Where is the "HIV-1 infectious molecular clone"? 13 July 2004
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Eleni Papadopulos-Eleopulos,
Biophysicist
Department of Medical Physics, Royal Perth Hospital,,
Valendar F Turner, John Papadimitriou, Barry Page, David

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Re: Where is the "HIV-1 infectious molecular clone"?

Where is the “HIV-1 infectious molecular clone”?

 

 

Throughout this debate Brian Foley has been claiming that:

 

(i)                 The Perth Group is ignorant of biology in general and molecular biology in particular;

 

(ii)               "people who understand molecular biology already know that the Perth Group has no clue what they are talking about….";

 

(iii)             although he has been "spoon feeding" us molecular biology (or so he thinks), we are "a group of unwilling students who have no interest in the subject matter, but only want to claim to have all the answers before doing any studying" ourselves. 

 

Brian Foley has repeatedly stated the existence of the “HIV-1 molecular clone” proves a 100% purity of “HIV-1” and the existence of the “HIV-1 infectious molecular clone” proves the existence of “HIV-1”.  When we asked him for a few references with evidence which proves the existence of the “HIV-1 infectious molecular clone” he gave us a long list of titles.  Upon investigation none of these papers contained such evidence.   When we informed him of this and asked him to provide one study and a few confirmatory studies in which, in his view, the evidence proves the existence of the “HIV infectious molecular clone”, he gave us two references.  Again, upon investigation it was seen the evidence presented in these two references did not satisfy his definition of the “HIV-1 infectious molecular clone”.  Hence we requested other references.  He replied in his rapid response “Absence of evidence is not evidence of absence” 8 June 2004:

“The Perth group wrote:
“…
It is clear that the evidence given in the Fisher et al study does not demonstrate the existence of an “HIV-1 infectious molecular clone” as defined by Brian Foley: “The clone must produce virus particles that are identical by serology, morphology, protein sequences, RFLP, Southern blotting, etc. to the parental virus, and the particles must also be infectious. If a cloned viral genome does not meet these criteria, it is not an INFECTIOUS molecular clone of the virus, be it HIV-1 or any other virus” (his emphasis). (See Brian Foley’s rapid response “Re: Re-phrasing our two questions to Brian Foley”,
11th May 2004)
…”

I did not state that ALL of those forms of evidence must be researched and described in each and every paper describing a clone. If I had meant that all lines of evidence must be researched and presented, then I would not have used the abbreviation “etc.” which means that there are many other lines of evidence that any infectious molecular clone would also meet IF it were studied…Nobody will ever publish a single paper in a scientific journal that describes all experiments that can ever possibly be done on a virus. Typically each paper in a peer-reviewed scientific journal makes just one point or a very few related points. It used to be common to publish a whole series of papers which in total just reported cloning a single gene. With modern technologies, cloning is much simpler, so few papers today even report on the details of the methods used.””

 

Brian Foley has spelt out criteria that “infectious molecular clones” must satisfy.   When we repeatedly asked him for references with evidence proving the so-called “HIV-1 infectious molecular clone” which satisfies his spelt-out criteria he gave references which supposedly he believed met his criteria but which, upon investigation, do not.

A scientist such as Brian Foley should not use the term “etc”.  Et cetera is Latin meaning “and the rest” (1) and if “there are many other lines of evidence that any infectious clone would meet IF it were studied”, then he should state what "it" is or they are.  If there are “many other lines of evidence” apart from “The clone must produce virus particles that are identical by serology, morphology, protein sequences, RFLP, Southern blotting”, what are they?  And why hasn’t Brian Foley mentioned them before?  Why provide readers of this Online debate with a list of properties which is incomplete?

Brian Foley states that evidence for the existence of the “HIV-1 infectious molecular clone” can be obtained from many “experiments” (studies).  Cloning of a viral gene or even of a viral genome is not the same thing as obtaining evidence for the existence of an “infectious molecular clone”.   Cloning of the viral genes and the genome can be obtained from several studies.   However, evidence for the existence of an “infectious molecular clone” must be obtained from one experimental study which sets out to confirm all the properties that Brian Foley defines as properties of an “infectious molecular clone”.

 

Brian Foley wrote: “If the Perth group has any evidence that any of the infectious molecular clones of HIV-1 that have been described are fraudulent, they should pursue that claim in a serious manner, rather than "debating" in unmoderated internet forums or trying to gain political support for their ideas.”

 

 

Since we do not know of any “HIV-1 infectious molecular clone” and so far Brian Foley has failed to give us any reference where “HIV-1 infectious molecular clones” are proven to exist, it is not possible for us to make any judgment regarding such clones.

 

 

In his rapid response “Re: New and repeated questions and requests to Brian Foley” 8 June 2004, Brian Foley wrote: “The Perth group wrote:

“…

Let us paraphrase our request: Would Brian Foley please give us a summary of the evidence (not just the title) of a study as well as the evidence from a few confirmatory studies where the existence of an “infectious molecular clone” (as defined by Brian Foley) of “HIV-1” has been proven.”
…”

Yes. I will give a summary of that, right after the Perth group gives me a summary of any one virus that they feel has been characterized to their satisfaction. This is not a one-way street, I have the right to ask a few questions too.”

 

 

The first step to characterize a retrovirus is to obtain it in a pure form.  We have provided references and detailed summaries of the evidence for retroviral purification in our papers as well as previous rapid responses.  For example, see our rapid response “A plea for the references on HIV purification” 3 July 2003.   Additional EMs of viruses purified by banding in density gradients can be found in the Spectra reference by Toplin (2) which can be accessed on our web site (http://www.theperthgroup.com/OTHER/Toplin.pdf).   So far we have been unable to find one EM for “HIV-1” similar to the EMs for the viruses in the above references, even if it was showing “a real soup” of retrovirus particles.   We are still waiting for Brian Foley to provide an appropriate reference.

 

Remember it is Brian Foley who has been insisting that EMs are not necessary and that we are wrong to claim there is no proof for the existence of “HIV-1”.   Brian Foley has repeatedly told us that if we knew molecular biology we would never question the existence of “HIV-1”.   He insists that the existence of the “HIV-1 infectious molecular clone” proves beyond reasonable doubt the existence of the virus.  Yet he has been unable to give us a single reference with evidence that satisfies his definition of an “infectious molecular clone”.   So we repeat our request:

Would Brian Foley please give us a summary of the evidence (not just the title) of a study as well as the evidence from a few confirmatory studies where the existence of an “infectious molecular clone” (as defined by Brian Foley) of “HIV-1” has been proven.

 

If Brian Foley fails to respond with his summaries and references then we must conclude his whole argument for the existence of “HIV-1”, based upon the existence of the “HIV-1 infectious molecular clone”, collapses.

 

References

1.      Ehrlich E.   Amo, Amas, Amat and More.  1987.   Harper and Row.  New York.

2.      Toplin I.   Tumor Virus Purification using Zonal Rotors.   Spectra 1973: 225-235.

Competing interests: None declared