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Cleaning up after XMRV

Discussion in 'Media, Interviews, Blogs, Talks, Events about XMRV' started by Ecoclimber, May 18, 2012.

  1. barbc56

    barbc56 Senior Member

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    It has nothing to do with anyone trying to discredit that another RV could be involved. Do you think I have always thought this? No, as the science changed so did my views and I don't blindly follow what any scientest says. I do a lot of reading and analyzing.

    I have edited my above post to say probable. Thanks Esther! :thumbsup:

    Barb C.:>)
  2. barbc56

    barbc56 Senior Member

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    I think I may be done with this thread. Shall we call a "truce" and just agree to disagree. I am just too tred to keep dong this and I think I have made my point(s).
    Barb C.:>)
  3. SOC

    SOC Moderator and Senior Member

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    What kind of science is that? We didn't find it, so it doesn't exist? They weren't even searching for any retrovirus, so why should we think a retrovirus would most probably be detected by now? We looked around a bit and didn't find it, so it must not exist? That's not the science I was taught. Even in high school we knew better than that.
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  4. ukxmrv

    ukxmrv Senior Member

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    Barb, please don't worry about this. My postings are purely aimed at the Retrovirologists and their claims not you.
  5. ukxmrv

    ukxmrv Senior Member

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    Here's an example of what some scientists do when they have a pet theory or want to look at virus activity in patients.

    Close to where I am in London is a group with an interst in retroviral activity in ALS

    http://www.neurology.org/content/70/4/278.abstract

    Conclusions: These findings further support the concept of retroviral involvement in amyotrophic lateral sclerosis (ALS) and demonstrate that serum is more suitable than CSF for assay of reverse transcriptase (RT) activity in this disease.

    Yet no retrovirologist has bothered to do the same thing for CFS patients.
    currer likes this.
  6. jace

    jace Off the fence

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  7. natasa778

    natasa778 Senior Member

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    Thanks for trying but no, actually I haven't seen any evidence of you trying to make your points or to explain 'what part of reading of science' makes you now believe that all XMRV testing would by now have 'probably' detected any other RV. This statement of yours is VERY intriguing and makes me think I am missing something. Please enlighten us when you have a minute.
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  8. Mark

    Mark Acting CEO

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    My sympathies for the difficulties you're having with editing. But don't worry, we are talking about the same study, the one you linked to. The bullet points were from Racaniello's blog about that study, as you've clarified.

    You did, and indeed it is highly relevant to the theme, here's the link to the PDF:
    http://jvi.asm.org/content/early/2011/05/04/JVI.00693-11.full.pdf html


    No, the points definitely weren't talking about all the positive studies, this is definitely a list of problems with all the studies. Some of them apply to Lombardi et al, most of them don't, most of them apply to the negative papers.

    As your own quote states: "the authors note other problems with many of the studies of XMRV in CFS patients".

    This does not refer to the positive papers only. If it did mean that, likely it would have said so. And since it mentions problems with "many" studies, I ask you, how many positive studies were there, to classify as "many"?

    You can read the actual source for these bullet points of Racaniello's in the pdf:
    http://jvi.asm.org/content/early/2011/05/04/JVI.00693-11.full.pdf html

    Lines 65-78 describe the problems with the negative studies, and notably Singh echoes the many valid criticisms made of those studies by forum members here at the time. It is most heartening to see her do so, because regardless of the end result of the science she firmly vindicates the response of patients here to the poor methodology of those negative studies. All of these points were highlighted by patients here; I'll take you through them line by line...(I am dealing here only with the critique of the negative studies; the critique of the positive studies is in the previous lines).

    65 - 67: "In all but two studies that failed to detect virus in association with CFS, only PCR-based assays were used, thus relying heavily on conservation of retroviral sequences"

    67 - 69: "The limits of detection, reproducibility and precision of the assays used in different studies were not known, making it difficult to distinguish the lack of ability to detect XMRV from a genuine absence of XMRV from samples."

    70 - 71: "Furthermore, tests that had resulted in more frequent detection of XMRV, such as growth of virus in cultured cells (14), were not used in subsequent studies."

    72 - 73: "Adequate controls for each step of the analysis, such as controls that would flag contamination occurring during the nucleic acid extraction process, were mostly lacking.

    73 - 76: "Furthermore, the number of negative controls should equal or exceed the expected prevalence of the virus in the control population. It is not clear if any of the studies employed more than one negative control per experiment, which would be important for the detection of a low incidence of sample contamination.

    76 - 78: "Finally, none of the studies tested samples from the same patients that were found to be positive in the original study by Lombardi et al (12).



    I'm grateful to you for bringing these details of Singh's paper to my attention Barb, because they are a damning indictment of most of the negative studies, and as I've said, it echoes the criticism from patients here and elsewhere, and they illustrate very well why so many patients had such serious concerns about the negative studies, particularly the early ones.

    As Singh explains, and as we commented at the time:

    - the negative papers only used PCR assays, focusing on a specific sequence and omitting the other methods used in Lombardi et al (so they weren't a proper replication of Lombardi et al);
    - the precision and reproducability of the assays used in the negative papers were unknown (so it was difficult or impossible to say whether there was no XMRV there or whether they just couldn't find it).
    - the tests that had worked best in Lombardi et al - especially the crucial culture test - weren't used in any of the subsequent negative studies
    - controls, such as controls to flag contamination, were lacking in all the studies (so the criticism and innuendo heaped on Dr Mikovits over that issue was quite unfair because nobody else controlled for contamination any better)
    - it wasn't clear whether any of the studies used any more than one negative control (so again, that criticism applies to the other studies just as much as to Lombardi et al).
    - none of the studies re-tested samples from the original Lombardi study (and very clearly indeed, that criticism can hardly be levelled at the Lombardi study itself!)

    So when you say:

    Well yes, the last point specifically talks about the Lombardi paper, in that it blames all the other papers for not retesting samples from that study. But the other points listed above were definitely, emphatically talking about the papers that failed to detect XMRV (prior to Singh's own study).

    The only two of your bullet points that refer to weaknesses in Lombardi et al and Lo/Alter are these, which are discussed in the section before the one I've highlighted above, in lines 57-65 of the paper (and Racaniello missed the first of these I think):

    • Patient and control samples collected from different geographical regions (11, 12)
    • Patient and control samples collected at different times (11)
    • Investigators generally not blinded to sample identity (except in a subset of 12)
    Note "generally", because there was some blinding (in Lombardi et al - 12). And the second of these two bullets applies to Lo/Alter (11), not to Lombardi et al (12).

    So in fact, excepting the flaws that were present in every study, including the negative ones, the only one of these bullet points that applies to Lombardi et al is the point about collecting samples from different geographical regions. And even in that case, I am not quite sure that Singh is quite correct on this point, because the Lombardi samples were collected from about 10 different sites across the US (in surgeries in ME outbreak areas), but I thought Mikovits had clarified that, although not mentioned in the paper, the blood from controls was collected from the same locations.

    So I'm glad I've done the full analysis there, in the end, because the point I've been highlighting has quite unexpectedly got considerably stronger along the way: It turns out that, in fact, every item in Singh's list of criticisms of all XMRV studies up to that date either applies to the negative studies only, or applies equally to all the XMRV studies, including the negative ones.The only exceptions are the three listed above, of which two points apply to Lo/Alter only, and only one (geographical regions) applies to Lombardi et al - and I think even that point may well be incorrect!

    So in Singh's very thorough analysis of the XMRV studies, there's not a single direct hit on Lombardi et al's methodology, and the only criticisms which may apply to Lombardi et al are explicitly applied to all the studies, including all the negative ones. Rather a different picture from the image of weak methodology in Lombardi et al which one sees presented all too often...
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  9. Mark

    Mark Acting CEO

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    OK Barb if you like, we can agree to disagree. I'm sorry, but I'm afraid you are just flat out wrong when you maintain that the list of bullet points were criticisms of the studies that found XMRV: they were almost exclusively criticisms of the studies that didn't, and I've proved it, with references, above. So we might as well move on.
    currer likes this.
  10. FancyMyBlood

    FancyMyBlood Senior Member

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    I still believe a RV (albeit endogenous) might be involved. Huber already found HERV-K18 activation in a small study (unpublished) and a much bigger study should be completed this year.
  11. barbc56

    barbc56 Senior Member

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    I am willing to let the differences stand for now until I have read the study in full.

    However, I would appreciate any comments/opinions from those who are science based to chime in on Singh's study and what she was saying in general and the bullet points specifically. It would be interesting to here their feedback. Just in case I am mistaken. If I am, I have no problem admitting that.;)

    Thanks for the link.

    Barb C. :>)
  12. natasa778

    natasa778 Senior Member

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    Mark's comments are excellent and very detailed, have you actually read them barbc56?
  13. barbc56

    barbc56 Senior Member

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    I 'm glad I read the whole paper as there is indeed mention of the shortcomings of the negative studies This was not clear to me from the Racaniello blog. But all critisims do not apply to all the studies. The preponderance of shortcomings, however, were on the positive studies. If you hover your mouse on the, numbers next to the text, the study title(s) show up.

    But, and I think this is a big but, maybe the issue is not which studies were criticized more but that the factors that concerned the authors of all the studies were controlled for and thus the conclusion of not finding XMRV in CFS/ME patients is the more important point.

    I think we both got caught up in the minutia and missed the bigger picture. :lol:

    I have listed the shortcomings of the positive, negative and all of the studies below:

    The shortcomings of the negative studies:


    The shortcomings of the positive studies:


    Shortcomings of all papers:

    Ah, closure!!! At least for now. :)

    Barb C.:>)
  14. Mark

    Mark Acting CEO

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    Thank you. It has taken a while for you to accept this point, but we got that straight, at least.


    This is interesting, and I really encourage you to reflect on this.

    Because there was no ambiguity in the Racaniello blog on this point, and I pointed that out to you with direct quotes much earlier in this thread. Racaniello stated:

    "the authors note other problems with many of the studies of XMRV in CFS patients".

    Yet you interpreted that statement as referring only to the positive studies. He never said that; there was no ambiguity. Your reading of this was clearly coloured by your assumption that the positive studies were flawed - would you even have said "bad"? - and the negative studies weren't. But that caused you to read this whole section wrongly: it highlights various flaws in all the studies.

    Worse, the detail of some of the bullet points makes it blindingly obvious that many of the points can only apply to the negative studies, and yet you still consider them to be criticisms of the positive studies, even now. In particular, the last one: the failure of all studies to test the Lombardi samples. Obviously the Lombardi study - positive - is the exception to this criticism. Yet you weren't able to see this either, and read even that point as a criticism of the positive studies. This selective reading clearly suggests that your opinion on the matter seriously clouded your judgement here.



    Indeed: as I have been trying to explain. Several do apply to most or all studies, and some apply only to the negative studies.

    However - remarkably - as I've further analysed Singh's text, I've found that none of them were said to apply only to the positive studies.



    Definitely not so, as I have clearly laid out in detail above. Your characterisation is still wrong: you are still taking criticisms of the negative studies and wrongly taking them as applying to the positive studies. We can work through those errors one by one if we must. I would encourage you to stick with it, as I think it will be a most illuminating process: Singh's critique is very good indeed, and an excellent introduction to the methodological flaws.


    That's very helpful, but as a short cut, you can refer to the references I gave above to the two positive studies:

    Lo/Alter - 11
    Lombardi et al - 12

    The rest are all negative studies, unless you can pick another one out that is positive (there may perhaps be another).


    I'm not sure exactly what you mean, but if you are saying that Singh corrected the methodological flaws she highlights when she conducted her own study, and then found her findings of XMRV in ME/CFS patients to be due to contamination, you are correct. That is not to say, of course, that her own study was perfect, nor that it is the final word on the subject, but it is a very good paper and it concluded that:

    "at least some of the discrepancy in the previous studies is due to the presence of trace amounts of mouse DNA".
    and
    "our findings do not support an association between CFS and MLV-related viruses including XMRV".



    Unfortunately, you have again categorised them wrongly, and listed shortcomings of the negative studies under the heading of shortcomings of the positive studies.

    Having examined in detail, I can now see what you did: you made the assumption that the criticisms were grouped together in Singh's text: criticisms of all studies, then criticisms of positive ones, then criticisms of negative ones. But you've blocked them out in that way without looking at the detail, and in fact Singh did not categorise them like that; they are all jumbled up together and need untangling one by one in order to see which types of studies each point is critiquing.

    But your format for this comparison is admirably clear, and contains the references, so we can go through the process using that format and discuss the detail if necessary.

    For now I will just list them correctly, and I'll only highlight in detail the first example of the type of error you've made, because I have covered all of this in detail earlier in this thread:

    The very first clause of your 'shortcomings of the positive studies' (in #73 above) is this one:

    "Control populations were often small, with as few as 43 in one study (25)"

    That reference 25 refers to a negative study: in its conclusion it states:

    "
    This study failed to show the presence of XMRV in peripheral blood mononuclear cells of patients with chronic fatigue syndrome from a Dutch cohort. These data cast doubt on the claim that XMRV is associated with chronic fatigue syndrome in the majority of patients."

    Here's my version of the items in your list then (I think you've omitted a couple of points but I've re-categorised the items in your list only). I've bolded and underlined key words to clearly show why I've categorised them correctly in my version.

    Introductory general comments on 'confounding factors' (uncategorised, but most apply to both positive and negative studies)




    Shortcomings of negative studies only:


    Shortcomings of most studies (some of these include shortcomings of positive studies, others may not).

    On this very last point, note that the subset of Lombardi et al (12) that was blinded was the only part of any of the studies that was blinded, so it's curious that Lombardi et al has been criticised severely, since the outset, for failing to blind all of the study - and this double standard has been allowed to stand.


    I fear not, Barb. You can't call closure and imagine that ends the argument, unless you get it right. I do hope we can get there, but I implore you to read and think about these points much more carefully before you post again, and understand why your categorisation is wrong.
  15. Esther12

    Esther12 Senior Member

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    Sorry - not keeping up with this thread, but one brief point is that different groups being able to validate one another's results is important. With the BWG we've seen that Mikovits couldn't validate her own.

    Even if the one positive study was really well done, very careful, well designed, etc - it could still be the one that is wrong. If the samples from patients and controls were ever treated differently, then that would leave room for one-sided contamination, and from that point, it doesn't matter how good and thorough the study is.

    It seems that it was common for both positive and negative studies to use samples which had been collected in different ways, and we had the Huber (I think) study showing XMRV in the control samples but not the CFS patient ones.

    Singh started finding positives in CFS samples, prior to tracking down some contamination. (And her study came out seeming really thorough).

    There are (as readers of this threads will now have realised) lots of different points that can be debated, but with the BWG results and the pile of negative studies, the weight of evidence is strongly against an association between CFS and HGRVs. I don't know how much debate over the finer detail of things is really worthwhile (although I do often enjoy debating things, regardless of whether this does any good).
  16. Waverunner

    Waverunner Senior Member

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    Wouldn't it be nice to actually confront some scientists with these arguments and let us know the answers? In this case we have the chance to actually confront some scientists because there are many of them who made comments about XMRV. I would really enjoy reading an answer from Prof Racaniello to Marks comment.
  17. currer

    currer Senior Member

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    I think Racaniello might have some problems with that given Mark's fiendish intelligence!

    http://www.virology.ws/2012/05/18/cleaning-up-after-xmrv/#comments
    Eigerwand writes here that Mikovits and Ruscetti wrote to Alberts defending their work, but that the letter was not published - despite having been sent in good time - and the Science paper suppressed.(I wont say retracted because that suggests the authors acquiesced in this process)
    http://www.sciencemag.org/content/334/6063/1636.1.full
    Does anyone have any further information about this letter?
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  18. barbc56

    barbc56 Senior Member

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    Yeah, we could debate until the cows come home. Let's look at the bigger picture. Science is showing that xmrv is a contaminant, not harmful and not related to CFS/ME/Prostate Cancer. That does not mean another RV/virus whatever isn't responsible but specifically talking about xmrv.

    Mark, I have to admit that in this thread, I find your defensiveness and inablity to see that sometimes with this DD we get foggy due to pain, exhaustion, whatever, so it doesn't warrent the personal criticisms from you. Perhaps just stating the facts? You gave me this advice and it's helped me keep my perspective.

    But then we are only human. Take care.

    Barb C.:>)
  19. Mark

    Mark Acting CEO

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    Certainly a big problem, but notable that this was just one failed experiment, and a small one, and the upstream parts of sample collection, storage etc weren't under her control, plus the timing and circumstances made it difficult for the WPI. It's certainly a massive problem for Mikovits, and I did in fact say right from the outset that this kind of blinded test should have been done immediately, incorporating samples from multiple diseases, and this was a logical imperative that this was the right thing to do. But I don't think the BWG results can be considered conclusive; BWG plus Lipkin, maybe...

    That's absolutely right.

    I think I should emphasise that my above long discussion doesn't especially point to conclusions about who is right and who is wrong, precisely for the reasons you cite.

    What the criticisms of the negative studies do highlight, though, is that the flaws in methodology which we all highlighted here were valid, and that the negative (pseudo-replication) studies are at least as open to criticism as the positive studies - more so, I would argue, since there is a longer list of flaws for them.

    That's important because it is unfair that Dr Mikovits has received the criticism that she has and the implications of being a bad researcher: for multiple reasons, that just isn't a fair deal at all. Anything she may have done wrong, absolutely everybody else did wrong as well, and nobody knew it was a problem until these studies all highlighted the issues.


    You're right that Singh highlights that all studies failed to treated samples equally, and that the difference between the batches can potentially explain such discrepant results as the positive studies.

    I am not sure about the Huber example you cite, that's of great interest, that detail will be key to pin down, because as I just noted here:
    http://forums.phoenixrising.me/inde...-maureen-hanson-david-bell.17574/#post-267836
    as far as I'm aware, every one of the 7 published studies reporting positive detection results found more in patients than in controls. As you mention, Singh did at first too, and actually I thought Huber had at first too; those examples are additional to the 7 I mentioned. The chances of all the batch discrepancies affecting patients rather than controls are less than 1%. So we need a whole bunch of studies which found more in controls than in patients, but didn't tell anyone, to redress this probabilistic anomaly.

    I'd like to be a little more precise and say that the weight of evidence is that there is no clear evidence of an association between CFS and XMRV or MLVs, and no evidence demonstrating an association between CFS and HGRVs. But I haven't seen any evidence against an association between CFS and HGRVs in general.

    But I guess you're right, the debate probably isn't terribly worthwhile at the end of the day; like you, I do just find it fascinating and intellectually stimulating, really...
  20. Mark

    Mark Acting CEO

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    It would: I suppose I'm guilty here of living in a bubble and not engaging elsewhere; I should post those comments on Virology blog really. I just post this stuff in my spare time really, I happen to have a day off and have spent it musing about XMRV because I enjoy that. But this thread is public domain; I have to turn my attention back to the mundane tasks of a jobbing moderator now really, but anyone's welcome to invite a response from Racaniello to my posts. I hope I wasn't too harsh on him, if he does read it; I do think he has generally done a good job and I appreciate what he's doing in terms of communication, it's a really refreshing thing and I wish there was more of it about.

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