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Could this be an early XMRV? The JHK virus

Discussion in 'XMRV Research and Replication Studies' started by currer, Aug 15, 2011.

  1. currer

    currer Senior Member

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    Eco, noone has ever suggested that the JHK virus derives from XMRV.

    Thse significance of the JHK virus is that it shows that there are many variant murine leukaemia viruses which have tropism for human cells and have been found in human cells and cell lines.

    It seems to me there is a concerted effort going on to "disprove XMRV" by pretending that supporters of the HGRV hypothesis believe that all HGRVs are descended from one original crossover event (XMRV) and that this hypothesis can be disproved if it can be shown that XMRV is not related to other mouse derived viruses found in humans.

    This is also the aim of the Paprotka paper, to pretend that MLVs cannot be infecting humans if one variant can be shown to have been created in lab. mice at a particular time.

    But all Paprotka shows is that MLVs that can infect human cells are readily created in labs that carry out zenografting, and the inference must be that this has happened many times before, and that we are justified in searching in humans for signs of infection by variant X/P-MLVs.

    It is probable that there are many HGRVs, and that there were multiple crossovers into humans. Indeed, there were about eighteen infected human cell lines at the last count, and they were NOT all infected with the same P/X- MLV.

    You are mistaking nomenclature for reality.
    But the reality is what is real, controlling nomenclature will not control the truth of the situation.

    Though this is the attempt at control that we are witnessing. To control knowledge of what has happened by controlling the naming of "XMRV".

    It is just a big disinformation campaign. We need to keep the knowledge of what has truly happened alive.
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  2. RRM

    RRM

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    No, but you have suggested (in your opening post) that XMRV derived from JHK. This is clearly not the case.

    This is actually very much supportive of the notion that these are contaminants generated in the lab instead of genuine human pathogens.

    The irony is that the exact opposite has happened. As far as I know, everybody agrees that Paprotka et al. only applies to "true" XMRV.

    It is in fact the apparent obsession with the Paprotka et al. study by some of the "haters" that go on and on about the study. For instance, a very strange letter has been written to the editor of Science, 'rebuttals' have been posted all over the place, I have seen youtube videos that supposedly show that the study should be retracted for a nonsensical reason and I have even seen the occasional avatar with a screenshot of the paper with a big red cross obscuring it.

    Paprotka et al. is a very comprehensive study that is probably the best to date in this specific field. However, any claims about other MRV's are not directly attacked by Paprotka et al.

    Yes, and this supports the notion that these are not genuine human pathogens. Of course, theoretically, one of these viruses could jump from the lab to humans but there is no real evidence that this has occured.

    I am sure that 20 years from now, a handful of people will still think this was an organized campaign to bury the brilliant and groundbreaking findings.

    But for those, please remember how lucky the evil forces must have been with these viruses that were below the limit of detection (phew, that would have blown the lid of it), the antibody response which is below the limit of detection (phew again, and let's hope it stays that way or we're still gonna be exposed), even when they're not below this limit they go in and out of the blood, or hide in tissue, or disappear out of the sample because of the blood collection protocol, brand of tubes, freezing and thawing of samples, etcetera.

    Imagine that Mikovits (and/or Ruscetti and/or) would have been able to reliably detect these viruses in patients when being put to the test.

    John Coffin and most of the retrovirological field would have looked like fools for not being able to detect what these few people could detect.
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  3. RustyJ

    RustyJ Contaminated Cell Line 'RustyJ'

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    Yet we still have the same handful of posters, who are not patients, who have very little regard for me/cfs, who are always around to correct the slightest variance from the party line. What is so important that this policing action must be maintained?
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  4. RRM

    RRM

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    I don't see how you can regard this as "policing action".

    I don't have a problem whatsoever with people believing whatever they want to believe. However, posting one's beliefs on a public forum, or at public blogs, or at publicly available news articles goes further than that. When you are doing this, you are trying to persuade others to adapt your beliefs. And when you do that, you must welcome rational discourse from people that don't agree with you.

    If you don't accept this by questioning the motives of others, then, rather ironically, it is you who is engaing in "policing action".
  5. Bob

    Bob

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    RRM, I think that there is still a major question that hasn't been answered, that we need answered, in relation to this research.

    The question is: Have any XMRV-like or MLV-like retroviruses infected humans in the wild? (and if so, what are the consequences?) (ok, that's two questions!)

    It doesn't seem sensible to dismiss these questions. Especially when so little is known about these new viruses/variants being discovered in human tissue and cell lines.

    And it seems more than likely that any potential human infection with MLV-like viruses might follow the macaque model of infection, such that the virus disappears from the blood, and resides in tissue/s, possibly as a latent virus. This could possibly make the virus almost impossible to detect in human blood samples, even using the most advanced techniques, as latent viruses, by definition, are not easily detectable. (I acknowledge that this would not explain Mikovits and Ruscetti's research findings using human blood samples.)

    Seeing as very little research has been done with human tissue in this field, and seeing as Dr Singh has performed a very strong XMRV research study using human tissue, it does seem a little premature to deny these questions.

    It seems to me that there are many questions to be answered, and that this research is still in its infancy.

    At the very least it is important to highlight the dangers of using so many cell lines that are infected with potential human retroviruses, that have already been demonstrated to have tropism for human cells.

    And, as there is a consensus that XMRV does have tropism for human cells, then it seems sensible to make sure that XMRV has not infected humans, and does not exist as a latent virus, hidden in certain tissues.

    For many of us, these questions have not been fully answered yet.



    Even if Mikovits and Ruscetti have only detected contamination in their studies on human samples, that still does not resolve many unanswered questions in the wider field of MLVs and MLV-like viruses.


    I'm pretty sure that it has not been proved that XMRV was created within the 22RV1 cell line. It is said that MLV recombination events occur very frequently (i.e. all the time), and that there are very many recombination possibilities that could have led to the creation of XMRV. (Didn't the Switzer paper explain this to us?)*

    But even if XMRV was created in the 22RV1 cell line, then that doesn't mean that it, or very similar MLV-like viruses, couldn't have also infected humans.


    It seems to me that as they are only just detecting these novel MLV-like viruses and variants in human cell lines, then this research is really in it's infancy, and it has possibly peeled off the lid of a very large can of worms, in terms of contamination and potential human infection. At the very least, this research may have prevented a future human health catastrophe.





    * I might have missed some relevant discussions about recombination possibilities, because I haven't been following these discussions recently. If there is something that I should read, could someone please give me a link?
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  6. Enid

    Enid Senior Member

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    I think it is a can of worms here too Bob until all the reseearch and findings are revealed.
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  7. RustyJ

    RustyJ Contaminated Cell Line 'RustyJ'

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    This is a forum for me/cfs patients (says so at the top of the page). My beliefs are related to my illness, as are 99.9% of members on this site. Yours are not. As regards the policing action, I post on a wide variety of topics related to me/cfs and my search for answers to this illness, whereas you only post to 'correct' XMRV-related comment.

    Questioning the motives of those on the other side of a debate is a rational response when there is distrust, or no reason for trust. For example there is a requirement for researchers to state conflicting interests when a study is published. And certainly the need would not be there, if researchers were always honest.

    Perhaps we should demand that those with interests contrary to me/cfs patients state their conflicting interests in their post signatures.
  8. Bob

    Bob

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    When someone posts their 'beliefs' on a forum, it is not necessarily to try to persuade others to adapt to their beliefs.

    It can be simply a case of wishing to exchange ideas, wishing to explore ideas, wishing to develop one's understanding or wishing to further one's knowledge etc.
  9. RRM

    RRM

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    If the objective was truly to (merely) exchange ideas or to further one's knowledge (and not to advance a viewpoint), then surely ideas from persons that do not agree with him/her should be welcomed. Moreover, there is a easy to use ignore feature and a thread specifically designated for "constructive" XMRV talk if one is really not concerned about convincing others.

    So, while your additional reasons are certainly valid, I never stated that advancing one's views is always the sole purpose of discussions like these.
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  10. RRM

    RRM

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    It is sensible to now dismiss these questions. In science, nothing is absolute, and sure enough there is always the possibility that future research proves everybody wrong, but after an very extensive effort by many experts in the field, it's safe to conclude there is simply no evidence to support the notion that these retroviruses are infecting humans.

    If we would have (an unlimited budget and have) to screen for anything, it would be much wiser to screen humans for monkey viruses, in my opinion.

    You may find this, but I strongly disagree. If Mikovits (or the others) again fail to reliably discriminate between patients and controls, it is over regarding ME/CFS, and rightly so.

    Of course Mikovits may dedicate the rest of her career to studying these viruses in humans but not many other scientists will waste their resources pursuing this dead end.

    But the "hunt" is/was caused by the original ME/CFS and PC findings. If any of these findings are true, they should be reproducible. If nobody can reproduce them and the original scientists also fail at doing so, there is really no reason to just keep on going for the sake of it.

    Again I can't agree. The problem with the PC tissue findings is that they represent "true" XMRV, and as such are directly affected by the Paprotka et al. paper (unlike Lo et al.'s findings, for instance).

    Besides, the single study that seemed to independently support these findings through reporting human integration sites, was marred by contamination.

    No, this is not what the Switzer paper showed.

    The generation of XMRV through a recombination of preXMRV1 and preXMRV2 is about as certain as certain can get. Just as you consist of a (unique) combination of your father's DNA and your mother's, XMRV is a unique combination of preXMRV1 and preXMRV2.

    What can be discussed (although this is also near-certain) is where and when this recombination took place: In the 22Rv1 cell line or one of its ancestors (extremly likely), in another event in the lab (extremely unlikely), or in a "natural" event (more extremely unlikely).

    Anything is possible, really. It just is incredibly unlikely because of several lines of independent evidence.
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  11. Bob

    Bob

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    RRM,

    Absence of evidence is not evidence of absence and so, for this reason, your assertion that "it's safe to conclude there is simply no evidence to support the notion that these retroviruses are infecting humans", is not only wrong in my opinion, but it is totally irrelevant to a discussion about whether further research should be carried out.

    I do not agree with your view that MLV research has been thorough enough to dismiss the possibility that MLV-like viruses have infected human beings.

    But maybe we just have to disagree about that.


    I do agree with you that if Mikovits and Ruscetti do not get any meaningful positive results in the Lipkin study, then not many researchers will continue with XMRV research. That seems fairly obvious. But it will still leave unanswered questions, such as Singh's prostate cancer study.

    If the Lipkin study is negative, then I expect that many of us will then look forward to the results of Lipkin's other study, and focus on other interesting research, such as the Rituximab research. There seems to be an unusually large amount of very interesting research in the pipeline at the moment.

    But even though there is very much other interesting research in the pipeline, MLV research is still very interesting, whether it's related to ME or not. And there are still many unanswered questions.

    You say that the XMRV studies should be reproducible. I agree. But the prostate cancer studies have been reproduced. And that includes at least one very strong study, by Dr Singh. The research does seem to have stalled, and I agree that we would need more studies published. However, the prostate cancer studies have not been withdrawn or discredited, so I am of the opinion that it is definitely worth following up these studies.


    Most of your argument seems to rest on the Paprotka study. I think you are relying too much on a study which is based largely on assumptions and conjecture.
    The paper was not entirely based on hard evidence, and it was was not a conclusive paper; nor did the authors pretend that it was conclusive.

    Switzer, in a number of published papers/abstracts, strongly contradicts the Paprotka study.

    Switzer's paper that I referred to in my previous post (Prosperi et al) questioned the certainty and validity of the Paprotka study. Actually, it basically destroyed the premise and conclusions of the Paprotka study. (See details and quotes below.)

    It cannot be safely assumed that XMRV was created only from preXMRV1 and preXMRV2, unless you can find both of those viruses in a substrate that has had contact with, or is directly related to, the 22RV1 cell line.
    If you cannot find the two pre-viruses in the vicinity of the 22RV1 cell line, then other possibilities must be considered.
    Switzer says that XMRV could have originated in a myriad of different MLV recombination events.

    So XMRV is not necessarily a "unique combination of preXMRV1 and preXMRV2". This is just one possibility. You seem to be assuming that the second half of XMRV must have come from a single genetic source. But it could be a result of many other recombination possibilities, as per the Prosperi et al study. For example, it could be a recombination of preXMRV1 and genetic material from two other viruses.

    I don't see why it is so unlikely that XMRV could have been created somewhere, and then transmitted to the 22RV1 cell line. Why is that so unlikely? The Paprotka study cannot rule out this possibility. Actually the Paprotka study is a very weak study.

    One of Switzer's papers concluded that XMRV is a result of evolution in the wild, and he has published the relevant sequences in genbank. He concludes that his sequences are from a wild human virus.

    In his published study, Switzer specifically says that the XMRV sequence variation that he has detected is "consistent with virus evolution during spread and persistence." Switzer's evidence and conclusions directly contradict Coffins and his co-authors conclusions in relation to there being no variation in any XMRV sequences. Switzer indicates there is evidence of virus evolution expected during normal human infection in the wild.

    "the finding of a viral strain in three prostate cancer patients that is distinct from the XMRV seen in previous studies is significant and demonstrates a broader viral diversity. This would be an expected result consistent with virus evolution during spread and persistence."

    And this is another extract that contradicts Paprotka et al:

    "Conclusion:
    Given the evidence of inter-tropic recombination in MuLV, detection and classification of recombination in XMRV using different MuLV tropism prototypes should be interpreted with caution ... These results suggest that identification of parental strains of the potential recombinants is difficult and that recombination in the highly genetically related MuLV have been occurring for some time."



    So my conclusion is that there are very many unanswered questions, and no straightforward or certain answers.

    The field seems to be wide open, with a myriad of unanswered but intriguing questions. I honestly don't see how anyone can say that there is nothing interesting or important to research here. It's like a scene out of the Naked Gun movie: "move along, there's nothing to see here." I agree that the ME-related research has not been replicated successfully enough to be convincing, but when looking at the whole body of MLV-related research, it is definitely worth exploring further and seriously.

    It seems to me, RRM, that you may have based your opinions and conclusions on an incomplete picture of the total body of research.



    Sources:

    No Association of Xenotropic Murine Leukemia Virus-Related Viruses with Prostate Cancer
    William M. Switzer, Hongwei Jia, HaoQiang Zheng, Shaohua Tang, Walid Heneine
    http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019065#abstract0

    Murine leukemia viruses (MuLV) and Xenotropic MuLV-related viruses exhibit inter-tropic complex recombination patterns
    Mattia C F Prosperi , William M Switzer, Walid Heneine and Marco Salemi
    6 June 2011
    Abstract presented to the '15th International Conference on Human Retroviruses: HTLV and Related Viruses'
    Retrovirology 2011, 8(Suppl 1):A235doi:10.1186/1742-4690-8-S1-A235
    http://www.retrovirology.com/content/8/S1/A235

    Extensive Genetic Recombination in the XMRV Genome
    William Switzer, W Heneine, M Prosperi, and M Salemi
    http://retroconference.org/AbstractSearch/Default.aspx?Conf=20&Abs=40126

    "Conclusions: Our results suggest that XMRV is a complex mosaic resulting from multiple recombination events, possibly occurring over a significant period of time. More research will be necessary to further investigate the mosaic structure of XMRV and to determine if recombination occurred before or after crossing into humans. In addition, caution should be taken when using small genomic regions for phylogenetic inference of MLV and XMRV tropism since this analysis may be influenced by viral recombination."
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  12. RRM

    RRM

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    No, it isn't, and this is in fact a very fundamental scientific notion. I cannot prove that there is no invisible pink elephant virus in your blood - there is just no evidence that there is. Likewise, nobody can prove that there are no "MRV's" of unknown sequence diversity at undetectable levels in unknown parts of humans.

    No, it does not.

    One of the problems on other similar forums is that they make it very easy to reinforce one's beliefs. Some people make a (faulty) analysis of certain studies but the problem is that this analysis is not really critically examined by others. People agree with this position and this reinforces the position of all the people involved.

    In this case, the conference abstract does not at all contradic the Paprotka et al. findings (and on a side note, it is worth mentioning that both conference abstracts really refer to the very same study). The 'difficulty of identifying parental strains' that the conference abstract mentions, refers to phylogenetic analyses based on partial sequences. In the case of Paprotka et al., the parental strain was not identified based on phylogenetic analyses at all. Like I explained, the fact that XMRV is the perfect combination of preXMRV1 and preXMRV2 clinches the deal.

    Although this is more of a appeal to common sense, I think it is also worth mentioning that Switzer orally presented this very study at CROI 2011 (were Paprotka et al. was also first presented). In fact, Switzer sat on the very same discussion panel as Pathak to discuss the state of XMRV research after he had presented this study and a day after Pathak presented Paprotka et al. I would wonder why Switzer failed to raise any questions about Paprotka et al., not even pointing out that there was some data out that questioned the Paprotka results.

    If you really feel that this Switzer study destroys Paprotka et al., how do you seriously account for Switzer failing to even mention this at CROI (or thereafter)? Is it because Switzer or anyone else seeing both presentations was just not smart enough to see this obvious contradiction? Is it because he wasn't "allowed" to do so (or something similar) in order to "bury" the findings? However, in that case, it doesn't make sense at all to release a conference abstract that makes it apparently obvious to anyone reading it that it destroys the offical party line.

    Or is it that, perhaps, some people are misinterpreting this conference abstract?

    Yes, it can.

    Even if tomorrow it is somehow conclusively proven that these two pre-viruses were not in the vincinity of the 22RV1 cell line and that Paprotka et al. is wrong after all, it would mean that preXMRV1 and preXMRV2 formed XMRV somewhere else, not that it was formed by the recombination of two other viruses (or any other evolutionary mechanism).

    There are several things pointing against this, but your alternative hypothesis also fails based on heuristic principles (i.e. Occam's Razor). Because it is hard to explain this, I'll give an example.

    Suppose I support the idea that HIV was brought into the human population through vaccines. Suppose that tomorrow, someone conclusively shows that a monkey (or rather two, for both strains of HIV) is responsible after all, and even I agree with the data. Then still I could "easily" maintain my hypothesis by arguing that perhaps, a vaccine infected man, and this man then infected the monkey, which then infected another human that spread it to the rest of the world.

    There is really no "need" for adding another layer to the hypothesis without any evidence backing it. Yes, it could be true (as for every true hypothesis there is an unlimited amount of false ones), but would you not consider this to be extremely unlikely without any data backing it up?
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  13. Bob

    Bob

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    RRM, your whole argument seems to rest entirely on the Paprotka study.

    A study that is not absolutely conclusive, and which provides little hard evidence for the origin of XMRV.

    The conclusion of the study is almost purely theory and conjecture.

    I've just re-read the Paprotka study, and it is stronger than I previously thought it was.
    (I should know by now not to base my discussions on my memory of complex research papers!)

    However, it's conclusions are not absolute. They are based on hypothesis and theory, with some inconclusive supporting physical evidence.

    The following quote from the paper proves that it is not a conclusive paper:
    "The alternative possibility is that recombination between PreXMRV-1 and PreXMRV-2 occurred during mouse evolution, giving rise to an endogenous XMRV provirus that is present in mice and can occasionally infect humans."

    The authors do make a stronger conclusion than I had thought:

    "Because the probability that the same recombination event could occur independently by random chance is essentially negligible, any XMRV isolates with the same or nearly the same sequences identified elsewhere originated from this event.

    However, I question whether it is sensible to rely on a conclusion, in a single paper, that is based on theory.

    (Note that the conclusion does not apply to XMRV sequences with a wider genetic diversity:
    "...any XMRV isolates with the same or nearly the same sequences ... originated from this event")

    I think it is an interesting study, that may be helpful, but it certainly doesn't tell us anything conclusive about XMRV. Not without further research anyway.

    It is not possible to come to an absolute conclusion that XMRV was created from two preXMRVs in that specific cell line.

    The Paprokta study just doesn't conclude that based on hard evidence, but only by using hypothesis and theory.



    We are told all the time that we can't rely solely on a single positive XMRV study, and that Mikovits' work needs to be replicated.

    But, RRM, you are relying on the Paprokta study for your whole argument against the need for further XMRV research.
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  14. RRM

    RRM

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    No, it doesn't. The simple fact is that the Paprotka et al. conclusions would be completely annihilated by Mikovits (or any of the others) if she could reproducibly find XMRV (or HGRV's) in samples. The fact that she (or anyone else) can't is really the fatal problem.

    By the way, I have clearly stated above that the Lo et al. findings were not directly affected by Paprotka et al. It is just that the many people apparently feel the need to attack Paprotka et al. without good reason, that it may seem that I myself seem to rely on it so much.

    This is a bit of a semantic trap, as literally speaking, any conclusion is basically some sort of purely theoretical conjecture (that may or may not rely on actual experimental evidence). If you mean that the conclusions of the study are not backed by experimental evidence then I obviously disagree.

    On a side note, pure theory and conjecture is exactly what can be observed in certain discussions about all of the 'negative' studies. Without any experimental backing, people try to explain the overwhelming evidence away.

    First, this is an obvious strawman. I specifically divided two hyptheses: a) preXMRV1 and preXMRV2 are the "parents" of 22Rv1 XMRV, and b) the recombination event happened in the 22Rv1 cell line. I specifically stated that the first conclusion was more certain than the second. Therefore it really is a fallacy to say that I asserted that it was absolutely certain that XMRV was created in that specific cell line.

    Second, the Paprotka et al. study does not merely 'hypothesise' this. From the actual Paprotka et al paper. (bolding mine):

    You may be confused by a part of the paper in which the authors indeed say they hypothesize this. However, this is how science works: first you hypotheisize, and then you observe if the data backs up your hypothesis. If it does, then you conclude that the hypothesis must be right. When you read back this part, you'll see that the authors did exactly this.


    Again this is a strawman, as this is not my position at all. I am not saying that one should 'soley rely' on Paprotka et al. (see above and my earlier posts). The fact of the matter is that the study is in itself independently confirmatory of the hypothesis generated through other experiments, and subsequent findings (for instance by Dusty Miller) are consistent and confirmatory of the Paprotka et al. study.

    As such, I would rather see it as a piece of a large puzzle. Yes, it was an important piece in the sense that it made the whole picture more understandable and this also made it easier to fill in some of the other gaps in the puzzle. But even without these findings, I would still be completely satisfied that the results of Lombardi et al. were not true.

    No, that is simply not true. preXMRV1 and preXMRV2 were both not just partially sequenced. There was some talk at the other forum about one of the two sequences being constructed togther from multiple sources, but this is clearly not true and is based on a misunderstanding of some of the data/figures in the paper.

    Incidentally, I was the one that posted this study at this forum.

    But I try to refrain myself from addressing minor points as to not make my posts even longer.

    With this study, I think it is most important to note that this is totally incosistent with some sort of disinformation campagin and scientists having to conform to the "party line". Switzer found some sequences, thought they weren't contamination and "just" reported his data.

    Switzer's study is just one of some that find "something", but the problem is that many of these "positive" studies really contradict each other completely on other fronts.

    As for your "extracted from wild XMRV" comment, I genuinely do not understand what you mean by that.
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  15. Bob

    Bob

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    RRM, A crucial point that you have conveniently overlooked, is the fact that Switzer's published study concluded that the XMRV sequences that he has detected, and put on genbank, were extracted from wild, evolving XMRV viruses.

    The Paprotka study is only relevant to VP-62, so Switzer's findings make the Paprotka study irrelevant to the arguments you are making against continuing XMRV research.

    Switzer's research, and his published XMRV sequences, concludes that his XMRV sequences are extracted from wild XMRV viruses, that have been evolving, and are therefore not identical to VP-62 found in the 22RV1 cell line.

    This is a crucial point that cannot be ignored.

    Even if Switzer was only detecting contamination, he has still uncovered enough variation in his strains of XMRV to show that XMRV is evolving somewhere, and so it likely exists and replicates in a source other than the 22RV1 cell line.

    So we have conflicting evidence, and a wide body of evidence, and you are only focused on the (inconclusive) study that suits your own point of view.


    And as I said earlier, I don't understand this desire to see XMRV research halted.

    Even if there is no XMRV VP-62 in the wild, and even if no ME patients have been infected with MLV-like viruses, the field of MLVs is a huge and important one that will continue to be researched by many scientists.

    The very fact that XMRV is not a mouse virus (as far as we know), but is a novel MLV-like virus that infects human tissue, is both startling and intriguing, and worthy of a serious amount of investment in a lot of sophisticated research.

    Personally, I cannot see how that is debatable.
  16. Bob

    Bob

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    Yes, they do use the word "conclude", but that conclusion is based on theory, and not on hard evidence.
    The 'hard evidence' is the existence of the preXMRVs, but the presence of these viruses does not prove the case.
    It is hypothesis and theory which forms the basis of conclusion.

    This is demonstrated by the following quote taken from the paper:
    "The alternative possibility is that recombination between PreXMRV-1 and PreXMRV-2 occurred during mouse evolution, giving rise to an endogenous XMRV provirus that is present in mice and can occasionally infect humans."

    If you don't understand the basis of the conclusion then you haven't read the entire paper, but only the conclusion. It is not an absolute conclusion, and it does not rule out other possibilities. The conclusion fits their hypothesis only with the use of theory to support their case.


    No, I'm not confused. I think you might be though.
    The study is based on hypothesis, theory and conjecture. With some inconclusive physical evidence found which supports their hypothesis.

    I'm not saying that it's a useless study. But I am saying that it would not be sensible hang the future of XMRV research on it.



    I don't know how you got that version of my post - It was only up for about a minute before I took it down for editing.
    I had to re-read the paper, because I wasn't sure if i was correct about that point and a couple of other points.
    I rewrote my entire post before posting an edited version.


    That's just bad wording on my part. I mean that Switzer detected evolving XMRV, suggestive of a wild virus.
    By 'extracted', I am just assuming that his sequences were partial sequences rather than the whole genome (i.e an extract of the entire genome - a partial sequence). But I might be wrong about that - I'm not sure if he did full genome sequences or not.
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  17. RRM

    RRM

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    I've read the entire paper.

    The alternative possibility that the authors mention (before they essentially reject it), also assumes that preXMRV1 and preXMRV2 are XMRV's "parents". The difference is that the recombination event then happened somewhere else. The conclusion that XMRV derived from preXMRV1 and preXMRV2 is therefore not at all affected by the alternative possibility.

    And please also note that authors state their conclusions after they considered and rejected the alternative possibility (because they consider it "remote"). Thus, they do not conclude but offer a realistic alternative possibility, but conclude after they reject the alternative possibility.

    Finally, this is really a semantic argument. You say the authors do not conclude anything but merely hypothesize and when I point out that they do literally conclude, you basically assert that their conclusions are not conclusions by your definition of "conclusion". This is commonly referred to as the "no true Scotsman fallacy". In science, no conclusions are really 100% absolute and I am fully aware of this. Yes it is "possible" that you and your neighbour share the exact same DNA, but it is safe to "conclude" that you don't.


    You then apparently missed the PCR gels, cloning/sequencing data and phylogenetic analysis. Yet it is me who has only read the conclusions?

    But he didn't. No "evolving" XMRV was found by Switzer. There is zero data to suggest that his strain of "whatever you wanna call it" is either ancestral or derived from the "whatever you wanna call it" in 22Rv1 (or the "whatever you wanna call it" in any other patient sample. On the contrary, the finding of two exact same sequences in seperate and apparently unrelated patients strongly rejects recent evolution in my opnion. It is more consistent with the idea that two samples got contaminated from a single source.

    Finally, these authors published a paper after this one (except for Tang) in which they conclude that "MLV and mouse DNA contamination is more widespread in diagnostic reagents and clinical specimens than previously thought" and they therefore "call for careful interpretation of any murine retroviral sequences that are detected in these analyses"(source). Thus, they basically say 'don't trust our previous findings'.
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  18. Bob

    Bob

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    Their alternative possibility is not dismissed outright. They only dismiss it on the balance of probabliities, a decision which they have based on 'theory' and not hard physical evidence.
    Yes, their alternative possibility still rests on preXMRV1 and preXMRV2, but it suggests that XMRV could be an endogenous mouse virus.
    The reason I hightlight this is to demonstrate that this is just one other possibility. There are many possibilities, other than what is explored in the Paprotka paper.


    It has nothing to do with semantics.

    In my recent posts, I was clearly saying that the paper is not 'absolutely' conclusive.

    A 'conclusion' in a scientific paper, is not necessarily an 'absolute', as it is not in this case.

    After I re-read the paper, I realised that the authors did make a firm conclusion, as I explained in a previous post.

    But their 'conclusion' was based on their theory of the behaviour of retroviruses, and not on conclusive physical evidence.

    i.e. they cannot conclusively demonstrate the XMRV was created with the cell line, but they use a balance of probabilities, which is based on their theories which might not be shared by other researchers.

    In this case, the 'conclusion' is the authors' opinion based on their research.


    But my reason for highlighting all of this is not to dismiss the Paprotka paper outright, but it is just to point out that there are still unanswered questions, and other possibilities, as the Switzer papers also demonstrate. The Paprotka paper does not now conclude all XMRV research. It is just one research paper in a large body of other research.


    No I didn't miss anything, but you don't seem to be able to grasp the fact that the authors have based their 'conclusion' on a theory. A theory regarding the likelihood of recombination events. They also have made an assumption that their theory is sound and correct, and that there are not alternative unexpected possibilities. They conclude that XMRV was formed only once, and formed in the 22RV1 cell line, and formed only in the 22RV1 cell line. This is based on theory (with some supporting physical evidence to support their hypothesis), and I question their confidence about the theory, based on the other research that I have highlighted.

    But even if they are correct, it does not conclude XMRV research. They only investigated VP-62, and Switzer has detected other strains which he concludes have evolved in the wild. So this makes the Paprotka study partially redundant, as it does not take into account, or explain, the wider body of XMRV research.

    The Paprotka study dismisses the possibility that XMRV was created in more than one place, or was created externally to the 22RV1 cell line (to be introduced into it from an external source). Again, this all seems very premature based on the limited amount of research that has been done so far.


    Erm, OK, so you don't want to consider the evidence that I've clearly posted for you? It doesn't get much clearer than this:

    "...the finding of a viral strain in three prostate cancer patients that is distinct from the XMRV seen in previous studies is significant and demonstrates a broader viral diversity. This would be an expected result consistent with virus evolution during spread and persistence."


    No. If XMRV is replicating and evolving in substrates other than 22VR1, then that doesn't dismiss their previously research in its entirety. It just raises the possibility that XMRV is replicating in cell lines other than 22RV1, which again makes the Paprotka study partially redundant, and justifies calling for further research in the subject.


    I'm glad that you agree that further research in this field is needed.
  19. RRM

    RRM

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    As is the case with virtually the complete body of science.

    Which I explained is a strawman, as nothing in science is completely absolute.

    For instance, regarding Lombardi et al., it is also perfectly possible that the incidence of XMRV in ME/CFS subjects and controls is exactly equal, but that, by sheer chance, the investigators accidentally chose more patients infected with XMRV than controls.

    This is why scientists have generally agreed on a (totally arbitrary) cut-off rate of 95% for statistical significance. To be "absolutely" sure that ME/CFS is associated with XMRV, you would really need to sample hundreds of millions of samples.

    This is why, when your results are statistically significant, the burden of proof generally shifts (because it is easy to provide data that suggest that you are wrong if you are in fact wrong).

    All of science essentialy builds upon the existing accumulaton of knowledge. For instance, in the history of mankind, it has never been observed that two exact identical organisms have emerged independently. In this sense, it is quite surprising that the authors even calculated the possibility of two independent generation events of a 8000+ bp virus.

    Have you ever considered the odds of someone having the exact same DNA or having exactly the same fingerprint as you? You could say this is also based on "just a theory" but I can assure you that many people go to jail or even get convicted to death based on "theories" like these.

    I don't. If the exact same XMRV could have occured twice, then an almost exactly the same XMRV could have occured twice (or more). You would then expect to see almost endless variations of XMRV all over the place. We don't observe this, so the chances of exactly the same virus happening twice must also be infinitely small.

    This is a rather strange way of arguing. You explain away countless of negative studies with original thought, but counter my argument against a single, cherry-picked study with the literal wording of the study itself.

    Can you explain why my argument against evolution and that finding the exact same sequence in two seperate patients is not at all consistent with nomal evolutionary patterns, is invalid?

    You are missing the point of this study. This is not what this second study showed, at all.

    How did I agree to this? I merely explained that these very authors questioned their earlier conclusions through subsequent research. For someone that accuses others of 'conveniently overlooking' certain studies, it is a rather ironic omission to overlook this study yourself.
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  20. Bob

    Bob

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    So, I'm glad that we agree with most of the issues then RRM. ;)

    Seeing as this discussion seems to be entrenching us both in our previously held views, I think i'll back out after this post.


    My main point is that I think we should be open to the entire body of evidence, and not rely on just one study, whether it be by Mikovits or by Paprotka, to support our opinions.

    I do not consider Paprotka to be conclusive, any more than I consider Mikovits or Switzer or Singh to be conclusive. So I keep an open mind, but I prefer to see research continue.

    Indeed, even though Paprotka et al come to a 'conclusion', they themselves say that there are other possibilities which they have rejected as unlikely. I believe that there may also be other possibilities that they haven't considered.

    You say that the existence of preXMRV1 and preXMRV2 is almost conclusive evidence that XMRV was created in the 22RV1 cell line.

    But I say that, even if XMRV was formed by the recombination of preXMRV1 and preXMRV2, it could have been created in other substrates other than 22RV1, and introduced into 22RV1 by contamination. The Paprotka study cannot rule out that scenario.

    Also, as Paprotka et al say, XMRV could be an undiscovered endogenous mouse virus.

    Or XMRV VP62 could be a 22RV1 contaminant, but other variants could also be a human virus, as suggested by Switzer's variants, published in his paper.

    And there could be other strains of XMRV, or similar viruses, replicating in other cell lines. (Has info about this already been published? I haven't been following it all closely recently.)

    Whichever scenario might be the true one, there are many possibilities, and I do not believe that we have definitive answers yet.



    I'll just respond to a couple of your points...

    A paper has been published which demonstrates XMRV variation consistent with evolutionary changes.
    Although VP62, in itself, does not have the required genetic variation to suggest that it is a wild virus, there have been many other variants published now.
    So even if Mikovits' VP62 isolates were contamination, that does not prove that she, or every other researcher, detected only contamination, or that there are not other strains infecting humans.
    Yes, there is a lot of confusion, and a lot of unanswered questions, and there do seem to be a lot of coincidences related to contamination.
    But they do need to get the answers to all of this because, amongst other potential scenarios, XMRV VP-62 could potentially infect humans, mutate, and cause disease, if it hasn't already done so.



    OK, I admit that I hadn't got around to reading the paper you cited.
    I thought that you meant that they had detected whole viruses in the reagents, but I've read it now, and I see that they only detected partial sequences.

    But I can't see how you have concluded that the second Switzer paper nullifies the first Switzer paper that we discussed.
    Sure, it suggests that contamination with MLVs is widespread, but if they were detecting contamination in their first study, then they wouldn't have seen enough genetic variation in their XMRV sequences to demonstrate evolution.

    It would be perverse if Mikovits was accused of contamination because she did not have enough genetic variation, but Switzer was accused of contamination because he had a lot of genetic variation.

    Sure, in theory, they could both have contamination, but that would mean that Switzers' contaminants were coming from somewhere unknown? In which case his viruses would have to be either existing MLVs or novel viruses arising from more cell lines. But his sequence are not known MLVs.
    So, this surely requires further investigation.

    Or, as Switzer concluded in his paper, XMRV could be a wild human retrovirus. I can't see how his other paper contradicts that. Nor does the Paprotka study contradict that. The Paprotka study only contradicts the XMRV/human research if researchers are only detecting the VP-62 variant. But Switzer has detected other variants, thus making the Paprotka paper irrelevant with respect to possible human infection.

    VP-62 could have jumped from a cell-line (possibly 22RV1), into humans, and then evolved into the sequences that Switzer has detected. Or it could have arrived in humans via another route.
    Nothing you have said or shown me, RRM, contradicts that.

    But, as far as I am concerned, these are just possibilities that I remain open to, and I am not convinced that XMRV is a human virus anymore than i am convinced it is not a human virus. Time will tell.
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