Thursday, December 6, 2012


LETTER TO SCIENCE
Via http://www.submit2science.org/ws/begin.asp (I want to submit a letter to the editor)
Submission acknowledged by editors on August 25, 2009 via email (ID 137063)

Open Letter to Editor-in-Chief and AAAS CEO
Science/AAAS
1200 New York Avenue NW
Washington, DC, 20005

To: Bruce Alberts, Editor-in-Chief, Science
Cc: Alan Leschner, CEO, AAAS

“Frankly speaking, I never relied on electron microscopy. I don’t think electron microscopy does much, except for the person who’s a structural biologist and wants to look at real structure. No one uses electron microscopy [in] virology any more – nobody. It is as rare as
hen’s teeth.” Robert C Gallo (6)
 
The following “fresh look” at Gallo et al is derived from heightened scrutiny of Science V224, 497-508. Their claims leading to the classification of a human retrovirus originally known as HTLV III/LAV (1) as a “unique cytopathic variant” were not adequately peer-reviewed.

It was their and your rush to publish and run past crucial details that weakened its conclusion: Detection, Isolation and Continuous Production of Cytopathic Retroviruses (HTLV-III) from Patients with AIDS and Pre-AIDS. (2)

No “continuous production of cytopathic retroviruses” was demonstrated.

Is reverse transcriptase activity a valid surrogate for “continuous HTLV III production”?

The caption to Figure 2 (2, 499) describes how the “peak fraction” was measured for maximum “reverse transcripase (RT) activity” - incorporating nucleotides into a growing polymer chain - in the “1.16 g/ml sucrose density band”. Apparently. Peer review overlooked the nature of the synthetic template (poly(A)-oligo dT [15]) described in these captions. It is “the adenylate-containing strand” or the “synthetic homopolymer” polyriboadenylate annealed with oligothymidylate (3).

What does the dash before “oligo” mean? That a chemical polymer not a biomolecule (a) has a “primer” (15 T’s) hydrogen-bonded at its end to kick start and maintain a polymerase reaction that’s roughly 3 orders of magnitude higher than an “endogenous” RT reaction (b) where true “information transduction” or “transcription” takes place. The template is referred to as a “homopolymer”, meaning it’s a “Johnny-one-note” not recognized as RNA by living organisms.

Numerous kinetic comparisons made by 70’s RNA “tumor virus” researchers with “endogenous” RT experiments produce the fact of much greater RT “activity” with synthetic templates.

Was a virion counting procedure fraudulently stated and referenced?

This is answered by commenting on two items from 2, page 499:

(1) “Both virus production and cell viability of the infected clone H4 (H4/HTLV III) were monitored for several months. Although virus production fluctuated (Fig 2a), culture fluids harvested and assayed at approximately 14 day intervals consistently showed particulate RT activity which has been followed for over 5 months…Thus, the data show that the permanently growing T-cell population can continuously produce HTLV-III.”

The reference to “particulate RT activity” is not proven because no “endogenous” assays are documented. According to “working standards” of retrovirology, the evidence from synthetic template reactions was based on reverse transcription being unique to retroviruses. In retrospect, this was an assumption not recognized as an “article of faith” by the lights of current science.

(2) “As shown in Fig. 2b, the highest RT activity was shown at a density of 1.16g/ml, which is similar to other retroviruses. The highest RT activity was found in the fractions with the largest amount of virus, AS DETERMINED BY ELECTRON MICROSCOPY (c). The actual number of viral particles determined by this method was estimated to be about 10^11 per liter of culture fluid.”

Thanks to the now available I. Toplin paper (Tumor Virus Purification Using Zonal Rotors; Spectra 1973: 225-235), we can better understand the working standards of retroviral isolation that guided experiments 1970 to 1986.

The reference of Popovic/Gallo and Toplin for viral particle count is the SAME (4). Toplin gives more precision in description: “We adjust the viral level to 2 x 10^11 particles per ml using rapid quantitative negative stain electron microscopy to MEASURE the concentration”. (c) The Toplin paper includes type of EM (Fig 6, pg 231) that can be used to determine particle count based on “double sucrose zonal centrifugation”.

Thus, the EM Popovic/Gallo refer to is clearly not Fig 1 (pg 498), Fig 2 (pg 501) or Fig 4 (pg 504) which include “cells”.

The March 26, 1984 Gonda to Popovic letter - “I do not believe any of these particles are HTLV I, II, or III” – implies missing “micrographs for publication” that “Dr Gallo wanted”. (8)

Is there a deceptively NOT presented or missing EM for the required back-up of the particle count?

Thus, nothing in the four papers published in V224, 497-508 validates that particle number.

We know from this letter that Gonda looked at EMs sent to him by Popovic.

Was Gonda’s examination to check the particle count?

Finally, subsequent publications did not verify a singular isolation by unique-sequence method completed by three groups (Gallo - Levy - Montagnier) in 1985. (5)

Conclusion: there is an initial misrepresentation in V224 of “HIV” = unique cytopathic retrovirus “isolation and continuing production” for your consideration.
 
Eugene Semon, BChE, PE (retired)
160 Bergen Avenue, Apt 4
Ridgefield Park, NJ 07660
genesemon@hotmail.com

NOTES

a. Because the polymer contains no information.

b. Means, according to convention, RNA template directed.

c. emphasis added, Gallo’s ref 36, Toplin’s ref 2 and reference 4 below

REFERENCES

1. Hahn et al; Science V232 (20 June 1986) 1548 – 1553: “Genetic heterogeneity has been firmly established as a prominent characteristic of the AIDS virus, HTLV-III/LAV.”

2. Popovic, Sarngadharan, Read, Gallo; Detection, Isolation and Continuous Production of Cytopathic Retroviruses (HTLV-III) from Patients with AIDS and Pre-AIDS. Science V224, (4 May 1984), 497-500

3. McCaffrey, Smoling and Baltimore; DNA POLYMERASES IN LYMPHOID CELLS, pg 247- 255, in Rolf Neth, Robert C Gallo, Sol Spiegelman, Frederick Stohlman, eds: Modern Trends in Human Leukemia, J.F. Lehrnanns Verla M√ľnchen 1974. http://www.wilsede-science connections.com/books/moderntrends/trends1/005%20-%20Nucleic%20Acid%20Metabolism%20in%20Leukemic%20Cells/247%20-%20DNA%20Polymerases%20in%20Lymphoid%20Cells.pdf

4. Monroe and Brandt; 1970. Rapid semiquantitative method for screening large numbers of virus samples by negative staining electron microscopy. Appl. Microbiol. 20: 259 –262

5. Leitner et al; Yet Another Subtype of HIV-1? AIDS Research and Human Retroviruses,11, Number 8, 1995, 995-997:

”The growth of unclassified sequences indicates that it is becoming increasingly difficult to categorize the HIV-1 sequences by the proposed criteria (env/gag “star phylogeny”) … (W)e may eventually be faced with a continuum of genetic variants.”

“(I)t is possible that future studies will reveal important immunological and biological differences between genetic subtypes.” (NB, see 7)

6. Gallo Testimony at Parenzee, 1306; http://garlan.rethinkingaids.info/Cases/Parenzee/Gallo.html
 
7. Henderson et al, Direct Identification of Class II Histocompatibility DR Proteins in Preparations of Human T-Cell Lymphotropic Virus Type III, JOURNAL OF VIROLOGY, 61, 2, Feb. 1987, p. 629-632; Kolegraff et al, Characterization and Role of Lentivirus-Associated Host Proteins, Experimental Biology and Medicine 231:252-263 (2006); Gurer et al, Specific Incorporation of Heat Shock Protein 70 Family Members into Primate Lentiviral Virions, J. Virol. (2002) 76, 4666-4670: “Hsp70 was roughly equimolar with pol-encoded proteins in virions”.
 
8. Cited Documents, M. Gonda to M. Popovic (March 26, 1984 http://www.sciencefictions.net/documents.html
RESPONSE – rejected for publication on September 23, 2009 (BTW did not claim to be a doctor :)
MS# 1181147
Dear Dr. Semon,

Thank you for sending a Letter-to-the-Editor to Science. We have read over your contribution, but will not be able to publish it in the magazine. We are letting you know as a courtesy in case you wanted to seek another outlet for your letter.
 
Please do not reply to this email, as it will not be read by Science. Unfortunately the volume of submissions precludes specific discussions about individual submitted letters.

Sincerely,The Editors
Science Magazine