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Post XMRV - For those that think this is dead...

Discussion in 'XMRV Research and Replication Studies' started by JT1024, Oct 16, 2011.

  1. Bob

    Bob

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    Surely it would be better to say that "we currently have no conclusive evidence that HGRV's exist", rather than saying that they don't exist?
    That seems like a reasonable approach to me.
    To say something doesn't exist in science, just because you don't have complete evidence for it, seems wrong to me.

    In physics, they are always looking for yet-to-be-discovered but predicted sub-atomic particles, such as the 'Higgs Boson' which they currently have no physical evidence for, but only theories or hypotheses that the particle fits into.
    They don't say that the Higgs Boson doesn't exist at the moment, because that would preempt the search for it, and pre-judge the outcome of the research... They say that it could potentially exist but that they don't have physical evidence for it; and that they are currently looking for physical evidence for it.
    If a scientific consensus develops for some other theoretical model of physics, that the Higgs Boson doesn't fit into, based on findings in the actual physical research, then there might be a consensus that the Higgs Boson doesn't exist, in which case they would say that the Higgs Boson doesn't exist.
  2. Bob

    Bob

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    I'm not quite sure how the statement, quoted earlier (that HGRVs don't exist), fits with the prostate cancer research and VP35 and VP42 - Weren't VP35 and VP42 full HGRV sequences taken from human tissue?

  3. currer

    currer Senior Member

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    No-one knows whether viruses are "dead" or "alive"! Good question.
  4. currer

    currer Senior Member

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    Esse essentiae et esse existentiae, eh?
  5. Bob

    Bob

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    Is that an HGRV genetic sequence? :D
  6. currer

    currer Senior Member

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    Equally opaque and incomprehensible!
  7. Mya Symons

    Mya Symons Mya Symons

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    I would love for there to be a scientifically proven reason for this disease, even a retrovirus like XMRV -- to finally have an answer would be quite a relief. However, here is why 90% of me stopped believing: There were too many excuses! First, the other scientific research was wrong because they had the wrong cohort (due to them having the wrong definition of CFS); then it was the wrong PCR; then the wrong equipment (such as test tubes); then it was the wrong temperature; then the other side was mistaken because they weren't culturing the virus before PCR (this was said to be the only way to find it); and now it is because the antibody test (the VIPdx test) was faulty (this is why she could not distinguish between the positive and the negative samples? Why wouldn't she say something about the test before this?) Am I forgetting an excuse? I think I am. It is just too much! Further, whether you like ERV or not, she made a good argument (the matching slides).

    Now there is still 10% of me that wants to believe in XMRV. This part is telling me to reserve judgment until Dr. Lipkin is done with his study. Nevertheless, if the results of his study are negative, then that is it. I think that even the majority of those with CFS will know that it is the end of XMRV. Unless, of course, you can find another reputable scientist (not Judy Mikovitz) who can isolate the virus in another way and then prove to the world it does indeed exist.
    wdb and barbc56 like this.
  8. currer

    currer Senior Member

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    It is true that the Urisman et al paper claimed to find VP35, VP42 and VP62 in prostate cancer tumor tissue.

    Another point I've just noticed is that Urisman states that the XMRV sequence is not found in human genomic DNA, and none of the HERVs bear any significant similarity to the XMRV genome.
    (Didnt someone bring this question up a while back?)

    Interestingly, the paper points out that the genome is most similar to DG 75, a MLV from a human B - lymphoblastoid cell line.
  9. currer

    currer Senior Member

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    Mya, it is common for initial conceptions to change over time as new information (positive or negative) comes to light.

    For example, the Urisman / Silverman paper on prostate cancer and XMRV said that XMRV preferentially infected the R462Q genotype for RNaseL.
    But Singh showed that this was not the case.

    No-one has made a fuss about this.
  10. Lee

    Lee

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    "it is common for initial conceptions to change over time as new information (positive or negative) comes to light."

    Right. In this case, the initial conception after the Science paper, was that there was a specific retrovirus that looked like it was infecting ME/CFS patients at high percentages, and non-patients at about 4%, and might be a threat to the blood supplies.

    More than a dozen labs jumped in to confirm - presumably because if Lombardi 2009 was correct, this was hugely important to public safety, and also because there were career science possibilities here.

    We got negative after negative, after negative after negative after negative. From very good virology labs, nothing but negatives. Serology, PCR - negative. Only Alter and Lo found anything - and when presented with blind samples they were unable to replicate their results. And when presented with blind samples, the authors of the initial paper were unable to replicate their results. And the only part of the initial paper that actually identified the virus, was shown to be due to contamination, and withdrawn. And no additional published work from the initialting lab.

    So yes, currer, the initial conception has changed, from - 'oh hell, that's scary if its true, let find out' to 'there's nothing there' and a lot of irritation about the changed stories and excuses and modified descriptions of methods and sloppiness and - it turns out - omission of details like use of a methylating agent, and intentional misrepresentation of publicly presented data - that led to millions of wasted dollars and thousands of wasted man-hours of really smart productive people who spent this time accomplishing nothing other than to show it was a waste of time.
  11. Bob

    Bob

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    If this is the case, then it makes me wonder, even more, how relevant the 5AZA issue is - If the use of 5AZA exposed a human endogenous retrovirus, then that would be a known human DNA sequence, and not a MLV p30 gag protein sequence.
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  12. Bob

    Bob

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    - that led to the discovery that XMRV is a man-made novel retrovirus that infects human tissue, that contaminates many labs and is produced in a widely used cell line...
    - that possibly led to averting a potential outbreak of a novel human retrovirus and a new human disease somewhere in the future...

    That's money well 'wasted' in my opinion.
    jace likes this.
  13. Lee

    Lee

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    Bob, the only sequences reported in 2009 were contaminants. All the reported sequence was VP62.

    Everything else was serology. JM et al originally claimed that the serology was specific to XMLV, and they had adequately controlled for cross-reactivity.

    Then when it was shown that there is no XMLV, JM claimed it was crossreacting and detecting 'HGRVs'. So much for having adequately controlled for cross-reactivity.

    But if the reagents could cross-react to some unknown 'HGRV,' they could also cross-react to hERV sequences. Every serology result in 2009 can be explained as cross-reactivity to expression of ERVs induced by demethylation. Every one of them. But JM hasn't said where she used 5AZA, only that she did use it and didn't bother to tell us, and that it isn't important.
  14. Lee

    Lee

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    "that led to the discovery that XMRV is a man-made novel retrovirus"

    Its not man made - it is a result of a recombination during passage of human tumor cells in mice. retroviruses recombine - this is a recombination event. its cool that they were able to detect the actual recombination by comparing cell lines stored before and after it happened. And the work that discovered this came from the Prostate Cancer research, not JM et als work.

    "that doe that infects human tissue,"
    In culture. Exposure to human sera inactivates it, and there is no evidence that it infects humans. There is not one reproducible experiment finding it or anything like it in humans.

    "that contaminates many labs and is produced in a widely used cell line..."
    Which information came from the prostate cancer work, primarily. Jm et als work was essentially meaningless in this.

    "leading to possibly averting an outbreak of a novel human retrovirus and a new human disease somewhere in the future..."
    What outbreak? XMLV is not in humans. There is no evidence that it infects humans. There is pretty good evidence, the serum inactivation, that it can't infect humans.

    Waste of time.
  15. Bob

    Bob

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    Oh yes... and if there was a contaminant present, the 5AZA could uncover a non-human ERV sequence. Thank you for explanation.
  16. Lee

    Lee

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    "he 5AZA could uncover a non-human ERV sequence."

    What non-human ERV sequence?

    There was VP62 plasmid as contaminant, in the PBMCs used for PCR and sequence analysis. VP62 is a plasmid, not a virus. Use of 5AZA would not cause VP62 to express any proteins. her eon earth would there be a 'non-human erv sequence?' To get non-human erv expression induced by 5AZA, there would need to be non-human cells at significant numbers in the sample.
  17. Bob

    Bob

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    Well, it was created in a lab as a direct result of human activity and scientific research.
    So it just depends on how you define 'man made'.

    If human sera inactivates it, then that does not mean that infection is impossible. Have you not seen the monkey studies where the virus is quickly cleared from the blood but lives in tissue?

    There are plenty of research papers that have shown that XMRV can infect human cells.
    Indeed, 22R1 is a human cell line.

    Also, you are forgetting the various prostate cancer studies, which we cannot yet dismiss.

    But it wouldn't have happened in this time frame without the high profile CFS study.

    I should have added the word 'potential' - a potential outbreak. XMRV can infect human cells, so it has the potential to become a wild virus very easily, if it hasn't already. It can infect human cells, and the monkey model suggests that it might live in tissue even if cleared from the blood quickly.

    And don't forget the prostate cancer studies.
  18. Bob

    Bob

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    OK, I understand your point now...
    Protein expression can only be induced by 5AZA if a complete cell is present...
    And the issue here is cross-reactivity with human ERVs.
  19. Angela Kennedy

    Angela Kennedy *****

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    No - this is a highly ideological spin on what actually happened, and is easily contested.

    The first 'negative' paper was published in indecent haste, for just one example. They did not replicate. They used a COMPLETELY DIFFERENT COHORT than the Lombardi team and different methodology. Key co-authors had a vested interest in negating a biomedical causation to ME/CFS, because they are known proponents of psychogenic explanations for this illness.

    After this, the cohort and testing methodology were NOT replicative of Lombardi et al for the negative studies that followed. In addition, the various authors of the negative papers immediately began trumpeting these negative findings in the press (away from the DATA Lee, away from the data) as 'proof' that there was no association of XMRV with CFS, at a time when the DATA and the problems with METHODOLOGY demonstrated no such thing.

    Inevitably, the ME community became suspicious. I will refer you to my signature here for an excellent summation of what has bothered patients about this debacle.

    And this all takes place in a context in which biomedical research for ME/CFS is grossly underfunded and never followed up, and where biomedical evidence of organic disease is constantly ignored in favour of fundamentally flawed psychogenic explanations.

    All this money was not spent on attempts to confirm, but to 'disprove', but in doing so, they did not replicate, so their methodologies were incorrect. The testing methodology and the cohort selection were too different from Lombardi to be called replication.

    And the plebs (that's us, ME sufferers and their supporters) had to sit and watch that, KNOWING the methodologies were all to cock.

    And that's why so many people are scandalised by what has gone on. And why your story above is incorrect.
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  20. alex3619

    alex3619 Senior Member

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    Hi Lee, on this point specifically. Rhesus macaques also have the capacity to inactivate it in blood. Their blood is clear in only three weeks. Their tissues are infected however. It does not prevent infection, it limits it. There is no reason to think humans are any different, and so under the precautionary principle it should be presumed it can infect humans until it has been proven it can't ... and that has not happened yet. This is still the case even if no humans have yet been infected.

    On the arising of the virus during cell passage as a result of recombination, that is an hypothesis. It has some evidence. It may or may not be correct. The evidence for Lombardi etc was stronger than the evidence for this, and yet look at the challenge it faces now. The recombination theory deserves just as much scepticism. That does not mean they were not right, it means we should not meekly accept the results just yet.

    Bye
    Alex
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