Brian T Foley,
Los Alamos National Lab, Los Alamos, NM 87545
Send response to journal:
On Nov 4th, the Perth group wrote:
”... Would Christopher Noble please tell us what evidence “databases of genetic sequences and phylogenetic trees” give us regarding the existence of a virus? We have always thought that to prove the existence of the “HIV” virus, you have to isolate/purify it and then proceed to define its genome and genomic sequences and its proteins. Otherwise, how do you know that the genomic sequences are those of “HIV” and the proteins are coded by these sequences? It is obvious that you cannot start with impure material to define the origin of the genome. If Christopher Noble has another way would he please tell us what it is?
We have repeatedly told you that you thought wrong. No organism has ever been “purified” 100%, no virus has ever been “isolated” by the full criteria which you have designed to be impossible. The study of microorganisms has never involved 100% “purity” and “isolation” from all other living and non-living matter, and it never will. Separation techniques, such as passing a culture supernatant through a series of filters with progressively smaller pore sizes tells us if a pathogen is cell-sized (fungi, protist, cancer cell, etc.) bacteria-sized, or virus-sized. It is not necessary to show that the filtrate is 100% “pure”, only that the pathogen is in the filtrate. After size is determined, other methods such as serology and genomic sequencing can be employed to determine which component found in the infectious filtrate is the pathogen.
It was very clear by 1982, from conventional epidemiology, such as contact tracing of sex partners, needle sharing partners and blood donors, that AIDS was caused by a pathogen that was transmitted only by close contact and not by casual contact. It remains clear today that AIDS is not caused solely by environmental factors or toxins or malnutrition, even if other health problems somewhat similar to AIDS are sometimes caused by such factors (1-23).
As to the
utility of databases; if a freshman high-school student is asked to
write an original work of fiction and his or her essay begins with this
When a DNA sequence is determined from an organism, now that the DNA sequences of tens of thousands of organisms have been depositied in electronic databases, it is usually trivial to determine what type of organism the new DNA sequence is derived from. This is why it took only a few weeks of research, once samples began to be analyzed, to determine that the Sin nombre hantavirus was the cause of an unexplained group of deaths in the southwest USA. It is also the reason why it also took only weeks to determine that a previously undiscovered coronavirus was the cause of SARS. No coronavirus and no hantavirus has ever been 100% “purified” by any procedure similar to what you have described. Not only is your full procedure not necessary, it is impossible. Serology and DNA sequencing alone are often sufficient to get started until complete infectious molecular clones or other materials become available for confirmatory work.
The retroviruses and other viruses have been extensively studied since the early 1900s, long before either DNA sequencing or gradient density ultracentrifugation were discovered. The tools and techniques used to study viruses continue to evolve over time as new techniques are found to be superior to older techniques. Many techniques, such as serology have not been replaced, but only improved upon. The 1984 Nobel Prize in physiology or medicine for the techniques related to the production of monoclonal antibodies is one example of a major improvement.
The Perth group has been repeatedly informed that they are deluded in their beliefs about the techniques and procedures used to study viruses. See for example: Micheal Coon, August 2000 Robin Weiss, 1999
Yet they continue to repeat the same rhetoric, as if repetition will make it more true. The subject of these rapid responses is not the “isolation” of HIV, but the “The politics of AIDS in South Africa: beyond the controversies”. This non peer reviewed exchange cannot and will not have any impact whatsoever on viral research, nor setting ground rules for genomics. This discussion can only have a small impact on uncovering the thinking that has lead the Perth group to attempt to misinform the government of South Africa about what it should do to mitigate the AIDS epidemic in that country. The Perth groups’ use of quotes about influenza and polio viruses, shows that they are not ignorant of all aspects of virology. Instead they are quite clever about selecting tidbits of information in an attempt to support their ideology. It is my opinion that the South African government should have set rules for the discussion of HIV and AIDS by their panel (such as rules stipulationg that the participants tell the truth, the whole truth and nothing but the truth) and established penalties for breaking those rules. Without any such rules and penalties, in the South African panel deiscussion or here in Rapid Responses, there can be no expectation of a credible or fair outcome. This does not mean that such panels and discussions are worthless, but it does place some constraints on their usefulness.
For my own part in this, I feel I must clear up at least one point that I was incorrect or misleading on above:
1) Possible transfusion-associated acquired immune deficiency syndrome
(AIDS) - California.
2) Update on acquired immune deficiency syndrome (AIDS) among patients
with hemophilia A.
3) Screening for risk of acquired immune-deficiency syndrome.
4) Progressive multifocal leukoencephalopathy in a male homosexual with
T-cell immune deficiency.
5) Differentiation of precursor T lymphocytes in man and delineation of
the selective abnormalities in severe combined immune deficiency
6) Acquired immune deficiency syndrome (AIDS): precautions for clinical
and laboratory staffs.
7) The new epidemic. Immune deficiency, opportunistic infections and
8) Attempted immune stimulation in the "gay compromise syndrome".
9) Opportunistic infection in previously healthy women. Initial
manifestations of a community-acquired cellular immunodeficiency.
10) Update on acquired immune deficiency syndrome (AIDS)--United States.
11) Cytomegalovirus retinitis in a young homosexual male with acquired
12) Homosexual practices and immune deficits.
13) Opportunistic infections and immune deficiency in homosexual men.
14) The epidemic of acquired immune dysfunction in homosexual men and its
sequelae--opportunistic infections, Kaposi's sarcoma, and other
malignancies: an update and interpretation.
15) [Immune deficiency and Kaposi's disease in 2 young male homosexuals].
16) Immune deficiency states--evaluation and management.
17) Use of steroid creams as a possible cause of immunosuppression in
18) Opportunistic infections and Kaposi's sarcoma in homosexual men.
19) The immune suppression syndrome in homosexual men. An epidemiological
study from the Cancer Research Institute in Arhus.
20) Disseminated mycobacterial histiocytosis due to M. Fortuitum
associated with helper T-lymphocyte immune deficiency.
21) An outbreak of community-acquired Pneumocystis carinii pneumonia:
initial manifestation of cellular immune dysfunction.
22) Severe acquired immunodeficiency in male homosexuals, manifested by
chronic perianal ulcerative herpes simplex lesions.
23) Pneumocystis carinii pneumonia and mucosal candidiasis in previously
healthy homosexual men: evidence of a new acquired cellular
Competing interests: None declared