* from DXer … the DOJ should disclose the 2004 article provided by Dr. Bruce Ivins to the FBI regarding silica and Bacillus spore suspensions
Posted by DXer on March 11, 2010
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CASE CLOSED ... what really happened in the 2001 anthrax attacks? 
DXer said
Dr. Ivins was provided this article abstract by someone about adding silica to the spore coat. In light of Dr. Andrews articulate discussion of the issue in his recently produced civil deposition, it seems especially important that this document be obtained.
DXer said
This document attached to the 302 needs to be produced this week. It is not exempt from FOIA. It is published and publicly available at any good university library in electronic databases. It goes to the heart of the debate over the Silicon Signature. It was wrongfully withheld under FOIA.
Ike Solem said
http://biopreparat-mknaomi.blogspot.com/2010/03/complete-transcript-of-dr-joseph.html
Regarding the Meryl Nass post:
Ezzell claimed that his statement had not been conveyed accurately, and that he had referred only to the first set of letter anthrax, which was clumped, not free-flowing and contained extensive debris. This “rough” preparation of anthrax could have been made in the available speed vac.
That is in direct contradiction to Michael’s testimony:
JM: I think the conclusions are:
*The New York Post, Leahy and Daschle materials are basically indistinguishable, elementally, at the spore level, and they both have a similar fraction of the spores with the silicon and oxygen in or on the spore coat.
*We found the silicon and oxygen signature on an endospore in the New York Post material, which leads me to believe that this is something that is happening during the spore formation process, not something that’s added later on as an additive, once the spores have been formed.
*I believe that the letter powders are not unique. We’ve seen examples in the literature and examples from other samples grown for the FBI that show the silicon and oxygen signature – they do differ, though, in the percentage of spores that have the silicon and oxygen on the spore coat.
What are we to make of this? One curious fact is that Sandia never looked at any of the unprocessed Daschle material:
Michael: We were given I think 1.4 milligrams of Leahy material and about 14 milligrams of New York Post and were told to be careful how we used it…
Michael: Okay, here’s the New York Post – these are the only two samples that we had powders of that we could do the thin prep of, I think they ran out of Daschle material, or didn’t want to share it with us, and you can see again the same thing, calcium, in the spore body itself, silicon and oxygen co-located with the, ah, spore coat, and again we see the iron and tin signature – so that sort of links the two attacks together, maybe, they’re very similar on a spore-by-spore basis, if you look at single spores.
Here, by the way, we see a serious failure in the FBI methodology – no isotopic elemental analysis of the RMR-1029 and RMR-1030 flasks, which could be used in analysis. If I take two identical tubes of anthrax from RMR-1029/1030 and grow them at separate labs, it’s likely that they will use different growth media – only slightly different, but this can show up in the isotopic ratios, since different companies make different media from different sources. None of this type of isotopic matching work was done, apparently.
This isotopic issue was also raised in the NAS meeting:
QUESTION: Does this technology allow you to get a sense of the ratios of isotopes, so that – what I’m thinking of is, with the minor elements, from different parts of the country with different isotope compositions, that it may be possible for example to track down something? – [inaudible]-
JM: One of the problems is that the amounts of the material are quite small, so you can go back and look at that SIMS data, and you can see the isotopic ratio in the tin peak, for example. It looks very much like a naturally occurring – what you’d expect from nature for tin. Trying to geolocate from that data would be really tough. It wasn’t something we thought about at the time because the signal was so low. It really doesn’t lend itself to that sort of work – and it’s not the right tool to use for that anyway. There are better tools to do that sort of analysis in.
Yes – and why didn’t the FBI seek out those tools?
After transcribing this, it seems that the Sandia lab did careful work – with the samples they were given – but that those samples were prepared elsewhere. Take this oddity, for example:
And you notice in the New York Post are these fairly large chunks – this is a 100 micron bar, so these chunks are quite large – and in fact, they’re very hard little pieces of material. In fact, we like to break them up to see more of the internal structure of these clumps. And you can take a pair of tweezers and clamp them on there and kind of click them, to make these particles break apart – so they’re very hard, uh, little particles.
Now, that clearly conflicts with numerous descriptions of a very free-flowing powder – which is why the entire Hart Senate Office Building was heavily contaminated with a single letter, along with the Brentwood mail facility. So, what can we make of this? Did something happen to those powders before they were sent to Sandia?
QUESTION: Were the preparations for the surrogate Bt silica and these Leahy samples – were they prepared exactly the same way?
JM: I believe so.
Hence, preparations were done elsewhere. Now, we know that samples of Daschle, possibly Leahy were sent to Battelle’s West Jefferson lab by the FBI for a “second opinion” after the USAMRIID conclusion of a high-tech weaponized attack. The powders were then autoclaved – and fused into bricks as a result. Were these the samples that were then shipped to Sandia for careful analysis?
Notice also that this sample preparation method could easily remove large quantities of silica – hence creating artifacts:
Anyway, in specimen prep, this happens to be some pictures that we took when we were preparing a sample from a clump of spores, a large clump of spores, so we wanted to make a sample across here for transmission electron microscopy so we used our focus ion beam to remove this material and remove this material, and then gradually thinned this sample down to electron transparency on the order of 100 nm or less..
There’s quite a bit of literature on artifacts generated via ion beam sample preparation – but this isn’t even mentioned or addressed by the Sandia group, as far as I can tell. Do a google scholar search for this string: ” Specimen preparation FIB induced damage ” for example – and these are soft biological samples, not even metals. In any case, they should have been far more careful about how they standardized their method when applying it to biological samples for the first time.
DXer said
“Here, by the way, we see a serious failure in the FBI methodology – no isotopic elemental analysis of the RMR-1029 and RMR-1030 flasks, which could be used in analysis. If I take two identical tubes of anthrax from RMR-1029/1030 and grow them at separate labs, it’s likely that they will use different growth media – only slightly different, but this can show up in the isotopic ratios, since different companies make different media from different sources. None of this type of isotopic matching work was done, apparently.”
Lots of work was done on the isotopic elemental analysis. Pubilshed studies were done on both water and media. Kreuzer-Martin published a number of reports on media with the last being a Bayesian approach. The isotopes did not support their FBI Theory and so the FBI did not even present it to the NAS so that the NAS could review their conclusion that it was inconclusive.
Funny how that is. To take just one example: when the examination of the copier in the library shows it was not the copier used, the lawyer nonetheless includes it in the accusatory Summary without disclosing that the science shows that it was NOT the copier used. Then the FBI does not have the NAS review that evidence that is exculpatory. The only relevant science they have reviewed is the science that doesn’t point to Ivins any more than it points to 350 others (and anyone they could have given the anthrax to). And yet somehow Ivins is said by the DOJ spokesperson to be guilty because he made the murder weapon.
Similarly, the Federal Eagle envelope issue is far more narrowing than the genetics and yet the science is not presented to the NAS for review.
There is not even a single expert on the panel qualified to address the central issue presented — regarding the issues of creating an aerosol powder presented.
So it is not surprising that the lengthy summary doesn’t rely on any science.
Anonymous scientist said
Thanks for transcribing the Joe Michael presentation. Very valuable source material.
Old Atlantic said
” Specimen preparation FIB induced damage ” What an appropriate phrase.
Anonymous Scientist said
Interesting update on Meryl Nass’ blog:
——————————————————
http://anthraxvaccine.blogspot.com/
a) Means: Retired colleagues have said he did not have the equipment to make Daschle-quality anthrax in the amounts required using equipment available to him at Fort Detrick. Anonymous colleagues at Fort Detrick claim he could. FBI has failed to clarify this major issue. FBI has not been able to “reverse engineer” the anthrax and therefore does not know what equipment was needed to produce it. FBI has made a series of changing claims over time about silicon found in the spore preparation. UPDATE: Ezzell and Mohr (not anonymous colleagues) told Scott Shane/NYT that Ivins had the equipment to produce the anthrax powder. LATER UPDATE: After Ezzell was interviewed and allegedly said Ivins had the equipment to make the spores in the anthrax letters, another coworker queried Ezzell on this. Ezzell claimed that his statement had not been conveyed accurately, and that he had referred only to the first set of letter anthrax, which was clumped, not free-flowing and contained extensive debris. This “rough” preparation of anthrax could have been made in the available speed vac.
——————————————————————
I certainly agree that nobody at Detrick could have made the Daschle or Leahy powders – that’s a powder engineering job. This is clearly shown in the Dugway paper where they simulated the behavior of Daschle powder and had to engineer their product with a propietary azeotrpic drying technique and a pneumatic ball mill with mesh filters.
I would seriously question if a speed vac would be capable of drying gram quantities of spores for the New York Post and other media letters. The speed vac takes 72 hours just to dry mg of sample. Even then a solid lump would be produced which would have to be made into a powder.
DXer said
As Dr. Ivins explained to the FBI, John Ezzell made dry powdered anthrax at Ft. Detrick. (See alsoemail reported by FoxNews.
I spoke to Dr. Ezzell about it and he confirmed it — even though he noted that he was under a gag order and his phone likely was wiretapped.
And so if Dr. Ezzell, the FBI’s anthrax expert at USAMRIID (since 1996 when he was in the same unit as the FBI scientists) made dry powdered anthrax at Ft. Detrick, it pretty clearly is doable.
Then the relevant questions become: JE, what equipment did YOU use. (And then the observer can consider whether that equipment was available to Dr. Ivins). For example, he could start by describing the soil suspension he made using Ames he provided Edgewood. Why won’t the AFIP data, when produced, point to access of Ames in a soil suspension?
Did Dr. Ezzell use a mini-spraydryer?
Ike Solem said
No biological threat assessment program was ever authorized at Fort Detrick, was it? Biological threat assessment was Dugway’s specialty, I thought – or West Jefferson’s, although the West Jefferson group may have been the one tinkering with the anthrax genome in an effort to make it vaccine-resistant.
This seems dubious at best – do you have any corroborating evidence of any kind that dry powdered anthrax was made at Detrick? If it was done outside the biological threat assessment program – wouldn’t that be a serious crime? And if so, why would John Ezzell simply admit to it?
See this Michael testimony:
JM: And again, note the variability here. We see a couple spores in this field and we see a lot of spores in this field that have the silicon and oxygen on the spore coat. And as far as I can find out, this is Ames grown via fermentation at Dugway using a L-D media. That’s all the information I had about that sample.
If you read the transcipt, you also come up with things like this:
JM: If you look at this series of samples, though, we’ve analyzed quite a few spores, the interesting thing is here, this would be a great sample to mine for conditions to see why it went from 18% of the spores with the silicon and oxygen signature, down to 1.2. And there were others in this series that had nothing, in that batch of samples. So, just to bring this to your attention, this is a great sample that you might want to pull the string on a little bit if you can.
QUESTION: Pull the string – what are we pulling for?
JM: I don’t know anything about these or where they came from. Okay – and if they know the growth conditions, you may be able to associate this change in silicon content, or silica – the number of spores with silica – with the growth conditions.
Now, it seems that if you hire a cutting edge semiconductor/nuclear materials analysis lab at Sandia to look at bioweapon attacks, you would do all that work – growing bacteria in media with and without silica – being involved with all steps of the process so you know what you are looking at, what the variables are – and only then going to look at samples from crime scenes, etc.
The fact that the FBI so tightly compartmentalized all this work is what leads to suspicions of doctored samples, sampling bias and so on. That’s just the physical forensics work, too – some of the genetics “morph” analysis seems to suffer from similar flaws.
Ike Solem said
Here you go, from the NAS Committee – they haven’t made anything public since this date, despite having had two or three meetings, the last on Feb 2 – I can’t even find a list of witnesses or speakers.
http://biopreparat-mknaomi.blogspot.com/2010/03/complete-transcript-of-dr-joseph.html
Conclusion? The Sandia argument for “naturally occurring silica” doesn’t hold any water.
The clause under which the NAS is keeping the rest of their inquiry secret is this one, 5 USC 552 (b)
An agency head may exempt from release under paragraph (1) specific information, that would –
(A) constitute a clearly unwarranted invasion of personal privacy;
(B) reveal the identity of a confidential human source, or reveal information about the application of an intelligence source or method, or reveal the identity of a human intelligence source when the unauthorized disclosure of that source would clearly and demonstrably damage the national security interests of the United States;
(C) reveal information that would assist in the development or use of weapons of mass destruction;
(D) reveal information that would impair United States cryptologic systems or activities;
(E) reveal information that would impair the application of state-of-the-art technology within a United States weapon system;
(F) reveal actual United States military war plans that remain in effect;
(G) reveal information that would seriously and demonstrably impair relations between the United States and a foreign government, or seriously and demonstrably undermine ongoing diplomatic activities of the United States;
(H) reveal information that would clearly and demonstrably impair the current ability of United States Government officials to protect the President, Vice President, and other officials for whom protection services, in the interest of national security, are authorized;
(I) reveal information that would seriously and demonstrably impair current national security emergency preparedness plans.
(J) violate a treaty or international agreement.
Which ones are they worried about? (J), (G) and (C), maybe?
All roads lead back to the biological threat assessment program, don’t they?
DXer said
Where does Sandia use the phrase “naturally occurring silica”? Isn’t that just a straw man argument that folks keep unfairly raising? Doesn’t he say: “we can argue what natural means all day long.” Isn’t he really just identifying the location of the silicon — and beyond that, he doesn’t know anything about (or venture a hypothesis) how it got there? (He and his colleague note that they were told what an exosporium was). As for the natural tendency of the silicon to be absorbed into the spore coat, that is demonstrated by the literature.
Sandia’s JM would have no basis to deny that it results from a silanizing solution in the slurry before drying — first, it is consistent with the article that started the thread. Second, the Air Force experiments, if nothing else, demonstrate that silanizing solution can be added intentionally. And in fact the purpose may not relate to floatability.
BTW, on Van der waals and electrical charges generally, there is a Driks article within the past few months that addresses the issue complete with complicated formulas.
“QUESTION: So the fact that you see the silicon inside a vegetative cell is what really allows you to conclude that this is probably a natural process?
One, one of the things, sure, right, I believe that’s true – and by natural, we can argue what natural means all day long.”
DXer said
“and by natural, we can argue what natural means all day long.”
I don’t know anything about the scientific method but shouldn’t a scientist define his terms to avoid such disagreements arising from semantical differences?
Anonymous Scientist said
It’s probably just the Somlyo abstract. Which in 2004 was not news, since it had already been mentioned by Meselson as the explanation for the AFIP results.
Distribution of calcium and other elements in cryosectioned Bacillus cereus T spores, determined by high-resolution scanning electron probe x-ray microanalysis.
M Stewart, A P Somlyo, A V Somlyo, H Shuman, J A Lindsay, and W G Murrell
Abstract
The distribution of a number of key elements in Bacillus cereus T spores was determined by high-resolution scanning electron probe X-ray microanalysis. To circumvent the redistribution of soluble or weakly bound elements, freeze-dried cryosections of spores, which had been rapidly frozen in 50% aqueous polyvinyl pyrrolidone, were employed. The sections were examined by using a modified Philips EM400 electron microscope fitted with a field emission gun, scanning transmission electron microscopy attachment, and a computer-linked energy-dispersive X-ray microanalysis system. X-ray maps for selected elements and the corresponding electron image were produced simultaneously by scanning the cryosections with a fine electron beam in a raster pattern, using the scanning transmission electron microscopy attachment. The results indicated that almost all of the calcium, magnesium, and manganese, together with most of the phosphorus, was located in the core region. An unexpectedly high concentration of silicon was found in the cortex/coat layer. Granules containing high concentrations of calcium, manganese, and phosphorus were demonstrated in spores containing reduced levels of dipicolinic acid. Spot mode analyses, in which a stationary beam was located over the region of interest in the spore cryosection, confirmed the results obtained with the scanning mode and also provided a more accurate quantitation of the elemental concentrations on a dry weight bases.
DXer said
What passage in that 1980 article do you view as referring to the “addition of silica to the spore coat”?
Do you agree that given that has long been central to the DOJ’s view of the silicon signature issue that if their only suspect gave them an article, it should be provided pursuant to FOIA?
I mean, DIA gave people 100 pages of articles that Ayman Zawahiri had related to anthrax — certainly DOJ can give us this one submitted to them by Dr. Ivins (whatever it is)?
Anonymous Scientist said
I certainly agree that it should be disclosed.
And you are right – the abstract does not say addition of silica – but that may just be the way the Special Agent characterized it. I do think if an abstract from a science paper existed with the phrase “addition of silica to the spore coat” in it, we’d have found that article long ago.
I believe Ivins passing this on is simply another example of his innocence – what guilty man would try to help solve the crime he committed?
DXer said
Excerpts:
“Silicone antifoam agents were not employed.”
“The silicon content of the cortex/coat layer may result from specific incorporation or from contamination from glassware or from silicone vacuum oils employed in the apparatus used to freeze-dry the spores. Since there was considerable variation in silicon content both within and between different spore reparations, we considered it unlikely that the effect could be due entirely to contamination.”
Anonymous Scientist said
But the key is that the maximum concentration of silicon Somlyo found in one particular sample was 0.3%.
When Livermore tried to introduce silicon “naturally” to Ames spores, the highest they got was 0.01%.
There was 1.45% in the Leahy spores. That was not natural. That was more than one hundred times higher than the maximum Livermore got for Ames.
DXer said
And what was the highest percentage of silicon found in the spores examined in “W.G. Murrell, Chemical composition of spores and spore structures. … 215– 273 (Chapter 7).”
Anonymous scientist said
Irrelevant. A different species and silicon antifoam was used.
DXer said
And what was the highest percentage of silicon observed for this data you think irrelevant but Sandia’s Joe Michael does not.
And where do you see that antifoam was used given it was not used in the Soimlyo abstract above it was not used.
Anonymous scientist said
Just read the Murrell paper. He says he used silicone antifoam and that’s why he detected silicon.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2106236/
It’s all really very simple. If you deliberately add silicon you find it there later. If you don’t deliberately add it you won’t detect it in levels above 10 parts per million.
Anonymous scientist said
I should add that not all antifoam agents are silicon based – but the one Murrell used was.
The one Dugway uses in their fermemter is NOT silicon based. It is Dow antifoam 204.
http://aem.asm.org/cgi/content/full/75/13/4297
DXer said
The article states:
“The spores were grown in 14 liter lots of medium, vigorously aerated in 20 liter bottles, with silicone antifoam.”
Thanks very much and good work in understanding and helping me and others in understanding these fine points.
So I believe when Dr. Michael says from what he’s seen he surmises antifoam was not used, it seems that he may be mistaken. It would seem that any reliance he or the FBI scientists place on their assumption he did not use antifoam is mistaken.
For the sake of completeness, I am still looking for the highest percentage found in the Murrell Chapter. (I typed up copious passages from the Chapter and posted it but cannot find what I typed now). I believe it was comparable to the Leahy material.
DXer said
Note that the Al Qaeda manual on “poisonous letters” instructs to use a silicone spray on the inside of the letter so as to avoid killing the mailman.
Ike Solem said
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Is this your putative Al Qaeda link, then?
DXer said
A 2006 Washington Field Office memorandum explained about the aerosol challenges:
“Antifoam was used in aerosol challenges when the challenge material contained large amounts of protein. For this reason, antifoam was used more often with various toxins and viral preparations rather than bacteria. There were rare occasions when antifoam was added to the collison nebulizer in the challenges. It was added to the nebulizer if the nebulizer became foamy or gummy during a challenge. When antifoam was added to the AGI, it settled to the top of the solution. The purpose of antifoam was to prevent bubbling inside the nebulizer or AGI which caused poor aerosolization, or material loss when the material stuck to the sides of the container.
The primary aerosol technicians were questioned about the use of antifoam as part of the aerosol process. All commented that it was not standard operation procedure (SOP) to utilize antifoam with Ba. Because the Ba aerosols used only water in the process, there was not usually enough foam created to require the use of antifoam.”
Ike Solem said
Hello there – I just dug up that paper, and it looks like they got a maximum of 0.5% in their prep. However, despite the fact that this paper has been widely flogged as proof of the silica theory, if you read the discussion they state the following:
“The silicon content of the cortex/coat layer may result from specific incorporation or from contamination from glassware or from silicone vacuum oils employed in the apparatus used to freeze-dry the spores.”
There best literature claim is a probable artifact, in other words. Despite this, here is what Dr. Michael had to say about this paper before the NAS:
“So there are multiple examples from the literature where they found silicon. On both of these examples, none of them mentioned any silicon antifoam agents, that I could find.”
True enough – but they did mention silicon vacuum oils used in the spore preparation! Why was that conveniently omitted from the presentation? Furthermore, why didn’t they make any effort to replicate this work? Wait… they did… and got much lower levels of silicon when trying to get spores to coat themselves in liquid media.
Conclusion? The spores had to be processed in some kind of spray-drying apparatus in order to get that level of silicon – after they were harvested and purified away from cell debris, etc. For a discussion:
Several sources agreed that the most likely way to build the coated spores would be to use the fine glass particles, known generically as “fumed silica” or “solid smoke,” and mix them with the spores in a spray dryer. “I know of no other technique that might give you that finished product,” Spertzel said.
DXer said
I contacted the Air Force lab some years ago on the issue. The Air Force lab in April 2007 did controlled experiments in which a silanizing solution was used in the slurry before drying and a product comparable to the mailed anthrax resulted. The head of the lab shared images with me and I circulated them (for example, to AS). A spraydrier was not used. The lab is very experienced at making anthrax simulants.
The head of the lab said that the attack anthrax did not have the characteristics of anthrax that had been milled or lyophilized. He did not see eye-to-eye with the FBI scientists.
Dr. RS was not engaged in making anthrax simulants.
Dr. Michael, of course, has never made anthrax simulant or done any controlled experiments making anthax simulants.
There is no contradiction between the suggestion that the source was a silanizing solution and those who say it was intentionally added.
And there is a naturally tendency on the part of the spore coat to absorb the silicon.
DXer said
I spoke with RS for about an hour a few months ago and he said he had not talked about it for the last half decade because he was so frustrated at what he perceived as the USG’s obfuscation. But I understood him to be saying that he did not realize that the FBI was conceding that silicon had been absorbed by the spore coat. I understood him to be saying that he thought they were still denying the finding of the AFIP report. Although he no doubt is highly expert, I don’t think it is the Air Force lab’s controlled experiments that are the best guidance on the issue.
And 8 years ago when I spoke to Dr. Alibek who was giving his views publicly (e.g., June 2002 NYT), he had not yet heard of the AFIP report’s findings.
And so I think everyone might want to freshen up their expert opinion and not rely on ones from years ago.
BugMaster once said:
“Antifoam as the source of silica WITHIN THE SPORE COAT is quite unlikely. The silica that penetrated the spore coat would have to be in the form of a monomer (silicic acids as an example) or low molecular weight polymer. That rules out antifoam as the source of the silica within the spore coat, but does not rule out antifoam as one of the sources of silica in the attack material as a whole.
Silicic acids are POORLY soluble in water. Interestingly, a solution containing a high concentration of a certain compound can contain much more solubilized silicic acid that just water itself. If the solution is diluted out, the silicic acid precipitates out of solution (or perhaps becomes associated with a spore?!).
The possibility that the tin detected could be from a organo-tin catalyst used to polymerize silicon is quite disturbing.
I have never bought into the theory that the attack material had undergone any specialized treatment to enhance dispersability.
Now I am having some doubts.
The presence of silica and now tin has been revealed, with no reasonable explanation for their presence put forth so far.”
I understood the Air Force lab experiments to show that it was not for the purpose of floatability but may instead serve some other function.
All this science stuff is over my head, but my understanding is that the presence of iron in the culture medium tended to cause more silicon to be absorbed and that that the silicon increased lethality.
I think the best approach is to unite around the requirement under the rule of law that the DOJ, USAMRIID and other agencies comply with the Freedom of Information Act and provide all documents subject to applicable exemptions.
If these agencies like USAMRIID cannot efficiently share information under FOIA — and it takes 2 years (as it has) to produce a simple stack of emails — then why do they think that they are even capable of sharing information necessary to keep our country safe?
Of course, anyone who persists in withholding documents wrongfully needs to be fired.