The Investigative Summary (pdf) published by the FBI in closing the Amerithrax investigation into the anthrax attacks of 2001 is curiously silent on the presence of a second species of bacteria found in the New York Post and Brokaw letters.

One of the search warrant affidavits (page 5 of linked pdf) released previously had this to say about the presence of Bacillus subtilis:

Both of the anthrax spore powders recovered from the Post and Brokaw letters contain low levels of a bacterial contaminant identified as a strain of Bacillus subtilis. The Bacillus subtilis contaminant has not been detected in the anthrax spore powders recovered from the envelopes mailed to either Senator Leahy or Senator Daschle. Bacillus subtilis is a non-pathogenic bacterium found ubiquitously in the environment. However, genomic DNA sequencing of the specific isolate of Bacillus subtilis discovered within the Post and Brokaw powders reveals that it is genetically distinct from other known isolates of Bacillus subtilis. Analysis of the Bacillus subtilis from the Post and Brokaw envelopes revealed that these two isolates are identical.

In contrast to the highly detailed description of the genetic analyses carried out to pinpoint a set of four mutations present in the population of B. anthracis spores in the RMR-1029 flask and the subsequent comparison of this profile to other anthrax cultures in order to confine this particular profile only to cultures known to be derived from RMR-1029, the Investigative Summary has only one passing reference to B. subtilis (page 18, from list of suspects investigated and cleared):

A foreign-born scientist with particular expertise working with a Bacillus anthracis simulant known as Bacillus subtilis, and against whom there were allegations that s/he had connections with several individuals affiliated with the al-Qaeda and Ansar al-Islam terrorist networks.

Ah, but notice what has changed here in the description of B. subtilis. Instead of being "ubiquitous" and a "contaminant", this passage admits that B. subtilis is often used as a laboratory simulant of B. anthracis.

Clearly, if the FBI could have identified the strain of B. subtilis detected in the attack letters as available to Ivins, that finding would have played a prominent role in the Investigative Summary.

Even though Ivins can’t be linked to the particular B. subtilis strain used, there is a documented case of B. subtilis being used as a B. anthracis simulant at another facility where we already know that much of the material that went into RMR-1029 was produced. Recall from this diary that I analyzed the available information about the amount of B. anthracis used in the attacks and found it highly unlikely that Ivins could have cultured the large amount of spores used in the attacks with the equipment and time he had available. Much of the material in RMR-1029 was produced at Dugway.

On December 13, 2001, Judith Miller published an article in the New York Times, where she disclosed that "government officials have acknowledged that Army scientists in recent years have made anthrax in a powdered form that could be used as a weapon." She further pointed out that this work occurred at Dugway in 1998. It should be noted that the anthrax produced at Dugway for Ivins that went into RMR-1029 was cultured in 1997.

The Miller article then goes on to quote scientist William C. Patrick on how he coached scientists at Dugway in drying a pound of highly purified anthrax spores in 1998. Miller quotes a Dugway spokesperson as saying a strain different from Ames (the parent of RMR-1029) was used in the drying experiments. Note that a pound of spores is enough dried spores to produce hundreds of letters with the one to two grams of dried spores thought to be in each letter. But in a further bit from the Dugway spokesperson, we have this:

She said Dugway did make one- pound quantities of Bacillus subtilis, a benign germ sometimes used to simulate anthrax.

We know from scientific results discussed in this article that the material dried in 1998 is unlikely to have been in the letters because radiocarbon analysis suggested the attack material was no more than two years old in late 2001. However, both the facilities at Dugway and Batelle appear to have been carrying out anthrax projects in the appropriate time frame. Exactly one week prior to the 9/11 attacks, Judith Miller published two articles on biowarfare. The longer article discusses how US germ warfare research has pushed the limits of international law. She first describes work attributed to the CIA, but near the end of the article we have this, regarding work to replicate a feared Russian engineered strain of anthrax:

Eventually the C.I.A. drew up plans to replicate the strain, but intelligence officials said the agency hesitated because there was no specific report that an adversary was attempting to turn the superbug into a weapon.

This year, officials said, the project was taken over by the Pentagon’s intelligence arm, the Defense Intelligence Agency. Pentagon lawyers reviewed the proposal and said it complied with the treaty. Officials said the research would be part of Project Jefferson, yet another government effort to track the dangers posed by germ weapons.

A spokesman for Defense Intelligence, Lt. Cmdr. James Brooks, declined comment. Asked about the precautions at Battelle, which is to create the enhanced anthrax, Commander Brooks said security was ”entirely suitable for all work already conducted and planned for Project Jefferson.”

The second, shorter article discloses construction of a model germ warfare production facility at Dugway:

In a nondescript mustard-colored building that was once a military recreation hall and barbershop, the Pentagon has built a germ factory that could make enough lethal microbes to wipe out entire cities.

Adjacent to the pool tables, the shuffleboard and the bar stands a gleaming stainless steel cylinder, the 50-liter (53-quart) fermenter in which germs can be cultivated.

The apparatus, which includes a latticework of pipes and other equipment, was made entirely with commercially available components bought from hardware stores and other suppliers for about $1 million — a pittance for a weapon that could deliver death on such a large scale.

Miller goes on to claim that anthrax was never produced at the facility. Note that in my previous diary, I calculated that about 72 L of fermentation capacity would have been needed to produce the spores used in the attacks, so that would be just two "runs" of a fermenter the size of the one in this facility.

A key quote relating to the facility says "The project also showed us how relatively simple it would be for a terrorist to assemble such a facility without being detected". That’s very interesting given this bit from the Chemical and Engineering News article linked above:

Both Meselson and the former military scientist agree that making the purified preparations didn’t require an expensive laboratory setup. As the military scientist says, "A simple facility" is really all that’s needed. "I have concluded that maybe the hardest part is doing it safely so you don’t hurt yourself. Some experience is needed, but it’s probably more an art than a science," he says.

So, what we have now is the Defense Department taking over the lead on multiple anthrax projects from the CIA once the Bush-Cheney administration came into power. They inherited a demonstration facility at Dugway and they expanded a project at Batelle. And our primary source for much of this information is Judith Miller, who is infamous for her work in disseminating Defense Department lies about weapons of mass destruction in the lead-up to the invasion of Iraq.

Given what we know about the scientific analysis of the spores used in the attacks, culturing the spores is much more likely to have occurred at Dugway or Batelle than in Ivins’ lab. If we are to believe the isotopic analysis carried out (see the C&E News article) then Batelle seems more likely, but as I have previously pointed out, pre-packaged sterile water and culture media are readily available commercially from sources in the northeast,and would have produced the result seen even if used at Dugway. In fact, if the "simple" facility at Dugway were used, it seems likely that pre-packaged water and media would be employed. We also know that Dugway did extensive work with B. subtilis. The search warrant affidavit does not go into detail regarding the statement that the B. subtilis recovered from the attack spores did not match known isolates. It seems unlikely to me that a clandestine Defense Department program that was pushing the limits on legality would be entirely forthcoming in sharing its entire culture collection with an FBI investigation.

In conclusion, I fail to see how the FBI has eliminated the possibility that the spores used in the attacks were cultured and dried at Dugway or Batelle, with the Dugway "demonstration" facility being the most likely because of its remote location and secret status. Further, the disappearance of discussion of B. subtilis in the Investigative Summary is highly suspicious, and could reflect uncertainty on the part of the FBI that an exhaustive analysis was carried out to identify potential sources.

Under such a scenario, two batches of anthrax spores, using RMR-1029 material (known to have been shared with Dugway) to inoculate (start) the cultures, could have been grown in the demonstration facility, cleaned thoroughly, and dried. The spores for the Post and Brokaw letters would then have been mixed with a crude harvest of B. subtilis, used an "extender" or "carrier" to conserve the supply of purified material, which was used in its pure form in the Daschle and Leahy letters.

Alternatively, the two fermenter batches could have been harvested and purified separately, with the first batch having B. subtilis present either from improper cleaning of equipment after test runs with it or its inclusion as a carrier. The second harvest would then have produced the highly purified material in the second wave of letters.

We may never know what really happened. Given the history of deceit on the part of the CIA, the Defense Department and Judith Miller on the issue of weapons of mass destruction in general, discerning what is true in the various leaked reports on anthrax culturing and processing technology at the facilities at Dugway and Batelle will be difficult without Congressional hearings conducted under oath and threat of prosecution for perjury. Nevertheless, I remain unconvinced of the guilt of Bruce Ivins and strongly suspect a [non-USAMRIID] Defense Department, or a [non-USAMRIID] Defense Department-contracted source for the attack material.

Oh, and adding to the misdirection here, don’t forget the nonlethal fake anthrax letter that Miller received on October 12, 2001. I wonder how much analysis was carried out on that letter. There is nothing in the Investigative Report about it, either.