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!
August 8th - What is the one thing about suffering with severe ME that the world needs to know?
Andrew Gladman brings our coverage of the Understanding & Remembrance Day for Severe ME, airing the voice of patients ...
Discuss the article on the Forums.

Article: Four Viruses! Alter Paper Confirms Retroviral Findings in CFS

Discussion in 'Phoenix Rising Articles' started by Phoenix Rising Team, Aug 24, 2010.

Thread Status:
Not open for further replies.
  1. awol

    awol *****

    Messages:
    417
    Likes:
    0
    Yes, but you said the problem was not the methods.

    And the problem WAS in large part the methods because if their methods had been good, they would not have found NOTHING.

    I invite you to carefully read Gerwyn and company's rebuttal in Retrovirology, to understand, once and for all, why NONE of the negative studies are worth the paper they are written on, because their methods were bad.
  2. leaves

    leaves Senior Member

    Messages:
    1,193
    Likes:
    14
    I am not convinced about that at all, but if it is true you can respectfully point them out.
  3. Cort

    Cort Phoenix Rising Founder

    Messages:
    7,025
    Likes:
    430
    Raleigh, NC
    Your point being?

    No, not at all. Since they have now found 4 MLV's one of which is XMRV - then the singular fact that XMRV is present is not as important as it was before the paper. The most salient fact is that there are a swarm of MLV's present in CFS. Which part of that don't you get?

    I don't V99 - those are the facts. Did Alter find XMRV? No.......Does that mean that at some point the two findings have to be reconciled? Yes, do you disagree with that? (How can you disagree with that??)

    I almost feel like we are different planets reading different papers. Are you saying that the WPI group does not have other MLV's in it? And that the ALter group does not have XMRV? Actually I will change that sentence to the problem probably lies in both groups. XMrV and MLV's are probably present in both groups. A complete vindication would be Alter findings XMRV in his samples. That would have set the research world afire. We'll know when that happens.

    I don't know if I can bear to read the rest of it. I wouldn suggest you don't bother ever again. You are doing a disservice to every patient with the disease by posting nonsense like this.

    The FDA response did not, interestingly, suggest that they believed other problems with methodology played a role.


    Yes they did, here:

    "Indeed, it is possible that the PCR primers used in various studies may have different sensitivity in detecting the diverse group of MLV-related virus gag gene sequences that we found in the clinical samples. The 5′ gag leader sequence of previously described XMRVs represents the most divergent segment of the XMRV genome in comparison with the genomes of the other MLVs (4). In particular, there is evidently a unique 15-nt deletion in the 5′ gag leader region in all of the XMRVs previously identified in patients with prostate cancer and CFS (3, 4). To detect XMRVs in human samples with better sensitivity and specificity, some studies used a PCR primer spanning this unique deletion as the XMRV-specific primer (6). However, none of the viral gag gene sequences amplified from the blood samples of CFS patients and blood donors in our study has this particular deletion (Fig. S1). As a consequence, such primers might have been insensitive in detecting the MLV-related gag gene sequences that we have identified." Lo et al.
  4. Cort

    Cort Phoenix Rising Founder

    Messages:
    7,025
    Likes:
    430
    Raleigh, NC
    Yes they did, here:
    Dr. Lo in the Press Conference did not say anything about this - and neither did the FDA response which I noted was what I was referring to. Dr. Alter repeatedly referred to the fact that CFS is a spectrum disorder.

    However you have a good point. My thought was that sample preparation was a simple factor but it turns out that its not. In any case I am committed to getting to the bottom of this.
  5. Cloud

    Cloud Guest

    Great reporting....thanks Cort. The science is unfolding now with an increased momentum.

    (I would have been entirely willing to work at 1/2 Monroes salary to advise the FDA on the CDC cohort problem....:D)
  6. Cort

    Cort Phoenix Rising Founder

    Messages:
    7,025
    Likes:
    430
    Raleigh, NC
    They also found 4 MLV's, not 3, and even that is misleading
    You're the one that's interpreting that as "lazy'. I interpret that as having not enough time - and it is accurate.

    I didn't say it didn't. Where did I say that?
  7. Cort

    Cort Phoenix Rising Founder

    Messages:
    7,025
    Likes:
    430
    Raleigh, NC
    My question is how much does it matter?They picked patients then that met both the empiric and the Fukuda criteria. Everyone on this board probably meets the Empirical criteria and the Fukuda criteria and the Canadian criteria. So long as they had Fukuda patients in that subset (which, as I pointed out is not necessarily true) then the fact that they almost met a weaker criteria is not that relevant to me.
  8. Dolphin

    Dolphin Senior Member

    Messages:
    6,518
    Likes:
    4,897
    I think it's quite possible that the cohort was the issue with the CDC study. Indeed we have the statement that the FDA team (Lo etc) couldn't find XMRV/MLVs in the samples from that study: http://www.fda.gov/BiologicsBloodVaccines/SafetyAvailability/ucm223232.htm

  9. Cort

    Cort Phoenix Rising Founder

    Messages:
    7,025
    Likes:
    430
    Raleigh, NC
    That's a good point. I did the best with my ability with what I had, It turns out that Andrea was right, though; I did miss a very important piece of the puzzle and I am rectifying that now - it should be up soon.
  10. awol

    awol *****

    Messages:
    417
    Likes:
    0
    I agree that cohort was a big part of the problem, but the methods were also bad. Cohort definition had nothing to do wih finding ZERO in their controls, when we now have peer reviewed papers showing a possible prevalence of 1.7% in Japan, almost 3% in Northern Germany, the WPI's 4% and Alter's 6.8%. If their methods had been good, they would have found something.
  11. Dolphin

    Dolphin Senior Member

    Messages:
    6,518
    Likes:
    4,897
    I'm exactly sure what you are saying.
    I initially picked up on your statement:
    http://www.forums.aboutmecfs.org/sh...-Paper-Arrives&p=115948&viewfull=1#post115948 - I praised and thanked you, etc.

    We know that all the people picked satisfied the empiric criteria. That's the criteria that were used.

    A few might satisfy the Fukuda criteria (as normally used).
    A few might satisfy the Holmes criteria.
    A few might satisfy the Canadian criteria.
    But we don't know.

    It could be the case that:
    None might satisfy the Fukuda criteria (as normally used).
    None might satisfy the Holmes criteria.
    None might satisfy the Canadian criteria.

    We don't know anything about what criteria they satisfy except that they all satisfied the empiric criteria.
    And not just the CDC but also Lo couldn't find any XMRV/MLVs in them.

    This is a great way to bash the empiric criteria. So I just pointed out that it is more accurate to say that they all satisfy the empiric criteria.
    The empiric criteria have turned up in all sorts of psychobabble e.g. personality disorders, childhood abuse studies, rate of current and lifetime psychiatric disorders (89% were found to have lifetime psychiatric disorders and the CDC recommended more CFS patients need to see psychiatrists based on this study).
    I think it is an important issue.
    =============
    ETA: It is relevant because it shows the difference between the patients Komaroff, Cheney & Bell see and the empiric criteria that make up CDC studies. It shows that the CDC are not using patients that are representative of the CFS patients specialists are seeing. You did sort of make the point and I am pleased you did. But you asked above so I'm explaining it.

    I perfectly understand how you made the mistake as the Switzer article isn't clear.
    =============
    ETA: the CDC say that the empiric criteria are the Fukuda criteria. But nobody else says that. People can get tricked when they say patients satisfied the Fukuda criteria.
    If one says these patients satsify the Fukuda criteria patients, one should also says that applies to the two childhood abuse studies, the prevalence study that found 2.54%, the study that found a higher rate of personality disorders, the study that found 57% current psychiatric disorders and 89% lifetime psychiatric disorders, etc. The CDC says they used the Fukuda criteria for them as they say the empiric criteria are just a version of them. I think we need to emphasise to people over and over that empiric criteric are a very specialised set of criteria and we shouldn't call them Fukuda criteria.
  12. V99

    V99 *****

    Messages:
    1,471
    Likes:
    1
    UK
    They found gag gene sequences, not more than that as you imply.


    They found sequences, they would not have been looking if it were not for the 'Science' paper. You are jumping to conclusions about XMRV. It will most likely be found to also be mutating. You haven't thought this through. They also found three different types of MLV-related virus gag gene sequences in patients, and one in a control. XMRV is then another relative. That makes 5


    Well firstly Harvey Alter disagrees with that. He says they are not 'disparate findings'. The finding of other MLV sequences supports the finding of XMRV. It's that simple. It all fits, if they are mutating.


    Again I will direct you to Alter & Lo's comments. How on earth would finding similar MLV sequences rub out the existence of XMRV? because that is what you are saying. I'm saying what they have been saying, that they are finding them also. Cort, what problem are you talking about? There is no problem. Both studies back each other up. You have no idea what you are talking about. Your making it up.


    No, if you read the sentence I am clearly saying that you are misleading people into thinking that these were replication studies, and you should have expanded on this to explain why the method employed can still be wrong.
  13. V99

    V99 *****

    Messages:
    1,471
    Likes:
    1
    UK
    I put the following:
    You replied
    That's because it is from the PNAS paper, Lo et al. The one you should have read.
  14. Dolphin

    Dolphin Senior Member

    Messages:
    6,518
    Likes:
    4,897
    If something has a 1% chance of happening, the chances of it not happening in 104 goes is (.99)^104=0.3516.

    If something has a 2% chance of happening, the chances of it not happening in 104 goes is (.98)^104=0.1223.
  15. Cort

    Cort Phoenix Rising Founder

    Messages:
    7,025
    Likes:
    430
    Raleigh, NC
    Well, excuse me. You always have the opportunity to write the right paper.
  16. V99

    V99 *****

    Messages:
    1,471
    Likes:
    1
    UK
    No, that is what you are implying. They could have created enough time, they didn't give that as an explanation for not doing the additional experiments. As you say you are interpreting, I will find that quote and show you.

    You have now put a comment I made in a quote box, this one:
    And are now saying:
    Do you even remember what you have read? or copied?
  17. V99

    V99 *****

    Messages:
    1,471
    Likes:
    1
    UK
    Clearly you haven't read the paper. What's with the bit about 'write the paper'
  18. Cort

    Cort Phoenix Rising Founder

    Messages:
    7,025
    Likes:
    430
    Raleigh, NC
    I think you are (intentionally) misunderstanding what I'm saying. Who said XMRV was rubbed out? My intent was that the WPI missed part of the swarm....not that XMRV does not exist - You are, once again, for the umpteenth time, putting words into my mouth. With regard to the replication problem I agree you have a point. One part of the study did replicate an important element of the study - they were all looking for the same genetic sequence. My problem is that I misunderstood the complexities of PCR. Like I said I am clearing that up.

    So????

    I think you're uncomfortable with subtleties. I noted very clearly that the Alter paper and Harvey Alter himself stated that his findings validated the general findings of the Science paper. Did you miss this?

    They obviously did not confirm the presence of XMRV....If they didn't do that do you suggest that I act as if they did?
  19. Cort

    Cort Phoenix Rising Founder

    Messages:
    7,025
    Likes:
    430
    Raleigh, NC
    This is what I wrote:

    That is not untrue - they all did look for that sequence. In fact I did miss something - as I noted earlier - about that - and I am clearing it up. The second sequence, as it turns out, is the determinative one.
  20. V99

    V99 *****

    Messages:
    1,471
    Likes:
    1
    UK
    Again my comments are about you leaving out important information. As you have read.
Thread Status:
Not open for further replies.

See more popular forum discussions.

Share This Page