Monday, December 29, 2008


There are 2 errors in what I posted below about the forensic analysis discussed in Professor Jacques Ravel's slides. The first correction is that the over 1,100 samples submitted to the FBI were screened for genotypic differences, and may not have been screened for morphologic differences.

The second error is that the slides say wild-type Ames (isolated from a heifer that died in Texas in 1981) did not vary from an anthrax sample isolated from Bob Stevens' cerebrospinal fluid (over 5 million base pairs identical), rather than from the anthrax letters directly.

What I termed slide 16 has a list of 5 different isolates (morphotypes) from the Leahy letter and 3 from the NY Post letter. One of each is termed "wild-type" so you might say there are 4 (Leahy: A, B, C and E/Opaque) and 2 (NY Post: A and B) morphotypes distinct from the majority colony type listed on the slide.

Later the slides indicate that 3 genotypes were identified within the A morphotype. The slides do not indicate how many genotypes were found in the other morphotypes. Nor how these were determined. There are 2 slides on each page. So what I identified as slide 16 is actually page 16, slide 31.

Slide 45 indicates that 4 PCR assays were developed to distinguish genotypes. I don't know from which samples these distinctive genotypes were found, and used.

The over 1100 submitted samples were screened for PCR genotype differences. Some had 1 or 2 variants but only the sample from Ivins' flask had 4. (It is implied that 4 were found in the anthrax letters.)


I erred in mixing up morphotypes and PCR assays in my earlier statement. There is nothing in the slides that indicated the 1100 samples were screened for morphologic colony differences.

There is missing information so I cannot say what kinds of samples were used to discern the genotypic differences. But my guess is these were genetic differences within morphotypically distinct colonies.

However, the slides appear to indicate that the morphologic variants differed between the two letters.

If genotypic differences of rare morphotypes are what was used to nail Ivins' flask, the science may be questionable. If the morphotypes varied between the two letters, is it forensically valid to focus on qualitative genotypic differences in a subset of morphotypes? But I am guessing this is what was done. The FBI needs to tell us precisely what methods were used.

Tuesday, December 23, 2008

New details from the genomic forensic analysis

Dr. Jacques Ravel of U Maryland, formerly of the Institute for Genomic Research (TIGR), spoke at the MIT faculty club on December 16, 2008 to discuss the scientific evaluation of the anthrax letters' spores.

I requested but did not receive an invitation to the event (despite my Bachelor's degree in Biology from MIT and some expertise in the subject). The slides were shared with me later, but each is labeled "do not distribute."

So I will not share them. They should be posted soon on an MIT website associated with the program that brought Ravel to MIT.

Of interest, the morphologic variations in spore colonies were not entirely identical between the NY Post and Leahy letters. Slide 16 indicates that 5 variations were found in Leahy's anthrax, and (only) 3 of those 5 variations were found in the Post anthrax. No other samples had these 3 variations but some (of greater than 1,100 samples screened) had 1 or 2.

There were no genetic polymorphisms between the 2 samples or a wild-type Ames.

Also of interest, Professor Ravel pays a lot of attention to the criminal-legal aspects of the case and the rules of evidence for trial.

An early article on the genomic studies in the Times is worth a read for comparison.

Friday, December 19, 2008

Military: Repeat of anthrax attacks harder today/AP

From the Annapolis Capital, Maryland

"Lennox said military safety reviews in recent months endorsed many of the security changes already made, from improved cameras and lights to satellite surveillance. But other changes were deemed not workable or too expensive, including limits on scientists' hours or a system that would prohibit workers from being alone with a toxin... As for transporting toxins, there are now requirements that two workers be present at all times during transit and that there be satellite coverage of the shipment."

Terrific. Satellite coverage every time the courier or FedEx carrier goes inside a building or gets on an airplane. How is that going to prevent unauthorized transfers of microorganisms and toxins? Do two workers share a bathroom stall?

The army's PR people will have to do better than this to convince the public the next bioattack won't be originating from a government lab.

Sunday, December 14, 2008

Confirmation: Letter spores grown in medium to which silicon added

Although this conclusion is nothing new to many of us, it is gratifying to get confirmation from the National Academy of Engineering of the National Academy of Sciences, and to hear a Sandia National Labs scientist, Paul Kotula, acknowledge that 200 tries to reverse engineer the spores did not create an identical match. Which simply says it is likely the FBI does not know exactly how the spores were made, which makes it more difficult to pin their manufacture on any one individual.

Saturday, December 13, 2008

Who is Responsible for Zimbabwe's Current Anthrax and Cholera Epidemics?

Zimbabwe media are reporting that Zimbabwe government officials are blaming British operatives during the liberation struggle--and today--for cholera and anthrax epidemics currently affecting the country:
"Dr Ndlovu quoted a research by Tom Mangold, a researcher in Warfare and Jeff Goldberg, an investigative journalist based in Washington DC, who made the stunning revelations that the British operatives during the liberation struggle planted some anthrax and cholera bacterium to wipe away black Zimbabweans and their herds of cattle.

The minister also said the rains are activating the bacterium and there are some operatives currently in the country who are working on planting the epidemics.

Mangold and Goldberg's 1999 book Plague Wars (you can read the entire book if you click on it) recounted my research on Zimbabwe's anthrax epidemic in chapter 22, and discussed the use of other chem/bio agents during the liberation struggle.

I'd like to make clear that the current cholera outbreak is the result of Zimbabwe's failure to provide safe water to its citizens, and is not a form of biological warfare perpetrated from outside. Adding small amounts of bleach to water would prevent this epidemic--that is, if there were adequate water available. Cholera bacteria spread from infected stools. The bacteria produce a toxin that forces huge amounts of water out of the body in the stool. It is the dehydration which kills. If you could provide sufficient fluid to patients using oral rehydration fluids or intravenous fluids, no one would die.

In the 1990 cholera epidemic in Latin America, the death rate was 1% or less as a result of this treatment, which ought to be cheap and available. (The antibiotics used to kill the bacteria are also inexpensive.)

Zimbabwe's lack of clean water, the lack of toilet facilities, the lack of available health care produced this cholera epidemic, not foreign operatives.

As for the current anthrax outbreak, that is different. It is the result of anthrax spores spread
between 1978 and 1980 by unknown operatives working to prevent majority rule. The spores remain in the soil, causing unpredictable outbreaks in grazing animals for decades or longer, in areas where the soil supports regrowth of spores during special weather conditions.

Cholera was used to contaminate some rivers in the 1970s, but did not spread widely in Zimbabwe because clean water and medical facilities were available then, and it was rapidly diluted.

Saturday, December 6, 2008

Are We Safer From Bioterrorism?--ProPublica

A 3-part series of articles by Marcus Stern looks into the financial costs, usefulness and risks of the $48 billion dollars spent on bioterrorism responses since 9/11/01. Additional material with videos can be found at the thought-provoking, new web magazine FLYP (Nov. 25-Dec 12 issue, main story--and the visuals are lovely).

Off Topic: Egalitarian Approach to Improving the Health Care System

This is an introductory talk I gave in 1995 about health care reform. It seems equally relevant today. I will post additional thoughts on improving our health care system as the new administration considers ways to cover all Americans, improve quality and cut costs. I think it is doable!

Hint regarding a future post: we do not know much about what it costs to produce nor to purchase health care items. Virtually all reimbursements for healthcare are negotiated. Charges and prices have very little meaning, since the amounts that are paid for identical items or services vary widely between health care insurers, negotiating entities and individual practitioners.

Until we have transparency about what all these numbers really are, we will understand nothing about the cost of healthcare.

Monday, December 1, 2008

Anthrax poses new threat in cholera-hit Zimbabwe: charity (Agence France Presse)

If you drop anthrax spores in areas where livestock graze or wild animals roam, anthrax's bitter harvest may keep returning. Under the proper weather conditions, spores can regrow and multiply locally. Animals grazing close to the ground may ingest anthrax-infected soil. The animals die suddenly. And hungry humans who butcher, consume or even use the animals' hide or hair are likely to develop anthrax as well.

In nature, luckily, the human disease is less deadly than the animal disease. The vast majority of affected humans develop cutaneous (skin) anthrax. It is slower to develop, and responds nicely to inexpensive antibiotics... if you have the means to get it diagnosed and treated promptly. A wider epidemic can be prevented by vaccinating herds once the disease is recognized.

Zimbabwe's health services have taken an enormous hit lately and are in shambles. People are dying again from the anthrax that was used against them and their cattle 30 years ago, during a long and dirty civil war for majority rule. An FBI informant claimed that Steven Hatfill told friends he had been involved in the original Zimbabwe epidemic. This is one reason he was suspected of having a role in the anthrax letters. Very little is publicly known about who spread Zimbabwe's anthrax, and how it was done.

However, Zimbabwe's experience tells us that even without causing the deadlier (inhalation) form of the disease, anthrax is a terrible problem. Forming a spore that may be viable centuries later, anthrax cannot feasibly be removed from the soil once it lands there.

Zimbabwe teaches that even as we make plans (and spend 50 billion dollars) to mitigate the effects of a biological attack, we should hesitate. We should step back a few paces. Mitigation is a hopeful concept. It may sometimes be effective. But Prevention is guaranteed to work. That is where our focus in the biological arena should be.

WP Editorial: The Next Attorney General (and the anthrax letters)

Editorial from the Washington Post:
...The new attorney general also should ensure that an independent commission or the inspector general review the anthrax investigation. In the summer, the FBI identified Fort Detrick scientist Bruce E. Ivins as the lone suspect in the 2001 anthrax attacks that killed five and sickened many more. Mr. Ivins took his own life before he could be put on trial. An independent examination of the anthrax probe should review the methods used by the FBI in investigating Mr. Ivins and, before him, Steven J. Hatfill, who was the FBI's initial suspect before being exonerated this year. The review must also examine how Mr. Ivins maintained a security clearance despite apparently suffering from serious mental illness.