1. Patients launch a $1.27 million crowdfunding campaign for ME/CFS gut microbiome study.
    Check out the website, Facebook and Twitter. Join in donate and spread the word!
The Lipkin Microbiome Crowdfunding Campaign Launches!
An ambitious $1.27m international, patient-led fundraising campaign storms into action. Sasha invites you to join it!
Discuss the article on the Forums.

New WPI and CDC XMRV sequences in genbank

Discussion in 'XMRV Research and Replication Studies' started by Bob, May 17, 2011.

  1. Bob

    Bob

    Messages:
    6,319
    Likes:
    6,615
    England, UK
    Yes, I agree that XMRV could not 'evolve' into PMRV, or vica versa, in the time frames that we are talking about.

    I'm not sure if I understand exactly what you mean here RRM, but isn't it the case that not many full sequences have been carried out, so we only have a partial picture of exactly what MLVs/MRVs have allegedly been detected in humans?
  2. currer

    currer Senior Member

    Messages:
    1,324
    Likes:
    767
    http://books.google.co.uk/books/about/Retroviruses.html?id=Awcmfx8EaOAC&redir_esc=y
    Retroviruses. John Coffin. Google books.

    Mechanisms and Factors that Influence High Frequency Retroviral Recombination
    Krista Delviks-Frankenberry,1 Andrea Galli,2,3 Olga Nikolaitchik,2 Helene Mens,4 Vinay K. Pathak,1 and Wei-Shau Hu2
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187697/

    some reading material.

    Dr Snyderman wrote in December that the integration study of his blood revealed a virus integrated at a site unlike a site where XMRV integrates.

    The deep sequencing studies have not been done even though a sample was sent because the lab pulled out of the research.

    We need further research to show what viral strains (if any) are present in patients.
    Everyone who follows this research in an unbiased way knows that the search has to be broadened to look for other MLV strains and that restricting the debate to "XMRV" is an artificial diversion from the real issue.

    It is a shame that labs are afraid to do deep sequencing studies in these circumstances.
    RL_sparky likes this.
  3. Bob

    Bob

    Messages:
    6,319
    Likes:
    6,615
    England, UK
  4. Jemal

    Jemal Senior Member

    Messages:
    1,030
    Likes:
    54
    We have enough time, right? ;)
    Some of you could almost be getting degrees in virology by now I think... :D
  5. Bob

    Bob

    Messages:
    6,319
    Likes:
    6,615
    England, UK
    Well, if we all sat the same retrovirology exam, do you think we might be able to answer one or two questions between us? lol
  6. Jemal

    Jemal Senior Member

    Messages:
    1,030
    Likes:
    54
    If the questions were about XMRV? Sure :D
  7. RRM

    RRM

    Messages:
    94
    Likes:
    104
    Let me illustrate with yet another example. Twelve men have walked on the moon. Suppose all took ground samples and turned out to be (moon) rock. Now, you could still argue as follows:

    "Where these men have walked reflects less than 1% of the moon's surface. Therefore it's still entirely possible that the moon is primarily made of cheese."

    While this is theoretically possible, it's more like a "hypothesis between the observational gaps", so to say. It lacks experimental evidence. If the hypothesis were true, you would expect that one of the men that walked the moon would have accidentally stumbled upon the predominant cheese surface. And even disregarding this, the hypothesis lacks any evidence in support of it.

    The same really applies here.

    It is true that there are really only partial MLV/MRV sequences available. Most are about 5% of the (assumed) length of the full virus. So you could hypothesize that the "unkown" parts reflect parts of XMRV or of other strains of MLV/MRV that have been found in blood samples.

    While this hypothesis can be theoretically true, it lacks experimental evidence. There have been multiple partial strains sequenced. You would expect to see some evidence of (recent) recombinational patterns in at least some of the reported partial sequences if recombination was truly the driving factor for the sequence diversity.
    Firestormm likes this.
  8. currer

    currer Senior Member

    Messages:
    1,324
    Likes:
    767
  9. Mark

    Mark Acting CEO

    Messages:
    4,412
    Likes:
    1,717
    Sofa, UK
    What's interesting to me is that, while it has been well-known to retrovirologists since the 1970s (at least) that their experimental methods have been creating many novel and (at least) potentially human-infectious retroviruses, which have spread worldwide as laboratory contamination, this information is new to me in the last 2 years, and it is certainly not public knowledge.

    I don't pass any judgment on whether these methods are the best practical option in the battle against human diseases, whether there are better alternatives, or whether there is anything that can be done about this situation. What interests me is the fact that this entire discourse is taking place very much out of the public domain. That's quite understandable of course, because the public reaction to this revelation would quite likely be rather intense, but for people like ourselves, affected by what appear to be novel epidemics of diseases whose very existence is disputed - and people who know with certainty that our immune systems have gone wrong in a way that medical science persistently refuses to recognise or investigate - this revelation about the systematic artificial creation of novel retroviruses inevitably feels pretty significant.

    It might be true that, behind the scenes, scientists are indeed taking these dangers very seriously indeed. But out in the real world, people are getting sick in new ways, and that sickness is certainly not being properly investigated. So our starting point as patients is the understanding that these dangers are not being taken seriously enough, or if they are well understood behind the scenes, then we are being consciously factored in as 'collateral damage' and written off as the unfortunate victims of technological progress in other areas.

    If it were the case that illnesses such as those we suffer from really are the lesser of two evils in the global fight against human disease, then actually, I could accept that - provided that our collateral damage were recognised and compensated just as it is for the rest of society. But we are being swept under the carpet, and our experience makes it quite clear that there really isn't any serious attempt to investigate what is going on with us: on the basis of that shared experience alone, we can be confident that there are dangers here that are certainly not being taken seriously enough, whether those dangers are indeed related to these novel retroviruses or to something else. And the reason for all the furore is obvious enough: these retroviral theories are (from what I have seen) the best general explanatory model yet advanced for the cause of the illnesses we are all suffering from.
    Bob, Jemal and currer like this.
  10. currer

    currer Senior Member

    Messages:
    1,324
    Likes:
    767
    It will take a massive political shift in western society to acknowledge the collateral damage you mention, Mark, because the current system is still highly profitable for the "winners".

    I have to admit to some serious doubts about virology as a profession, too - they experiment on animals, create unnatural and lethal viruses which can earn them millions, many work in secret biological/bioweapons research, treat the public with disdain and suspicion...how right or ethical is this? And can we really assume that "good" can result from such activities - is it even right to benefit from technologies developed in such ways?

    OK we have "conquered" polio and TB, but we have swopped them for AIDS and ME and autism. Perhaps this is not the way to progress. Can your civilisation genuinely progress if its actions are immoral? Dont you just exchange one form of suffering for another?
    Angela Kennedy likes this.
  11. natasa778

    natasa778 Senior Member

    Messages:
    1,246
    Likes:
    825
    London UK
    Especially since WHO CDC and other regulatory agencies have been well aware of the risks and actual confirmed instances of contamination of biologicals by those agents, MulVs included, for quite some time. The push to explain these contaminants away as harmless to humans is nothing new, it is just playing out on a bigger scale and more out in the open this time around.
    jace likes this.
  12. barbc56

    barbc56 Senior Member

    Messages:
    1,118
    Likes:
    490
    Really? I find this statement puzzling. Virology has helped us conquer polio as well as other diseases. Do you want to go back to those times? I have two friends who contacted polio when I was growing up. One died. The other has post polio syndrome. Even though I was very young at the time, I remember having to stay inside, the pools closing down. I would think many here would be too young to remember this, but it was scary.

    What are the instances of the confirmed instances of contamination of biologicals? Not saying there aren't any, but I have to say I have missed this.

    One thing I have always wondered about is some say that lab workers are tested for XMRV/whatever but think it's because the labs are afraid people will catch something. Couldn't it be the other way around? Since the lab workers have been in various labs, and xmrv is a very prevalent contaminant, might they carry the contaminate unknowingly into the lab and that's why they are tested, though tbh, I don't know how often testing of lab workers happens.

    Both?

    As far as biological weapons, I think that is always possible just as many Satellites are used for spying. I am not sure what the real world consequences are of this and wonder if this was more prevalent during the cold war before scientiest were more accountable. However, since then we have had the war in Iraq, so who knows? Would I be surprised there is something like this happening? No.

    But just because this is possible I'm not sure what the odds it could be an explanation for our illness. I would think there would be other, more logical reasons. Think occam's razor.

    Barb C. :>)
  13. RustyJ

    RustyJ Contaminated Cell Line 'RustyJ'

    Messages:
    873
    Likes:
    267
    Brisbane, Aust
    Thanks currer for reminding us of what is important. JHK-3 is an X-MRV. Whether it is XMRV is a non-issue in light of recent events. I am concerned more with finding a cure for my illness, not scoring points in some technical debate which not only does nothing to further the search for a cause, but retards further progress.
    jace and Bob like this.
  14. RustyJ

    RustyJ Contaminated Cell Line 'RustyJ'

    Messages:
    873
    Likes:
    267
    Brisbane, Aust
    This debate is not new. There have been moves in the UK to tighten up regulations, because of perceived problems (although cynically, the measures seemed to be more about managing public reactions). I think that in any area of science there is pushing of ethical boundaries, particularly when commercial interests are involved. I think it is an important debate to have. These sorts of questions need to be asked. To say otherwise is a little naive.
    currer, jace and Angela Kennedy like this.
  15. Mark

    Mark Acting CEO

    Messages:
    4,412
    Likes:
    1,717
    Sofa, UK
    I'm afraid that I've been far too busy with other matters for the last week to respond to the comments earlier in this thread about this forum being a 'denialist' forum, and there is far too much there for me to go through and respond to everything now. So all I can do is do my best to sum up the situation as I see it. I'm reluctant to do so really, because this thread seems to be back on topic now, and my post might drag it off topic again, but there were comments made which should be responded to. I don't want to get into a protracted discussion about this though, because the bottom line is that anyone who has concerns about how the forum is moderated, or about members who post here, can only address those concerns by raising those issues with moderators (via 'Report Posts'), and public discussions like the one above serve little or no purpose. Nevertheless, I'll respond to the points made earlier in this thread...

    I have to agree that there have been one or two members (and really no more than that) who have in the past been provocative, unreasonable and insulting in the way they've expressed their 'denialist' comments about XMRV. We've moderated a number of such posts recently, and one member has recently been suspended, and in fact the majority of the posts we've moderated were not even reported to us by anybody, we just happened to come across them ourselves. We have done a lot of work behind the scenes to make clear to members who've breached the rules what is and what is not acceptable behaviour here, and we have banned some members for trolling. I'm also quite confident that we have checked out the post history of those members who some see as trolls considerably more carefully than the members who are making those claims have done. There is a lot of work involved there, we do work hard on issues like this, and we deal with them as fairly as we can.

    So actually we do deal with trolling and deliberately provocative patterns of posting, but if anybody wants to criticise any failure on our part to deal with particular instances or individuals, and that person has not themselves reported the offending posts to us, then they haven't got a leg to stand on as far as I'm concerned. And there are plenty of people who posted in the discussion above who have criticised the forum in a general way for allowing posts and members they don't like, but who have never reported anything to the moderators. If you don't report posts, it's quite unreasonable and unrealistic to expect that the moderators should scour every thread looking for posts that might offend you. If you have a legitimate complaint, then report it, and we will deal with it fairly.

    Having noted that there have indeed been some legitimate concerns there in the past, I must also say that, in general, I don't see any problem with the posts by members who have raised questions about XMRV/HGRV. I don't like to name names, and I don't know who the people complaining about 'denialism' are actually talking about, since they have not reported the incidents they refer to, nor have they privately named to us the people they accuse of trolling (as would be appropriate), nor have they supplied us with any evidence of the alleged trolling behaviour they have mentioned. But I can say that my views and my interest in HGRV science should be fairly well known by now, and I read as much of these threads as time permits, and I have found all those members who are currently posting on this subject to be entirely reasonable, fair, and well-mannered in their posts on this subject (with the exception of one member who has recently been suspended). Contrary to what some members have suggested, I actually think that we have a good standard of polite and respectful debate on this subject here now, with strong opinions on both sides, but expressed in a quite reasonable way. I actually want to thank and praise our members for that - on both sides of the argument.

    This is not a place where one side of a debate like this can expect to be favoured. Phoenix Rising aims to be a place where contentious issues can be discussed in a polite and respectful environment, and where different points of view are to be expected. By sticking to the issues and discussing them rationally, it should be possible for the discussions to generate more light than heat, and that is not always the case elsewhere on the internet.

    There is one particular aspect of some of the comments about 'denialism' in particular that I want to challenge, and that is the suggestion that people who do not believe in the XMRV/HGRV hypothesis are not themselves ME patients (seemingly, by definition). This theme of seeking to exclude anyone who does not agree with a particular 'politically correct' party line from a particular group, and arguing that because you do not believe x, y or z, you must therefore not have ME, but must be some form of troll or infiltrator, is one of the most pernicious and profoundly damaging concepts that afflicts the online ME community. It pits patients against patients, projects an inaccurate and unreasonable image of patients, mires us all in suspicion and confusion, and fatally undermines the argument of anyone who makes the claim. Resorting to ad hominem arguments such as this is effectively an admission of defeat - and it is most certainly self-defeating.

    Due to the wide variety of people with whom I am in contact in my role as moderator, both virtually and in the real world, I happen to know that there is no shortage of patients who are sceptical about XMRV and HGRV. ME is no respecter of political inclinations, and though the biopsychosocial experience of the mistreatment of ME patients tends to be a radicalising one, the disease affects conservatives and radicals alike. Few of those patients who are sceptical about HGRV/XMRV post their views about XMRV here, though there are certainly those who would like to do so and who have been intimidated out of doing so. And the frustration about repeating old arguments, about not being able to convince other people to change their point of view - all of that frustration certainly applies to both sides of this argument. There most certainly are patients who are sceptical about XMRV/HGRV who are feeling just as tired of rehashing old arguments as the supporters of the theory are.

    It's also been acknowledged, above, that there is a thread here that's dedicated to constructive discussion of XMRV/HGRV. When we agreed that policy, we stated in that thread that, where necessary, members may post a thread and stipulate that it is intended only for positive contributions on a particular topic. We noted that, in fairness, other members might post a separate thread on the same subject, with different criteria for the discussion. So there is already a mechanism for pro-HGRV members to have a 'private' discussion on this subject, if they feel that would be more productive. I also secured agreement from the board for the principle of future 'micro-sites' within PR, on this issue and perhaps on other subjects in the future. We are still working on the technical infrastructure to provide that facility, and I'm confident we will roll out something of that nature later this year. So we do have some provision for special interest discussions, but I do not think there is much more we could reasonably be expected to do to restrict the more open discussion of XMRV/HGRV issues. If supporters of HGRV/XMRV are concerned about the balance of the general XMRV threads here, they can only address that by posting on them to balance out the views they disagree with; members should not expect that this issue will ever be discussed here in a one-sided way, and I think people just have to accept that is not what this forum is about. Instead, what everyone has a right to expect here is a fair, calm, and rational environment where their right to respectfully express their opinion is respected. As moderators we do our best to live up to that goal.

    In the end, though, this whole discussion about this forum being 'denialist' about XMRV/HGRV is really rather pointless. My personal views on the subject should be quite easy for anyone to see, and I'm in charge of moderation now, so if anyone accuses us of a bias against XMRV/HGRV then I am bound to question that claim. I do try to moderate here as fairly as I possibly can, based on the evidence available to me, and I'm grateful to Bob for his kind words earlier about the job I do. And I would add that I have absolute confidence in the rest of my new team to do a better job of it than I can myself, and I believe we have an excellent and very hard-working team of moderators here now.

    So to those who have concerns about the moderation here, or about certain posts, or about certain members, the bottom line is that there is not much value in complaining about that within forum threads. Instead, report your evidence to the moderators, and make your case via reported posts, and we will deal with those reports as fairly as we can. But please don't expect that we will ban members for rejecting the XMRV/HGRV theory because, like the majority of PR members, I want to be a member of a forum where diverse opinions and arguments can be respectfully expressed, and where an honest and intelligent debate can shed light on the many issues of concern to us all. So if you have specific concerns, then please report them and supply evidence in support of your concerns; I really don't see what I can do to deal with vague and general complaints like those above.
  16. Bob

    Bob

    Messages:
    6,319
    Likes:
    6,615
    England, UK
    Hi Mark,

    Thank you for taking the time and effort to respond to the concerns raised. It's really appreciated. You've been fair, thorough, thoughtful and balanced, as always.

    I hope i was careful in my own posts to separate genuine forum members who have legitimate concerns about XMRV, from people who I consider to be on the forum purely to energetically promote a certain point of view against XMRV (people who have no legitimate interest in ME). There have been quite a number of the latter type of members who have been removed from the forum over the past six months, so I think that my public complaints about these type of members are valid.

    I do acknowledge that it is impossible to make a public forum perfect for everybody's use, and I am grateful for the continuous hard work that the mod team all put into making the forum better. But after feeling like i had experienced harassment which led to me taking a break from the forum, I thought it was fair to publicly share my perspective on the subject, at least once. I don't usually publicly vent like that, but I felt I needed to say it. I hope my posts were perceived as constructive, although I was having a bit of a rant, so maybe they weren't as balanced as they could have been. And maybe my perspective is too one-sided because I come from a place of being receptive and enthusiastic about XMRV research.

    Personally, I would really welcome a respectful discussion, from both sides of the XMRV argument, and I wouldn't have a problem with that at all. But unfortunately it hasn't felt at all respectful over the past few months, from my perspective, due to a small number of energetic posters. But I hope that the discussion we've now had about this subject will help both sides of the debate have a bit more awareness of each others' concerns, and that it will help us all to consider each other a bit more and to continue the respectful discussion that we've had recently in this thread.

    Thanks for the reminder to always report posts that we have an issue with.
    jace likes this.
  17. Firestormm

    Firestormm Content Team Lead

    Messages:
    5,278
    Likes:
    4,669
    Cornwall England
    Morning Mark,

    From my own perspective, I have only been aware of such issues in the past two years simply because of the publication of Lombardi and the connection to my condition.

    Once that was 'out of the bag' only then did I begin looking back at other issues of which I had not been aware. I think in that respect it was natural for me at least to think these issues pertaining to contamination and/or murine infection were something new, that 'science' became more focused as a result of Lombardi.

    To some limited extent I still think this is true - to judge by the number of papers on the subject at any rate - and perhaps murine infections have come into the spotlight. But that is not to say 'science' was not aware of them before and their potential.

    I may sound naive and even silly but I do believe in and trust science - but it is for them - as it is for us - a learning curve and new studies cast more light on things that hadn't been considered in as much depth previously (or indeed may contradict previous research). Each new paper sheds more light on past papers and past understanding - you know how it goes - and this is one reason why I am reluctant to ever conclude anything definitive from a single paper alone.

    Science hasn't closed the door on any of this - if anything I think they have increased their efforts - a single paper or even papers might not stand up to the test of time; but that's science!

    Science will continue to study XMRV and any other identified murine retrovirus; they will keep looking for others currently unknown; and - should human infection be confirmed - they will have a far better understanding as a result.

    My interest - apart from breaking up the monotony of my existence - and a genuine desire to learn - is to remain abreast of developments IN CASE human infection is ever confirmed.

    Of course everyone's interest will be heightened again if a paper is forthcoming linking any of this to our condition I suspect - for now though it is less of a focus I would imagine.
    Bob and Sam Carter like this.
  18. barbc56

    barbc56 Senior Member

    Messages:
    1,118
    Likes:
    490
    Mark, thank you for your post. I just did what you recommended.

    Part of the problem lies with some people thinking that anyone who disagrees with another person is inherently being disrespectful. Not talking about either side particularly, but have to be honest that I have seen posts where people are complaining about another person's opinion but did not see any disrespect.

    I know you and I disagree with a lot of things but probably agree as many of us, more than not on issues of respect, an open forum and realizing that not everyone is going to have the same perspective on topics. Issues are not just black and white but somewhere in the grays.

    People's personal perspective and how it affects others is a hard issue to moderate. One persons respect may be seen as disrespect by others simply on the basis of opposing opinions. It doesn't have to be that way. Kudos to you and the other mods.

    I have also been attacked and no one, whatever side(s) you are on, deserve to be treated that way.

    Barb C.:>)
  19. natasa778

    natasa778 Senior Member

    Messages:
    1,246
    Likes:
    825
    London UK
    There is a whole long thread on this forum somewhere, with lots of documents posted, go look in the Testing folder. Or could be in this folder...
  20. bullybeef

    bullybeef Senior Member

    Messages:
    476
    Likes:
    44
    North West, England, UK
    I have been thinking about government acceptance of a new global plague, and how this could cause differing countries relationships could become frayed.


    If the majority of Europe and North America have private healthcare and welfare systems, so in some way, a global plague could be accepted eventually, but what happens when a country has a "free" healthcare/welfare system or a National Health Service?


    If UK had a NHS during the turn of the 20th century during the influenza outbreak, the costs to government would have been astronomical, particularly at the time after WWI there was a global depression back then. So what happens if a new, long term epidemic is brought to the governments attentions, and countries with national healthcare systems are reluctant to accept it, particualarly during another global economic depression?


    Would this cause relationship problems for countries on opposing sides of eventual acceptance based upon their healthcare and welfare systems?


    In our case, we have seen much of the anti HGRV debate stem from the UK. Much of the denialism and contamination accusations first came from the UK. The swiftness of the UKs attack on XMRV spoke volumes for me, based upon their reluctance to accept the situation and ramifications, but is this much of a surprise? And could a time come were capitalism demands cashing in on a chronic epidemic, which would leave the likes of the UK hung and dry?


    Or should a new human retrovirus be accepted by some countries, could this cause the likes of the UK attempt to say it doesn't travel like HTLV to avoid monetary cost to treat the potentially infected?

See more popular forum discussions.

Share This Page