* new NAS response asserts that “much” of the FBI material it has received is exempt from FOIA disclosure, but fails to cite specific legal authority for such exemption; is this a wilful breach of NAS’s responsibility under FOIA?
Posted by DXer on September 10, 2009
* buy CASE CLOSED at amazon *
NOTE: for prior correspondence between NAS and LMW on this topic, see related post … * the NAS has sequestered FBI submitted documents and will not make these available until the end of the study, over a year hence … the legal rationale for this sequestering is now expected next week.
******
Update 9/11/09 …
email from LMW to NAS …
BILL … I’m forwarding to you excerpts from a comment received on the CASE CLOSED blog after posting your response earlier today. I hope you will respond to the issues raised in that comment as well the underlying issue of whatever legal authority you are claiming to withhold FBI material … LEW
Excerpts from comment by DXer …
- Lew, start with an easy one. Have him put a copy of the contract in the Public Access File or quote language that the FBI included that prevented its release and the release of those documents not exempt under FOIA.
- There is nothing in the statute that permits the withholding until after their review is done. To the contrary, it holds the opposite and makes FOIA applicable.
- If it is producible at the end of their review, it is producible now. Thus, his present position constitutes a wilful breach.
- Why is the Public Relations person giving NAS’ legal opinion rather than the General Counsel?
- Charging for the 100 pages also is inconsistent with FOIA.
******
Update 9/10/09 … email from LMW to NAS …
BILL
Thank you for your response, although I must say it seems inadequate.
You say that much of the FBI material is exempt from release under the FOIA law, but you do not cite the specific legal authority under which such exemptions are claimed.
It is my understanding that there are several reasons for possible exemption from release. Which reasons do you specifically cite for each category of FBI material you claim is exempt?
Also … I note that you say “much” of the FBI material is exempt, which means that some is not exempt.
Could you please advise which FBI material you believe is not exempt, and how the non-exempt FBI material differs from the FBI material which you say is exempt?
Finally, how does one go about requesting the FBI material which you say is not exempt?
I’m sure you agree that release of “thousands of pages” of FBI materials at the end of your study is very different from release of these materials as they become available during the course of the study. There are many people who wish to assist in the analysis of the FBI material, and who can provide the kind of help I believe NAS has stated it wants from the public.
You can facilitate that assistance by releasing material promptly; you will surely inhibit such assistance by holding it all until the end, when it will be too late to be meaningful.
LEW
******
Update … email from NAS to LMW (9/10/09) …
Lew, below is my response to how we’re handling material from FBI. Before it is a link to FACA sections applying to NAS and under which we operate, so you can see the language with which we comply. Sorry it took me a few days to get back to you.
http://www.nasonline.org/site/PageServer?pagename=ABOUT_FACA
The study committee expects to receive thousands of pages of material from the F.B.I. in the course of its study. Some has already been received; more will be coming as the study progresses.
Much of this material is exempt from mandatory release to the public under the Freedom of Information Act.
However, we have an agreement with the F.B.I. that all of the material will be made available to the public at the same time that our report is released, so that everyone will be able to review the information that was available to the committee in reaching its conclusions.
CASE CLOSED ... what really happened in the 2001 anthrax attacks? 
DXer said
The recent NAS report states:
“The review comments and draft manuscript remain confidential to protect the integrity of the process. We thank the following
individuals for their review of this report:
R. John Collier, Harvard Medical School
Rita R. Colwell, University of Maryland
M. Bonner Denton, University of Arizona
Ashlee M. Earl, Broad Institute of the Massachusetts Institute of Technology and
Harvard University
Philip C. Hanna, University of Michigan Medical School
Stephen A. Johnston, Arizona State University
David H. Kaye, Arizona State University
Cato T. Laurencin, University of Connecticut Health Center
M. S. Meselson, Harvard University
Randall S. Murch, Virginia Polytechnic Institute and State University
Pauline Newman, U.S. Court of Appeals for the Federal Circuit
Stanley A. Plotkin, University of Pennsylvania (emeritus)
Elizabeth Rindskopf Parker, University of the Pacific
R. Paul Schaudies, GenArraytion, Inc.
James M. Tiedje, Michigan State University
Bruce Weir, University of Washington
Although the reviewers listed above provided many constructive comments and
suggestions, they were not asked to endorse the conclusions or recommendations, nor did they
see the final draft of the report before its release. The review of this report was overseen by
Stephen Fienberg, Carnegie Mellon University, and Floyd Bloom, The Scripps Research
Institute. Appointed by the National Research Council, they were responsible for making certain
that an independent examination of this report was carried out in accordance with institutional
procedures and that all review comments were carefully considered. Responsibility for the final
content of this report rests entirely with the authoring committee and the institution.”
DXer said
An April 2003 profile on Dr. Budowie in Science discusses his role on putting DNA genetic fingerprinting on a scientific ground and his role in Amerithrax. Dr. Keim is quoted “He’s really a scientist, and a good one — not a cop.”
***
“After the anthrax letters killed five people and sickened 17 others, the bureau came under withering attacks from Congress, the media, and bioterrorism attacks from Congress, the media and bioterrorism experts for its alleged clumsiness. Clueless field agents asked all the wrong questions, critics said, and the bureau even gave Iowa State University in Ames the go-ahead to destroy a collection of historical anthrax samples that may have contained valuable information.”
“Although few people understand what really goes on in such an investigation, the FBI will always be held to a high standard, [Dr. Budowie] says, adding that it should be. But he concedes that the bureau has much work to do if it wants to deter future bioterrorists — or nab them. … The Hazardous Materials Response Unit was started in 1996, but until the anthrax mailings, every suspected bioterror attack turned out to be a hoax or a false alarm.”
“But much remains to be done, a panel assembled by the American Academy of Microbiology concluded in a report issued in February (Science, 21 February, p. 1164). To make sure microbial DNA evidence holds up in court, for instance, a “chain of custody” will have to be preserved from every incident, meaning that everyone from first responders to lab technicians will have to follow standardized protocols.”
***
“We have to prepare for the fact that every piece of evidence is going to be challenged,” Budowie says. “That’s the way the system works.”
***
“The best way to get feedback is to expose yourself,” he says. “it works much better than a dictatorial approach.”
Question:
Did the FBI provide the NAS panel all documents relating to the contents of the collection destroyed in Iowa and the process by which the FBI permitted the collection to be destroyed? No. Did the FBI’s federal hazardous materials response unit acquiesce in its destruction? Did other FBI decision-makers not consult its experts? (Dr. Keim reports that he was not consulted.)
Bruce Ivins wrote Patricia Fellows saying that he had heard [and he names his source, a scientist involved in the investigation], that the aerosolized Ames anthrax closest to the attack anthrax had been made by the FBI’s leading anthrax expert, Dr. Ezzell, who forthrightly confirms to me that he made aerosolized Ames for DARPA. He has been the anthrax expert for the federal hazardous materials response unit since 1996. (JE noted to me that he is under gag and that the phone likely was being wiretapped). Was Dr. Ezzell consulted concerning the destruction of Ames? I haven’t wanted to impose further given that these same issues are addressed by documents obligated to be produced under FOIA but are being withheld.
Virulent Ames was supplied by Bruce Ivins to a former Zawahiri associate who worked for DARPA which is the only reason I was asking Dr. Ezzell if he had ever aerosolized Ames and given it to DARPA. He says that at the request of DARPA he gave it to John Hopkins Applied Physics lab. I contacted the DARPA Program Manager overseeing research there at the APL (she is a radiation expert) to see who confirmed that radiation had rendered the virulent Ames inactive. (In 2001, shipments were being made where the radiation was not effective and live spores were delivered). But she did not respond. Neither did the main university researcher there long funded by DARPA.
On a separate question, Dr. Keim is of the view that the same mutants could arise in any large collection of Ames but says that contrary to his recommendation, the hypothesis was not tested. Why not?
The Infiltration of US Biodefense
http://www.anthraxandalqaeda.com
DXer said
Let’s take an example on the subject of contamination and this issue of “touch DNA”, assuming the panel members explore it. It was urged by WMD CIA analyst Jennifer Smith who had also been a key FBI Special Agent working on Amerithrax science. Dr. Smith from her presentation seemed to be making a very pointed and informed suggestion.
Contamination is an issue that is within the panel’s expressly tasked mission. The scientist that Dr. Ivins says made powderized Ames for DARPA that was rumored to be closest to the mailed anthrax, Dr. Ezzell, accidentally dipped the bottom of the envelope put in bleach in analyzing it for the FBI. How does that bear on the issue of touch DNA?
Ed Lake writes:
“To Err Is Human
Ezzell accidentally placed the bottom edge of the envelope into a groove … filled with bleach. There was no way to correct the mistake, but fortu- …
http://www.anthraxinvestigation.com/Sample.pdf”
Dr. Ezzell worked for the FBI hazardous materials response unit since 1996. As I vaguely recall, by 1998 (see citations in the thread), Dr. Budowie was publishing about touch DNA even though it did not become widely known until a few years ago. This accidental bleaching of the envelope might be fairly understood by the experts as an act of contamination — putting aside the huge concerns relating to contamination when the DNA technology is relying on 15 human cells or fewer.
If the documents are withheld without regard to the particular application of FOIA exemptions, we have no way of knowing whether the FBI is producing what needs to be produced for a meaningless check on its work. The NAS would be out of compliance with the governing legislation notwithstanding the commitment and good faith of its expert panel. The ones responsible for the decision perhaps are the staff paid a million dollars or whatever who agreed to the FBI request that they withhold the documents without an applicable justification under FOIA.
If the NAS is not prepared to do a particularized and thorough job complying with the FOIA obligation, that does not bode well for the review on the merits. It’s one thing to say the right things in a press release, and quite another to press for documents from someone strongly motivated not to give them to you.
DXer said
Dr. Budowie and Dr. Smith co-authored on Low Copy Number Human DNA.
LOW COPY NUMBER – CONSIDERATION AND CAUTION
Bruce Budowle, Deborah L. Hobson, Jill B. Smerick, and Jenifer A.L. Smith
Laboratory Division, FBI, Washington, DC
ACKNOWLEDGMENT
This is publication number 01-26 of the Laboratory Division of the Federal Bureau of Investigation. Names
of commercial manufacturers are provided for identification only, and inclusion does not imply
endorsement by the Federal Bureau of Investigation.
REFERENCES
10. Budowle B, Smith JA, Moretti T, DiZinno J (2000) DNA Typing Protocols: Molecular Biology and
Forensic Analysis, BioTechniques Books, BioForensic Sciences Series, Eaton Publishing, Natick, MA.
DXer said
Dr. Schultzer, Budowie and Atlas write on the importance of preserving evidence in “Biocrimes, Microbial Forensics, and the Physician.”
Steven E. Schutzer*, Bruce Budowle, Ronald M. Atlas
***
The Physician’s Role in Collecting Evidence Top
Although finding the perpetrator of a crime is a law enforcement function, the actions of attending physicians can help with microbial forensics—the scientific discipline dedicated to analyzing evidence from a biocrime or an act of bioterrorism, and that seeks to authenticate a piece of the puzzle for attribution. Implicit in the term attribution is the identification of the responsible party or the exclusion of the innocent [13].
Many physicians are familiar with the treatment of sexual assault victims, and the need to collect and preserve evidence when the patient consents. Sexual assault analysis kits have been validated to preserve semen, saliva, hair, blood, and skin. They also provide instructions on how to maintain a chain of custody to ensure that there has been no tampering with the evidence. Chain of custody is the process that assures integrity of the evidence, and ensures that there is documentation of the time the evidence is handled and each individual handling or examining the evidence. Courses exist in crime scene investigation, evidence collection, and chain of custody of the evidence in suspected sexual assault cases, and there are often well-trained support personnel who can assist patients and physicians. Such evidence collection guidance and support structures are not well-developed for biocrimes.
***
Law enforcement authorities can assist with such documentation processes.
Microbial Forensics
***
A major thrust of microbial forensics will, therefore, be the analysis of nucleic acids that can relate the genome of the pathogen to specific sources. This analysis is analogous to human DNA forensic analysis, which is being widely used to prosecute criminals and to exonerate the innocent [19]. But there are important differences between the analyses of microbial genomes and those used in human DNA forensics. Because of the sheer number of potential pathogens that could be employed as a weapon, identifying genetic markers for microbes is a more daunting task than identifying human DNA.
***
If physicians suspect a biocrime, they should take steps to ensure the preservation of the diagnostic samples so that they are not prematurely destroyed. Physicians may also advise the patient to preserve additional material that may prove useful for a criminal investigation. Just as in sexual assaults, in a suspected biocrime, the patient’s personal articles may carry traditional forensic evidence that is of equal value to the information revealed by the microbe itself. Unlike sexual assault evidence, in a suspected biocrime, procedures used to preserve one particular microbe may be deleterious for other microbes and for physical evidence (such as fingerprints, culture media, isotopes, hair, and environmental material). In addition, procedures useful for preserving one microbe may be insufficient to preserve another that may be unknown at the time.
citing, inter alia,
• Breeze R, Budowie B, Schutzer S (2005) Microbial Forensics. San Diego: Academic Press. 448 p.
DXer said
Low-level Human DNA Evidence
Jennifer Smith pointed out to the NAS panel the current debate over techniques for getting the most information out of low-level human DNA. She told the NAS panel in late July 2009 that if the FBI explored the issue (hint: they did), it would be interesting for the panel members to see it. FBI agents, in fact, did swab Bruce Ivins for human DNA.
Separately, she explained that she expected that the FBI would be giving the panel members Brady-material, evidence that might be exculpatory.
Separately, she said that the FBI did not share all the information that the CIA needed to make an assessment of the evidence in Amerithrax.
DXer said
Of course, there is no way to judge whether the FBI is complying Brady-material relating to “touch DNA” because of the NAS’ failure to comply with the Government in the Sunshine Act (FOIA) as required by FACA.
DXer said
Re: Explosion of human DNA articles by Dr. Budowie, including some submitted while he was still at the FBI working on Amerithrax.
In addition to Dr. Beecher’s article Ike mentions,
Beecher, Douglas J., “Forensic Application of Microbiological Culture Analysis To Identify Mail Intentionally Contaminated with Bacillus anthracis Spores,” Applied and Environmental Microbiology, Aug. 2006, p. 5304-5310
FBI general contributions to microbial forensics include a number of sophisticated publications by Dr. Budowie. Dr. Budowie spoke before the panel.
Everyone on the panel, I would think, would benefit from a copy of the extensive treatise Dr. Budowie edited in 2007 or so titled MICROBIAL FORENSICS. (One panel member co-authored with Dr. Keim about the Amerithrax genetics).
Although further below I also gather up some articles that are relevant to Amerithrax, I wanted to note separately an explosion of article by Dr. Budowie on human DNA in the last few months. I cite only some.
Do they have what former FBI agent (and later lead CIA WMD analyst) Jennifer Smith referred to as low level DNA? What an intriguing possibility!
Are the 10 or so additional studies being published right under our noses without us realizing it?
First, here are Dr. B’s articles about Microbial Forensics (and I think I’m missing a recent one in Coat Med J.):
Budowle B, Harmon R., “HIV legal precedent useful for microbial forensics,” Croat Med J. 46(4):514-21 (Aug 2005).
Budowle, B., M. D. Johnson, C. M. Fraser, T. J. Leighton, R. S. Murch, and R. Chakraborty. 2005. “Genetic analysis and attribution of microbial forensics evidence,” Crit. Rev. Microbiol. 31:233-254.
Budowle B, Murch R, Chakraborty R., “Microbial forensics: the next forensic challenge,” Int J Legal Med. 119(6):317-30 (Nov 2005).
Budowle, B., S. E. Schutzer, M. S. Ascher, R. M. Atlas, J. P. Burans, R. Chakraborty, J. J. Dunn, C. M. Fraser, D. R. Franz, T. J. Leighton, S. A. Morse, R. S. Murch, J. Ravel, D. L. Rock, T. R. Slezak, S. P. Velsko, A. C. Walsh, and R. A. Walters. “Toward a system of microbial forensics: from sample collection to interpretation of evidence,” Appl. Environ. Microbiol. 71:2209-2213 (2005).
Budowle, B., S. E. Schutzer, A. Einseln, L. C. Kelley, A. C. Walsh, J. A. L. Smith, B. L. Marrone, J. Robertson, and J. Campos. Building microbial forensics as a response to bioterrorism. Science 301:1852-1853 (2003).
But here are are some on human DNA in just the past few months:
Biotechniques. 2008 Apr;44(5):603-8, 610.
Forensically relevant SNP classes.
Budowle B, van Daal A.
FBI Laboratory, Quantico, VA, USA. Bruce.Budowle@ic.fbi.gov
Forensic samples that contain too little template DNA or are too degraded require alternate genetic marker analyses or approaches to what is currently used for routine casework. Single nucleotide polymorphisms (SNPs) offer promise to support forensic DNA analyses because of an abundance of potential markers, amenability to automation, and potential reduction in required fragment length to only 60-80 bp. The SNP markers will serve an important role in analyzing challenging forensic samples, such as those that are very degraded, for augmenting the power of kinship analyses and family reconstructions for missing persons and unidentified human remains, as well as for providing investigative lead value in some cases without a suspect (and no genetic profile match in CODIS). The SNPs for forensic analyses can be divided into four categories: identity-testing SNPs; lineage informative SNPs; ancestry informative SNPs; and phenotype informative SNPs. In addition to discussing the applications of these different types of SNPs, this article provides some discussion on privacy issues so that society and policymakers can be more informed.
PMID: 18474034 [PubMed – indexed for MEDLINE]
See also , for example,
Croat Med J. 2009 Jun;50(3):207-17.
Validity of low copy number typing and applications to forensic science.
Budowle B, Eisenberg AJ, van Daal A.
Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Ft Worth, TX 76107, USA. eisenber@unt.hsc.edu
Low copy number (LCN) typing, particularly for current short tandem repeat (STR) typing, refers to the analysis of any sample that contains less than 200 pg of template DNA. Generally, LCN typing simply can be defined as the analysis of any DNA sample where the results are below the stochastic threshold for reliable interpretation. There are a number of methodologies to increase sensitivity of detection to enable LCN typing. These approaches encompass modifications during the polymerase chain reaction (PCR) and/or post-PCR manipulations. Regardless of the manipulations, when processing a small number of starting templates during the PCR exaggerated stochastic sampling effects will occur. The result is that several phenomena can occur: a substantial imbalance of 2 alleles at a given heterozygous locus, allelic dropout, or increased stutter. With increased sensitivity of detection there is a concomitant increased risk of contamination. Recently, a commission reviewed LCN typing and found it to be “robust” and “fit for purpose.” Because LCN analysis by its nature is not reproducible, it cannot be considered as robust as that associated with conventional DNA typing. The findings of the commission seem inconsistent with the nature of LCN typing. While LCN typing is appropriate for identification of missing persons and human remains and for developing investigative leads, caution should be taken with its use in other endeavors until developments are made that overcome the vagaries of LCN typing. A more in-depth evaluation by the greater scientific community is warranted. The issues to consider include: training and education, evidence handling and collection procedures, the application or purpose for which the LCN result will be used, the reliability of current LCN methods, replicate analyses, interpretation and uncertainty, report writing, validation requirements, and alternate methodologies for better performance.
Anal Chem. 2009 Aug 17. [Epub ahead of print]
Mixture interpretation: defining the relevant features for guidelines for the assessment of mixed DNA profiles in forensic casework.
Budowle B, Onorato AJ, Callaghan TF, Della Manna A, Gross AM, Guerrieri RA, Luttman JC, McClure DL.
J Forensic Sci. 2009 Jul;54(4):810-21. Epub 2009 Apr 2.
PMID: 19368620 [PubMed – in process]
Related Articles
10:
Local population structure in Arabian Peninsula revealed by Y-STR diversity.
Alshamali F, Pereira L, Budowle B, Poloni ES, Currat M.
Hum Hered. 2009;68(1):45-54. Epub 2009 Apr 1.
PMID: 19339785 [PubMed – indexed for MEDLINE]
Related Articles
11:
Validation of SRY marker for forensic casework analysis.
Kastelic V, Budowle B, Drobnic K.
J Forensic Sci. 2009 May;54(3):551-5. Epub 2009 Mar 16.
PMID: 19302388 [PubMed – indexed for MEDLINE]
Also, as just one more example,
J Forensic Sci. 2009 Jul;54(4):810-21. Epub 2009 Apr 2.
Mixture interpretation: defining the relevant features for guidelines for the assessment of mixed DNA profiles in forensic casework.
Budowle B, Onorato AJ, Callaghan TF, Della Manna A, Gross AM, Guerrieri RA, Luttman JC, McClure DL.
FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22134, USA. bbudowle@ic.fbi.gov
As a start, other peer reviewed publications on microbial forensics I would note as relevant include:
Edgewood Chemical Biological Center, “Production of Bacillus Spores as a Simulant for Biological Warfare Agents,” Final rept. Sep 2002-Sep 2003
Investigation of Bioterrorism-Related Anthrax, United States, 2001: Epidemiologic Findings,” Emerging Infectious Diseases, October 2002
“First Case of Bioterrorism-Related Inhalational Anthrax in the United States,” Palm Beach County, Florida, 2001, Emerging Infectious Diseases, October 2002
“Inhalational Anthrax Outbreak among Postal Workers, Washington, D.C., 2001,” Emerging Infectious Diseases, October 2002
“Bacillus anthracis Aerosolization Associated with a Contaminated Mail Sorting Machine,” Emerging Infectious Diseases, October 2002
“Epidemiologic Investigations of Bioterrorism-Related Anthrax, New Jersey, 2001,” Emerging Infectious Diseases, October 2002
“Surveillance for Anthrax Cases Associated with Contaminated Letters, New Jersey, Delaware, and Pennsylvania, 2001,” Emerging Infectious Diseases, October 2002
Beecher, Douglas J., “Forensic Application of Microbiological Culture Analysis To Identify Mail Intentionally Contaminated with Bacillus anthracis Spores,” Applied and Environmental Microbiology, Aug. 2006, p. 5304-5310
Bowen, G. J., J. R. Ehleringer, L. Chesson, E. Stange, and C. E. Cerling.. “Stable isotope ratios of tap water in the contiguous USA,” Water Resour. Res. 43 (2007)
Budowle B, Harmon R., “HIV legal precedent useful for microbial forensics,” Croat Med J. 46(4):514-21 (Aug 2005).
Budowle, B., M. D. Johnson, C. M. Fraser, T. J. Leighton, R. S. Murch, and R. Chakraborty. 2005. “Genetic analysis and attribution of microbial forensics evidence,” Crit. Rev. Microbiol. 31:233-254.
Budowle B, Murch R, Chakraborty R., “Microbial forensics: the next forensic challenge,” Int J Legal Med. 119(6):317-30 (Nov 2005).
Budowle, B., S. E. Schutzer, M. S. Ascher, R. M. Atlas, J. P. Burans, R. Chakraborty, J. J. Dunn, C. M. Fraser, D. R. Franz, T. J. Leighton, S. A. Morse, R. S. Murch, J. Ravel, D. L. Rock, T. R. Slezak, S. P. Velsko, A. C. Walsh, and R. A. Walters. “Toward a system of microbial forensics: from sample collection to interpretation of evidence,” Appl. Environ. Microbiol. 71:2209-2213 (2005).
Budowle, B., S. E. Schutzer, A. Einseln, L. C. Kelley, A. C. Walsh, J. A. L. Smith, B. L. Marrone, J. Robertson, and J. Campos. Building microbial forensics as a response to bioterrorism. Science 301:1852-1853 (2003).
Bush, Larry M. et al., “Index Case of Fatal Inhalational Anthrax Due to Bioterrorism in the United States,” New England Journal of Medicine, 345:1607-1610, November 29, 2001
Cliff, J. B., K. H. Jarman, N. B. Valentine, S. L. Golledge, D. J. Gaspar, D. S. Wunschel, and K. L. Wahl, “Differentiation of spores of Bacillus subtilis grown in different media by elemental characterization using time-of-flight secondary ion mass spectrometry,” Appl. Environ. Microbiol. 71:6524-6530 (2005)
Horita, J., and A. A. Vass, “Stable-isotope fingerprints of biological agents as forensic tools,” J. Forensic Sci. 48:122-126 (2003).
Keim et al., “Microbial forensics: DNA fingerprinting of Bacillus anthracis (anthrax),” Analytical Chemistry, 2008 Jul; 80 (13): 4791-9
Kiel, at al, Geographical Distribution of Genotypic and Phenotypic Markers Among Bacillus anthracis Isolates and Related Species by Historical Movement and Horizontal Transfer, Folia Microbiol. 53 (6), 472–478 (2008)
Kreuzer-Martin, H. W., L. A. Chesson, M. J. Lott, J. V. Dorigan, and J. R. Ehleringer, “Stable isotope ratios as a tool in microbial forensics. 2. Isotopic variation among different growth media as a tool for sourcing origins of bacterial cells or spores,” J. Forensic Sci. 49:961-967 (2004).
Kreuzer-Martin, H. W., L. A. Chesson, M. J. Lott, and J. R. Ehleringer, “Stable isotope ratios as a tool in microbial forensics. 3. Effect of culturing on agar-containing growth media,” J. Forensic Sci. 50:1372-1379 (2005).
Kreuzer-Martin, H. W., M. J. Lott, J. Dorigan, and J. R. Ehleringer, “Microbe forensics: oxygen and hydrogen stable isotope ratios in Bacillus subtilis cells and spores,” Proc. Natl. Acad. Sci. USA 100:815-819 (2003).
Kreuzer-Martin, H. W. et al., “Microbe forensics: Oxygen and hydrogen stable isotope ratios in Bacillus subtilis cells and spores,” Proceedings of the National Academy of Sciences,” February 4, 2003
J.B. Petro, and D.A Relman, “Understanding Threats to Scientific Openness, Science, December 12, 2003
Shoham, Dany & Jacobsen, Stuart “Technical Intelligence in Retrospect: 2001 Anthrax Letters Powder,” International Journal for Intelligence and Counterintelligence, October 2006
Whiteaker, J., C. Fenselau, D. Fetteroff, D. Steele, and D. Wilson. 2004. Quantitative determination of heme for forensic characterization of Bacillus spores using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal. Chem. 76:2836-2841. [PubMed].
Wunschel, D. S., E. A. Hill, J. S. McLean, K. Jarman, Y. A. Gorby, N. Valentine, and K. Wahl. 2005. Effects of varied pH, growth rate and temperature using controlled fermentation and batch culture on matrix assisted laser desorption/ionization whole cell protein fingerprints. J. Microbiol. Methods 62:259-271. [PubMed].
Wunschel, S. C., K. H. Jarman, C. E. Petersen, N. B. Valentine, K. L. Wahl, D. Shauki, J. Jackman, S. P. Nelson, and E. White. 2005. Bacterial analysis by MALDI-TOF MS: an interlaboratory comparison. J. Am. Soc. Mass Spectrom. 16:456-462. [PubMed].
DXer said
Here is another example of a recent article by Dr. Budowie on low level human DNA. Consider whether we are not seeing the publication of the long-awaited articles being relied upon in reaching the FBI’s solution in Amerithrax. In considering the hypothesis, someone could study the dates of submission.
J Forensic Sci. 2009 Jul;54(4):798-809. Epub 2009 May 26. Links
A perspective on errors, bias, and interpretation in the forensic sciences and direction for continuing advancement.
Budowle B, Bottrell MC, Bunch SG, Fram R, Harrison D, Meagher S, Oien CT, Peterson PE, Seiger DP, Smith MB, Smrz MA, Soltis GL, Stacey RB.
FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA. bbudowle@ic.fbi.gov
The forensic sciences are under review more so than ever before. Such review is necessary and healthy and should be a continuous process. It identifies areas for improvement in quality practices and services. The issues surrounding error, i.e., measurement error, human error, contextual bias, and confirmatory bias, and interpretation are discussed. Infrastructure is already in place to support reliability. However, more definition and clarity of terms and interpretation would facilitate communication and understanding. Material improvement across the disciplines should be sought through national programs in education and training, focused on science, the scientific method, statistics, and ethics. To provide direction for advancing the forensic sciences a list of recommendations ranging from further documentation to new research and validation to education and to accreditation is provided for consideration. The list is a starting point for discussion that could foster further thought and input in developing an overarching strategic plan for enhancing the forensic sciences.
DXer said
Here are some more recent articles by Dr. Budowie on the subject.
But let’s go back to a question raised by one of the Senators. Why did the FBI swab Bruce Ivins for DNA so late in the process? (In July, I believe). Was it as a further check on DNA they already had obtained? (From television and news reports, we have seen that clever investigators are commonly able to obtain DNA surreptitiously; was this a second sampling or had they really not yet obtained his DNA?)
Leg Med (Tokyo). 2009 May;11(3):159-61. Epub 2009 Mar 13.
Population data for 15 STR loci (Identifiler((R)) kit) in a Filipino population.
Smith BG, Lee B, Budowle B, Allen RW.
Kern County District Attorney, Forensic Science Division, 1300 18th street fourth floor, Bakersfield, CA 93301, USA.
Allele frequencies for fifteen STR loci, D3S1358, TH01, D21S11, D18S51, D2S1338, D5S818, D13S317, D7S820, D16S539, CSF1PO, D19S433, vWA, D8S1179, TPOX and FGA, were investigated in a Filipino ethnic group resident in the United States and in the Philippines. Statistical evaluation of the data collected indicated the population to be in Hardy-Weinberg equilibrium and therefore acceptable for calculations in forensic and family relatedness casework.
J Forensic Sci. 2009 Sep;54(5):1016-21. Epub 2009 Jul 15.
Texas population substructure and its impact on estimating the rarity of Y STR haplotypes from DNA evidence*.
Budowle B, Ge J, Aranda XG, Planz JV, Eisenberg AJ, Chakraborty R.
Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center at Ft Worth, TX 76107, USA.
Three sampled populations of unrelated males–African American, Caucasian, and Hispanic, all from Texas-were typed for 16 Y short tandem repeat (STR) markers using the AmpFlSTR Yfiler kit. These samples also were typed previously for the 13 core CODIS autosomal STR loci. Most of the 16 marker haplotypes (2478 out of 2551 distinct haplotypes) were observed only once in the data sets. Haplotype diversities were 99.88%, 99.89%, and 99.87% for the African American, Caucasian, and Hispanic sample populations, respectively. F(ST) values were very small when a haplotype comprised 10-16 markers. This suggests that inclusion of substructure correction is not required. However, haplotypes consisting of fewer loci may require the inclusion of F(ST) corrections. The testing of independence of autosomal and Y STRs supports the proposition that the frequencies of autosomal and Y STR profiles can be combined using the product rule.
PMID: 19627418 [PubMed – in process]
Forensic Sci Int Genet. 2009 Jun;3(3):179-84. Epub 2009 Feb 14.
Mutation rates at Y chromosome short tandem repeats in Texas populations.
Ge J, Budowle B, Aranda XG, Planz JV, Eisenberg AJ, Chakraborty R.
Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45221, USA.
Father-son pairs from three populations (African American, Caucasian, and Hispanic) of Texas were typed for the 17 Y STR markers DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS456, DYS458, DYS635, DYS448, and Y GATA H4 using the AmpFlSTR YfilerTM kit. With 49,578 allele transfers, 102 mutations were detected. One three-step and four two-step mutations were found, and all others (95.1%) were one-step mutations. The number of gains (48) and losses (54) of repeats were nearly similar. The average mutation rate in the total population is 2.1 x 10(-3) per locus (95% CI (1.7-2.5)x10(-3)). African Americans showed a higher mutation rate (3.0 x 10(-3); 95% CI (2.4-4.0)x10(-3)) than the Caucasians (1.7 x 10(-3); 95% CI (1.1-2.5)x10(-3)) and Hispanics (1.5 x 10(-3); 95% CI (1.0-2.2)x10(-3)), but grouped by repeat-lengths, such differences were not significant. Mutation is correlated with relative length of alleles, i.e., longer alleles are more likely to mutate compared with the shorter ones at the same locus. Mutation rates are also correlated with the absolute number of repeats, namely, alleles with higher number of repeats are more likely to mutate than the shorter ones (p-value=0.030). Finally, occurrences of none, one, and two mutations over the father-son transmission of alleles were consistent with the assumption of independence of mutation rates across loci.
The effects of Asian population substructure on Y STR forensic analyses.
Budowle B, Ge J, Low J, Lai C, Yee WH, Law G, Tan WF, Chang YM, Perumal R, Keat PY, Mizuno N, Kasai K, Sekiguchi K, Chakraborty R.
Leg Med (Tokyo). 2009 Mar;11(2):64-9. Epub 2008 Nov 26.
PMID: 19038565 [PubMed – in process]
Post-injection hybridization of complementary DNA strands on capillary electrophoresis platforms: a novel solution for dsDNA artifacts.
McLaren RS, Ensenberger MG, Budowle B, Rabbach D, Fulmer PM, Sprecher CJ, Bessetti J, Sundquist TM, Storts DR.
Forensic Sci Int Genet. 2008 Sep;2(4):257-73. Epub 2008 May 5.
DXer said
I believe the FBI swabbed Dr. Bruce Ivins for human DNA on July 22, about a week before he committed suicide.
http://www.nytimes.com/2008/09/07/world/americas/07iht-anthrax.1.15943837.html
U.S. lawmakers want details of anthrax investigation
By Scott Shane and Eric Lichtblau
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Bureau officials say they are certain that they have solved the nation’s first major bioterrorism attack, in which anthrax-laced letters killed five people, after a long and troubled investigation that by several measures was the most complex in the bureau’s history.
But in interviews last week, two dozen bioterrorism specialists, veteran investigators and members of Congress expressed doubts about the bureau’s conclusions. Some called for an independent review of the case to reassure the public and assess policies on the handling of dangerous pathogens like anthrax.
Meanwhile, new details of the investigation, revealed in recent interviews, raised questions about when the bureau focused on Ivins as the likely perpetrator and how solid its evidence was.
In April 2007, after the mailed anthrax was genetically linked to Ivins’s laboratory and after he was questioned about late-night work in the laboratory before the letters were mailed, prosecutors sent Ivins a formal letter saying he was “not a target” of the investigation. And only a week before Ivins died did agents first take a mouth swab to collect a DNA sample, officials said.
Justice Department officials, who said in early August that the investigation was likely to be closed formally within days or weeks, now say it is likely to remain open for three to six more months.
In the meantime, agents are continuing to conduct interviews with acquaintances of Ivins and are examining computers he used, seeking information that could strengthen the case.
But bureau and Justice Department officials insist that the delay, which they say is necessary to tie up loose ends in a complex investigation, reflects no doubts about their ultimate verdict. “People feel just as strongly as they did a month ago that this was the guy,” said a department official who spoke on the condition of anonymity.
In interviews, FBI officials said they knew their findings would face intense scrutiny after the bureau admitted that for years it had pursued the wrong man, Steven Hatfill, whom the government paid $4.6 million in June to settle a lawsuit that accused the government of leaking information about him to the news media.
Officials also acknowledged that they did not have a single, definitive piece of evidence indisputably proving that Ivins mailed the letters – no confession, no trace of his DNA on the letters, no security camera recording the mailings in Princeton, New Jersey.
But they said the case consisted of a powerfully persuasive accumulation of incriminating details. Dr. Vahid Majidi, head of the FBI’s weapons of mass destruction directorate, said the accumulation of evidence against Ivins was overwhelming: his oversight of the anthrax supply, his night hours, his mental problems and his habit of driving to far-off locations at night to mail anonymous packages.
“Who had the means, motive and opportunity?” said John Miller, assistant FBI director for public affairs. “Some potential suspects may have had one, some had two, but on the cumulative scale, Dr. Ivins had many more of these elements than any other potential suspect.”
DXer said
Dr. Budowie’s “Extracting evidence from forensic DNA analyses: future molecular biology directions” is one of the recent articles addressing touch DNA or Low Copy Number (LCN) . It is more accessible than others to non-scientists and its full-text is online.
For his longstanding expertise on the subject, see
1.) Budowle, B., and A.J. Eisenberg Rimoin, D.L., J.M., R.E. and B.R.. 2007. Forensic Genetics Emery and Rimoin’s Principles and Practice of Medical Genetics5th ed, Elsevier, Philadelphia: 501-517
2.) Budowle, B., J.V. Planz, R. Campbell, and A.J. Eisenberg Patrinos, G. and W.. 2005. Molecular diagnostic applications in forensic science Molecular Diagnostics, Elsevier, Amsterdam:267-280
3.) Budowle, B., and A. van Daal. 2008. Forensically relevant SNP classes. BioTechniques 44:603-610
4.) Budowle, B., H.A. Deadman, R.S. Murch, and F.S. Baechtel. 1988. An introduction to the methods of DNA analysis under investigation in the FBI Laboratory. Crime Lab. Dig. 15:8-21
5.) Scientific Working Group on DNA Analysis Methods (SWGDAM) 2004. Revised Validation Guidelines, Forensic Sci. Commun.
6.) Budowle, B., and F.S. Baechtel. 1990. Modifications to improve the effectiveness of restriction fragment length polymorphism typing. Appl. Theor. Electrophor. 1:181-187
7.) Budowle, B., J.A. Smith, T. Moretti, and J. DiZinno. 2000.DNA Typing Protocols: Molecular Biology and Forensic Analysis, Eaton Publishing Company/BioTechniques Books, Natick
DXer said
Who collected the “touch DNA” from the letters for the FBI?
http://www.scientificamerican.com/article.cfm?id=experts-touch-dna-jonbenet-ramsey
August 8, 2008
What is touch DNA?
The technology that cleared JonBenet Ramsey’s family of her murder can detect the slightest bit of genetic material. Husband and wife forensic experts Max and Lucy Houck explain:
So what’s touch DNA?
The touch DNA method—named for the fact that it analyzes skin cells left behind when assailants touch victims, weapons or something else at a crime scene—has been around for the last five years. In fact, the prosecutor in the Ramsey case, Boulder County District Attorney Mary Lacy, learned about touch DNA when she attended a course here at the West Virginia University Forensic Science Initiative in the summer of 2007.
The technique has dramatically increased the number of items of evidence that can be used for DNA detection. In the 1980s, in order to perform DNA analysis on a crime scene or victim, forensic investigators needed a blood or semen stain about the size of a quarter. The sample size fell in the 1990s to the size of a dime and then became: “If you can see it, you can analyze it.”
Touch DNA doesn’t require you to see anything, or any blood or semen at all. It only requires seven or eight cells from the outermost layer of our skin.
Here’s how it works: Investigators recover cells from the scene, then use a process called polymerase chain reaction (PCR) to make lots of copies of the genes. Next, scientists mix in fluorescent compounds that attach themselves to 13 specific locations on the DNA and give a highly specific genetic portrait of that person. The whole process takes a few days, and forensic labs are often backed up analyzing data from other cases.
These 13 locations were carefully chosen because they are highly variable between people and do not give away any specific information, such as race, gender, personal health or genetic disease. The reason: authorities don’t want personal health information being used for law-enforcement purposes, such as interrogations. The chance of DNA profiles from two different people having the same genetic signature is vanishingly small.
The trick to finding these cells: context. If clothing is removed from the victim, as it was in the Ramsey case, a forensic specialist could try to guess where it might have been handled—perhaps the waistband of a pair of pants—and swab those areas with a Q-tip or a blade. But in cases like the JonBenet Ramsey murder, which has tripped up authorities for over a decade, it can provide information that leads to a killer—or at least exonerates the innocent.
DXer said
USA TODAY
http://www.usatoday.com/tech/science/2008-09-22-touchdna_N.htm
‘Touch’ DNA offers hope in cold investigations
Kevin Johnson, USA TODAY
Evidence supported the “likelihood” that JonBenet’s attacker removed her clothing and then redressed her, the statement says. Analysts scraped the waist areas of long johns JonBenet had on when her body was discovered in the basement of her home Dec. 26, 1996. Williamson says they were able to retrieve enough cells to produce an unidentified male profile.
The findings did not resolve the murder, but they excluded the 6-year-old’s parents and brother. Lacy cleared the family and apologized for the suspicions that made their lives “an ongoing living hell.”
Davis worries the Ramsey case will spur “unrealistic” expectations about touch DNA. “We have to be cool-headed, scientific and look at its limitations,” he says.
Yet Cordle and others hope for similar results in cases that have dogged them for years. “Word is spreading, and lots of agencies are responding,” Cordle says.
BODE
http://www.bodetech.com/technologies/touch-dna/touch-dna-overview
Touch DNA – Overview
• Touch DNA – Overview
Touch DNA Evidence – Overview
As forensic DNA technology has become a common tool in criminal investigations, scientists have attempted to obtain DNA evidence from what were once considered unlikely sources. “Touch DNA” refers to the DNA that is left behind from skin cells when a person touches or comes into contact with an item.
Bode’s recent success of using a Touch DNA collection method to obtain a DNA profile from the long johns worn by JonBenet Ramsey has created an increased interest in better understanding Touch DNA methods.
What is Touch DNA?
• Touch DNA is not Low Copy Number (LCN) DNA. LCN DNA profiling allows a very small amount of DNA to be analyzed, from as little as 5 to 20 cells. Because of the small amount of starting DNA in LCN samples, many more cycles of amplification are necessary.
• Touch DNA samples at Bode are processed/amplified exactly the same way as blood, semen, saliva etc, and are therefore admissible in court.
Humans shed tens of thousands of skin cells each day, and these cells are transferred to every surface our skin contacts. When a crime is committed, if the perpetrator deposits a sufficient number of skin cells on an item at the scene, and that item is collected as possible evidence, touch DNA analysis may be able to link the perpetrator to the crime scene. Touch DNA has been successfully sampled from countless items including gun grips, steering wheels, eating utensils, and luggage handles, just to name a few.
However, since Touch DNA is usually deposited in smaller amounts than the DNA found in bloodstains or other body fluids, it is more difficult to obtain DNA profiles from touch DNA samples. The key to obtaining successful Touch DNA results depends on recognizing items which may be suitable for Touch DNA analysis and using the sampling technique that will recover the highest number of skin cells.
Many labs test for Touch DNA using either the swabbing or cutting method. In the “swabbing method”, the surface of the item is rubbed with a cotton swab to collect possible cells. This method is preferred for hard items such as glass or plastic. The “cutting method” may be used for soft items, such as clothing, in which fabric from areas of interest is cut to collect possible cells. These two approaches can be successful on many items of evidence and both are used by Bode Technology; however they both have the limitation of placing unnecessary substrate (the cotton swab itself or the fabric cuttings) into the small DNA processing tube. There is a limited amount of substrate that can be placed in a tube, and the substrate itself may “trap” some cells during processing, which would decrease the likelihood of obtaining results.
In addition to the commonly used swabbing and cutting methods, Bode has recently started using the “Scraping” and “Tape Lift” methods, in which the surface of soft items (such as clothing) are either scraped with a blade, or sampled with a small piece of tape, to collect possible cells. Due to the lack of unnecessary substrate generated by these methods (scraping produces a small “pile” of fiber, cells, and debris that can easily be placed in the DNA processing tube), a larger surface area can be sampled. An increase in surface area increases the number of possible cells recovered; therefore, increasing the chances of obtaining a DNA profile.
The scraping/tape lift methods are ideal in situations where the scientist can locate areas on the item which are most likely to contain the perpetrator’s skin cells. If clothing were left at the crime scene by the perpetrator, pressure points on the clothing such as the interior neck of a shirt or the band inside a hat, are excellent candidates for these sampling methods. In addition, in a sexual assault case in which the victim’s clothing had been removed by the perpetrator, areas such as the waistband may contain sufficient cells belonging to the perpetrator to produce a profile.
Through improvements in sampling methods corresponding to increasingly sensitive DNA testing methods, and through continual education of the criminal justice community regarding the testing possibilities, Touch DNA is enabling forensic scientists to provide information in cases which were once unsolvable.
BBC News
http://news.bbc.co.uk/2/hi/uk_news/7341251.stm
DNA technique ‘fit for purpose’
The technique has been used in high-profile cases around the world
A controversial method of obtaining DNA profiles is “fit for purpose” in court, an independent review has concluded.
The government-commissioned study said low copy number DNA analysis, which can establish a profile from just a few cells, was “scientifically robust”.
But it recommended improvements in how police forensic teams collect the cells to ensure there is no contamination.
Use of the method was briefly suspended last year after the Omagh bombing trial judge questioned its credibility.
Professor Brian Caddy’s report concluded the technique was fundamentally sound, but not being used as effectively as possible.
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LOW COPY NUMBER DNA TESTING
LCN DNA evidence has been used by the Forensic Science Service since 1999
It enables DNA profiles to be produced from minute amounts – often invisible to the naked eye
The tiny particles used vastly increase the potential for contamination
It recommended an advisory panel guide the courts on how to interpret such low template DNA evidence and said any profile obtained using the technique should be presented to a jury in a criminal trial with caveats.
Professor Caddy said: “I am satisfied low template DNA is fit for purpose within the criminal justice system.
“I found that the technique, as developed by all the forensic suppliers, is scientifically robust and appropriate for use in police investigations.”
Failure rates
He added: “The drive is towards the setting of standards of recovering DNA from crime scenes, and having set those standards, making sure they are properly implemented.”
Andrew Rennison, the Forensic Science Regulator, said: “I’m satisfied the science is safe and fit for purpose, but there is work to be done around collection and interpretation.”
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Case by case
Forensic expert Professor Allan Jamieson, who questioned the validity of LCN DNA when he gave evidence for the defence in the Omagh bomb trial, said its use should be carefully considered.
“The real issue is: do we know what it means when you see a profile?” said Prof Jamieson, director of The Forensic Institute in Glasgow.
“For example, when you mix two people’s DNA together, it’s like mixing the coins in their pockets together. They end up on the table and you have to say which coin came from which person.
“You simply can’t do that.”
Ike Solem said
This is a scientific review of the forensic evidence, right? Under the FBI’s initial approach, that would be the Amerithrax 2 investigation. FOIA search terms might include the following names:
David Lee Wilson – FBI agent in charge of the “Amerithrax 2” case, the scientific investigation.
James Buran – a Navy expert in anthrax who worked for David Wilson.
Kenneth C. Kohl – an assistant U.S. attorney who was assigned full time to both Amerithrax squads
Michael Kuhlman – Battelle scientist, Vice President and Manager, Aerosol and Process Technologies , National Security Division. He initially claimed that the Daschle anthrax spores were ten to fifty times less potent than the Army estimates indicated.
Douglas Beecher – FBI lab scientist, the only scientist involved in the investigation who was allowed to publish anything (although the FBI would not allow reporters to interview him). He supported the low-tech lone wolf-with-a-lyophilizer theory.
Dr. Cindy Friedman – a CDC epidemiologist who worked for Wilson on Amerithrax 2.
Those names might be useful to include in any FOIA request for documents related to Amerithrax 2.
There is also a long list of contractors and other institutions that handled the Amerithrax 2 material:
TIGR genomics insitute – they did the DNA sequencing.
Ibis Biosciences – they designed the “sophisticated genetic tests” – see this article in the LA Times:
http://articles.latimes.com/2008/aug/04/nation/na-anthrax4
Fort Detrick, MD – where the initial analysis was carried out.
Battelle, West Jefferson, OH – where the FBI sent the samples for a second opinion.
Armed Forced Institute of Pathology – initial spore analysis for physical properties, as opposed to genetic analysis.
Sandia National Labs – secondary spore analysis for physical properties.
There are some others that might be worth looking into – for example, the cleanup crew for the Hart Senate Office building was based down in Oak Ridge, TN (Camp Dresser McKee was one of them). They might have produced technical reports on their cleanup effort.
P.S., for some background info on the microbial genetic forensics issue, the central issue the NAS is looking at:
Bacillus anthracis is part of the larger Bacillus cereus group, which also includes Bacillus thuringiensis, which is an insect predator. (On one hand, BT is used by organic farmers in wet culture form as an insecticide; on the other, the toxin has been engineered into corn plants (Bt-Corn), where it is expressed inside the plant tissues – yuk!).
Bacillus anthracis itself is a new evolutionary species (maybe 10,000 years old) according to the genetic analysis that have been done. It has low genetic diversity and reproduces only by cloning inside animal hosts. It may have arisen along with animal husbandry (in stable muck, maybe). Unlike Bt toxin, anthrax toxin attacks mammalian white blood cells. The toxin allows the bacteria to proliferate without interference, followed by the death of the host from septic shock. The bacteria then turn themselves into sealed spores, drain out into the soil, and wait around (for many years) for the next hoofed mammal to come along and ingest them.
There are many different Bacillus strains, but due to low genetic diversity they were difficult to distinguish from one another using simple methods – but much effort was expended to meet that problem. Thus, there is now a good genetic map of the diversity of Bacillus anthracis, mostly created by people like Paul Keim and Northern Arizona and the folks at Craig Venter’s TIGR institute (I recall when they published their first microbial genome – and now it only costs $1000!).
Once you have a good map of the diversity, it is possible to develop all kinds of tricky rapid tests that can assign a particular isolate or spore sample to a particular strain of anthrax – and that can be used to rapidly screen 1000’s of samples.
That work was also done by a group from Northern Arizona Univ and TIGR, That is here:
http://www.ncbi.nlm.nih.gov/pubmed/17093023 (2007)
A similar paper is here:
http://www.cdc.gov/EID/content/14/4/653.htm
Note that this paper does have a member of Ibis Biosciences on their publication, so it should be safe to assume that Ibis does have access to the latest anthrax-detection technology. However, the only initial claim made was that the team developed a rapid test that can selectively and rapidly identify the Ames strain of anthrax using a PCR (polymerase chain reaction, the basic workhorse of molecular biology these days) method.
“The use of these SNPs coupled with real-time PCR allows specific and sensitive (<100 fg of template DNA) identification of the Ames strain."
For the genetic analysis, the claim is that the flask contained a certain mixture of Ames strains that differed from one another by one base pair out of five million, and that this specific mixture of Ames strains was identical to that found in the spore powder. They found those 1 bp changes 'serendipitously' but that's a separate issue – let's say they found them, using whole-genome sequencing strategies. They then designed a PCR test based on these 1 bp changes. That, to say the least, is a tricky bit of business, and it's not clear if the whole claim was ever peer-reviewed or published.
However, samples from that flask were widely distributed, as the Ames strain is the anthrax vaccine challenge strain, so anyone doing anthrax vaccine development would be using Ames to test vaccinated rabbits and so on. Likewise, any "biological threat assessment" program that was testing anthrax bomblets would also use Ames, in order to compare it to past research.
Thus, the FBI press release stating that the flask had a 'unique fingerprint' much like a human fingerprint was deceptive nonsense. Imagine if you were able to clone yourself a dozen times – all those clones would have your fingerprints as well. This is how anthrax bacteria reproduce, so if the famous flask had been used as seed culture for a dozen different clients, those descendants would have the same fingerprint – and Bacillus anthracis has a notably slow rate of mutation, so those 'unique fingerprints' would all be identical.
That's assuming that the Ivins flask samples themselves were not cross-contaminated with powder from the Daschle-Leahy anthrax letters, and that the genomic sequencing and PCR work was all done correctly. In that case, the entire thing just falls apart. However, even if there was no contamination, the 'fingerprint' business is scientific nonsense.
The other one issue is the nature of the spore aerosol preparation, which is not a topic in genetics so much as in materials science. I'm still not clear as to whether the NAS has agreed to look at this second topic as well as the genetics issue.
DXer said
I spoke to one of the hardworking people overseeing the FOI production from USAMRIID. He says they are processing 1,000 more pages of emails from Dr. Ivins.
Why does the USAMRIID find itself able to comply with FOIA but NAS does not?
DXer said
Lew, start with an easy one. Have him put a copy of the contract in the Public Access File or quote language that the FBI included that prevented its release and the release of those documents not exempt under FOIA. There is nothing in the statute that permits the witholding until after their review is done. To the contrary, it holds the opposite and makes FOIA applicable. If it is produceable at the end of their review, it is produceable now. Thus, his present position constitutes a wilful breach. Why is the Public Relations person giving NAS’ legal opinion rather than the General Counsel? There is nothing wrong to withhold things exempt from FOIA — indeed, such documents should be withheld. But “to prevent meaningful input” by experts like John Kiel and Serge Popov is not one of them. And he himself is saying that they are subject to production at the end of the NAS review (confirming they are not exempt). Charging for the 100 pages also is inconsistent with FOIA.
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(3) in developing the advice or recommendation, the academy complied with–
***
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