could find a replacement not merely equally qualified on the issue of how a spore coat folds over upon upon drying, but one who has experience with aerosols.

      • Anonymous Scientist said

        Concerning the FBI’s claims about a lypholizer being used to prepare the powder here’s what Serge Popov had to say on that one:

        “The disappointment was that the lyophilizer turned out to be a speedvac device useful for drying small amounts of liquids into solid films on the walls of the microtubes, but not into the fluffy powder.”


        In other words, yet another scientifically childish leak the FBI threw out there, hoping nobody with any intelligence would challenge it. This is similar to the leak they made to the NYT’s Scott Shane about the so-called “chemical signature of the water” pointing to Detrick and only Detrick. After this absurd notion was shown to be patently scientifically possible, the FBI had to issue a denial and the NYT had to issue a postscript:
        Postscript: February 28, 2009
        A front-page article on Jan. 4 about Bruce E. Ivins, the late Army scientist who the Federal Bureau of Investigation says was responsible for the anthrax letter attacks of 2001, reported that F.B.I. scientists had concluded in 2004 that out of 60 domestic and foreign water samples, only water from near Fort Detrick, Md., where Dr. Ivins worked, had the same chemical signature as the water that had been used to grow the mailed anthrax. That information, provided by a former senior law enforcement official who did not want to be named in the article, suggested that the anthrax could not have come from military and intelligence research programs in Utah and Ohio, as some defenders of Dr. Ivins’s innocence had speculated. The F.B.I. declined to answer questions for that article, which said that the evidence against Dr. Ivins was circumstantial and that many of his colleagues believed the F.B.I.’s conclusion was wrong.

        On Tuesday at an American Society for Microbiology conference in Baltimore, an F.B.I. scientist, Jason D. Bannan, said the water research ultimately was inconclusive about where the anthrax was grown. An F.B.I. spokeswoman, Ann Todd, said on Wednesday that the bureau “stands by the statements” of Dr. Bannan. The case will be reviewed this year by the National Academy of Sciences.

  3. DXer said

    Inventory Procedures Did Not Impede Insider Misuse of Agents

    Prior to the fall of 2001, there were no effective inventory control procedures at USAMRIID — or indeed other institutions that worked with select agents — that would have impeded insider misuse of such agents. Anthrax spores were held in a liquid solution in a flask (RMR-1029) that originally (October 22, 1997) contained 1000 ml of spore suspension with a concentration of 3×10 10 spores/ml. While the flask had been under the control of Dr. Ivins since 1997, other laboratory staff may also have had access to it. However, no one in USAMRIID was specifically responsible for monitoring the use of materials by scientists. According to USAMRIID officials, Dr. Ivins’s laboratory notebook contained a record of the amounts of material removed at various times between 1997 and 2004, when the FBI finally removed the flask from USAMRIID. Additional undocumented removals from the flask could have been disguised simply by adding water to restore the volume. This would have reduced the spore concentration, but this concentration was apparently never checked. Even if it had been, experts told us that the normal biological experimental error involved in counting spores could have disguised the loss of up to 5 percent of the material.

    • anonymous scientist said

      I’ve been pointing out for months on this forum exactly what this GAO report states today. It would have been trivial to remove even 100ml of spores and replace it with water. It would never have been noticed – even if it was checked with a spore count.

      • DXer said

        “The overarching purpose here is to prevent terrorism,” said Ken Wainstein, former Justice Department national-security chief and White House Homeland Security adviser. “It’s always a tough call when to pull the trigger and arrest a terrorist suspect during these threat investigations. You want to keep surveillance on him and collect intelligence about his network and his associates, but you don’t want to leave him out there so long that he carries out a terrorist attack or detects your surveillance and disappears.”

        Comment: Ken Wainstein was FBI Director Mueller’s Chief of Staff; head of the National Security Division; the US Attorney for DC, and then the national security person at the White House.

    • BugMaster said

      I don’t think repeating the spore counts could detect even a 5% difference. Viable counts at this level can vary by 20% or more, depending on the technique used and the skill of the technician.

  4. DXer said

    The GAO report issued today states:

    “On July 10, 2008, “[Ivins’ access rights to the entirety of USAMRIID were withdrawn by the laboratory commander. An order was susequently issued to installation security to prevent Dr. Ivins from entering the installation unescorted. A written bar order was signed with a plan to serve the document to Dr. Ivins. Before service of the order occurred, he died of a drug overdose on July 29, 2008.”

    Ed Lakes reasons that his suicide proves he was guilty of murder — that he otherwise had no reason to commit suicide. Such reasoning is unsound. USAMRIID had been his world all of his adult life. He lived very nearby. He had just spent $68,000 on attorneys fees and was cashing in EE Savings Bonds. Dr. Ivins had independent reasons to commit suicide.

  5. DXer said

    GAO report issued today at p. 37.

    “Immediately following the anthrax mailings in 2001, FBI took contaminated evidence to USAMRIID for analysis. Dr. Ivins was tasked by USAMRIID management to analyze the samples of spores sent through the mail and was also a technical consultant to the FBI in the early months of investigation.”

    At least we now know one of the reasons he was working overtime in October, November and December.

    • DXer said

      After describing the first incident where a lab technician had expressed concern there was contamination due to unsafe handling procedures and Dr. Ivins took clean-up steps without reporting them, the GAO report continued:

      “After a spill incident inside of suite B03 in building 1425 in April 2002, Dr. Ivins conducted a second round of unauthorized sampling of his shared office space and cold side areas outside of suite B-3. These findings were reported and sparked a buildingwide sampling inspection. An inspection conducted by the Army 8 months after the anthrax mailing found that suite B-3 in building 1425 at USAMRIID was contaminated with anthrax in four rooms of suite B-3 (306, 304, cold room, and 313 (Dr. Ivins laboratory)) and that bacteria had escaped from secure to unprotected areas in the building. All the areas outside of suite B-3 that tested positive were associated with Dr. Ivins and members of the Bacteriology Division. The inspection report stated that “safety procedures at the facility and in individual laboratories were lax and inadequately documented; that safety supervision sometimes was carried out by junior personnel with inadequate training; and that exposures of dangerous bacteria at the laboratory, including anthrax, had not been adequately reported.”

  6. DXer said

    Dr. Hassell at the roundable says that when they seized it was down to several hundred ml. (He explains it was originally had started in two flasks).

    It was last at several hundred ml in Spring 2002. Did they seize it then?

    Or when he said “several hundred milliliters” did he mean 37 ml or 137 ml. with the flask having been first seized in November 2007.
    Or is there some other way of reconciling the comments and photo with the flask 1029 record produced pursuant to FOIA.

  7. Anonymous Scientist said

    Majidi writes, in his letter to the NAS : “Can BA spores dried with a rudimentrary methodology pose an inhlational hazrd resulting in pulmonary anthrax”?

    This question is totally unscientific. Obviously the answer is yes. The drum-maker a few years back certainly dried his spores in a rudimentary manner (from a dried animal skin) – and he contracted pulmonary anthrax. But it was probably a 1 in a thousand shot. Another 999 drum-makers did the same thing that week and they DIDN’T contract pulmonary anthrax.

    This is science, FBI style. No quantities – no benchmarks – no statistics. No quantitative analysis whatsover.

    The question Majidi SHOULD have asked is “Can BA spores dried with a rudimentary methodology escape from envelopes and contaminate 20 people in different floors of a building and can these spores re-aerosolize from surfaces weeks later after being disturbed by normal office activities and have airborne median particle sizes of 1-2um as found by the EPA study in the Hart building”?

    • BugMaster said

      Are there any reliable methods that can be used to accurately geolocate the facility / location where BA spores may have been grown?

      Yes. From that location, you should be able to isolate the genetically identical b. subtilis!

      • Anonymous Scientist said

        And you should be able to find BA spores in that location with the same silicon signature found in the mailed spores !!!

  8. DXer said

    Dr. Fraser-Liggett summarized:

    “I was hopeful that perhaps genomics would provide sufficient amount of information to be able to track the material to its source, but I then [in late 2001], and have always, asserted that in no way did I ever believe that this kind of genomics-based investigation was ever going to lead to the perpetrator,” Fraser-Liggett said. “That was going to require much more traditional police investigation.”

  9. DXer said

    Dr. Fraser Liggett said that as she understood it, based on what the FBI told her, “there were no other samples that were screened that had 3 out of the 4”

    Yet, to the contrary, as I recall his testimony, Dr. Budowie there was one that had 3 morphs and that the NAS panel members should consider it.

    What explains the difference?

  10. DXer said

    Natureblog summarizes:

    “Other speakers included … retired FBI Special Agent Jennifer Smith, who urged the panel to “continue to probe” and push the FBI to release all the relevant documentation.”

    My intelligence source says that the FBI has produced only a small fraction of the relevant documents.

    What we need is federal district court judge Rakoff, given his experience in these matters, to take over responsibility for the sufficiency of the document production

  11. DXer said

    The following topics were discussed in the closed sessions:

    Opening Remarks and Introductions
    Discussion of Study Charge
    Overview of the NRC Study Process
    Handling of Restricted Information
    Security Related Issues
    Review of Morning Session
    Committee Member Presentations
    Discussion of Future Meeting Schedule
    Conflict of Interest/Bias/Balance and Committee Composition
    Preliminary Evaluation of Documents
    Discussion of Additional Data Needs and Future Speakers

  12. DXer said

    Dr. Read, a scientist helping with the Amerithrax investigation in the DNA sequencing, long ago published the news that the anthrax was a 50/50% mixture of genotype 62 (Ames) and genotype 62 with an inversion on the plasmid. This would mean two distinct nucleic acids were detected in the sample. This means that some of the Ames had a segment of DNA that is inverted, or flipped, relative to the remainder of the plasmid. Years ago one expert (RJE) advised me that no properly trained microbiologist would propagate or archive a mixture. Standard microbiological procedure calls for isolation of single colonies – i.e., single, unmixed cells and their clonal, unmixed progeny — at each step. (Inversions are not an uncommon class of mutational events, however. It would only be especially probative if it were a rare inversion and if samples were to be present among samples collected from laboratory archives.) It was always possible that the anthrax used was highly distinctive (pinpointing a single lab) and the authorities just didn’t have that sample collected. But given that since 2002 they have known it was a mix of Ames strains, it is surprising that they did not zero in on Ivins flask a half decade ago given that any description of how it was created would have revealed it to be a mix of two sources.

    The FBI in August 2008 announced that 8 samples were an exact match. (MSNBC previously had reported that the 16 labs had been narrowed to 4). The FBI reports that 100+ individuals had access. Unnamed Ft. Detrick sources report that 200-300 individuals had access in light of the FBI’s mistaken assumption it had always been stored in 1425. The field thus has been narrowed from 1,000 who had access to 100-300. But to talk about the genetics as if it related to Dr. Ivins guilt — rather than the 100-300 who had access — is fallacious. It is a good thing that the NAS task to confirm that aspect of the inquiry. They can use the term “M&Ms”, if they like, to describe the morphs, and it won’t bear much on Dr. Ivins’ guilt. Why isn’t the finding that it was a mixture of two samples just as probative (and at the same time corroborative)? And why wasn’t that knowable in 2002?

  13. There are 4 pictures or frameworks to think about the lineage or tree of Ames strain and the identification of the letters relative to that tree.

    1) There is a tree of lineages going back to the origin of the Ames strain. We can put every flask and the letters exactly on the right spot of the tree. This is a deterministic mode of thinking. Sometimes the tree has gaps and we have to think about stochastic issues.

    2) We have a deck of cards and we deal out a bridge hand. There is one deal. We compute probabilities for what cards (morphs) are in what hand. For this we need to define what is the starting deck.

    3) We have a game like blackjack where we can count cards. So the state of the system evolves and we have information. In blackjack, there is a single branch to track.

    4) Fully stochastic. The entire generation of the tree of lineages is a stochastic process.

    These different pictures are used at different times. We switch in our minds between them. The NAS should lay these pictures out carefully and carefully expose the assumptions and flaws in each picture.

    The deterministic tree has gaps. We need to think about what to do about those. That requires us to think about the stochastic pictures.

    If we think of the bridge hand, what is the state of the deck of cards? That isn’t very well defined. This is what I meant by defining the starting gate in comments earlier.

    What gets you into the running to produce the 4 morph identification?

    Does tree mapping get us beyond thinking of the 4 morphs? Is 4 morph thinking closer to the bridge deal thinking?

    NAS should think about these and write out with little card game and other examples what it is they are doing. Committees like this typically meet and don’t work out a table of examples working from easy to complicated. Because of that the committee itself is usually confused. They often argue over points that are because they didn’t write the Schaum’s Outline of whatever it is they are doing. Writing the Schaum’s Outline of example calculations from easy to hard is what will shed light on this.

    Are we going to end up with probability numbers like .05 or .5 or .9? Are these numbers stable? That is where you need to think about the examples and the stochastic process issue carefully.

    • Question 3 has the deck of cards picture as its implicit assumption. It says if you start with 0, 1 or 2 of the mutations, what is the chance you can get to the 4. This depends on quantities of growth, which is like number of cards dealt.

      If we used the tree of lineages of picture, then we would ask can we find a morph in one of the letters not in RMR 1029. Then we would ask if that morph could have appeared randomly in the growths for that letter.

      Is there a branching subtree for the letters themselves? Did the second letters for example grow from the growths for the first letters? Were each set of letters done in a single batch, or was it sequential? Can we tell that from the morphs or other info from the samples?

      This is why the NAS should state each picture and give the answer for each picture for each of the FBI questions.

  14. It would be useful for the panel to develop or point out and use a terminology for the probability calculations.

    It would also be useful to build up examples of calculations.

    One spore by itself that lies dormant and does not contain any of the 4 morphs to start with. What is the probability that this spore has one of the 4 morphs after 5 years? Obviously its zero. But it emphasizes that the number of spores and what they are doing matter.

    • By terminology I mean things like what gets you to the starting gate? Is it Ames strain? Or is it a sub-strain of Ames?

      Strains branch into what? Sub-strains? Each morph set is a type of sub-strain? Or each morph set is a sub-sub-strain, and there already is a definition for sub-strain?

      “Here we identified SNPs that define the lineage of B. anthracis that contains the Ames strain, the strain used in the 2001 bioterrorist attacks in the United States. Sequencing and real-time PCR were used to validate these SNPs across B. anthracis strains, including (i) 88 globally and genetically diverse isolates; (ii) isolates that were shown to be genetic relatives of the Ames strain by multiple-locus variable number tandem repeat analysis (MLVA); and (iii) several different lab stocks of the Ames strain, including a clinical isolate from the 2001 letter attack.”

      Does begin Ames strain qualify a sample to be a possible entrant to produce the 4 morphs? Has this paper gone beyond the conceptual framework of talking about 4 morphs and more morphs can be analyzed?

      Can the branching tree of Ames be mapped? I.e. every sample in the world put on the tree that branches out from whatever they consider the root of the Ames tree? Does that allow a more precise placement of the Ames in the sample letters? Is such a map possible? Does it resolve the question more precisely?

      Is the Ames in the letters the same branch exactly as the RMR 1029 or does it fit better as having branched once or twice already from being in some other lab and being grown and regrown?

      A terminology for this tree, if a standard exists, or has to be invented would help communicate the situation.

  15. Also some other issues to mull over. The origins tree in time of the relevant strains or close enough anthrax has to be considered and its relevance to any probability calculations or parameter estimations carefully analyzed. The following questions should be considered.

    Is part of the origins tree in time of anthrax flasks now existing unobserved? Should you compute a stochastic expectation over those variables? How does that depend on your model? How do you model the stochastic expectation? Can you do it in closed form or do you need to do computer simulations? Did you budget for that? Time and money? Who is going to program it? Lehman quants? Did NAS and FBI not understand the problem when they came up with the budget?

    • DXer said

      Meanwhile, as to the whodunnit, “here’s what happened.”

      Dr. Claire Fraser-Liggett told the panel assembled by the National Academies of Sciences in July 2009 that she began her work to find a match began in late 2001. “I was hopeful that perhaps genomics would provide sufficient amount of information to be able to track the material to its source, but I then, and have always, asserted that in no way did I ever believe that this kind of genomics-based investigation was ever going to lead to the perpetrator,” Fraser-Liggett said. “That was going to require much more traditional police investigation.”

      In February 2002, one senior FBI agent told the Wall Street Journal that access to anthrax was “absolutely so lax,” that even if the lab is identified, it may not be possible to discover where the terror strain was sent or who had access to it. The WSJ article noted: “At Dugway Proving Ground, a large military facility in Utah currently under investigation, a former scientist said security was slipshod. ‘Somebody could have walked out of a hot area with a couple of spores in a briefcase or lunch pail,’ he said.”

      As one news account noted: “Ask Keim [the FBI’s key scientist on the issue] if he thinks Ivins was the anthrax letters terrorist and he says he just doesn’t know. ‘It remains to be seen.’ ”

      Claire Fraser-Liggett, professor at the University of Maryland School of Medicine and director of the University of Maryland Institute for Genome Sciences and an adviser to the FBI on Amerithrax, asked, “What would have happened in this investigation had Dr. Hatfill not been so forceful in his response to being named a person of interest. What if he, instead of fighting back, had committed suicide because of the pressure? Would that have been the end of the investigation?” It was Fraser-Liggett’s genetic analysis of the anthrax spores in the letters led to Ivins’ flask, and the other 7 isolates with the same genetic profile. “The part that seems still hotly debated is whether there was sufficient evidence to name Dr. Ivins as the perpetrator,” Fraser-Liggett says. “I have complete confidence in the accuracy of our data,” Fraser-Liggett says, but she says it does not indicate Ivins is guilty.

      “What would have happened in this investigation had Dr. Hatfill not been so forceful in his response to being named a person of interest. What if he, instead of fighting back, had committed suicide because of the pressure? Would that have been the end of the investigation?” — FBI genetics expert Claire Fraser-Liggett

      Preliminary research was first reported in 2002 in Science. The analysis is directed to showing the similarity between various samples of Ames. The institutions known to have fully virulent B. anthracis Ames include USAMRIID, Naval Medical Research Center, Dugway in Utah, CDC, CAMR-Porton [in Great Britain], Battelle in Ohio, University of Northern Arizona (Keim), University of New Mexico, Louisiana State University (Hugh-Jones), and University of Scranton (DelVecchio). Samples from RMR1029, for example, were shipped to UNM and Battelle. The UNM shipment was sent Federal Express in March 2001. University of New Mexico, like University of Michigan, was doing DARPA doing vaccine work when Bruce Ivins supplied them with virulent anthrax from flask 1029 in March 2001. (March 2001 was when the Koehler lab upgraded to BL-3; Dr. Koehler was a researcher specialized in virulence. She had a $100,000 grant from the CIA that year to work with anthrax in soil. The lab was devastated by millions of gallons of water in a June 2001 flood from a tropical storm.)

      Given that the documentary evidence establishes UNM received virulent Ames from flask 1029 in March 2001, why is UNM not on the list of places that received Ames from 1029? (as distinguished from 1028 and 1030). Why isn’t University of Michigan? Michael Hayes, a lab tech there, reported on killing virulent Ames supplied by Dr. Ivins in a petri dish. In October 2001, LSU and University of Michigan were subpoenaed. A DARPA Program Manager at the time privately told a friend of mine that they knew where the attack Ames came from and even the machine used to make it. LSU and University of Michigan were subpoenaed out of the gate. According to Richard Hidalgo, assistant to the dean of the school of veterinary medicine at LSU, the DOJ asked the school to provide by Oct. 23 a log of all visitors and employees at the Hugh-Jones Special Pathogens Lab since Jan. 1, 2000, including their Social Security numbers and dates of birth. The subpoena also asked for information on shipments of pathogens to and from the lab. “Besides Dr. Hugh-Jones and his lab director, only three others have been in the lab” during the time in question, Hidalgo said. “I’ve never been there myself.” Why did the FBI limit the October 2001 subpoena of LSU Special Pathogens Lab to visitors after January 1, 2000. Wasn’t the DARPA research involving virulent Ames supplied by Bruce Ivins occurred prior to that?

      Newsday reported:

      “A subpoena also was delivered to the University of Michigan, according to a source who asked not to be identified. “All research institutions are being contacted by the FBI and asked for information,” the source said. “They were seeking personnel records for those who may be working with select agents.” …”LSU’s Hidalgo said the FBI appears to be looking for any breach in the strict handling procedures for anthrax and other select agents. It could not be determined yesterday how many institutions have received subpoenas. In some cases, the FBI has made investigative inquiries without court orders.”

      Alibek says Russia had Ames. Porton Down reportedly provided it to four unnamed researchers. (That, for example, is where Martin Hugh-Jones at LSU got some Ames in the late 1990s). American Type Culture Collection (“ATCC”) has written me to say that as a matter of policy, they will not address whether their patent repository (as distinguished from their online catalog) had virulent Ames prior to 9/11.( Although ATCC did not take the opportunity to deny it, one can infer from the FBI’s affidavit in connection the search of Ivins’ residence that no lab in Virginia is known by the FBI to have had virulent Ames. Thus, FBI, in its “Ivins Theory,” was working on the understanding that ATCC did not have Ames in its patent repository.)

      Ari Fleischer explained: “What you have to keep in mind is the difference between knowledge about what type of information you have to have to produce it, and who could have sent it. They are totally separate topics that could involve totally separate people. It could be the same person or people. It could be totally different people. The information does not apply to who sent it.” Ken Alibek, the former head of the Soviet bio-weapons program suggests that ‘If I were a terrorist, I would certainly not use a strain known to be from my country.'” To the same effect, it seems that Bruce Ivins would not have used the strain — a special mixture of the US Army strain — for which he was the “go-to” person.

      The Washington Post explained in a late October 2008 article: “While some FBI scientists were analyzing genetic mutations, others were scouring the planet for repositories of Ames-strain bacteria. To their surprise, Ames turned out to be quite rare, with only 15 U.S. institutions and three foreign ones possessing live, virulent Ames. Samples of Ames were collected and added to a repository the FBI had established at Fort Detrick. In a process that ended only in late 2006, bureau scientists picked up 1,072 samples of anthrax bacteria and tested each for mutations identical to the ones in the bioterrorist’s letters.” “Back at the bureau’s Washington field office, agents were reconstructing the history of RMR-1029. A giant flow chart, covering most of a wall, recorded each discovery about the origins of the spores and what Ivins did with them. But the agents wondered: Could others, besides Ivins, have gotten access to the flask of spores?” The Post article continues: “The question drives much of the skepticism about the FBI’s case. At a news conference in August, bureau officials estimated that as many as 100 people potentially had access to the biocontainment lab where Ivins kept his collections. Investigators have maintained that other possible suspects were ruled out, but they have never explained how. It is one of the gaps that independent experts and lawmakers have raised since Ivins’s death.” Journalist Joby Warrick writes: “In interviews, FBI officials said the list of 100 names included USAMRIID scientists as well as anyone with even a tenuous connection to Ivins’s lab, such as visitors or janitors. Each person was investigated, though most could not have gotten to the spores under any reasonable scenario the investigators could construct.” “Still, dozens of people were cleared at various times to enter USAMRIID’s Building 1425, where Ivins worked and kept his spore collection. Each had to be investigated, even those who lacked the basic knowledge to handle highly lethal bacteria.” Joby Warrick of the Washington Post reports that “In late October 2001, lab technician Terry Abshire placed a tray of anthrax cells under a microscope and spotted something so peculiar she had to look twice.” “Abshire focused her lens on a moldlike clump. Anthrax bacteria were growing here, but some of the cells were odd: strange shapes, strange textures, strange colors. These were mutants, or ‘morphs,’ genetic deviants scattered among the ordinary anthrax cells like chocolate chips in a cookie batter.” Although it would take years to develop the science, this discovery led to proving that the origin of the anthrax was originally Ivins reference flask.

      There was no requirement to document transfers prior to 1997. One former USAMRIID-sponsored vaccine researcher at UMass, Dr. Curtis Thorne reports that samples used to be sent by ordinary mail. In 2001, his research on virulence of genetically altered anthrax strains was being built upon at the University of Texas (Houston) by Theresa Koehler under a grant from the CIA, the National Institutes of Health and others. The Ames strain, along with other strains, would be distributed not for nefarious purposes, but for veterinary and other research, to include use in challenging vaccines in development.

      “We just don’t know how many hands it went through before it got to the ultimate user,” explained Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota and once a consultant to the government’s investigation. One expert, Dr. C.J. Peters, summarizes: “Knowing that this strain was originally isolated in the U.S. has absolutely nothing to do with where the weapon may have been prepared because, as I tried to make the point, these strains move around. A post doc in somebody’s laboratory could have taken this strain to another lab and it could have been taken overseas and it could have ended up absolutely anywhere. Tiny quantities of anthrax that you couldn’t see, that you couldn’t detect in an inventory can be used to propagate as much as you want. So that’s just not, in fact, very helpful.” The FBI estimates that, at a minimum, 100 had access to the flask in Bruce Ivins’ lab. Ft. Detrick scientists point out that it used to be stored in a different lab in 1997, bringing the number to 200-300 people. The New York Post reports that “multiple facilities outside of Fort Detrick were sent RMR-1029 for their own research, including government laboratories, the Battelle lab and academic institutions like the University of New Mexico.” The Post explains: “In April 2007, the FBI sent Ivins a letter saying he was “not a target of the investigation” and said it was investigating 42 people who had access to RMR-1029 at the Battelle labs in Ohio, [Ivins attorney] Kemp said.” Dean Boyd, a Justice Department spokesman, commented in February 2009: “The recent inventory issues at USAMRIID highlight the difficulties confronted by the FBI in their efforts to trace the evidentiary material back to its source at USAMRIID, and reinforce our conclusion that samples of anthrax could easily have been removed from the facility undetected.”

      “Another lab might take a couple of milliliters of that spore preparation and create a daughter preparation,” Gerry Andrews, Ivins former boss and now a Professor at the University of Wyoming, says. “How many [samples] Ivins gave out I have no idea, but he did it through official channels, and there is a chain of custody records that indicates which labs got RMR-1029 and how much of the material they got.”

      The exact match to what was known to be in Ivins flask was at “one other institution” with the word “institution” being parsed to be different from the word laboratory.

      DR. MAJIDI: The total body — the total universe of people at some point were associated with RMR-029 — I’ll qualify that. Roughly, about 100-plus.

      QUESTION: Hundred-plus. Were those all at Detrick, or other labs —

      DR. MAJIDI: No, they were at Detrick and other labs.


      DR. MAJIDI: So a hundred people are within the universe of this RMR-1029 sample, and everyone was investigated. We looked a number of different factors that go into the investigation, and we were able to include and exclude specific individuals in that list.


      QUESTION: You’ve already told us a hundred people; right? So —

      DR. MAJIDI: Yeah.

      QUESTION: — how many labs?

      DR. MAJIDI: Hmm —

      QUESTION: Is it one?

      DR. MAJIDI: It’s more than one.


      DR. MAJIDI: Hmm —

      QUESTION: Can we keep guessing?


      QUESTION: Two?

      QUESTION: Is it ten?

      DR. MAJIDI: Okay, it’s total two laboratories.

      QUESTION: Total two. Including USAMRIID? Or —

      BACKGROUND OFFICIAL: Two institutions.

      DR. MAJIDI: Two institutions.

      BACKGROUND OFFICIAL: Because when you say “laboratories,” you got to figure, remember —

      QUESTION: Yeah.

      DR. MAJIDI: Two institutions —

      QUESTION: So that means USAMRIID and two other institutions?

      DR. MAJIDI: No, that means USAMRIID and one other institution.

      QUESTION: USAMRIID and one other institution?

      DR. MAJIDI: Yes.”

      The FBI WMD head implied that the other institution might be deemed “quasi-governmental” rather than what we call government.

      “DR. MAJIDI: Those locations — it is not eight laboratories. I got to be clear about that. They came from different locations. A good number of them came from USAMRIID itself. And we’re not disclosing the location.

      QUESTION: How many were outside of the United States, and how many were non-governmental labs?

      DR. MAJIDI: None outside the United States.

      QUESTION: Were they all government labs?

      DR. MAJIDI: There’s a fine distinction there and I don’t know really what we call government and what we call quasi-governmental, so we’re going just going to leave that as is.

      QUESTION: When you said that eight have them had four markers —

      DR. MAJIDI: Roughly eight of them had four markers.”

      Dr. Majidi took his guidance at the conference from Battelle employee James Buran, who had been head of the Navy biological defense program.

      In a March 6, 2009 Press Release, the FBI explained:

      “Only eight of the anthrax samples collected during the course of the investigation matched the genetic profile in the letter material and all were linked back to RMR-1029. This conclusion was the most significant and relevant scientific finding in the case.

      By analogy, if one were to grow a corn stalk from a specific corn seed, the trace chemical fingerprint of the stalk might differ from that of the seed due to different compositions—for example iron—in the respective fertilizers used to grow each; however, the genetic profile of the seed and the stalk would be identical.”

      The strain referenced in documents on Khalid Mohammed’s computer seized in March 2003 was not Ames and perhaps not even virulent. It is reasonable to assume that the anthrax purchased from the North Korea supplier was not Ames (if that report of an early acquisition is credited). Thus, the question relevant to an Al Qaeda theory is what access to the US Army strain might have been accomplished by someone with 1) an organization supported by funds diverted from charities backing his play, and 2) a lot of educated and technically-trained Salafists who believe in his Islamist cause. A former KGB spy master says that the Russians had a spy at Ft. Detrick who provided samples of all specimens by diplomatic pouch. But it seems more likely that Al Qaeda got it directly from a western laboratory. For example, Ayman had a trusted scientist attending conferences sponsored by Porton Down scheduling 10-day lab visit as early as 1999. In the US, he had the support of other scientists (such as GMU’s Al-Timimi) who did advanced research alongside researchers working with the Ames strain under a contract with USAMRIID for DARPA. NBC once reported that the 16 labs known to have Ames had been winnowed to 4 that were a match.

      On NPR, Attorney Paul Kemp, attorney for the family of the late Bruce Ivins, said that Ames from Ivins’ flask was known to have gone to Battelle and University of New Mexico. Warrick explains: “Ivins, the FBI discovered, had spent more than a year perfecting what agents called his ‘ultimate creation’ — his signature blend of highly lethal anthrax spores — and guarded it so carefully that his lab assistants did not know where he kept it.” “Ivins’s talents also helped give him away, investigators told the Washington Post said. Exceptionally pure concentrations of anthrax spores were Ivins’s trademark and placed him in an exclusive class. In the end, the FBI concluded, he was the only one with access to the deadly spores who also possessed the skills and equipment needed to create the extraordinarily powerful bioweapon that was mailed to U.S. Senate offices and news organizations in the fall of 2001.”

      The Washington Post’s Warrick writes: “It was intended for garden-variety animal experiments, but the collection of anthrax spores known as RMR-1029 was anything but ordinary. Ivins, its creator, had devoted a year to perfecting it, mixing 34 different batches of bacteria-laden broth and distilling them into a single liter of pure lethality. The finished product, a muddy, off-white liquid in a glass flask the size of a small coffee pot, was the greatest single concentration of deadly anthrax bacteria in the country, FBI investigators said.” Ivins began work on it in 1996 with the goal of creating a large repository of highly virulent Bacillus anthracis spores that could be used by his fellow scientists at the U.S. Army Medical Research Institute for Infectious Diseases, or USAMRIID, for years to come. To measure the effectiveness of new anthrax vaccines, the drugs have to be tested against a potent form of bacteria that remained the same from one experiment to the next.” “It was his ultimate creation,” Jason D. Bannan said of the flask, an FBI microbiologist assigned to the Amerithrax case told the Washington Post. “This was the culmination of a lot of hard work.” Warrick writes: “He wasn’t an expert. He was the expert,” said a senior FBI investigator, who answered questions about the still-open case on the condition of anonymity.” “Bruce Ivins was a victim of a vicious plot,” said Ayaad Assaad, a toxicologist who once worked with Ivins at Fort Detrick, in Maryland.

      In a number of patents by University of Michigan researchers in Ann Arbor, Tarek Hamouda and James R. Baker, Jr., including some filed before 9/11, the inventors thank Bruce Ivins of Ft. Detrick for supplying them with Ames. The University of Michigan patents stated: “B. anthracis spores, Ames and Vollum 1 B strains, were kindly supplied by Dr. Bruce Ivins (USAMRIID, Fort Detrick, Frederick, Md.), and prepared as previously described (Ivins et al., 1995). Dr. Hamouda served as group leader on the DARPA Anti-infective project. A patent application filed April 2000 by the University of Michigan inventors explained:

      “The release of such agents as biological weapons could be catastrophic in light of the fact that such diseases will readily spread the air.
      In light of the foregoing discussion, it becomes increasingly clear that cheap, fast and effective methods of killing bacterial spores are needed for decontaminating purposes. The inventive compounds have great potential as environmental decontamination agents and for treatments of casualties in both military and terrorist attacks. The inactivation of a broad range of pathogens … and bacterial spores (Hamouda et al., 1999), combined with low toxicity in experimental animals, make them (i.e., the inventive compounds) particularly well suited for use as general decontamination agents before a specific pathogen is identified.”

      In late August 2001, NanoBio relocated from a small office with 12 year-old furniture to an expanded office on Green Road located at Plymouth Park. After the mailings, DARPA reportedly asked for some of their product them to decontaminate some of the Senate offices. The company pitched hand cream to postal workers. The inventors company, NanoBio, is funded by DARPA. NanoBio received a $3,150,000 defense contract in 2003. Dr. Hamouda graduated Cairo Medical in December 1982. He married in 1986. His wife was on the Cairo University dental faculty for 10 years. Upon coming to the United States in 1994 after finishing his microbiology PhD at Cairo Medical where Zawahiri’s sister Heba taught antimicrobials and his father taught pharmacology, Dr. Hamouda was a post-doctoral fellow at the Wayne State University School of Medicine in downtown Detroit. His immunology department biography at Wayne indicates that he then came to the University of Michigan and began work on the DARPA-funded work with anthrax bio-defense applications with James R. Baker at their company NanoBio.

      The University of Michigan researchers presented in part at various listed meetings and conferences in 1998 and 1999. The December 1999 article titled “A Novel Surfactant Nanoemulsion with Broad-Spectrum Sporicidal Activity of against Bacillus Species” in the Journal for Infectious Diseases states: “B. anthracis spores, Ames and Vollum 1B strains, were supplied by Bruce Ivins (US Army Medical Research Institute of Infectious Diseases [USAMRIID], Fort Detrick, Frederick, MD) and were prepared as described elsewhere [i.e., using a lyophilizer]. Four other strains of B. anthracis were provided by Martin Hugh-Jones (Louisiana State University, Baton Rouge.” Dr. Baker reports the work NanoBio’s research with virulent Ames was “done at USAMRIID by a microbiologist under Dr. Ivins’ direct supervision and at LSU under the direction of Dr. Hugh Jones. ”

      In the acknowledgements section, the University of Michigan authors thank:

      Shaun B. Jones, Jane Alexander, and Lawrence DuBois (Defense Science Office, Defense Advanced Research Project Agency) for their support.

      Bruce Ivins, Patricia Fellows, Mara Linscott, Arthur Friedlander, and the staff of USAMRIID for their technical support and helpful suggestions in the performance of the initial anthrax studies.

      Martin-Hugh-Jones, Kimothy Smith, and Pamela Coker for supplying the characterized B. anthracis strains and the space at Louisiana State University (Baton Rouge).

      Robin Kunkel (Department of Pathology, University of Michigan) for her help with electron microscopy and a couple of others for technical assistance and manuscript preparation.

      The researchers found that their nanoemulsion incorporated into the growth medium completely inhibited the growth of the spores. Transmission electron microscope was used to examine the spores.

      In 1999, [Dr.Kimothy Smith] moved to the Arizona lab, bringing with him the lab’s first samples of anthrax”.

      The patent explained that “The nanoemulsions can be rapidly produced in large quantities and are stable for many months *** Undiluted, they have the texture of a semisolid cream and can be applied topically by hand or mixed with water. Diluted, they have a consistency and appearance similar to skim milk and can be sprayed to decontaminate surfaces or potentially interact with aerosolized spores before inhalation.”

      A March 18, 1998 press release had provided some background to the novel DARPA-funded work. It was titled “Novavax Microbicides Undergoing Testing at University of Michigan Against Biological Warfare Agents; Novavax Technology Being Supplied to U.S. Military Program At University of Michigan as Possible Defense Against Germ Warfare.” The release stated that “The Novavax Biologics Division has designed several potent microbicides and is supplying these materials to the University of Michigan for testing under a subcontract. Various formulations are being tested as topical creams or sprays for nasal and environmental usage. The biocidal agent’s detergent degrades and then explodes the interior of the spore. Funding, the press release explains, was provided by the Defense Advanced Research Projects Agency of the Department of Defense. In a presentation at the Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC) on September 26, 1998, Michael Hayes, a research associate in the U-Michigan Medical School, presented experimental evidence of BCTP’s ability to destroy anthrax spores both in a culture dish and in mice exposed to anthrax through a skin incision. “In his conference presentation, Hayes described how even low concentrations of BCTP killed more than 90 percent of virulent strains of Bacillus anthracis spores in a culture dish.” Its website explains that the Interscience Conference on Antimicrobial Agents and Chemotherapy is the “[p]remier meeting on infectious diseases and antimicrobial agents, organized by the American Society for Microbiology.”

      An University of Michigan Medical school, Medicine at Michigan, (Vol. 1, No. 1, Spring 1999) explained:

      “In studies with rats and mice in the U-M Medical School under the direction of James R. Baker, Jr., M.D., professor of internal medicine and director of the Center for Biologic Nanotechnology, the mixture, known as BCTP, attacked anthrax spores and healed wounds caused by a closely related species of bacteria, Bacillus cereus. (The letters BCTP stand for Bi-Component, Triton X-100 n-tributyl Phosphate.)

      Baker describes the process as follows: “The tiny lipid droplets in BCTP fuse with anthrax spores, causing the spores to revert to their active bacterial state. During this process, which takes 4-5 hours, the spore’s tough outer membrane changes, allowing BCTP’s solvent to strip away the exterior membrane. The detergent then degrades the spores’ interior contents. In scanning electron microscope images, the spores appear to explode.” The rapid inactivation of anthrax bacteria and spores combined with BCTP’s low toxicity thus make the emulsion a promising candidate for use as a broad-spectrum, post-exposure decontamination agent.
      The research is sponsored by the Defense Advanced Research Projects Agency (DARPA), the central research and development organization for the U.S. Department of Defense.”

      Dr. Baker, by email, advises me that Ivins did the studies involving Ames for them at USAMRIID. He reports: “We never had Ames and could not have it at our UM facilities.” Before September 2001, it’s office was described as in the basement of a downtown bank which seems to describe 912 N. Main St., Ann Arbor, just west of University of Michigan campus.

      An article in the Summer of 2000 in Medicine at Michigan explains:

      “Victory Site: Last December [December 1999] Tarek Hamouda, Amy Shih and Jim Baker traveled to a remote military station in the Utah desert. There they demonstrated for the U.S. Army Research and Development Command the amazing ability of non-toxic nanoemulsions (petite droplets of fat mixed with water and detergent) developed at Michigan to wipe out deadly anthrax-like bacterial spores. The square vertical surfaces shown here were covered with bacterial spores; Michigan’s innocuous nanoemulsion was most effective in killing the spores even when compared to highly toxic chemicals.”

      In 2001, a Dugway scientist explained to NPR and print media that it was sometimes necessary to use virulent Ames in testing decontamination agents in order to know the kill rate.

      An EPA report explains:

      “In December 1999, the U.S. Army tested a broad spectrum nanoemulsion and nine other biodecontamination technologies in Dugway, Utah, against an anthrax surrogate, Bacillus globigii. Nanoemulsion was one of four technologies that proved effective and was the only nontoxic formulation available. Other tests against the vaccine strain of B. anthracis (Sterne strain) were conducted by the John Hopkins University Applied Physics Laboratory and by the U.S. Army Institute of Surgical Research.”

      As Fortune magazine explained in November 2001 about NanoBio: “Then bioterror struck…. It moved to a bland corporate park where its office has no name on the door. It yanked its street address off its Website, whose hit rate jumped from 350 a month to 1,000 a day.” NanoBio was part of the solution: “in the back of NanoBio’s office sit two dozen empty white 55-gallon barrels. A few days before, DARPA had asked Annis and Baker if they could make enough decontaminant to clean several anthrax-tainted offices in the Senate. NanoBio’s small lab mixers will have to run day and night to fill the barrels. ‘This is not the way we want to do this,’ sighs [its key investor], shaking his head. ‘This is all a duct-tape solution.’ ” James Baker, founder of Ann Arbor’s NanoBio’s likes to quote a Chinese proverb: “When there are no lions and tigers in the jungle, the monkeys rule.”

      It’s naive to think that Al Qaeda could not have obtained Ames just because it tended to be in labs associated with or funded by the US military. US Army Al Qaeda operative Sgt. Ali Mohammed accompanied Zawahiri in his travels in the US. (Ali Mohamed had been a major in the same unit of the Egyptian Army that produced Sadat’s assassin, Khaled Islambouli). Ali Al-Timimi was working in the building housing the Center for Biodefense funded by the Defense Advanced Research Projects Agency (“DARPA”) and had access to the facilities at both the Center for Biodefense and the adjacent American Type Culture Collection. Michael Ray Stubbs was an HVAC system technician at Lawrence Livermore Lab with a high-level security clearance permitting access. That was where the effort to combat the perceived Bin Laden anthrax threat was launched in 1998. Aafia Siddiqui, who attended classes at a building with the virulent Vollum strain. She later married a 9/11 plotter al-Balucchi, who was in UAE with al-Hawsawi, whose laptop, when seized at the home of a bacteriologist, had anthrax spraydrying documents on it. She had previously attended classes and her sister-in-law, an MD, worked in the building where the Koehler lab was in Texas. The reality is that a lab technician, researcher, or other person similarly situated might simply have walked out of some lab that had it. What was NanoBio’s old street address? Why is Aafia Siddiqui associated with an address at 1915 Woodbury Drive in Ann Arbor? An Assistant United States Attorney has claimed in open court (in the opening argument in United States v. Paracha) that Aafia was willing to participate in an anthrax attack if asked. The affidavit submitted by her defense psychiatrist says she reports that she was tasked to research germ weapons.

      Among the documents found in Afghanistan in 2001 were letters and notes written in English to Ayman Zawahiri by a scientist about his attempts to obtain an anthrax sample. One handwritten letter was on the letterhead of the Society for Applied Microbiology, the UK’s oldest microbiological society. The Society for Applied Microbiology of Bedford, UK, recognizes that “the development and exploitation of Applied Microbiology requires the maintenance and improvement of the microbiological resources in the UK, such as culture collections and other specialized facilities.” Thus, Zawahiri’s access to the Ames strain is still yet to be proved or disclosed, but there was no shortage of possibilities or recruitment attempts by Ayman. One colleague of his estimates that he made 15 recruitment attempts over a many year period. Dr. Keim observes: “Whoever perpetrated the first crime must realize that we have the capability to identify material and to track the material back to its source. Whoever did this is presumably aware of what’s going on, and if the person is a scientist, they can read the study. Hopefully, the person is out there thinking: When am I going to get caught?”

      After the February 2009 presentation, the New Scientist summarized: “Eight samples had all four. One came from a flask labelled RMR-1029 that Ivins was responsible for at USAMRIID. The other seven came from cultures taken from that flask, only one of which was not located at USAMRIID. So while these findings show the attack spores came from one of these cultures, the FBI has gone further in concluding the attack came directly from the RMR-1029 flask.” The FBI has not yet identified the location of the 8 isolates downstram from Ivins’ flask known to be an identical match — or the 100+people it says had access. (Mr. Persichini, the DC Field Office has assured us that will never happen). For the US Attorney Jeff Taylor to make it seem, however, that only Ivins had control over anthrax that was genetically identical was specious. The more commonsensical point would be that Ivins would have no reason to use anthrax so directly traceable to him by reason of being a distinctive mix of Ames strains, which was first announced in the 2002 Science article by Dr. Keim et al.

      In June 2001, in addition to the conference at Annapolis organized by Bruce Ivins, a conference was held at Aberdeen Proving Ground (Edgewood) for small businesses that might contribute to the biodefense effort. It showcased APG’s world class facillities that had the full range of relevant equipment, as well as the range of activities and research featured by presenters at such conferences. It was called “Team APG Showcase 2001.″ Edgewood maintains a database of simulant properties. The info and equipment, including spraydrying equipment, is available to participants in the SBIR — promoting small business innovation. So might the anthrax attack have required the learning of a state? Well, to get that, all you needed to do was go to the program that shares such research for the purpose of innovation in the area of biodefense. APG built a Biolevel-3 facility and, according to a Baltimore Sun report, by October 2002 had 19 virulent strains of anthrax, including Ames. Here is a 1996 report on a study done at Edgewood involving irradiated virulent Ames provided by John Ezzell that was used in a soil suspension. Dr. Ezzell tells me that he made aerosolized Ames that year at the request of DARPA. (He pointed out that he was under a gag order and that the phone was wiretapped he presumed.) Another article discusses Delta Ames supplied to Edgewood by the Battelle-managed Dugway, subtilis, and use of sheep blood agar.

      Did Battelle have virulent Ames across I-95? Edgewood tested nanoemulsion biocidal agents during this time period, according to a national nanobiotechnology initiative report issued June 2002.

  16. Those who answer these questions should also be able to answer questions like the biology exams here:

    How many flasks in the world are there with Ames and how much in each flask? Make up an assumption. What is the probability distribution of the distribution of mutations in those flasks. Does this depend on the tree backward in time of their origin? If it does, how? Should you take that tree as given or consider it stochastic? Does that change your answer? If stochastic, how should you model it?

    Does it depend on the quantity in each flask? Does it depend on how they were grown? Plates v. fermentor for example?

    Does your final answer depend on the estimator used to determine parameters? If you use maximum likelihood are there model assumptions that your answer depends on? Should you use Generalized Method of Moments?

    • DXer said

      A simpler approach would be for an NAS panel member just to ask Dr. Keim:

      Would an equally large collection likely have the same 4 morphs?

      He will answer “Yes, I think so.”

      Was the hypothesis ever tested?

      He will answer “I recommended it but the recommendation was not accepted. I don’t know why.”

  17. Questions 2 and 3 on probability open a lot of doors. The probability of whether 4 mutations are produced and tested depends on the size of the quantities at each stage. You have a test result at the end of a multistage process that goes back in time to the date of common origin or related origin of the anthrax in RMR-1029 as well as whatever other Ames existed that is considered relevant.

    The probabilities of some other source along the timeline to a common relevant ancestor depends on many factors and variables including who had what closely related stocks where in what quantities.

    A Bayesian analysis of this would also raise issues on many variables of this type.

    How likely are the mutations used for the id? Answering that requires knowing a lot.

    2 and 3 are tricky questions that are easy to get wrong. Mitochondrial DNA dating of Eve was at first very simplistic in probability reasoning. There are opportunities to make mistakes here too.

  18. This gives the committee some, albeit limited, room to answer on whether Ivins could have done this. One question on subtilis. If its used first to test the procedure, and then a run is done with anthrax, is the subtilis gone? I.e. if you do a second run without cleaning, does the second run have subtilis or not?

    What needs to be done to prevent in cleaning to prevent this?

    Is it more likely that the October batch was done on different equipment?

    Does it matter which equipment we are talking about? Centrifuge is harder to clean?

    How big was the equipment used by Ivins? Could it be immersed in some cleanser? If the September mailing was 5 grams and took large pieces of equipment to make, could Ivins get them in his glove box? Sterilize them?

    For centrifuges and other equipment needed for a 5 gram run, could they be sterilized inside Ivins’ glove box?

    What about the glove box itself?

    Was the inside of the glove box tested for subtilis? If so when? The rest of the equipment?

    How big were centrifuges or other equipment inside Suite B3? What size flasks were there?

    The production questions link to the questions asked so that the NAS should answer those to answer the questions asked properly. These are foundation questions that need to be answered.

    How long would it take to do these runs? For example, these all relate to question 4 as well. The size of the equipment needed for the job relates to how easy it is to recover bacterial DNA from them. Big equipment that can’t be immersed are more likely to have recoverable DNA.

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