Thursday, June 18, 2015

Dugway does not just make anthrax. What else got sent out live?

USA Today reported that a CDC study found that anthrax spore killing had not been standardized using control spore samples at Dugway.  Tests of different spore concentrations and volumes had not been tested against different radiation doses to ascertain the degree of lethality of the process under varying conditions.

It seems remarkable to me that this could actually go on for ten or more years.  But putting my doubts aside, there is another issue:  what else was irradiated and shipped out with live pathogens?

All the select agents come to mind, including Ebola, Marburg, and anything else that many US labs are creating defenses against, and for which they are developing better and quicker detection methods.  This is a considerable collection of bad bugs.  So anthrax aside, what else went out "live" and what happened as a result?  Presumably gamma killing of the rest was not standardized or tested either, right?

Why do only anthrax scientists keep getting thrown under the bus?

UPDATE: Great source on Ivins' emails and the irradiation problem.  Ivins thought the problem was due to a new irradiation machine.

An Anonymous made a comment that Dugway is only approved as a BSL 3, not a BSL 4, which is required for work with Ebola and Marburg, and thus they do not work with those viruses. When meaning to approve the comment I erased it by mistake.

I certainly could have been wrong about which pathogens are present at Dugway, but my recollection is that Dugway did have BSL 4 status.  However, I think this is based on a document from the 1980s. It comes from an environmental impact statement for a proposed lab, which is discussed in this book. However, I also find links to army statements that Dugway has only BSL 3 labs.  USA Today claims there is a BSL-4 at Dugway.  It seems I can't resolve the discrepancy tonight.

My original point stands, which is that if Dugway's gamma irradiation did not inactivate all anthrax spores, the gamma irradiation of other pathogens was likely inadequate as well.

UPDATE September 9, 2015: USAT reported that Congressmembers were concerned: 
"that the Pentagon's problems containing live anthrax spores could extend to other lethal toxins that could be used as weapons against troops and civilians, members of Congress and their staff told USA TODAY... The worry is that procedures that did not contain anthrax won't prevent the escape of other toxins the labs study, said a senior Capitol Hill staffer who studies the issue but spoke on condition of anonymity because staff members are not authorized to speak publicly about it. Those toxins include chemical and biological agents the military fears could be turned into a weapon..."

Thursday, June 11, 2015

USA Freedom Act: Lies the Government is Telling You/ Judge Andrew Napolitano

From the Washington Times:

Last week, Republicans and Democrats in Congress joined President Obama in congratulating themselves for taming the National Security Agency’s voracious appetite for spying. By permitting one section of the Patriot Act to expire and by replacing it with the USA Freedom Act, the federal government is taking credit for taming beasts of its own creation.
In reality, nothing substantial has changed.
Under the Patriot Act, the NSA had access to and possessed digital versions of the content of all telephone conversations, emails and text messages sent between and among all people in America since 2009. Under the USA Freedom Act, it has the same. The USA Freedom Act changes slightly the mechanisms for acquiring this bulk data, but it does not change the amount or nature of the data the NSA acquires.
Under the Patriot Act, the NSA installed its computers in every main switching station of every telecom carrier and Internet service provider in the United States. It did this by getting Congress to immunize the carriers and providers from liability for permitting the feds to snoop on their customers and by getting the Department of Justice to prosecute the only CEO of a carrier who had the courage to send the feds packing.
In order to operate its computers at these facilities, the NSA placed its own computer analysts physically at those computers 24/7. It then went to the U.S. Foreign Intelligence Surveillance Act (FISA) Court and asked for search warrants directing the telecoms and Internet service providers to make available to it all the identifying metadata — the times, locations, durations, email addresses and telephone numbers used — for all callers and email users in a given ZIP code or area code or on a customer list.
The first document revealed by Edward Snowden two years ago was a FISA court search warrant directed to Verizon ordering it to make available to NSA agents the metadata of all its customers — more than 113 million at the time. Once the court granted that search warrant and others like it, the NSAcomputers simply downloaded all that metadata and the digital recordings of content. Because the FISA court renewed every order it issued, this arrangement became permanent.
Under the USA Freedom Act, the NSA computers remain at the carriers’ and service providers’ switching offices, but the NSA computer analysts return to theirs; and from there they operate remotely the same computers they were operating directly in the Patriot Act days. The NSA will continue to ask the FISA court for search warrants permitting the download of metadata, and that court will still grant those search warrants permitting the downloading. And the NSA will continue to take both metadata and content.
The Supreme Court has ruled consistently that the government must obtain a search warrant in order to intercept any nonpublic communication. The Constitution requires probable cause as a precondition for a judge to issue a search warrant for any purpose, and the warrant must “particularly [describe] the place to be searched, and the persons or things to be seized.” Because this is expressly set forth in the Constitution itself, Congress and the president are bound by it. They cannot change it. They cannot avoid or evade it.
Probable cause is evidence about a person or place sufficient to permit a judge to conclude that evidence of a crime will probably be found. Both the Patriot Act and the USA Freedom Act disregard the “probable cause” standard and substitute instead a “government need” standard. This is, of course, no standard at all, as the NSA has claimed under the Patriot Act — and the FISA court bought the argument — that it needs all telephone calls, all emails and all text messages of all people in America. Today it may legally obtain them by making the same claim under the USA Freedom Act.
When politicians tell you that the NSA needs a court order in order to listen to your phone calls or read your emails, they are talking about a FISA court order that is based on government need — not a constitutional court order, which can only be based on probable cause. This is an insidious and unconstitutional bait and switch.
All this may start with the NSA, but it does not end there. Last week, we learned that the FBI is operating low-flying planes over 100 American cities to monitor folks on the streets and intercept their cellphone use — without any search warrants. Earlier this week, we learned that the Drug Enforcement Administration has intercepted the telephone calls of more than 11,000 people in three years — without any search warrants. We already know that local police have been using government surplus cell towers to intercept the cellphone signals of innocent automobile drivers for about a year — without search warrants.
How dangerous this is. The Constitution is the supreme law of the land. It applies in good times and in bad, in war and in peace. It regulates the governed and the governors. Yet if the government that it regulates can change it by ordinary legislation, then it is not a constitution but a charade.
Suppose the Congress wants to redefine the freedom of speech, the free exercise of religion or the right to keep and bear arms, just as it did the standards for issuing search warrants. What is the value of a constitutional guarantee if the people into whose hands we repose the Constitution for safekeeping can change it as they see fit and negate the guarantee?
What do you call a negated constitutional guarantee? Government need.

Tuesday, June 9, 2015

As the Anthrax Story Keeps on Coming: 68 labs, 5 countries

On June 9, two weeks since this story first burst forth, we are up to 68 labs that likely got some live anthrax from Dugway.  And another country has been added, the UK.

If the story is accurate as told so far, what probably happened is that there was incomplete inactivation due to inadequate doses of gamma irradiation.  Those responsible for the inactivation process (usually exposing spores to cesium or cobalt sources of gamma rays) may not have recalibrated the radiation dose for larger collections of spores, and for different containers, media, etc. Bacterial killing is not like killing cows.  A cow is either alive or dead.  But collections of bacteria die at log rates, and killing that very last spore can require a much higher dose of radiation than is needed for the first 99.99% of the batch.

The good news is that it takes, in general, many thousands of inhaled spores to produce an infection. So small numbers of live spores won't generally make anyone sick.  Though even one can be used to grow a deadly batch of new anthrax spores.

Live Anthrax Sent to 66 Labs in 19 States, Washington DC and 3 Countries: But Nobody Discovered This for Years? It Strains Credulity.

I will be writing more about the US DoD assertion that up to 66 laboratories in 19 states, the District of Columbia and three countries  (Australia, South Korea and Canada) received live anthrax spores by mistake from an Army lab at Dugway Proving Ground in Utah. The June 4 WSJ (behind a paywall) says the problem has existed for "over a decade".

The story seems improbable to me, since the mistake should have been caught fairly quickly, not many years later.  Scientists who work with potentially deadly organisms generally don't take claims of their inactivation by others, elsewhere, on faith:  they plate them out and incubate them and check whether there is growth, to be sure there are no live spores, before exposing themselves to a deadly agent.  To imply that scientists at 66 laboratories all failed to perform this procedure, which is SOP, strains credulity.

In 2014 it was found that CDC had a similar issue: it was reported that anthrax spores had been 'inactivated' using a chemical procedure that was sufficient for anthrax in its vegetative form, but not in its spore form. This was said to have exposed about 80 people at CDC to potentially aerosolized spores.  The mistake was discovered when plates were left by chance for a week in an incubator, and late growth was discovered.

The story was that after the chemical treatment, spore growth on plates (into vegetative cells) was delayed but not prevented.  The incident exposed several levels of incompetence. Any idiot working with anthrax should have understood that anthrax' niche as a bioweapon stems from its ability to retain growth potential even after being exposed to extremes of pressure, temperature and dryness (dropped from bombs or airplanes), while in spore form. A spore is anthrax in 'suspended animation.' But during active growth, in the vegetative stage, anthrax is very easily killed.  (Though you must be sure none of it forms spores before it is killed.) As a spore, anthrax is inactivated only with great difficulty.  Which is reflected by how it can start to grow, given the right conditions, even after spending one hundred years or more in spore form.

The CDC mishap informed researchers that they should be alert for delayed growth, when anthrax has been exposed to a procedure intended to kill or damage it, so plates testing anthrax growth should be incubated for longer than normal.  

Below are excerpts from 2 abstracts pointing out that irradiation of spores may not always kill them.  Many factors influence the dose of radiation required to kill all spores in a bundle, including whether spores are wet or dry, the type of diluent, the geometry of how spores are packaged together during irradiation, type of packaging and spore concentration. These factors are only partly understood.  Furthermore, bacteria and spores undergo log killing (as opposed to an all-or-nothing process): a low radiation dose allows, for example, 1/1,000 spores to survive, while a higher dose only allows 1/1,000,000 to survive.

But that is why you test your batch to ensure it is fully inactivated before you expose yourself to it. And Dugway would have been required to do so before shipping it out to others.  Dugway produced most of the anthrax that was stored in Bruce Ivins' flask RMR1029.  Dugway has been making large production runs of anthrax for many years. It is not a newcomer to this enterprise.

Also note that when spores are shipped, their packaging within packaging is supposed to prevent any leakage of contents, no matter what type of indignities the package may be subjected to, en route. (There are federal rules that were enacted after leakage many decades ago.) And packages must be tracked carefully as well.

For example:  here is part of an SOP published by University of Pittsburgh investigators on what it takes to approve a method for inactivation of select agents (those microbes, like anthrax, designated as high threat agents for bioterrorism):

Standard Operating Procedure for Obtaining Approval and Safety Testing of a Sample Inactivation Method
  • 1. For all sample inactivation procedures, the investigator  and  his  or  her  staff must  notify the  Team  of the intent to  inactivate  biological  materials  for  removal  from  the  RBL  BSL­3/registered Select Agent facility. 
  • 2. The proposed inactivation procedure must be discussed  either at a strategy meeting prior to initiation of a project or  at  the  investigator’s  standing  monthly  meeting  with  the  Team. 
  • 3. Each proposed inactivation method must be described  in  detail,  along  with  corresponding  safety  testing  procedures that demonstrate the lack of viable infectious material  after the inactivation procedure. 
  • 4. An investigator may use an original inactivation procedure, or  he  or  she may  use an existing inactivation  procedure published elsewhere or developed by another investigator and listed in this SOP. 
  • 5. Once  the  Team  has  been  notified  of  the  inactivation  procedure,  the  investigator  may  proceed  with  performing  safety testing on the inactivated materials. Safety testing is  required  for  both  original  inactivation  procedures  and  for  existing inactivation procedures developed by other investigators or published in the literature. 
  • 6. If  an inactivation method is to  be  used  for more than  one pathogen, safety testing data must be provided for each  pathogen or type of pathogen. 
  • 7. It is  recommended to  use  a  high­ titer  or  concentrated stock of infectious agent in the safety testing to provide the  most rigorous challenge to the inactivation procedure...
1.    2006 Sep;101(3):514-25. 
Spores of Bacillus subtilis: their resistance to and killing by radiation, heat and chemicals.
Setlow P1.
A number of mechanisms are responsible for the resistance of spores of Bacillus species to heat, radiation and chemicals and for spore killing by these agents... Both UV and gamma-radiation also kill spores via DNA damage. The mechanism of spore resistance to gamma-radiation is not well understood, although the alpha/beta-type SASP are not involved...  Given the importance of the killing of spores of Bacillus species in the food and medical products industry, a deeper understanding of the mechanisms of spore resistance and killing may lead to improved methods for spore destruction.

2.    2008 Jul;74(14):4427-33. doi: 10.1128/AEM.00557-08. Epub 2008 May 30

Gamma irradiation can be used to inactivate Bacillus anthracis spores without compromising the sensitivity of diagnostic assays.

Dauphin LA1Newton BRRasmussen MVMeyer RFBowen MD

The use of Bacillus anthracis as a biological weapon in 2001 heightened awareness of the need for validated methods for the inactivation of B. anthracis spores. This study determined the gamma irradiation dose for inactivating virulent B. anthracis spores in suspension and its effects on real-time PCR and antigen detection assays. Strains representing eight genetic groups of B. anthracis were exposed to gamma radiation, and it was found that subjecting spores at a concentration of 10(7) CFU/ml to a dose of 2.5 x 10(6) rads resulted in a 6-log-unit reduction of spore viability...