Thursday, March 18, 2010

Anthrax Investigation: What About the Silicon?/ Science

Science Magazine asks, "What about the Silicon?"  The 19 March 2010 issue contains an article by Yudhijit Bhattacharjee detailing all we don't know about the silicon in the anthrax spores sent to Senators Daschle and Leahy and to the NY Post, and the absence of spores containing silicon in Ivins' flask.  Excerpts follow:
That question has confounded investigators throughout the probe into the 2001 anthrax letter attacks, which the U.S. government formally concluded in February. Scientists inside and outside the government say there is clear evidence that the high levels of silicon found in the anthrax came not from anything added to "weaponize" the anthrax spores—as researchers had suggested early in the probe—but from the culture in which the spores were grown. That evidence may have settled the issue of whether the anthrax was weaponized, at least for scientists familiar with the case. But it raises a different question: Why did the mailed anthrax have such a high proportion of spores with a silicon signature in comparison to most other anthrax samples?
... The FBI's scientific case against Ivins rests on DNA tests showing that the mailed anthrax came from a flask under Ivins's control at the U.S. Army Medical Research Institute of Infectious Diseases in Frederick, Maryland. Investigators also had the attack material chemically analyzed, first at the Armed Forces Institute of Pathology (AFIP) in Washington, D.C., within weeks of the attack. Examining the spores under a scanning electron microscope, AFIP scientists detected silicon and oxygen and concluded that the spores had been coated with silica to make them float easily, enhancing their power to kill.
But the Sandia study, presented last September to a National Academies panel reviewing the science behind the investigation, still leaves questions. Out of 124 spores from a letter mailed to Senator Patrick Leahy of Vermont, Michael found the silicon-and-oxygen signature in 97—78% of the sample. The signature was present in 66% of a sample from a letter to former Senator Tom Daschle and in 65% of spores from a letter sent to the New York Post.
Out of nearly 200 other anthrax samples from different labs, none came close to displaying such a prominent silicon signature. The highest, in a sample from Dugway Proving Ground in Utah, was 29%. The researchers couldn't find silicon in the coat of a single spore out of some 300 taken from RMR-1029, the flask in Ivins's lab identified as the source of the bacteria used in the attacks; they concluded that all the silicon had come from the culture.
The unusually high percentage of silicon-bearing spores in the attack material "is a bit of a strange thing," says Michael. "We have no way of knowing how they were really grown." An anthrax researcher who did not wish to be named calls it "awfully weird" and "a particularly inconvenient exception" because it leaves a gap in the case. However, neither scientist thinks the anomaly casts doubt on the broader investigation...


Ross said...

Kathryn Crockett, Ken Alibek’s assistant — just a couple doors down from Ali Al-Timimi — addressed the microencapsulation in her 2006 thesis, “A historical analysis of Bacillus anthracis as a biological weapon and its application to the development of nonproliferation and defense strategies.” She expressed her special thanks to bioweaponeering experts Dr. Ken Alibek and Dr. Bill Patrick. Dr. Patrick consulted with the FBI. Dr. Crockett successfully defended the thesis before a panel that included USAMRIID head and Ames strain researcher Charles Bailey, Ali Al-Timimi’s other Department colleague. In 2001 he said he did not want to discuss silica because he did not want to give terrorists any ideas. Oops! Too late. The scientist coordinating with the 911 imam and Bin Laden’s Sheik was 15 feet away.

Dr. Crockett in her PhD thesis says that scientists who analyzed the powder through viewing micrographs or actual contact are divided over the quality of the powder. She cites Gary Matsumoto’s “Science” article in summarizing the debate. She says the FBI has vacillated on silica. The AFIP data, if released, would point to the high level of silica in the first batch of letters.

On the issue of encapsulation, Crockett reports that “many experts who examined the powder stated the spores were encapsulated. Encapsulation involves coating bacteria with a polymer which is usually done to protect fragile bacteria from harsh conditions such as extreme heat and pressure that occurs at the time of detonation (if in a bomb), as well as from moisture and ultraviolet light. The process was not originally developed for biological weapons purposes but rather to improve the delivery of various drugs to target organs or systems before they were destroyed by enzymes in the circulatory system” (citing Alibek and Crockett, 2005). “The US and Soviet Union, however, ” she explains, “used this technique in their biological weapons programs for pathogens that were not stable in aerosol form… Since spores have hardy shells that provide the same protection as encapsulation would, there is no need to cover them with a polymer.“ She explains that one “possible explanation is that the spore was in fact encapsulated but not for protective purpose. Encapsulation also reduces the need for milling when producing a dry formulation.” She wrote: “If the perpetrator was knowledgeable of the use of encapsulation for this purpose, then he or she may have employed it because sophisticated equipment was not at his disposal.”

Ross said...

One military scientist who has made anthrax simulants (unlike Joe Michael) described the GMU patents to me as relating to a silicon encapsulation technique which serves to increase the viability of a wide range of pathogens.

In the past, the Sandia scientists in their public comments seemed to be making inferences and conclusions about whether the silica would be useful in making mailed anthrax — and whether it would be highly probative — that went beyond both their field of expertise and the data apparently available to them. But their powerpoints seemed solid and conservatively framed in the conclusion drawn. Now to the press Dr. Michael waxes broad again in a way that goes beyond his field and beyond his data.

I find Peter Setlow’s commentary on the recent Japanese article about silicon encapsulation to be thoughtful and would have preferred that he address the issue before the NAS.

I respect the government view, if it is the government’s view, that these are not issues that should be discussed public necessarily. To my way of thinking, outsiders, in my opinion, need only enough information to know whether “they got the right guy.” Presently, most people think the FBI did not — and the FBI’s interference with USAMRIID’s FOIA production in the past has only served as Exhibit A in that argument. From where I sit, for all I know, it is the FBI’s Dr. Bannan, formerly the collections scientist at the American Type Culture Collection (“ATCC”) at GMU which sponsored Al-Timimi’s program, who is supporting the decision to withhold the AFIP data. Given the government assures us that it does not relate to “weaponization,” then it would seem that there is no reason not to release it. The only previous reasons related to the fact that the investigation was ongoing and it would reveal the test that was done. (But of course the AFIP newsletter disclosed the test that was done and so that is not justification for withholding).

Ross said...

Once the AFIP data is released, experts like Peter Setlow can consider the source of the reason for the silica such as whether it was putting virulent Ames soil (silica) suspension such as the FBI scientist John Ezzell did in 1996 for DARPA when he made dry powdered anthrax at Ft. Detrick. Or we can turn to the “Microdroplet Cell Culture” patent filed by Ali Al-Timimi’s Discovery Hall colleagues at the DARPA-funded Center for Biodefense and see if there is a connection. The silica would be in the culture medium and then would be removed by repeated centrifugation.

Alternatively, experts can consider that if Flask 1030 has 6 % of spores containing the silicon signal, and flask 1030 constitute leftovers from aerosol experiments, perhaps the attack anthrax was stolen leftovers from animal aerosol challenge experiments which were left unguarded in the basement of 1412 in garbage bags until someone got around to using the autoclave. Antifoam sometimes would be used to unclog the nebulizer.

Or we can explore the other hypotheses relating to the reason for the Silicon Signature, such as it being due to rice hull contamination (silicon) in a spraydryer. Or whether it is due to use of a silicone sealant sprayed on the inside of the envelope such as the Al Qaeda chapter on “poisonous letters” instructs be used (to avoid killing the mailman).

I’m not a scientist which is why it seems that the data and pictures need to be released so that we can have experts like the Center for Biodefense’s Sergeui Popov and the government’s John Kiel review it. If we learned anything from 9/11, it is that there are times that information needs to be shared so that people can connect the dots. This is such a time. Any one with a conflict of interest should recuse himself from the particular aspect of Amerithrax. Anyone without the relevant qualification to address an issue should sit down and have a qualified expert, who has done controlled experiments, address the question. John Kiel is such a scientist. Head of the Air Force lab, his lab did controlled experiments on the issue independent of the FBI and could report to Congress on the issue.

Anonymous said...

Would growing spores with a high silicone content, give the same effect as treating spores with a aerosol gel ?

Anonymous said...

Incredible. Is this guy Bhattacharjee on drugs?

When did Science Magazine start using quotes like "is a bit of a strange thing", "awfully weird" and "a particularly inconvenient exception"? This is not science.

Science deals with data and hard numbers.

The article rejected the AFIP conclusions of silicon weaponization without even seeing the AFIP data. That's not what scientists do. Scientists look at ALL the data and explain it.

So - what exactly does that pesky AFIP data contain that Bhattacharjee and the editors of Science Magazine decided was not important to see or discuss?

Old Atlantic Lighthouse said...

We are told that silicon helps anthrax resist stomach acid.

We are told that Sandia found no silicon on the outside of the anthrax spores.

We are told the silicon was added to promote lethality not dispersibility.

So the conclusion is that the anthrax mailer intended the recipients of the letters to eat the anthrax. This despite the warning to take "penacilin".

Of course the other possibility is that during prep of the spores for Sandia's analysis, or as a result of the method of analysis itself, the silicon on the outside was moved or removed somewhere else.

Anonymous said...

There is no basis to suggest that the method of analysis itself or during pre the silicon was moved or removed somewhere else. See pictures contained in MICROBIAL FORENSICS and in Sandia powerpoints.

The Japanese study is by no means the extent of learning on the functions of microencapsulation.

Old Atlantic Lighthouse said...

The link below considers a lengthy hypothesis to explain how Brownian motion could have striped off an artificial coating of the anthrax spores leaving silicon inside them.

In a nutshell, an artificial coating would produce a low drag coefficient on the coated spore. This would lead to a high diffusion coefficient and a high mean and standard deviation of velocity of the artificially coated spores by a random walk diffusion process in the velocity of the spores.

Some artificially coated spores would have higher velocities from the combined effect of high mean and standard deviation in velocity. When they collided head on, they would widen cracks and holes. The original outer coating may have had its own flaws plus only weakly been bound to the spore or to silicon inside the spore coat. Over time, the collisions would weaken the bonds.

When the artificial coating is stripped, the drag coefficient goes up and the spore acts like a normal spore with low velocity mean and standard deviation from Brownian motion. These spores are then stable. But silicon and other elements inside them are trapped and stay in them.

This hypothesis and mechanism reconciles the initial lab observations of high velocity spores with the later observation of silicon inside the spores but no artificial coating outside them.

Anonymous said...


I recommend you read the excellent MICROBIAL FORENSICS (Bruce Budowie editor) available for free through your local public library's interlibrary loan.

Old Atlantic Lighthouse said...

The formulas for the velocity distribution of a spore under from random collisions in a media of smaller particles is given here:

I apologize for the unsightly link, but its the best I could find.

The formulas show that the variance of the velocity is inverse proportional to the drag coefficient. The drag coefficient just means the tendency of the velocity to revert back to zero from friction.

F = - gamma m v

where m is the mass of the spore, gamma is the drag coefficient, and v is the velocity. There is an additional random forcing term from random collisions with molecules.

When gamma is low, the drag is low, i.e. friction is low. In this case, the variance of signed velocity is high. In that case, we get some very high velocities compared to a spore which has a high drag coefficient gamma.

In October 2001, the labs directly observed high velocity movements of the spores under the microscope. The spores flew off the slides. This was observing the Brownian motion of the spores. The original observations by Brown were on pollen. Brown was a botanist.

The high velocity of the spores in October 2001 under the microscope was not due to em fields since it had no particular direction. It could only be from Brownian motion. Which means they directly observed the velocity distribution as high compared to normal spores they were familiar with. This was equivalent to directly observing the drag coefficient as low.

Unless silicon in the coat causes this, there was an outer coating. In either case, the spores had a high velocity distribution from Brownian motion. That is just fancy math talk for saying they dispersed. The math of dispersion is the formulas of the velocity distribution under Brownian motion at the above link.

Since coated spores have a higher velocity then uncoated, over time, coated spores will suffer higher velocity collisions. This will widen cracks and holes just like pot holes in a road. Eventually, the coating is knocked off leaving the silicon inside the coat still there. The uncoated particles have a high drag coefficient like normal spores and thus a low velocity distribution.

Anonymous said...

The FBI stated that the Dugway Proving Grounds could not "reproduce" the anthrax letter spores. Yet they claim the spores came from the 1029 batch in Ivins possession. Ivins notebook records that the spores for the 1029 batch were received from Dugway.

Maybe you better read that again. The spores came from Dugway...the same spores that were supposedly used for the anthrax letters. That shipment was noted in Bruce Ivins notebook. One vial was of highly purified spores similar in make-up to the Daschle letter spores. Yet Dugway, could not reproduce their own spores ?

Old Atlantic Lighthouse said...

Peter Hagedorn "Approaches to systems biology" Ph.D. thesis.

Page 82 of pdf (numbered page 70) he studies the Ornstein Uhlenbeck model of the velocity distribution of cells and spores from Brownian motion with actual cell data. This is presented in the thesis. He then studies modifications to the OU model to better describe the data.

The point is not whether the OU formulas need some modifications for actual cells, but that this overall approach is sound. The data here show that.

For spores the results are likely to be better than for cells.

Old Atlantic Lighthouse said...

"A Nonparametric Approach to Cells Dispersal"
Christina Surulescu, Nicolae Surulescu

They study various generalizations of the Ornstein Uhlenbeck in studying living cell movement and dispersal.

They mention subtilis in the introduction and consider various models including OU and generalizations. They reference some other papers in this area as well.