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The Race to Retract Lombardi 2009...

Discussion in 'XMRV Research and Replication Studies' started by jace, Oct 10, 2011.

  1. Bob

    Bob

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    It's been a long time since I read the original Science paper, but I believe that the non-retracted part of the paper refers to partial genetic sequences and not whole XMRV isolates, and that's why it's not been retracted by the authors. I believe that the WPI are currently getting some more isolates fully sequenced, but they are a long time coming, and long overdue, and I don't know if they are isolates obtained for the Science paper or if they are more recent isolates.


    I agree. I don't know what the exact issue is with Mikovits getting published, but she has been talking about other studies, in which she has been finding other HGRVs, for more than a year now. I don't know if her papers have been rejected, and if they have I don't know for what reasons. But I think she has said that she has unpublished papers sitting in her drawer, which she can't get published. But if they aren't published, then they are meaningless for the rest of us, which is very unfortunate.


    I have to admit, that for me personally, the BWG study seems to be a very strong study, and the original Science paper XMRV findings have now been retracted. I haven't heard Judy Mikovits dispute the BWG's findings either. She seems to have signed up to its conclusions, and is now looking for other HGRVs, other than VP62.
    I can't comment on how the BWG results affects the Science paper without reading the paper again. But if the sequences found in the Science paper could be attributed to other HGRVs then I don't think that it is invalidated.
    Although, to many people, the Science paper looks like a definite result of contamination, it could be the case that there are HGRVs present in the patient blood samples, and that the whole study was confounded by the presence of the VP62 contamination.
    So to me it now looks like it's either contamination or a coincidence. But I haven't ruled out a coincidence, which is why I am still interested in the subject.

    I hope that the Lipkin study is completed, and that Judy Mikovits is still involved.
    Once those results come back, then I think that will clarify things for most of us.
     
  2. currer

    currer Senior Member

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    Hi

    I am currently going through the IiME talk by JM and will post a bit more about it later.

    She clearly states in this talk, though, that she is finding sequences which definitely are not VP62, and confirming it with antibody work.

    Remember that her initial interest was provoked by positive results for MLVs from the virochip array, and this would be before the arrival of the VP62 clone in her lab.

    This has been said on other threads., so I dont want to repeat myself at length here, but if Silverman feels his results in PC are invalidated by the VP62 contamination why are there not calls for the retraction of his and Singh's work also?
     
  3. Lee

    Lee

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    currer:
    "..Judy Mikovits was unable to get any further retoviral papers published..."

    i dont buy it - and that's the polite way to say it. There are literally dozens of virology journals out there, from different publishers, different editors, as well as appropriate general-interest journals. If JM was 'unable' to get published, it's because she didn't have anything publishable.

    Alter/Lo got published, even with their methodological problems and shortcomings - sequences falling into 4 classes identical within those classes (suggesting ERV, not replicating virus), and sequences nearly identical to known mouse ERVs, but no insertion site work to demonstrate independent origins, but it got published with little trouble. All the followup studies got published. There was no broad, mu.ti-publisher, dozens-of-editors conspiracy to cover anything up here.

    "...our understanding of what we find will inevitably be enlarged by further research."
    Or, it will be shown not to be true. Almost no one out there can find this alleged virus, including some of the premier retrovirology labs on the planet. The labs that report they can find a virus in almost all patients but only a very few controls, JM and WPI, VIPDx, Alter and Lo, when given blind samples and allowed their choice of assays, find a few 'positives' in both patient and control samples.

    Initial positive which cant be confirmed when blinded(JM), someone trying to make money off that initial positive, cant confirm when blinded (VIPDx), weird mouse ERV results which cant be confirmed when blinded (Alter an Lo), and negative, negative, negative, negative, negative, negative...

    And then, retraction of the key piece of data saying this is a GRV (the sequence data, which was just a contaminant), admission from JM and Ruscetti that another key piece of the data they showed us didn't actually show the experiment they claimed it showed (comparison of patient and control) but instead showed a demethylation induction experiment without any known controls.

    The ONLY positive results here are from people who cant replicate it and have admitted to falsifying data (JM and Ruscetti), from a lab trying to make money that cant replicate their own work (VIPDx), and from a lab that found mouse ERVs and can't replicate their work (Alter and Lo).

    And no, saying that JM and Ruscetti falsified data is not a 'witch hunt.' It is just restating what they themselves said. They admitted it - they changed labels on a publically-presented western blot, intentionally, to make it 'less confusing.' They presented a demethylation experiment in their Science paper, and labeled it as and described it as a comparison experiment. That is falsification of data, and it is NEVER, EVER justified in science. And to me, it means that nothing else they say can be trusted.

    And they cant replicate their work blind.

    Where is the evidence for a virus? I don't see any.
     
    kurt likes this.
  4. Lee

    Lee

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    Bob,

    The only sequences in the Science paper were the sequences that have been retracted. Everything else is microoscopy, serology, cell biology, all of it now called into doubt because JM and Ruscetti have admitted to using demethylating agents, which can induce ERVs and explain all that data, but didn't tell us or show the controls. I look at that paper, and I see cross-reactivity of retrovirus-specific probes to induced ERV sequences, with no controls to rule it out.
     
  5. Bob

    Bob

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    That's not what I understood. I understood that the partial sequences in the paper still stand. So I think this needs to be double-checked.
     
  6. currer

    currer Senior Member

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  7. Lee

    Lee

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    currer, JM has stated a lot of stuff. She has also changed her story, on experiment details for example, multiple times. She has also admitted to having intentionally said things about her data that are not true, and to omitting key details that make the experiment different from what she claims.

    No one else has been able to replicate what she claims. Why on earth do you believe her?
     
  8. currer

    currer Senior Member

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    Hi Lee,


    I believe Dr Mikovits because she is an accomplished retrovirologist, who knows more about retrovirology than I suspect you do.

    Modifying scientific theory in the light of fuller knowledge, does not invalidate a theory, as I explained in my earlier post.
     
    jace and ukxmrv like this.
  9. Lee

    Lee

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    Bob,

    The only sequences in the science paper are the gag sequences they got from the PCR products, reported in the supplement Figure S1. They sequenced VP62, the contaminant.
     
  10. Lee

    Lee

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    currer:

    "Thanks for coming here to impose it on us."

    Us?

    Oh, that's cute. You apparently speak for the entire ME/CFS community? And anyone who disagrees with you is 'coming here to impose it on' the ME/CFS community?

    Yes, JM certainly knows more virology that I do. She does not know more virology than all those labs that could not confirm her work, and she cant back up her own work with reproducible data. But apparently, she isn't imposing anything on you?
     
    being and kurt like this.
  11. currer

    currer Senior Member

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    Hi again, Lee.

    In her talk, which gives information Dr Mikovits has sadly been denied the opportunity to publish, she is sequencing pol/env genes.

    Now I must get back to the DVD so I will have to leave you to your own devices!
     
    jace likes this.
  12. Lee

    Lee

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    "information Dr Mikovits has sadly been denied the opportunity to publish"

    Is JM running around telling this to people? Or is it an urban legend?

    Either way, i cant use language strong enough to say how absurd it is. There are no conspiracies involving many dozens of journals and many more editors to deny one author publication.

    If JM has been unable to publish, either she hasn't bothered to submit to appropriate journals, or she wasn't submitting publishable material.
     
    Jenny likes this.
  13. Esther12

    Esther12 Senior Member

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    I wouldn't be surprised if it would be extremely difficult for Mikovits to publish work in remotely respectable journals at the moment.

    If I was an editor, I'd only be willing to publish work from her which claimed an association between CFS and an identified virus if her testing had been done under independently blinded conditions - which is rarely expected. The controversy that surrounds her work, and some of her own behaviour, mean that it could well be that studies which would normally be seen as fit for publishing are now being rejected.
     
    busybee likes this.
  14. Bob

    Bob

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    The partial retraction only relates to the full sequences, as far as I understand, as follows:
    "Sequences of full-length XMRVgenomes from
    two CFS patients and a partial genome from a third
    patient were generated (table S1).
    "

    Interestingly, the paper said that the complete genomes were more than 99% identical to VP62, so this doesn't look like the massive fraud, cover-up, or misleading paper, as some would have us believe:
    "Thus, the complete XMRV genomes in these CFS patients were >99% identical in sequence to those detected in patients with prostate cancer."

    Env genes were also sequenced:
    "Of the 101 CFS samples analyzed, 68 (67%) contained
    XMRV gag sequence. Detection of XMRV was
    confirmed in 7 of 11 WPI CFS samples at the
    Cleveland Clinic by PCR-amplifying and sequencing
    segments of XMRVenv [352 nucleotides (nt)]
    and gag (736 nt) in CFS PBMC DNA
    "

    Lee, this is yet another opinion that you post have posted as 'fact'.
    The gag sequences could possibly be from contamination, but that has not yet been established as fact.
     
    jace likes this.
  15. Firestormm

    Firestormm Guest

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    Thanks for the earlier replies - I will post some replies tomorrow but am off to bed now.

    Esther - the only thing I would add is that Mikovits has been saying this almost ever since Lombardi et al was published. It was said in response to almost every critique or question - at least it seemed so at the various times.

    I mean before the BWG results she claimed to have a drawer full of results that would vindicate her claims - maybe these will form the basis of that NIH study she received (or WPI received) that Grant for? Don't know, can't remember the details now.

    Night :cool:
     
  16. Lee

    Lee

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    Bob,

    Silverman's retraction specifically looked at the env PCR fragment - the sources of the env sequences that they talked about but did not show. Silverman showed taht the endv sequences come from VP62 contaminatin.

    This is not opinion - this was th ekey peice of data in tehanalsyis taht led Silverman to retract.
    Quotes:

    "However, all of the CFS samples that were positive for XMRV env DNA were also positive for neo DNA, a part of XMRV VP62 plasmid (Fig. 1), whereas none of the control samples were positive for neo DNA."

    "There were no examples of XMRV env DNA in the absence of plasmid sequences (Fig. 2). Two of the sequence-confirmed junction sequences (WPI-1104 and WPI-1178) were from same samples used to generate Table S1 (sequences of XMRV genomes) and Figure S2 (the phylogenetic tree) (1)."

    Figures S1 and S2 were based on VP62 gag sequence, and have been retracted. Silverman's retraction showed that the env sequences also derive from VP62.

    All of the sequence data, the gag data they showed, and the env data they did not show, derive from VP62 contaminants. This is not opinion - this is what Silverman showed.
     
  17. Lee

    Lee

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    Esther12:
    "I wouldn't be surprised if it would be extremely difficult for Mikovits to publish work in remotely respectable journals at the moment."

    At the moment, yes. Two weeks ago she admitted to falsifying data - that's a death knell. But prior to that? If she had publishable work she could have gotten it published.
     
  18. Bob

    Bob

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    Lee, I'd be very grateful if you could refrain from repeating those opinions and accusations until we know all of the facts.

    The 5AZA issue does not necessarily relate to the whole paper, and we do not know its significance.

    Science are doing an investigation into the issue, so why don't we leave it for them to determine the facts?

    As far as I understand it, the 5AZA issue only relates to proteins (specifically MLV p30 gag) in a single Western Blot test, and it does not relate to the PCR results.

    Is MLV p30 gag found in the human genome? If not, then is the 5AZA issue relevant anyway?

    "To determine whether XMRV proteins were
    expressed in PBMCs from CFS patients, we developed
    intracellular flow cytometry (IFC) and
    Western blot assays, using antibodies (Abs) with
    novel viral specificities. These antibodies included,
    among others, (i) rat monoclonal antibody (mAb)
    to the spleen focus-forming virus (SFFV) envelope
    (Env), which reacts with all polytropic and
    xenotropic MLVs (7); (ii) goat antisera to whole
    mouse NZB xenotropicMLV; and (iii) a rat mAb
    to MLV p30 Gag (8). All of these Abs detected
    the human VP62 XMRV strain grown in human
    Raji, LNCaP, and Sup-T1 cells (fig. S3) (5). IFC
    of activated lymphocytes (6, 9) revealed that 19
    of 30 PBMC samples from CFS patients reacted
    with the mAb to MLV p30 Gag (Fig. 2A). The
    majority of the 19 positive samples also reacted
    with antisera to other purifiedMLV proteins (fig.
    S4A). In contrast, 16 healthy control PBMC cultures
    tested negative (Fig. 2A and fig. S4A). These
    results were confirmed by Western blots (Fig. 2,
    B and C) (6) using Abs to SFFV Env, mouse
    xenotropic MLV, and MLV p30 Gag.
    "
     
  19. Lee

    Lee

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    Bob, I'm not talking about the 5AZA - although that is also falsification IMO (yes, that is opinion).

    I'm talking about the fact that she admitted changing controls to patients in the labeling of at least one of the versions of that blot, and doing it intentionally to 'make it less confusing.'

    Knowing that data is one thing, and telling or audience that it is something else, is falsification of data. No opinion involved - thats pretty much the definition of falsified data. She not only admitted she did it, she defended it. Those are facts.

    Even more, she said that is is even more acceptable because the audience that she presented data to, was an audience of 'primarily patients.' (note single quotes - i'm paraphrasing from memory. Get that? She defended falsifying data, because it was to patients.

    And you are ok with this?
     
  20. currer

    currer Senior Member

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    Lee, I am OK with it.


    No I absolutely reject any accusation af "fraud" leveled at Dr Mikovits. It is clear to any unbiased observer that she has done her work in good faith.

    What on earth do you suggest she would gain? Why commit a "fraud" which would inevitably and rapidly come to light? There is no credible motive here, and for you to suggest that anyone could behave in such an untenable way puts your own motives in question.

    And why do you conveniently forget that if you accuse Mikovits of fraud you also have to accuse Ruscetti?

    Do you seriously believe the retrovirology community is going to go along with such contemptible accusations against a man of distinction?
     
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