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Re: Re: Re: A critical examination of the evidence for the existence of HIV

There is no such thing as defeat or victory in any of this business. We all wish that AIDS did not exist, or that it would go away if we burried our heads in the sand. But the reality is that the AIDS epidemic is claiming thousands of lives per day, and "debating" about it will do no good. There is a lot of real work to be done. Anyone can "armchair quarterback" and claim that the work being done is not good enough. But you should notice that the Perth Group is not attempting to do any work. They are not gathering any data on AIDS, they are not working with viruses. They just read the literature and make up clever misinformation about the conclusions reached in those papers.

Alan also wrote:
"...A major part of that paper is an analysis of the work of the Montagnier and Gallo groups,published in 1983 and 1984, which was taken to establish the existence of a retrovirus which was later named HIV. He will read in the conclusion:

"The phenomena they interpreted as HIV are all non-specific and were known to be so long before the AIDS era.In fact given the origin of the cells and the culture conditions one would (be) expect to find all these phenomena even if the cultures are not infected with a retrovirus."

Can anyone deny (refute) this? Can everyone ignore it? ..."

This is the type of misinformation known as telling a half-truth. It is true that each of the tests applied by Gallo et al. in 1982 through 1984 are not 100% specific. But what the Perth Group is leaving out, is that several less than 100% specific tests, when used together, can indeed lead to a 100% specific result. As an analogy, there are probably 600 people on earth with the name "Alexander Jones"; so that name is not specific. There are probably hundreds of addresses in the world that are "100 Cherry Street"; so that is not specific. There are hundreds of homes in the town with ZIP code 03111; so that is not specific. But there is only one person on earth who is named Alexander Jones who lives at the 100 Cherry Street address in the town with ZIP code 03111. So added together all this "non specific" data becomes very specific.

The world of AIDS research neither began nor ended in April of 1984. There were hundreds of researchers working on AIDS from dozens of angles from 1981 to the present time. The conclusion that AIDS was caused by a microorganism that could pass through a submicron filter, and be transmitted sexually and via blood products but not via casual contact was clearly reached by mid 1982 and has been reconfirmed over and over again since then.

Possible transfusion-associated acquired immune deficiency
syndrome (AIDS) - California.
MMWR Morb Mortal Wkly Rep. 1982 Dec 10;31(48):652-4.
PMID: 6819440

Update on acquired immune deficiency syndrome (AIDS) among
patients with hemophilia A.
MMWR Morb Mortal Wkly Rep. 1982 Dec 10;31(48):644-6, 652.
PMID: 6819439

Gerstoft J, Malchow-Moller A, Bygbjerg I, Dickmeiss E, Enk C,
Halberg P, Haahr S, Jacobsen M, Jensen K, Mejer J, Nielsen JO,
Thomsen HK, Sondergaard J, Lorenzen I.
Severe acquired immunodeficiency in European homosexual men.
Br Med J (Clin Res Ed). 1982 Jul 3;285(6334):17-9.
PMID: 6805793

Pitchenik AE, Fischl MA, Dickinson GM, Becker DM, Fournier AM,
O'Connell MT, Colton RM, Spira TJ.
Opportunistic infections and Kaposi's sarcoma among Haitians:
evidence of a new acquired immunodeficiency state.
Ann Intern Med. 1983 Mar;98(3):277-84.
PMID: 6299151
Schroff RW, Gottlieb MS, Prince HE, Chai LL, Fahey JL.
Immunological studies of homosexual men with immunodeficiency
and Kaposi's sarcoma.
Clin Immunol Immunopathol. 1983 Jun;27(3):300-14.
PMID: 6603314

etc...

Although all lentiviruses look alike by electron microscopy, and thus electron microscopy is of very limitted value in the study of retroviruses, DNA sequence analysis is 100% specific. No two retroviruses are exactly alike, due to the error rate of their reverse transcriptase. So the DNA sequence of each virus is unique. Just as there are only 26 letters in the English alphabet, yet billions of different books can be published, so too can the 4 bases of DNA or RNA be used to create a seemingly infinite variety of different viruses and other organisms. In my analogy above, I showed how just a few letters and numbers can be used to positively identify one individual of the more than 6 billion humans on the planet. So too, can just small regions of any retroviral genome (less than 300 bases in most cases) be used to positively identify any retrovirus.

As both the Perth Group and Chris Noble have pointed out, the tempo and mode of evolution can also provide clues as to where a virus came from. In the example of the 1977, H1N1 influenza A virus, which reappeared in the human population after 27 years of complete absense, the fact that DNA sequences from the 1977 isolates were nearly identical to the last isolates from the 1950s proved that this virus had been in a freezer, and not replicating and thus evolving in some small isolated group of humans, or in an animal reservoir.

Many analyses have shown that the viral transmission can be accurately traced between individuals in a mini-epidemic or local cluster:
Leitner T, Escanilla D, Franzen C, Uhlen M, Albert J.
Accurate reconstruction of a known HIV-1 transmission
history by phylogenetic tree analysis.
Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):10864-9.
PMID: 8855273

Leitner T, Kumar S, Albert J.
Tempo and mode of nucleotide substitutions in gag and
env gene fragments in human immunodeficiency virus type 1
populations with a known transmission history.
J Virol. 1997 Jun;71(6):4761-70.
PMID: 9151870

Machuca R, Jorgensen LB, Theilade P, Nielsen C.
Molecular investigation of transmission of human
immunodeficiency virus type 1 in a criminal case.
Clin Diagn Lab Immunol. 2001 Sep;8(5):884-90.
PMID: 11527797

Blanchard A, Ferris S, Chamaret S, Guetard D, Montagnier L.
Molecular evidence for nosocomial transmission of human
immunodeficiency virus from a surgeon to one of his patients.
J Virol. 1998 May;72(5):4537-40.
PMID: 9557756

Leitner T, Escanilla D, Franzen C, Uhlen M, Albert J.
Accurate reconstruction of a known HIV-1 transmission
history by phylogenetic tree analysis.
Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):10864-9.
PMID: 8855273

Leitner T, Kumar S, Albert J.
Tempo and mode of nucleotide substitutions in gag and
env gene fragments in human immunodeficiency virus type 1
populations with a known transmission history.
J Virol. 1997 Jun;71(6):4761-70.
PMID: 9151870

Machuca R, Jorgensen LB, Theilade P, Nielsen C.
Molecular investigation of transmission of human
immunodeficiency virus type 1 in a criminal case.
Clin Diagn Lab Immunol. 2001 Sep;8(5):884-90.
PMID: 11527797

Robbins KE, Weidle PJ, Brown TM, Saekhou AM, Coles B,
Holmberg SD, Folks TM, Kalish ML.
Molecular analysis in support of an investigation of a cluster of
HIV-1-infected women.
AIDS Res Hum Retroviruses. 2002 Oct 10;18(15):1157-61.
PMID: 12402955

Blanchard A, Ferris S, Chamaret S, Guetard D, Montagnier L.
Molecular evidence for nosocomial transmission of human
immunodeficiency virus from a surgeon to one of his patients.
J Virol. 1998 May;72(5):4537-40.
PMID: 9557756

etc...

And hundreds more have traced the spread of HIV among larger groups of people:

Motomura K, Kusagawa S, Lwin HH, Thwe M, Kato K, Oishi K,
Yamamoto N, Zaw M, Nagatake T, Takebe Y.
Different subtype distributions in two cities in Myanmar:
evidence for independent clusters of HIV-1 transmission.
AIDS. 2003 Mar 7;17(4):633-6.
PMID: 12598785

Gianella A, Andrade R, Sanchez JL, Carrion G, Sanchez JL,
Russell K, Robb M, Birx D, McCutchan F, Carr JK.
Molecular Epidemiology of HIV Type 1 in Ecuador, Peru,
Bolivia, Uruguay, and Argentina.
AIDS Res Hum Retroviruses. 2002 Dec 10;18(18):1339-50.
PMID: 12487805

Carr JK, Avila M, Gomez Carrillo M, Salomon H, Hierholzer J,
Watanaveeradej V, Pando MA, Negrete M, Russell KL, Sanchez J,
Birx DL, Andrade R, Vinoles J, McCutchan FE.
Diverse BF recombinants have spread widely since the introduction
of HIV-1 into South America.
AIDS. 2001 Oct 19;15(15):F41-7.
PMID: 11600844

Velarde-Dunois KG, Guimaraes ML, La Fuente C, Andrade R,
Arevalo R, Pantoja S, Mariscal R, Sandoval R, Iriarte F,
Chamon V, Melgar ML, Carvajal R, Morgado MG.
Molecular characterization of human immunodeficiency virus
type 1-infected individuals from bolivia reveals the presence of two
distinct genetic subtypes B and F.
AIDS Res Hum Retroviruses. 2000 Nov 20;16(17):1921-6.
PMID: 11118078

Peeters M, Esu-Williams E, Vergne L, Montavon C, Mulanga-Kabeya C,
Harry T, Ibironke A, Lesage D, Patrel D, Delaporte E.
Predominance of subtype A and G HIV type 1 in Nigeria, with
geographical differences in their distribution.
AIDS Res Hum Retroviruses. 2000 Mar 1;16(4):315-25.
PMID: 10716369

etc...

The molecular epidemiology of HIV-1 is not unique. The exact same methods are used to trace other infectious diseases. They are also used to trace human population movements over the past 100,000 years and the geographic biodiversity of any other species of plant, animal, fungi, bacteria or protozoan. Here is a random sampling of recent papers and news articles:
Fungal Metabolism Under The Snow

...

Whitaker RJ, Grogan DW, Taylor JW.
Geographic barriers isolate endemic populations of
hyperthermophilic archaea.
Science. 2003 Aug 15;301(5635):976-8. Epub 2003 Jul 24.
PMID: 12881573

Fuller NJ, Marie D, Partensky F, Vaulot D, Post AF, Scanlan DJ.
Clade-specific 16S ribosomal DNA oligonucleotides reveal the
predominance of a single marine Synechococcus clade throughout a
stratified water column in the Red Sea.
Appl Environ Microbiol. 2003 May;69(5):2430-43.
PMID: 12732508

Symula R, Schulte R, Summers K.
Molecular systematics and phylogeography of Amazonian
poison frogs of the genus Dendrobates.
Mol Phylogenet Evol. 2003 Mar;26(3):452-75.
PMID: 12644404

Volobouev VT, Aniskin VM, Lecompte E, Ducroz JF.
Patterns of karyotype evolution in complexes of sibling species
within three genera of African murid rodents inferred from the
comparison of cytogenetic and molecular data.
Cytogenet Genome Res. 2002;96(1-4):261-75.
PMID: 12438808

Stone KD, Flynn RW, Cook JA.
Post-glacial colonization of northwestern North America by
the forest-associated American marten (Martes americana,
Mammalia: Carnivora: Mustelidae).
Mol Ecol. 2002 Oct;11(10):2049-63.
PMID: 12296948

etc...

In summary, the data from HIV-1 and other lentiviruses is both internally and externally consistent. The spread of HIV and AIDS has been traced around the globe by dozens of methods, from clinical features, to serology, to DNA sequence analsysis. If the Perth Group, or any other denialist group actually had any data or science of any sort on their side, they could make millions of dollars defending the people who loose millions of dollars each year to AIDS: for example the companies that paid over six hundred million dollars into the Ricky Ray fund for hemophiliacs. If the HIV tests were not specific enough, they could challenge laws in any country in the world where HIV seropositive people can be legally denied life insurance, based upon positive serology alone. Or they could scam the viatical settlement industry which buys life insurance policies pre-death, from HIV seropositive people who bought insurance before testing positive. Unfortunately for them, and for countries such as South Africa which are at a loss for how to deal with their epidemics, HIV is real, and empty rhetoric, lies or denial cannot make it go away.

Competing interests:   None declared