Thursday, December 23, 2010

Dr. Coffin Responds

While waiting for sources to get back to me, I thought I’d post preliminary comments from Tufts University’s Dr. John Coffin.  Coffin co-authored two of the four studies in Retrovirology on Monday that postulated that XMRV may be merely contamination from mouse DNA, as opposed to a new human retrovirus that has jumped species from mouse to man and has been found in patients with ME/CFS and prostate cancer.

CFS Central:  In your papers, you write that you obtained samples of WPI's [Whittemore Peterson Institute] XMRV positive lymphoblastoid cells.  Your papers, however, don't discuss testing these cells for evidence of mouse DNA….  Did you test these cells for evidence of mouse DNA?  If so, did you find contamination? If you did not test the 1282 cells for contamination, why did you decide not to test them?

JOHN COFFIN:  Not to my knowledge, since there was no particular reason to do so.  We have tested [prostate cancer] 22Rv1 cells, and some other human cell lines, with negative results.

CFS Central:  Were the cell lines you tested that had no mouse contamination (the 22Rv1 cells, for instance) XMRV positive or XMRV negative?

JOHN COFFIN:  22Rv1 is XMRV positive. It's the standard positive control.

CFS Central:  Have you tested or do you have plans to test XMRV positive patient samples from WPI or MLV [-related virus] positive patient samples from Drs. Alter and Lo?  

JOHN COFFIN:  We have no plans to do so at Tufts. However, the group I work with in the NCI [National Cancer Institute] is collaborating with the Blood Working Group, and we will look at samples from both the WPI patients as well as the same patients that Lo and Alter studied. [Lo and Alter are the principal investigators of the NIH/FDA/Harvard study published in August, which found XMRV-related retroviruses in the majority of ME/CFS patients and 7 percent of controls.]

CFS CENTRAL:  If you’ve already tested these retroviral positive samples from WPI and Alter/Lo, did you find mouse DNA contamination?  

JOHN COFFIN:  We haven't done that yet.

CFS CENTRAL:  If Tufts hasn’t tested these samples and has no plans to, wouldn’t that be the definitive way to determine whether there is mouse DNA contamination?

JOHN COFFIN:  We will test at NCI using the same assay.


  1. Yes, she's baaacck!

    Go get 'em, Mindy!

    So very disappointing to see a scientist of Dr. Coffin's stature dissembling and equivocating when faced with your direct questions. This kind of weasel-ing behaviour should be beneath him. It is a sad day for science to see him succumb to this.

  2. p.s. Mindy, please correct your post:

    '... from WPI and Alter/Low'

    '... from Drs. Alter and Low'

    (you wouldn't want a blogger to refer to you as Kiteiw...)

    Also, they did not find MLV in patients, they found MLV-related viruses. Please correct terminology.

    [don't post this comment, it's just for correction purposes]

  3. Thank you, Mindy. You are asking the hard questions that need to be asked. If they're not careful, you are going to get some of these people to give some real answers.

    Keep up the great work!

    Patricia Carter
    XMRV+, 24 years M.E.

  4. Glad to see you on the case again, Mindy!

    One point: The viral sequences found by Lo et al do not belong to any known MLV, so the only correct term to use for them MLV-related viruses (XMRV is itself an MLV-related virus). The term MRV should become common parlance... Calling them MLVs is for now problematic because of all the speculation by contaminationists (I can make up words, too!) about MLV contamination; any confusion of terms favors that group.

    I really look forward to the next installment!

  5. Your investigative journalism is a wonderful asset to us all. -- rivka

  6. Great work...can't figure out what the upside is for these scientists. It's true that many academics in science are not great communicators but they are not stupid and they are purposefully troublemaking and not getting to the root issues to evade the truth. They are obvuscating...the question is why? Elisabeth

  7. Thanks for all your hard work and honest reporting.


  8. Thanx Mindy. This interview reads like fiction. I have to remind myself constantly that this is nothing but the truth (so help me God ;-).

  9. Thanks Mindy.

    It is really odd that Dr. Coffin has put his name to the 2 papers highlighting the risks of contamination and yet doesn't appear to have done the fairly obvious (and basic) testing that you have highlighted.
    I wonder what his motives are for behaving in this way and for not doing these tests? Having initially praised Lombardi et al, he seems to be doing certain things which undermine them. People may start to conclude that his intentions are not entirely genuine - contrary to what his prodigy (Dr. Stoye)would have us believe.

  10. Nice one Mindy - an example to all the embedded journos out there picking up fat salries for doing nowt (diddly)

  11. Thank-you for the direct questions. We appreciate all you do. Lynn

  12. With all the other events of this week, I haven't given those five papers the full scrutiny they deserve. I note that Prof. Racaniello made a serious error in his initial judgment on them, which was unfortunately reported by Trine Tsouderos as the end of XMRV. He has since retracted the quoted statement in a gracious way.

    The hidden discovery of this debacle is that Eric Klein had published results showing provirus integrated into human chromosomes in cells flash frozen in the operating room, and nobody denying the reality of XMRV in ME/CFS appears to have noticed. This says the virus is not simply an artifact introduced in the laboratory, and is actually present in some humans -- irrespective of ME/CFS.

    Since this is a retrovirus, it should be natural that a cell line derived from prostate cancer would show viral sequences, and sometimes express them as actual virions. Thus, tracing the sequence to a cell line does not necessarily invalidate research using other cell lines. The cell line acquired those sequences from real infections. Since the infections were in prostate cancer, this is an important link in the chain of evidence for causation.

    Caution is appropriate for results derived from cell lines. The published positive results did come from groups which made extensive use of negative controls. They did test their reagents and equipment in advance, and again later. They used laboratories which had never handled mouse samples. This should rule out the kind of contamination reported by Huber.

    Since one negative study used water as a negative control, and none of them took the extraordinary step of working in laboratory rooms never exposed to potential contaminants, I conclude the groups with positive results were more careful. Deniers appear to have relied on the rule of thumb that you can rule out all positive results due to contamination if you avoid all positive results. This is true, but hardly requires research.

    I'm afraid people who accepted the conclusions reported by many parts of the press without reading the actual papers and checking statements will wake up next week to find they have bought a motorized tie rack.


  13. I think it is important to remember how scientists structure their experiments and look at data determine emperical research results. I recommend reading Thomas kuhn's "The Structure of Scientific Revolutions" to help understand the nature of what is occurring in XMRV research.

    Thanks for the comments by Coffin. It is interesting to see where people are lining up on the novel XMRV discovery.

    Happy holidays everyone! I look forward to a new year with answers and treatments for us patients!

  14. Thank you so much for getting into the nitty gritty.

    You're one of the very few that does.

    Enjoy the festive holidays knowing that 'you done good'.

    hugs@ya fly

  15. Thank you, Mindy, for asking the right questions, and pushing a bit for answers. Anything to keep these guys honest! You are helping us all--thanks again for your good work.
    Best, Chris

  16. Yay Mindy! Sock it to 'em. Thanks for using your intelligence and persistence for the good of so many.


  17. One Dr Alan Rein, retrovirologist at the National Cancer Institute has said, on Dr Rancaniello's podcast today, that 'yes, XMRV could be a human pathogen, but that it also might not be' and he is concerned that research money might be wasted on XMRV and MLVs in CFS and/or cancer.

    Wasted? ME/CFS research is already getting nothing more than token amounts of money to investigate an illness that has felled more people than AIDS and costs more in lost income, taxes and productivity than, say, erectile dysfunction or malaria.

    IMO, this is a huge clue to the timing and thrust of this effort to end research on these MLVs. Money. These men, and yes, they are all men, are still heavily invested in HIV which still affects a lot more men than women, in the northern hemisphere. ME/CFS is still seen as mainly a woman's illness and it doesn't kill those patients right away. Keeping it a mystery and/or a quasi-mental illness keeps costs down.

    Either excuse, 'it's too big a mystery' or 'it's mental', allows the unconscious sexism and the unconscious bias against looking into something that is too "mysterious" to dominate the flow of research money.

    All his co-speakers, including Rancaniello, were careful to be a little more openminded-seeming regarding the contaminatin papers, but their overall bias still comes out against MLVs and XMRV. One of them, Rancaniello I think, also included the usual gratuitous insult to ME/CFS activists who insist on following up the lead provided by the WPI research and supported by the Alter/Lo paper. He quoted some email he had received, stated in authoritatative terms, that ME/CFS patients so want this finding to be "it" that we, as usual, are just crazy, stupid and delusional. He totally doesn't get the fact that we just want the leads followed up and proven or disproven scientifically, not politically or from purely economic motivation or cultural bias against women.

    Dr Coffin, who's name is all over HIV research is no exception. He and the others who first infered the contamination accusation is the end of XMRV research and then backed off from it haven't 'seen the light'. They have just adapted to the fact that their attack and resistance stategies to keep funding their pet projects will have to be more subtle than they have been so far.

  18. I used googleScholar to find papers with Dr Coffin's name on them. I found about 397, mostly paid for by US governmental bodies such as NIH.

    Of the first 100 papers whose titles I skimmed, 24% were about avian viruses - chicken tumor viruses, like Rous sarcoma (8% of the first 100 papers).

    Dr Stoye's name was on many of Coffin's papers. Stoye seems mesmerized by mice. His research, including fascinating papers on the hairless mutation in lab mice, are all based on mice as subjects of study.

    No wonder these two researchers become discombobulated when human patients talk back and question their motives. The mice and the chickens never did that!

    The remaining papers were mostly about HIV. It seems that those researchers deeply embedded in HIV research money pipelines do not want any money diverted to the potentially huge subject of viral infection in the 1-4 million Americans with ME/CFS.

    Mindy, I'd love for you to ask Dr Coffin if he thinks investigating chicken tumor viruses is more important that the possibility of a new retrovirus causing neuroimmune disease in humans.

  19. From me/cfs forums, by Wildaisy (not me who is just reposting):

    This is an attempt to summarize what has happened, so far, towards the forum nominating some people. I have taken my name, Roy's, and Dr. Yes' names off the list because we have declined. If anyone else on the list either agrees or declines, please let me know and I'll add that information to this list.

    I have also included Dr. Yes' excellent summary of what we would like for the patient representative(s) on this committee to do.

    I hope this gives us a starting point. Please add your suggestions.


    Steering Committee for the NIH State of Knowledge Workshop on ME/CFS

    Proposed mecfsforums nominees:

    Andrea Whittemore-Goad -- agreed
    Annette Whittemore
    Chris Cairns-agreed
    Heidi Bauer-agreed-
    Hillary Johnson
    Jamie Decker-Jones, MD
    Joan Grobstein, MD
    Judy Frederiksen-agreed
    Keith Baker-agreed
    Mary Schweitzer
    Mindy Kitei
    Pat Fero
    Tom Hennessy

    We need people who represent to, among other things:

    (1) Pressure the NIH to fund the WPI

    (2) Pressure the NIH to endorse and fund carefully controlled clinical trials of pharmaceuticals for HMRV positive CFS patients.

    (3) Demand that ME/CFS be recognized as a legitimate, severely disabling PHYSICAL disease - and NOT a psychosomatic one - by all government agencies in such a manner that insurance companies are obliged to treat it as such.

    (4) Pressure the NIH to allocate adequate funds for research into the HMRV-CFS association that will use the same criteria used by the WPI/NCI studies, and also to greatly increase funds for other research examining the neurological, immunological, and other biomedical components of ME/CFS.

    (5) Push for the formal recognition of the Canadian Consensus Criteria as the primary tool for ME/CFS diagnosis


  20. Great to see your blog again! you always ask the real "inside your face" questions.

    Happy New Year Mindy! Keep up the good up!

  21. Why Dusty Millers study is fatally flawed

    Please see this:


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