TWiV 136: Exit XMRV

June 5, 2011

nude mouseHosts: Vincent Racaniello, Alan Dove, Rich Condit, and Stephen Goff

Retrovirologist Stephen Goff joins Vincent, Rich, and Alan for a discussion of recent papers on the retrovirus XMRV and its association with chronic fatigue syndrome and prostate cancer.

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Alan – The Demon-Haunted World by Carl Sagan
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  • RRM

    Note it was between parantheses, usually a sign to say it’s additional information. and when you first addressed it, I literally specified that it was a “minor issue”, Gob. You are again diverging away from the issue at hand.

    What’s important is that all those other three primers did not target the non-identical region your argument hinges on. To be really clear:

    NONE OF THE PRIMERS IN THE ENV REGION WERE (JUST) XMRV SPECIFIC

    Therefore it is patently stupid to conclude that they conclusively detected XMRV using ONLY env primers, Gob. You cannot conclusively detect something if your primers are not specific.

    And you are very welcome to copy my posts for future reference. I am not even aware of the fact that I could alter them.

  • Anonymous

    You have also altered this post since I replied.

  • Anonymous

    You have altered this post since I replied.

  • RRM

    I have never altered any post here, Gob. It must be your memory. Or a vast CONSPIRACY!!!

  • Anonymous

    You have altered your posts.  

  • Anonymous

    What is important is that Paprotka et al detected XMRV in the earlier xenografts.

    If they had wanted to give their belief any validity they would have used XMRV specific primers and in fact state:

    “We used the same XMRV-specific primer sets to amplify and sequence DNA from early passage xenografts (736, 777, 8L, 8R, 16R, and 18R; Fig. 2B); the results showed that XMRV env, but not gag sequences were present (sequencing coverage summarized in fig. S3),”

  • Anonymous

    RRM post

    “Note it was between parantheses, usually a sign to say it’s additional information. and when you first addressed it, I literally specified that it was a “minor issue”, Gob. You are again diverging away from the issue at hand.What’s important is that all those other three primers did not target the non-identical region your argument hinges on. To be really clear:NONE OF THE PRIMERS IN THE ENV REGION WERE (JUST) XMRV SPECIFICTherefore it is patently stupid to conclude that they conclusively detected XMRV using ONLY env primers, Gob. You cannot conclusively detect something if your primers are not specific.And you are very welcome to copy my posts for future reference. I am not even aware of the fact that I could alter them.”

  • Anonymous

    RRM post:

    “I have never altered any post here, Gob. It must be your memory. Or a vast CONSPIRACY!!!”

  • RRM

    No sir, I have not.

  • RRM

    Yes, they attempted to find XMRV, but because only their env primers would return positives, they (unlike you) started thinking what the reason for that may be. The reason was the presence of preXMRV-1, WHICH IS IDENTICAL TO XMRV IN THE ENV REGIONS THAT THOSE PRIMERS TARGETED.

    Paprotka did check for XMRV in the earleir xenografts, because they targeted these xenografts with more than just env primers. While the env primers weren’t specific for XMRV (and therefore only idiots think that you can specifically detect XMRV using such a primer), the assays combined ARE specific for the detection XMRV.

  • RRM

    I understand how you’d like to think that but no, I have not.

  • Anonymous

    Where is the proof it was PreXMRV-1 and not XMRV?

    They say the primers used were, “XMRV-specific primer sets”.  

    You have now claimed that those who say the primers were specific are idiots.  Paprotka et al did say that.

  • Anonymous

    RRM post

    “Yes, they attempted to find XMRV, but because only their env primers would return positives, they (unlike you) started thinking what the reason for that may be. The reason was the presence of preXMRV-1, WHICH IS IDENTICAL TO XMRV IN THE ENV REGIONS THAT THOSE PRIMERS TARGETED.
    Paprotka did check for XMRV in the earleir xenografts, because they targeted these xenografts with more than just env primers. While the env primers weren’t specific for XMRV (and therefore only idiots think that you can specifically detect XMRV using such a primer), the assays combined ARE specific for the detection XMRV.”

  • RRM

    I have not altered a single letter, Gob. I am not even aware of the fact that I can alter posts here.

    The fact that you conclude this however, says a lot about your ability to objectively and critically evaluate relevant data.

  • RRM

    Like I have explained, Paprotka said it in another context. They were merely reporting this at the time when they thought the env primers were specific for XMRV. As you can clearly see from the now infamous red square picture, they are not.

    And the proof is in the fact that the other primers that were targeted for XMRV (and didn’t target preXMRV-1) did not detect the thing. I know what you are going to say, Gob, but remember (the wisest thing I have seen you write here) that science is not absolute. Regardless, it still makes the conclusion on the forums incredibly stupid: “He was infect!” 

  • RRM

    Whatever makes you reduce all that cognitive dissonance, Gobster.

  • RRM

    “You have also claimed that it is not enough to use none [sic] specific primers to look for XMRV.”
    I wouldn’t call it a claim; it’s undisputable logic. Suppose I have a method that detects apples and oranges. I can NEVER specifically detect apples with just that assay (or oranges, but let’s keep it simple). Only when (for instance) I have another assay that detects (a portion of)  an orange and it returns a negative result, I can conclude that I have detected an apple.
    That is exactly why none of those three env primers from Paprotka et al. can differentiate XMRV from preXMRV-1. Yes, there is a sentence in the paper that implies otherwise (in the eyes of dumb people), but  please at least say you understand this very basic logic.

  • Anonymous

    In the paper they state:

    “We used the same XMRV-specific primer sets to amplify and sequence DNA from early passage xenografts (736, 777, 8L, 8R, 16R, and 18R; Fig. 2B); the results showed that XMRV env, but not gag sequences were present (sequencing coverage summarized in fig. S3),”

    They clearly show they detected XMRV env, not PreXMRV-1 or 2.   

    Are you now claiming that Paprotka et al should not have said this?

  • Anonymous

    RRM post

    Like I have explained, Paprotka said it in another context. They were merely reporting this at the time when they thought the env primers were specific for XMRV. As you can clearly see from the now infamous red square picture, they are not.

    And the proof is in the fact that the other primers that were targeted for XMRV (and didn’t target preXMRV-1) did not detect the thing. I know what you are going to say, Gob, but remember (the wisest thing I have seen you write here) that science is not absolute. Regardless, it still makes the conclusion on the forums incredibly stupid: “He was infect!”

  • Anonymous

    RRM Post

    “I have not altered a single letter, Gob. I am not even aware of the fact that I can alter posts here.
    The fact that you conclude this however, says a lot about your ability to objectively and critically evaluate relevant data.”

  • Anonymous

    Thank you for doing so.

  • Anonymous

    Thank you for doing so.

  • RRM

    It’s no problem to me, as I understand what they are saying.

  • Anonymous

    Pick one then?  Are the primers XMRV env specific and found the virus in the earlier xenografts, or were they not specific and should have been, as you say it is stupid if they are not?

  • Anonymous

    RRM Post

    “It’s no problem to me, as I understand what they are saying.”

  • Anonymous

    That is a good idea, retract Paprotka et al.

  • RRM

    You apparently find this strange, I don’t, but whatever.

    The point is that it is no way an indication that Gallo calibrated his assays to “known positives” he received from Montagnier.

    Come one, Gob. Everybody knows this. Nobody has ever used your proposed methodology in the history of (retro)virology.

  • Tiggerkenwood

    Why doesn’t someone take some tissue from the cervix, stomach, or prostate of a few of the people who tested positive under the VIPdx antibody test and look for XMRV.  We could end this now!   Like many women, I have had a biopsy of my cervix before.  It is easy, quick and painless.  We could start with cervix biopsies or only do those.  

     All this back and forth bickering by everyone (including the cfs’ers, doctors, scientists, and radom people) is getting us nowhere.  It is all so very frustating.

  • Tiggerkenwood

    If you think someone is constantly altering posts here, why not keep a copy of the original post for proof ?

  • Anonymous

    Why don’t they replicate?  

    The people on this podcast are all aware of what that means. You can use the same variables.

    To shine a light on Shin et al., as a way to conduct research and not get contamination, when they had contamination, is laughable.

  • Anonymous

    That is why he wanted positives.  Every school child to fully fledged scientists knows you cannot claim an assay works without evidence.  Ila Singh has also stated that it is not good enough to use a spiked sample as the matrix is different and then proceeded to do the opposite.  

  • Anonymous

    That is what I am doing now I know they are.

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