XMRV = Lab contaminant.

Posted by ERV on February 25, 2011
(83)
More »

After all the XMRV on ERV, as Wendy would say, “Im finished!”

Its over.

At this point, there are innumerable lines of evidence suggesting that XMRV is not a real human pathogen– from its magical ability to be spread despite no virus in any body fluid, including blood, including in HIV-1 patients, to its inability to infect its ‘target cell’ while it infects other cells, to its refusal to mutate more than two nucleotides on its own or in response to human mutagens in vivo, except that it does in vitro, its inability to give rhesus macaques even the most menial symptoms after being administered at a should-have-probably-been-lethal dose, to the fact not one lab on the planet can reliably detect it in humans, to the fact ‘XMRV infected’ people dont make antibodies ‘to’ XMRV, while healthy controls do– For XMRV to be a real human pathogen, it literally has to be an alien time-traveler from another dimension with some sort of Romulan cloaking device and/or Harry Potters magic cloak thingie.

It makes a lot more sense that ‘XMRV’ is really a lab contaminant, and once you start ‘looking’ for a contaminant, you can find it (whether you want to or not).

But pro-XMRV labs did have one good leg left to stand on: They mapped XMRV integration sites in prostate tumors from ‘XMRV’ prostate cancers.

*nod* There you go. They didnt just find the virus or evidence the virus was somewhere (or was somewhere, at some point), they found *it* and *exactly* where it integrated.

Except, apparently they didnt.

Analysis of XMRV integration sites from human prostate cancer tissues suggests PCR contamination rather than genuine human infection
XMRV is a gammaretrovirus associated in some studies with human prostate cancer and chronic fatigue syndrome. Central to the hypothesis of XMRV as a human pathogen is the description of integration sites in DNA from prostate tumour tissues. Here we demonstrate that 2 of 14 patient-derived sites are identical to sites cloned in the same laboratory from experimentally infected DU145 cells. Identical integration sites have never previously been described in any retrovirus infection. We propose that the patient-derived sites are the result of PCR contamination. This observation further undermines the notion that XMRV is a genuine human pathogen.

Oh for fucks sake.

Long time readers of ERV know what this means from my list of Creationist Claims about ERVs:

The first paper simply states that some retroviruses like to insert in genes, some like to insert near promoters of genes, and some like to insert in the middle of no where. The specific insertion sites, what base pairs on on the left, which ones are on the right, is random.

The odds of having the ‘same’ virus at the ‘same’ location in two independent organisms is fucking astronomical, to the point where we havent ever observed it. Ever. UNTIL XMRV, AMIRITE!! No. The ‘mapped integration sites’ are fucking contaminations from cell lines infected with XMRV.

For fucks sake.

It is striking that there have been no independent reports of patient-derived XMRV integration sites nor have there been any descriptions of polytropic or modified polytropic MLV integration sites in human samples despite the apparent detection of these viruses in CFS patients [5].

Hey.. hey guys. Why dont you all try to guess who [5] is. Ill give you a hint: It is Shyh-Ching Lo, Natalia Pripuzova, Bingjie Li, Anthony L. Komaroff, Guo-Chiuan Hung, Richard Wang, and Harvey J. Alter. The group who ignored their reviewers request for them to map their integration sites, because Alter is a NAS member, and they could. It is striking that they didnt ever do that, isnt it, Jeremy A. Garson, Paul Kellam, and Greg J. Towers?

Neither did Judy “NO ONE CAN FIND THE VIRUS BUT ME!!!!! I AM THE MESSIAH!!!” Mikovits.

Striking!

But maybe not so striking considering how the prostate cancer lab ‘mapped’ their sites. ‘Normal’ PCR? Meh, 30-40 cycles, whether youre doing regular or real-time. Sometimes you need a second round of PCR to bump up your signal more, or nested PCR, doubling that.

Jeremy A. Garson, Paul Kellam, and Greg J. Towers generously called the labs protocol ‘unusual’:

The propensity for PCR contamination is increased due to the unusual technique used for cloning the prostate tissue-derived integration sites which involved an extraordinary degree of PCR amplification with 80 preliminary amplification cycles followed by nested PCR consisting of 29 cycles and then an additional 18 cycles [8]. PCR tubes were opened during the procedure for the addition of fresh DNA polymerase after 40 cycles.

I do some weird PCR. I do. I have done some crazy ass shit to get my stuff to work, but I could tell you the exact biochemistry behind what I was doing, thus why I was doing it. And *I* think their method goes beyond ‘unusual’ and well into ‘convoluted and bizarre, to the point where I dont trust this data without further information’. And then theres this:

No negative controls were mentioned in the published method [8].

Oh for fucks sake.

Ugh.

Ugh.

Whatever.

I suppose I must give credit where credit is due– Mikovits was quoted as saying something recently at a conference hosted by (SHOCK!) a troupe of woo-peddlers, ‘Gordon Medical Associates’:

The subject I’ve stayed away from, that was discussed intermittently, was the politics of it all. Our government’s involvement, or lack thereof. I’d like to close with a quote from Mikovits, when asked about the politics and all the second guessing that has occurred regarding her research today. Very confidently, and quickly she retorted, “I think the politics will go away shortly.” Period. All she said. There was a gasp in the room, and she moved on as if she had just said “please pass me a glass of water.”

*shrug* She was right. Its over.

PS– Also, no XMRV associated with autism or families of autistic people. Still:

Lack of Infection with XMRV or Other MLV-Related Viruses in Blood, Post-Mortem Brains and Paternal Gametes of Autistic Individuals

Keywords:
(83)
More »

Comments

  1. #1 JohnV
    February 25, 2011

    holy lord 167 pcr cycles……………

    At cycle 39-40 I had RT-qPCR detecting single digit template copies (which I wouldn’t have trusted if it wasn’t right in the line plotted by the other dilutions and was mostly included for the gee whiz factor). They’re doing some kind of crazy homeopathic PCR I guess.

  2. #2 Poodle Stomper
    February 25, 2011

    But I find XMRV in all of my PCR assays also! My protocols are less orthodox though, requiring 90 cycles, addition of extra Taq and mixing of samples with the tail of one of my mice but it’s real!!!!

  3. #3 ERV
    February 25, 2011

    John– No, I think its only 127. They added the Taq after 40 cycles, at some point. lol, ‘only 127′.

    I want to know where the hell all their Taq went. Where did it go? Why the hell did they need to add more?? Hell, I can take reactions that have been in the fridge for a week, throw them in the thermocycler for a few minutes, and Taq still adds As on just fine if I decide I need to do a TOPO-TA reaction. Taq hasnt degraded so much that Ive needed to add more. I have never had to ‘add more Taq’. WHERE DID THEIR TAQ GO??? lol.

  4. #4 windy
    February 25, 2011

    There is a sort of logic there. Taq polymerase is heat-resistant, but not perfectly so, and supposedly a little bit of the Taq degrades during each denaturation step. But their procedure still seems unnecessary – half-life of Taq is about 40 mins at 95 degrees, so they could run a very long reaction before the polymerase becomes limiting.

    Extra cycles and and an additional two steps of nested PCR seems just overkill and inviting trouble. Unless their PCR is really non-specific, after 127 cycles they should have astronomical amounts of the target. What’s the initial amplification supposed to do that the nested PCR can’t do?

  5. #5 gillt
    February 25, 2011

    No negative controls were mentioned in the published method

    Maybe because after 127 cycles they were contaminated?

  6. #6 Amenhotepstein
    February 25, 2011

    You mean, after all this time, it was just a….

    Foreign Contaminant?

  7. #7 Amenhotepstein
    February 25, 2011

    Crap! Link borked! Try again!

    You mean, after all this time, it was just a…

    Foreign Contaminant?

  8. #8 chris
    February 25, 2011

    hey erv. you know you probably are an aspie, right?

  9. #9 Jay
    February 26, 2011

    But I woke up this morning and XMRV was in bed next to me!

  10. #10 andrew
    February 26, 2011

    from Human Test Subject Reveals Bacteria Responsible for Ulcers

    Dec 28, 2010 by Stephen Allen Christensen

    Read more at Suite101: Human Test Subject Reveals Bacteria

    Despite finding bacteria in tissue samples taken from the stomachs of people with ulcers, generations of physicians doggedly clung to the belief that most ulcers resulted from stress and poor dietary habits, and they exhorted their patients to make lifestyle changes that would supposedly cure them.

    Even though scientists acknowledged that the bacteria found in specimens from different people all looked the same, they presumed these microorganisms resulted from contamination. After all, they claimed, the stomach’s interior is essentially a sterile environment, made so by high concentrations of hydrochloric acid that kill bacteria.

    Ads by Google

    I feel this article shows that the so called experts can get it wrong and they have used the contamination argument before in the past.

  11. #11 ZenMonkey
    February 26, 2011

    ‘XMRV infected’ people dont make antibodies ‘to’ XMRV

    Little off-topic, but I’ve been wondering about CFS patients who have been tested for XMRV and the results have come back positive. I’m unclear on how XMRV is so ridiculously hard to find in CFS patients, yet there’s accurate tests for it? (One of which is of course provided by the WPI, at rates of $400 or so, which is not covered by any insurance.)

    What kind of information are these patients receiving? I have to say I haven’t yet come across one CFS patient who says she is XMRV-positive who a) has a scientific or skeptical perspective or b) wasn’t pro-XMRV to begin with. Naturally that’s not any kind of useful data, and I’m sure such people exist. But I haven’t been able to get good information from XMRV-positive patients thus far other than “I feel vindicated” and “Yay Mikovits” and so forth.

  12. #12 Poodle Stomper
    February 26, 2011

    Andrew,

    Yes, science does have it wrong at times. Science is a self-correcting field. However, there is a difference between helicobacter pylori and retroviruses. Retroviruses are known to have a very high rate of mutation. To observe the identical sequence in unrelated cases is extremely unlikely (see nigh impossible). As ERV pointed out, for a retrovirus from two unrelated cases to have identical insertion sites is also very, very unlikely. So yes, science does make mistakes but don’t confuse retroviruses for bacteria. They are completely different.

  13. #13 RRM
    February 26, 2011

    @andrew

    Suppose you fall out of an airplane mid-flight. On your way to almost certain death, you start thinking: “oh, I once read about this guy falling out of an airplane from the same height as me. It look like our cases are very comparable. This means I have a good chance of survival”.

    No, you don’t. Millions of others have been in the same position as you and have died under identical circumstances. The luck of one crazy exception you can think of doesn’t enhance your chances of survival. For you to compare yourself with the lucky guy, you must have fallen from a plane AND have survived.

  14. #14 RRM
    February 26, 2011

    @Zenmonkey

    This guy (the below forum’s owner BTW) has tested positive at WPI (or VIPdx) and seems pretty skeptical:

    http://forums.aboutmecfs.org/showthread.php?10261-Your-daily-negative-XMRV-study-XMRV-is-PCR-contamination&p=160094&viewfull=1#post160094

    Of course, on the “other” forum, posters have concluded that this guy is an afwul human being. It reminds me of that Monty Python bit:

    http://www.youtube.com/watch?v=gb_qHP7VaZE

  15. #15 jaranath
    February 26, 2011

    Andrew:

    Abbie’s posts and the research article highlight plenty of reasons why XMRV is different from the ulcer case. And don’t forget it was the scientists who discovered the bacteria and convinced the rest of the scientific community, and doctors (who are not scientists).

    If you want to know why this is different, read the post. If you don’t understand the science, ask. “Science has been wrong before!” is, by itself, a meaningless objection.

  16. #16 Scramton
    February 26, 2011

    Not following the scientific method just never seems to work out.

  17. #17 Azkyroth
    February 26, 2011

    I’m still struggling to understand the significance of this XMRV thing. Is it like that guy who comments sometimes who thinks every single human behavior or ailment is triggered by changes in NO levels, only it’s gained an audience?

  18. #18 ERV
    February 26, 2011

    ZenMonkey– I find it particularly disgusting and manipulative that WPI et ass make it clear that ‘a negative test doesnt mean you are negative’. If you keep paying for tests, they will keep testing you until its positive.

    Ive been wondering about the legality of this– telling people they are infected with viruses with non-FDA approved, unlicensed tests. None of the reagents we use in the lab are licensed for clinical testing– all companies put NOT FOR CLINICAL OR DIAGNOSTIC USE in their inserts to protect themselves, legally, from back-door ‘testing’ like this. And then I realized their ‘super special viral culture’ method used reagents that I dont think come with that warning, while PCR, flow, Western, etc reagents absolutely 100% do. What a strange coincidence…

  19. #19 theshortearedowl
    February 26, 2011

    To quote my previous lab manager: “Yeah, well they could have amplified bloody anything with that protocol…”

  20. #20 John
    February 26, 2011

    I took Mikovits at her word at the beginning, with the whole ‘you have to culture the sample to find the virus’, etc., until it apparently came out that WPI found the virus without culturing (err, what? still not sure about that whole situation), but the evidence is mounting and I’m now basically to the point of being an XMRV atheist, so props to you, ERV, you called it. This paper kind of seals the deal for me. (obligatory ‘if it weren’t for you damn kids I’d have gotten away with it!’, and ‘next time, Inspector Gadget, next tiiiiiiiime….!’, etc.)

    I’ve been wondering about the XMRV testing thing too, man. I think the WPI fucked up fairly royally by selling those tests. They’re kind of cash-strapped as it is, do they really have the money to refund several hundred thousand dollars to testees if the XMRV thing is finally, conclusively (as in court of law conclusively) shown to be a contaminant? Dr. Peterson, the P in WPI, ‘semi-retired’ and left his position as medical director at WPI shortly after the XMRV thing broke. I even spoke with someone over email who said she was a patient of his and was in the process of selling her home to move to Reno to be closer for treatment at the WPI, ie that’s how sudden it was. Was Annette Whittemore penny wise and pound foolish to head up the WPI herself instead of hiring someone with experience to do the job?

    That said, the one thing that I still have questions about is that Dr. Peterson has presented numerous times on a cohort of patients he sees who have all developed either mantle cell lymphomas, gamma clonal T-cell rearrangements (indicative of long term viral infection and predictive of MCL), etc. and all had CFS for a long long time prior to developing cancer. What the fuck is up with that? It’s stuff like that that keeps me from completely dismissing XMRV, but I’m not gonna argue with anyone anymore trying to support it.

    There’s just a lot of stuff that doesn’t make sense even besides the XMRV PCR stuff, like how ME, the disease renamed CFS, has been reported numerous times to occur in epidemic outbreaks which are entirely consistant with enterovirus outbreaks, yet one of the arguments about XMRV is that it has a long latency period, which doesn’t make sense.

    Supposedly the new theory is that XMRV is really a recombinant of two mouse MLV’s which occured when human cell lines were passaged through mice, and that’s why they haven’t found XMRV as such in mice.

    Stuff due to be presented at CROI in Boston-

    XMRV

    91LB: XMRV Probably Originated through Recombination between Two Endogenous Murine Retroviruses during in vivo Passage of a Human Prostate Cancer Xenograft.
    T Paprotka, K Delviks-Frankenberry, O Cingoz, A Martinez, H-J Kung, C Tepper, W-S Hu, J Coffin and Vinay Pathak

    In Poster Abstracts:

    Session 55: XMRV: New Findings and Controversies

    Session 58: XMRV and GBV Virus–Host Interaction

    Session 41: Biomarkers Linked to cognitive Dysfunction

    Session 43: XMRV: New findings and Controversies
    Discussants: Kathryn Jones, NCI; Jonathan Stoye

    215: Development of a GFP-indicator Cell Line for the Detection of XMRV
    KyeongEun Lee, F Ruscetti, P Lloyd, A Rein, G Fanning-Heidecker, and V KewalRamani

    216: XMRV Induces a Nonproductive Infection in Human Lymphoid Tissue

    217: Presence of XMRV Sequences in B Cells Are Restricted by APOBEC

    218: Single Copy and Single Genome Sequencing Assays to Detect XMRV in Human Blood Products
    Mary Kearney, A Wiegand, J Spindler, F Maldarelli, J Mellors, J Coffin and Blood XMRV SciRes Working Group

    219: Discordant XMRV Test Results and Non-reproducible Mouse Endogenous Retroviral Detection in an XMRV-prevalence Study
    Timothy Heinrich, et al

    220: Serologic and PCR Testing of Persons with Chronic Fatigue Syndrome in the US Shows No Association with XMRV
    William Switzer, H Jia, H Zheng, S Tang, R Garcia, and B Satterfield

    221: Extensive Genetic Recombination in the XMRV Genome
    William Switzer, W Heneine, M Prosperi and M Salemi

    222: Disease-associated XMRV Sequences Explained by Laboratory Contamination
    Stephane Hue, E Gray, A Gall, A Katsourakis, CP Tan, C Houldcroft, J Garson, O Pybus, P Kellam and G Towers

    223: Identification of a Novel Endogenous MLV as an XMRV Ancestor
    Oya Cingoz and J Coffin

    Session 58

    Poster Abstracts
    XMRV and GBV-virus–Host Interaction

    235: Determination of Host Range and Cellular Tropism of XMRV

    236: Lack of the Detection of XMRV or Polytropic MLV-related Sequences in Blood Cells from HIV-1-infected Patients in Spain

    237: A Sensitive Real-time PCR Assay for the Detection and Quantification of XMRV

    238: No Evidence for XMRV Infection in Transplant Recipients from Germany

    239: Limited Evidence of XMRV Infection in Different Populations in Spain, Including Patients with Chronic Fatigue Syndrome and Prostate Cancer

  21. #21 Charl
    February 26, 2011

    John: there is certainly something strange going on in CFS/ME. Just because XMRV isn’t the cause doesn’t mean that there isn’t immune dysfunction triggered by a past or on-going viral infection in many people with those conditions. The fact is fact is, we know no more about the cause of CFS and ME than we did 18 months ago, other than that XMRV isn’t involved (nor in prostate cancer either). What’s truly rotten is the amount of money, time and resources wasted on this dead end that should have been shut down in about 2008, and which could have been use so much better employed trying to find the real cause(es).

  22. #22 daedalus2u
    February 26, 2011

    Azkyroth, XMRV is like cold fusion, homeopathy, chiropractic, acupuncture. An initial mistake that people got their egos invested in and later couldn’t admit that they were wrong. It is not at all like nitric oxide (which does happen to be an actual cause of CFS). See this post.

    http://www.chronicfatiguetreatments.com/wordpress/treatments/chronic-fatigue-syndrome-nitric-oxide/

    The idea of low NO being the cause of many disorders is a correct idea that hasn’t caught on yet. It is the opposite of XMRV which is a wrong idea that caught on and persisted much longer than it should have.

  23. #23 Azkyroth
    February 27, 2011

    That would be more immediately credible if you hadn’t previously ascribed spousal abuse to an evolved tendency to subject women to stress that would increase their NO levels during pregnancy, and I vaguely remember you brought it up in a context that had to do with regularity of bathing…

  24. #24 Poodle Stomper
    February 27, 2011

    Stating that nitric oxide (whether a lack or excess) is the cause of CFS is also not credible without a load of evidence to back it up, especially when there is no consensus on the cause of CFS in the scientific community. Saying things like that is no different that what the wooers do when they claim their magic virus is the cause.

  25. #25 ZenMonkey
    February 27, 2011

    It is not at all like nitric oxide (which does happen to be an actual cause of CFS)

    The idea of low NO being the cause of many disorders is a correct idea that hasn’t caught on yet.

    Because it’s only a hypothesis on which you have done no studies or experiments of any kind in humans? And the whole thing is based on your personal decision that post-exertional malaise is the “major” symptom of CFS. It is extremely irresponsible to go around naming your pet NO project as a definitive and “correct” cause of CFS when there is literally no scientific evidence to confirm it. Additionally there’s been a considerable amount of research since November 2008 when you wrote that post you keep flogging.

    There are currently zero definitive causes of CFS. None. Nothing. Nobody knows. (I’m not talking about etiologies, obviously.) Claiming that you have “the answer” with no medical science to back you up is akin to quackery, and CFS patients are flooded with more than enough of that.

    Personally I’m much more interested in the recent spinal fluid study than in XMRV at this point, although of course if the scientific consensus on XMRV (or NO, for that reason) ever winds up positive, I will change my mind.

  26. #26 Andrew
    February 27, 2011

    A virus and bacteria are totally different as I know myself.
    I was however pointing out the politics which go on to discredit Helicobacter Pylori the cause of stomach ulcers and xmrv have been the same. Using psychiatrists to say a disorder like ME CFS Is down to psychological factors such as illness beliefs is as unscientific as it was to put ulcers down to stress. Before J Marshalls discovery Stomach ulcers were seen as down to stress by science no argument!
    Your blog points out Mikovits as exploiting people for her own ends you fail to point out THE medical psychiatric camp being funded in the UK by the tax payers were most negative studies originate. They would lose that funding and there reputations if XMRV was found to be the cause of ME CFS.
    It is easy to come up with a test to not find what you are looking for and call it scientific. As I have explained and will add J Marshall as a Nobel prize winner scientist states that no one could replicate his results which he says himself was not true and they called his bacteria contamination o a harmless commensals. Which are the same reasons given as not finding XMRV for ME CFS? Can I trust the establishment’s negative research into XMRV?
    .So as you see if the results don’t fit the science can be ignored overlooked or subverted by the prejudices of the scientific majority especially when it is seen as totally a psychiatric condition. The idea that science is not compromised or influenced by the politics is naïve.
    You can find J marshalls own words on this
    http://nobelprize.org/nobel_prizes/medicine/laureates/2005/marshall-autobio.html

  27. #27 In Vitro Infidelium
    February 27, 2011

    Oh for heaven’s sake you scientists simply don’t understand science – you need a part time psychology student to tell you just how wrong you all are (apart from Judy Mikovits who knows everything) http://www.retrovirology.com/content/8/1/13/comments#471696

    @ ZenMonkey I’m unclear on how XMRV is so ridiculously hard to find in CFS patients, yet there’s accurate tests for it? (One of which is of course provided by the WPI, at rates of $400 or so, which is not covered by any insurance.)

    WPI (even if unintentionally) is creating its own patent ‘illness (XMRV infection) based on the WPI licensed test. XMRV + is considered = to HIV + by many M.E/CFS sufferers who have had the test and who now firmly believe that XMRV is the cause of their M.E/CFS symptoms because, they have a test that tells them they are infected with a retrovirus. The logic that you present >if XMRV is so secretive, how come WPI can find it so easily in so many M.E.CFS sufferers ?< is reversed by the XMRV+ crowd who see the WPI test as being the one perfect lens which no one else but WPI has been able to create. So long as WPI keep returning tests which say CFS = XMRV+ then there will be no acceptance by the pro WPI faction that XMRV is a dead end. The very fact that such a high proportion of CFS sufferers do return a positive result should be seen as problem, after all why should a Syndrome defined by a group of disparate symptoms have a single infectious agency ? The clinical symptoms of HIV infection are not unique to HIV, even though the process of AIDS may be. If XMRV can cause M.E/CFS symptoms, other viruses ought to be able to do the same and be as hard to find within the affected individual, in which case M.E/CFS would be expected to have multiple disease agencies across the human population.

    @ Andrew. Puleeease, not another WPI generated meme, it was stupid when Annette Whittemore put it out in her new year’s message to the world and it only grows more ridiculous in repetition. No one ever seriously doubted the existence of H.pylori, the only questions were whether it could survive in the human stomach and whether it could cause disease. Science didn’t make a mistake regarding H.pylori, it simply awaited the evidence that the organism could survive in the stomach and could cause disease. XMRV by contrast has no reliable scientific means of being assessed as anything more than a laboratory artefact. As for your selective reading of Marshall’s biography, you missed the key point – “I was unsuccessfully attempting to infect an animal model.” – his adoption of himself as the animal model is what led to wider acceptance i.e ‘it was the science what done it’.

  28. #28 ERV
    February 27, 2011

    LOL!

    “The authors are clearly not familiar with MLV viruses”

    I mean, this is straight from the wooers playbook– the arrogance of someone to think their laymens understanding of viruses/vaccines/evolution is superior to that of THE ENTIRE FIELD OF VIROLOGY/IMMUNOLOGY/EVOLUTION composed of EXPERTS WHO HAVE STUDIED VIRUSES/VACCINES/EVOLUTION FOR THEIR ENTIRE LIVES.

    Ugh.

    Its like me going up to an airline pilot “Excuse me, MR EXPERT, but clearly you are unfamiliar with the intricacies of flight. Ive been flying X-wings in video games for years, I think I know a little more about how to fly than you do.”

  29. #29 RRM
    February 27, 2011

    Worse is that his fellow forum members now believe this study has been ‘debunked’.

    The funny thing is that a true expert once explained to this person how silly his comments were. Of course, this retrovirologist (and a graduate student from his lab) were subsequently banned from the forums:
    http://www.mecfsforums.com/index.php/topic,4637.msg51094.html#msg51094

  30. #30 andrew
    February 27, 2011

    I would try to stop the pilot from crashing into a mountain if he had a bucket over his head .

  31. #31 daedalus2u
    February 27, 2011

    If you want to reject what I say because you don’t understand it, that is fine. That is what you should do. The correct response is to say “I don’t know”.

    Azkyroth, abuse lowers NO levels. When pregnant women are abused, the low NO produced is what mediates the physiology of the “cycle of violence” in their unborn child. If you are going to be growing up in a violent environment, having a violent-type phenotype is a “feature”.

    Abuse can be a causative factor in CFS too. The coupling between PTSD and CFS is due to the common pathways involving NO.

    PS, there is a “load of evidence”. There are not clinical trials because I don’t have funding to do them. Largely that is because this idea is considered too “far out” and people are not willing to put the time in to understand the background, that would be the “load of evidence” that I have based it on.

    Zen, and is there any data in the literature that contradicts the low NO hypothesis of CFS? Any data that is not compatible with the low NO hypothesis of CFS?

    *Crickets chirping*

    There wasn’t any before 2008, and there still isn’t any. I am pretty sure there never will be any because the low NO hypothesis of CFS is actually correct.

    Prior to the acceptance of the Helicobacter pylori hypothesis of ulcer causation, there was also no data inconsistent with the hypothesis that Helicobacter pylori caused ulcers. The reason there was no data inconsistent with it is because the hypothesis of Helicobacteri pylori causation was actually correct.

    I do recommend reading the Nobel Prize writeup by Marshall. Politics and the popular media played a big role in the acceptance by the scientific community that Marshall was correct. That and his satisfying Koch’s postulate by inducing gastritis in himself by drinking a H. pylori culture. Which by the way was merely an n=1 anecdote.

  32. #32 Poodle Stomper
    February 27, 2011

    “PS, there is a “load of evidence”. There are not clinical trials because I don’t have funding to do them. Largely that is because this idea is considered too “far out” and people are not willing to put the time in to understand the background, that would be the “load of evidence” that I have based it on.”

    Is this load of evidence available from peer reviewed sources? Has this load of evidence been replicated? You ask Az “Zen, and is there any data in the literature that contradicts the low NO hypothesis of CFS? Any data that is not compatible with the low NO hypothesis of CFS?
     but to do so is to ask him to prove a negative. The burden of proof is on you. Until you can show reliable evidence that your hypothesis is correct, claiming that it is so is no different than what woo-meisters and snake oil salesmen do.

  33. #33 Jay
    February 27, 2011

    Anyone who still uses Taq should have their funding pulled. Come on people.

  34. #34 jaranath
    February 27, 2011

    Andrew, as has been pointed out several times already, read this post. Read Abbie’s, and others’, past posts on the topic. Read the article in question. The reasons why XMRV is a non-issue are laid out plainly. Pylori had data, XMRV doesn’t. Waving your hands around vaguely and yelling “politics!” and “conspiracy!” won’t change that. But yes, “lalalalalaIcan’thearyou” IS easier.

  35. #35 daedalus2u
    February 27, 2011

    PS, the “load of evidence” is from the peer reviewed literature. I am not presenting the low NO hypothesis of CFS as other than a hypothesis. I am not charging people $400 for a test, and then subjecting them to HAART with no basis. That makes me different than the woo-peddlers.

    If people want to understand the low NO hypothesis of CFS, it is up to them to get the background to understand it. I can’t *force* anyone to learn the background.

  37. #37 ZenMonkey
    February 28, 2011

    Zen, and is there any data in the literature that contradicts the low NO hypothesis of CFS? Any data that is not compatible with the low NO hypothesis of CFS?

    As Poodle Stomper pointed out, this is the exact same question as “Prove that aliens didn’t land at Area 51″ or “Prove that Jesus wasn’t the son of God.” That’s not my job. It’s your job is to prove that your hypothesis is solid, which you have never done. Constantly repeating yourself and reposting a 3-year-old article do not constitute evidence of any kind. As you claim to be a skeptic it’s astonishing you don’t know this.

    I am pretty sure there never will be any because the low NO hypothesis of CFS is actually correct.

    Again, this is scientifically and logically bizarre. I am pretty sure there will never be any research showing that tiny pretty pink ponies visit my backyard at night, because they really do. What?

    However, I did send you an article that refuted your NO hypothesis this year. I never received a response.

    Finally, not all woo-peddlers are out to scam patients. Some have good intentions (ahem) and are somehow deluded into thinking that they have the answer. They are just as dangerous, if not more so, than the obvious scammers.

    Please leave the medical science to medical scientists. Again, we patients do not need yet more garbled and unproven “theories” for the desperate to chase. I dearly wish you could understand this part as your ego seems to be overpowering your interest in actually aiding patients. This is not a game and you are currently adding to the problem.

  38. #38 ERV
    February 28, 2011

    Dany– Did you read this post and follow the links? What do you think that table means? I know what the psych major thinks it means (its what Creationists think it means), but what do you think it means?

  39. #39 daedalus2u
    February 28, 2011

    Zen, if you are so ignorant of nitric oxide physiology that you equate it with little pink ponies, we can’t have a conversation about it because you don’t have the background to understand it. If you do a search on PubMed, there are 107,704 citations listed under “nitric oxide”. Under “pink ponies” there is only a single citation.

    There is wrong stuff in the nitric oxide literature (just like there is wrong stuff in every field). It takes a sophisticated understanding to be able to understand it. You are not going to get a sophisticated understanding of it in a few days, a few weeks or a few months. This bogus XMRV stuff took a couple of years to shoot down and probably cost tens of millions in time from sophisticated and knowledgeable researchers.

    When real skeptics don’t have the background to understand something, they say “I don’t know”.

    If you read and understood what I wrote some years ago, and feel it is wrong, what is wrong with it? If you can’t articulate why you feel it is wrong, then (if you are a skeptic) you have to default to “I don’t know”. If you can’t bring yourself to default to “I don’t know” then you either need to learn the background so you can articulate what is wrong with it, or you need more practice at being a skeptic.

    I agree with you, that CFS patients do not need more incorrect hypotheses (like XMRV) siphoning off resources and energy from productive research avenues. What CFS patients need are correct hypotheses and further research on those correct hypotheses. I am quite sure that I have a correct hypothesis. I don’t have the resources to do the kind of research on it that should be undertaken.

  40. #40 ZenMonkey
    February 28, 2011

    Zen, if you are so ignorant of nitric oxide physiology that you equate it with little pink ponies, we can’t have a conversation about it because you don’t have the background to understand it.

    daedalus2u, if you seriously don’t understand why I gave that example, and since you keep calling your unproven hypothesis “true,” I have no idea what you’re doing calling yourself a skeptic.

  41. #41 daedalus2u
    February 28, 2011

    Zen, if you are a skeptic, you know you can’t “prove” anything, you can only disprove it and then you know it is wrong. You can never know it is right.

    No *real* scientist ever talks of *scientific proof*.

    When I say that something is “true”, what I mean that it has been confirmed to me to such a degree that it would be perverse to withhold provisional assent. That is the same definition of “true” that any other skeptic has.

    If you want some kind of “proof” before thinking something is “true” you are using a non-skeptical standard.

    I understand why you gave that example, and it was a poor example. NO is known to be involved in each and every physiological system that is disrupted in CFS. What triggers mitochondrial biogenesis is NO. What regulates steroid synthesis is NO. What regulates blood flow is NO. What regulates oxygen consumption is NO. What regulates ATP levels is NO. What regulates the immune system is NO. What regulates expression of glycolytic enzymes is NO. What regulates erythropoeisis is NO. What regulates bone density is NO. It would be perverse to think that NO was not involved in CFS.

    CFS is a long term state. A long term state can only be a consequence of a long term disruption of normal physiological control systems. Essentially all of the physiological systems that are known to be out of whack in CFS are regulated by NO, and they are all out of whack in the direction that would be expected from a chronic state of low NO.

    Does that constitute “proof”? No, it doesn’t. But that and a whole lot more has convinced me that it would be perverse to not provisionally accept the hypothesis that CFS is due to low NO.

    I appreciate that you don’t have the background to understand the details of NO physiology the way that I do. My understanding is not unique, or magical, or somehow out of the mainstream. It is considerably deeper and broader than most mainstream NO researchers and is focused in a different direction, mostly on NO as a signaling and control mechanism and how perturbations in the basal NO level affect NO mediated signaling pathways and what are the long term consequences of those disruptions.

  42. #42 Cheng Vang
    February 28, 2011

    If you do a search on PubMed, there are 107,704 citations listed under “nitric oxide”.

    *face palm* Search engine fail.

    If you want some kind of “proof” before thinking something is “true” you are using a non-skeptical standard.

    *face palm* Skeptic fail.

    I am quite sure that I have a correct hypothesis.

    You know, people who are sure they have a correct hypothesis usually have a shit load of credible experiments to go along with that hypothesis.

  43. #43 Poodle Stomper
    February 28, 2011

    “My understanding is not unique, or magical, or somehow out of the mainstream. It is considerably deeper and broader than most mainstream NO researchers and is focused in a different direction,”

    You know, it really irks me something fierce when people with no relevant background in a subject claim that they know more/better than those people actually doing the research. On what are you basing this claim? Do you know the limits of their knowledge? I’m sorry but words like that are cheap and used by antivaxers, AIDS deniers and every other form of woo and stupidity out there. If you truly know better then put your money where your mouth is and actually do the research. Otherwise, you are simply accepting your own idea with no experimental evidence to back it up and, again, this is exactly what the wooers do.

  44. #44 Levi
    March 1, 2011

    ERV,

    You state at #18: “Ive been wondering about the legality of this– telling people they are infected with viruses with non-FDA approved, unlicensed tests.”

    In your studied opinion, would this concept also apply to Brent C. Satterfield of Cooperative Diagnostics, who offered the first commercially available XMRV to the public ahead of VIPdx/WPI? Who sold hundreds of “blood dot” tests to be sent thru the mail by patients who were charged $400 a pop? He may have seen the light and closed his operation down, but all of those test results are still out there.

    Its been a while since I practiced law, but it would sorta seem to be a similar problem in both cases. If so, why are Satterfield, Cooperative Diagnostics, and the CDC not properly disclosing this potential conflict of interest due to a possible legal author liability in the latest 0/0 XMRV paper published in Retrovirology?
    http://www.retrovirology.com/content/8/1/12

    If serious competing interests undeclared by scientists in publications are a problem for you, then why do you repeatedly use Satterfield’s research to support your claims about XMRV on your site? Just wondering. You explain the science of PCR testing well and I have enjoyed your adventures in Antarctica. I hope you keep writing about XMRV on your blog, at least until Ian Lipkin completes his work and releases his findings, which will most likely be definative on the subject of XMRV.

    Then you will either have a gloatfest, or have some tall explaining about your theories to blog about. Good luck either way!

  45. #45 Kiwi
    March 1, 2011

    “Zen, and is there any data in the literature that contradicts the low NO hypothesis of CFS? Any data that is not compatible with the low NO hypothesis of CFS?”

    Yep. There’s the slight problem with your theory that NO levels aren’t low in CFS. A few studies have looked at it now, I can’t be arsed finding any others now but if you can get the full text of that they’ll probably reference them where they note that CFS patients often have elevated NO levels.

  46. #46 ZenMonkey
    March 1, 2011

    (erv, I apologize for this brief hijack.)

    Poodle Stomper, I would like to get in touch with you. If you’re so inclined, could you click on my name and leave a random comment somewhere so I can get your email address? If not, no worries at all.

  47. #47 daedalus2u
    March 1, 2011

    PS, project much? I am just back from the Gordon Conference on NO. I have been working with NO for ~10 years. There was considerable improvement in the general level of understanding since the last Gordon conference that I went to where I presented on the opening night on basal NO.

    kiwi, NO levels are not higher in CFS. Nitrate and nitrite levels might be higher, but that is not the same thing. Yes, many NO researchers make the same mistake and confuse high nitrite plus nitrate with high NO. Nitrate and nitrite are metabolites of NO. Their concentration (in micromolar levels) reflect the production rate of NO, not the NO concentration (which is nanomolar or less).

    At the Gordon Conference there was an excellent presentation on NO levels in the brain by the worlds expert on measuring NO levels in the brain (in vitro). The first slide was on what levels of NO people have reported in the brain, it went up to micromolar. Then he showed his results. His highest measurement was a few nanomolar. His lowest was maybe 10 picomolar. That is moles per liter. 10 picomolar is 0.3 parts per trillion. That is extremely challenging to measure on the time (sub second) and length (sub micron) scales that it is important. The trip was worth it just for that.

  48. #48 Poodle Stomper
    March 1, 2011

    Daedalus,

    Define “working with NO”. If you’ve been doing research linking it to CFS and have evidence to back it up then great. However, making statements definitively linking CFS to low nitric oxide despite no evidence to back it up leads me to have serious doubts about the nature of your research (i.e. how scientific it is). The last you mentioned regarding this, you had tested giving one person a concoction of bacteria to supposedly raise their levels of nitric oxide and that they felt better. You did not however present any evidence that the bacteria you gave them actually raised their NO levels nor that their NO levels were low to begin with. So all you had was a very probable placebo. So no, I’m not projecting at all. I simply very much dislike crap science. If your science is legit then by all means publish it and let your results be replicated and I’d be more than happy to apologize.

  49. #49 W. Kevin Vicklund
    March 1, 2011

    kiwi, NO levels are not higher in CFS.

    I have found numerous studies supporting elevated levels (of production?) of NO in patients with CFS. I was unable to find any studies showing that NO is depressed in CFS patients. Please provide links or cites to such research articles.

  50. #50 ERV
    March 1, 2011

    Sorry, Levi– You got caught in the spam trap :(

    Cooperative Diagnostics pulled the plug on their commercial testing once it became clear that there was more to the story than the 2009 Science paper. Via the Cooperative Diagnostics page:
    Within weeks, results from those being tested commercially questioned the connection between XMRV and CFS. Cooperative Diagnostics immediately posted a warning to its customers that XMRV may or may not be found in persons with CFS and that purchase of a test would aid in research only. Once peer-reviewed publications confirmed that XMRV was not found in CFS or controls, Cooperative Diagnostics elected to remove its test from the market. It seemed unethical to continue to sell a test for a virus that the majority of peer-reviewed publications indicated may not even exist in the human population.

    That was the responsible thing to do. VIPDX/REDLABS should have, as well.

    why are Satterfield, Cooperative Diagnostics, and the CDC not properly disclosing this potential conflict of interest due to a possible legal author liability in the latest 0/0 XMRV paper published in Retrovirology?

    From the paper you linked to:
    COMPETING INTERESTS
    Cooperative Diagnostics is a commercial enterprise that owns the rights to one of the XMRV PCR tests described in this manuscript. Publication of these results will likely reduce the potential market that Cooperative Diagnostics could reach with its XMRV test.

    They clearly disclosed their financial interest in this issue. Their negative findings will negatively impact their business. Its in the paper. Freely available, to anyone.

    *weirdlook*

  51. #51 Levi
    March 1, 2011

    ERV,

    No worries about the spam filter. I did read the paper and the “disclosure” statements about competing interests that you to speak of above. They are misleading. Had they said “Well, one of our authors owns a business that sold XMRV tests to hundreds of folks that could get him sued if XMRV turns out to be a viable pathogen and the test missed it. Not to mentioned thier sex partners. So he may be a bit biased.”

    THEN it would be an accurate and meaningful disclosure. Its just a small point, but I think you may be missing it.

  52. #52 daedalus2u
    March 1, 2011

    PS, it is ok, I do have data. I have instrumental data of NO production by these bacteria in vivo. Instrumental measurements showing that some of it is absorbed. Instrumental measures of a physiological effect known to be mediated by NO coincident with spontaneous and instrumentally measured NO production by these bacteria in vivo, human. It is instrumental data of many sigma above background in multiple events. But it is n=1. What I don’t have is the resources to get higher n data.

    I have presented my data at conferences, I haven’t published it because it is n=1. It isn’t wrong because it is n=1. Marshall’s data was n=1 too. He had other data as well. At these conferences no one has shown me how my data is wrong, they just say I need higher n.

  53. #53 Poodle Stomper
    March 1, 2011

    I truly would like to hope that you are right and that CFS is that easy to treat. I also hope that you continue on then and get a much higher n. I also hope that you agree that an n=1 does not warrant such statements as “CFS is caused by low NO”. Not yet anyway.

  54. #54 RRM
    March 1, 2011

    Meanwhile, in Boston:

    http://www.retroconference.org/2011/Abstracts/42508.htm

    Conclusions: We conclude that XMRV was not present in the original CWR22 prostate tumor but was generated by recombination between PreXMRV-1 and PreXMRV-2 during in vivo passages of the CWR22 xenograft. The probability of an identical recombinant arising multiple times is vanishingly small, raising the possibility that contamination of human samples with XMRV originating from the 22Rv1 cell line is responsible for its reported association with PC and CFS.

  55. #55 ERV
    March 1, 2011

    Christ:

    We could reliably detect 1 env copy and 10 gag copies of XMRV control plasmid… XMRV was not detected in 2 patients with previous positive test results.

    Obviously WPI ‘diagnoses’, since they said one person was XMRV and one was ‘MLV-X-whatever’.

  56. #56 Kiwi
    March 1, 2011

    PS, it is ok, I do have data. I have instrumental data of NO production by these bacteria in vivo. Instrumental measurements showing that some of it is absorbed. Instrumental measures of a physiological effect known to be mediated by NO coincident with spontaneous and instrumentally measured NO production by these bacteria in vivo, human.

    But no data showing that has any relevance to CFS. You’d be a bit more convincing if NO levels actually were low.

  57. #57 John
    March 1, 2011

    ‘Vanishingly small’ is scientific lingo for ‘your ass is cooked’, isn’t it? …and one of the authors’ names is Frankenberry!

    CFS patients, tonight we mourn the loss of something which didn’t even make much sense in the first place. Let us now sing our blues-
    http://www.youtube.com/watch?v=KowJb0s1TIE

    ——————————–

    http://www.retroconference.org/2011/Abstracts/42508.htm

    Paper #:91LB
    Title:XMRV Probably Originated through Recombination between 2 Endogenous Murine Retroviruses during in vivo Passage of a Human Prostate Cancer Xenograft
    Authors and Affiliations:T Paprotka1, K Delviks-Frankenberry1, O Cingoz2, A Martinez3, H-J Kung3, C Tepper3, W-S Hu1, J Coffin2, and Vinay Pathak*1
    1NCI-Frederick, MD, US; 2Tufts Univ Sch of Med, Boston, MA, US; and 3Univ of California, Davis, Sacramento, US

    Background: Xenotropic murine leukemia virus–related virus (XMRV) has recently been associated with human prostate cancer (PC) and chronic fatigue syndrome (CFS). However, other studies have failed to detect XMRV in PC and CFS patients. A human PC cell line, 22Rv1, produces XMRV that is virtually identical to virus isolated from PC and CFS
    patients. The 22Rv1 and CWR-R1 cell lines were derived from a human PC xenograft, CWR22, which was serially passaged in nude mice. To evaluate the genetic variation and evolutionary potential of XMRV, nucleic acid extracts of early and later passages of the CWR22 xenografts and CWR-R1 were analyzed.

    Methods: DNA isolated from early (3rd and 7th) and later passage CWR22 xenografts consisted of a mixture of tumor DNA and nude mouse DNA. Short tandem repeat analysis was used to confirm that the tumor DNA were derived from the same person as the 22Rv1 and CWR-R1 cell lines. XMRV-specific PCR primers and qPCR assays were developed and used for the analysis of xenograft and nude mouse nucleic acids. We explored the origin of XMRV by analyzing xenograft-associated nude mouse DNA and DNA from other nude mouse strains; the data revealed the presence of two previously undescribed endogenous proviruses, PreXMRV-1 and PreXMRV-2, which contained >3.2-kb stretches of their genomes with ~99.92% identity to XMRV.

    Results: PCR assays showed that both cell lines and later passage xenografts contained XMRV but the early passage xenografts did not, indicating that XMRV was not present in either the original CWR22 tumor or associated nude mouse tissue, but became prevalent in later passage xenografts. Retroviral recombination between PreXMRV-1 and PreXMRV-2 involving a few template switching events can generate a
    replication-competent virus that differs from XMRV by only 5
    nucleotides (99.94% identity). Analysis of 15 nude mouse strains indicated that none contained XMRV, but some strains potentially used to passage the xenograft contained both PreXMRV-1 and PreXMRV-2.

    Conclusions: We conclude that XMRV was not present in the original CWR22 prostate tumor but was generated by recombination between PreXMRV-1 and PreXMRV-2 during in vivo passages of the CWR22 xenograft. The probability of an identical recombinant arising multiple times is vanishingly small, raising the possibility that contamination of human samples with XMRV originating from the 22Rv1 cell line is responsible for its reported association with PC and CFS.

  58. #58 RRM
    March 2, 2011

    To the idiots at the MECFSforums:

    The point of Miller’s reply at Retrovirlogy is that common integration sites are not the same as identical integration sites.

    It’s like saying “I have parked the car at the same spot as I did yesterday” vs “I have parked my car exactly where I did yesterday and when I say exactly I mean to the fermimeter”.

  59. #59 Patrick Moore
    March 6, 2011

    Occam’s Razor of Virology: When you find a virus that causes disease, the disease should be easier to understand and not harder.

    If you have to come up with more explanations for the virus than you would without it, then you are wrong (e.g., XMRV infection is not a HERV and is restricted to a rare form of prostate cancer and CFS–diseases which share no apparent common features. Somehow, these prostate cancer and CFS patients have a common exposure to this virus as a risk factor despite there being no common epidemiologic patterns. Although XMRV is clearly a murine ERV, people with exposure to mice are not at noticeable risk for prostate cancer or CFS).

    It makes more sense that XMRV is a murine ERV that jumped to a human prostate cancer cell line decades ago when it was passaged through a nude mouse as a xenograft (a common practice) as elegantly shown by the Hue et al Retrovirology article. It has since been detected as an intermittent PCR contaminant.

    My advice, above all else, is to test samples blindly and randomly. If you have PCR contamination, your results will be “biased toward the mean” of no significant relationship. This is the easiest and least costly confirmation possible. When your postulated virus-disease relationship survives this stringent test, then you possibly have something. Then, the science begins. Randomized and blinded testing has saved me, on multiple occasions, from appearing to be a bigger idiot than my natural talents for idiocy allow.

    For what it is worth, when the CFS-XMRV paper was first published, we had severe concerns about its methodology and conclusions, which was published in F1000 (subscription required so it is reprinted below). I think it it is still valid:

    Detection of an infectious retrovirus, XMRV, in blood cells of patients with chronic fatigue syndrome.
    Lombardi VC, Ruscetti FW, …, Silverman RH, Mikovits JA
    Science 2009 Oct 23 326(5952):585 -9 [abstract on PubMed] [full text]
    DOI: 10.1126/science.1179052 PMID: 19815723
    Competing interests: None declared

    Comments

    The discovery of the cause of chronic fatigue syndrome would be an extraordinary finding. Rather than providing extraordinary proof, this manuscript has flaws that leave the reader unsure of knowing precisely what was measured. To detect the xenotropic murine leukemia-like virus (XMRV), the authors used nested-PCR on non-randomized and non-blinded samples, a recipe for uncontrolled PCR contamination. This technique re-amplifies previously cycled products and is inherently prone to intermittent false positivity that has occurred in our lab and many others (e.g. {1} and {2} on which I am the author). This is a concern in light of post-publication claims that XMRV detection rates among chronic fatigue syndrome (CFS) patients have climbed from 67% to 95%, and XMRV tests are now being sold and advertised on the internet at [http://www.redlabsusa.com/ http://www.redlabsusa.com . Southern blotting, which would allay this suspicion, was not done. Other results in the study also lack support. Flow cytometry and immunostaining with murine leukemia virus (MLV) antibodies were used to directly detect viral proteins in patient cells (see Figure 2A of the paper). The CFS peripheral blood cells have robust monotonic staining rather than the bimodal peaks that are expected from a mixture of infected and uninfected populations of peripheral blood cells. It is not certain whether this level of viremia for an exogenous retrovirus is medically possible. It may, perhaps, be possible but it seems improbable and is a pattern more consistent with a cross-reactive endogenous retroviral antigen. To confirm this finding, CFS peripheral blood cells (without negative controls in Figure 2B) were immunoblotted using cross-reactive spleen focus-forming virus (SFFV) and MLV antibodies. XMRV gp70 and p30 proteins are found at higher levels in 2 out of 5 CFS peripheral blood samples (1150 and 1221) than in the positive control — HCD-57 cells directly infected with SFFV — a very remarkable result. Repetition with negative control samples (see Figure 2C of the paper) has the higher molecular weight bands cut from the photograph, thus we cannot interpret potential positivity for p30 gag precursor proteins among the control samples (see CFS samples 1199 and 1220 in Figure 2B). Finally, the positive control HCD-57 cell lane in Figure 2C lane 8 has a completely different banding pattern from the very same control in Figure 2B lane 7 for the p30 gag protein. The elementary issue of whether the authors are measuring XMRV has to be clarified. The fundamental basis for the CFS case and control samples is also not defined at an appropriate level. The samples (supplementary online material) were “selected for this study from patients fulfilling the 1994 CDC Fukuda Criteria for Chronic Fatigue Syndrome (S1) and the 2003 Canadian Consensus Criteria for Chronic Fatigue Syndrome/myalgic encephalomyelitis (CFS/ME) and presenting with severe disability”. These are two separate definitions, the latter published in the “Journal of Chronic Fatigue Syndrome” (which is no longer in print). It is unclear how the samples were selected from these two criteria. No references or cut-offs are given for tests used to clinically define the CFS patients as cases so we are unable to interpret the essential basis for the study. In addition, no description is given to indicate that controls were tested in the same manner as CFS patients; in fact, there is no description for negative control samples at all. For a disease whose diagnosis is controversial, a clear statement of where and how the cases and controls were selected is a critical first step.

  60. #60 Patrick Moore
    March 6, 2011

    P.S. Thanks for your comments on our JVI paper on Merkel cell polyomavirus. It sure felt good that someone outside our field read it critically

    http://scienceblogs.com/erv/2010/11/new_cancer_virus_merkel_cell_p.php

    P.P.S. Your logo on God, gag, pol, env, etc. is…perfect. Just perfect.

  61. #61 ERV
    March 6, 2011

    *points up* I will be printing that comment off when Im looking for a post-doc in a year or so :P

  62. #62 ken
    March 6, 2011

    http://www.retrovirology.com/content/8/1/13/comments
    ERV It looks this fellow from mecfs.forums is taking you and Miller to task on your analysis! What about his analysis. Some of it makes sense.

  63. #63 Ken
    March 7, 2011

    http://www.retrovirology.com/content/8/1/13/comments
    Who is this Gerwyn fellow trashing Towers, Miller and You Erv. Is there anyone on here that has expertise to counter his arguments. Miller tried but got no where with Gerwyn as he keeps spinning out abstracts and assumptions on the scientific method versus guesstimate which he throws at the Tower study and Miller. Maybe Miller will give some brownie points to refute some of Gerwyn analysis if you call it that. Any takers. I don’t have the background, it only confuses everything. If at all with the outbreaks, I believe that CFS may be caused by entrovirus since everyone agrees its replication is to slow for such a dramatic outbreak at one time. thoughts or takers anyone????

  64. #64 John
    March 9, 2011

    Mr. Morris apparently didn’t understand that the paper he was commenting on was dealing with the subject of identical integration sites, a finding which had never been reported before yet according to the paper was reported twice by the same lab which ‘discovered’ the virus to begin with, and not preferential integration into genes (someone please feel free to correct me if I’m using incorrect terminology). Seeing as how the paper was only a short correspondance dealing with that one topic it doesn’t exactly instill me with confidance that he is truly taking anyone to task in his subsequent remarks.

  65. #65 RRM
    March 10, 2011

    His later explanation for this tiny error was very convincing though:

    “When the authors describe integration sites they appear to be discussing integration into the same genome or region of a genome rather than a single nucleotide as raised by Miller.”

    Let’s see, from the actual paper:

    “Nucleotide BLAST searches (…) revealed that 2 of the 14 integration sites (..), obtained from two different patients, were identical to XMRV integration sites.”

    And: “Two mismatched nucleotides were noted in the LTR region (…)”

    Also, check Figure 1 (http://www.retrovirology.com/content/8/1/13/figure/F1?highres=y), which has the title “Nucleotide alignments of XMRV integration site sequences derived from patients’ prostate cancer tissues and the experimentally infected human tumour cell line DU145.”

    So yes, the authors are certainly at fault for not making it clearer for the dyslectic.

  66. #66 Charl
    March 11, 2011

    Erlwein and McClure retest their samples using Lombardi et al’s primers, and an ELISA assay: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0017592

  67. #67 anonymouse
    March 11, 2011

    Could someone comment on Gerwindbags latest revelation —
    http://www.mecfsforums.com/index.php/topic,6122.0.html

    I am as dumb as a stump regarding these issues but does this research actually show what he is claiming or is he bending research again.

    Thanks so much.

  68. #68 ERV
    March 11, 2011

    Mouse– Ive dealt with Creationists/Deniers/Anti-vaxers for so long, I usually can interpret blather into what they think they mean. I have no idea what he thinks his point is in that particular post. Your guess is as good as mine.

    Apparently its a ‘great find’, though… :-/

  69. #69 Charl
    March 11, 2011

    There are s***loads of different lab mouse strains – new ones are constantly being created to mimic different human pathologies all the time, and occasionally the mice get put in the wrong both together, do what mice do best, and you get a brand new cross strain. Some common lab strains have been bred to be sensitive to XMLVs (which they should normally lack a functional receptor for), but wild mice (by which I mean the little blighters who ate my trainers one winter when I left them in the garage, get into our room space and scurry around, and used to steal my rabbit’s food) should be immune. No idea about wild-type lab mouse strains, as I don’t know how close they are to real wild house/field mice. Not sure why Gerwyn is getting excited.

  70. #70 anonymouse
    March 11, 2011

    Thanks so much for the replies.

    Can the conclusion “XMRV is capable of infecting laboratory mice as well as humans” be drawn from the research he cited and does it actually mean anything. I really don’t know know what, in all his arrogance of I know more than retrovirologists, he is trying to prove here except maybe XMRV found in samples from the WPI were not due to contamination. Seems like a huge leap in logic to me.

  71. #71 ERV
    March 11, 2011

    With Teh Crazy, sometimes I find it useful to grant their premise. If his premise is “XMRV can replicate in wild mice/donkeys/lady bugs” fine.

    If XMRV can replicate in wild mice/donkeys/lady bugs, why is there functionally *zero* sequence diversity in the reported sequences?

    I just made a neat graphic of ~150 HIV variants. Its only a stretch of ~100 nucleotides (not the whole genome). Every single one of these variants is clearly different from the others.

    And yet the XMRV sequences published, to date, are LESS DIVERSE than expected by *DNA* mutation rates, certainly not mutating like a real wild-type pathogen that is actively replicating (mutations via RT and recombination and in proviral DNA) and under selective pressure from constantly shifting environments (every newly infected individual is a new environment, and as their immune response responds, the environment changes).

    Its absurd to posit that XMRV is actively replicating in wild anything. Its a contaminant.

  72. #72 John
    March 13, 2011

    link #1- http://treatingxmrv.blogspot.com/2011/03/cover-up-and-contamination-theories.html
    ‘Cover-up and contamination theories’ by Jamie Deckoff-Jones MD

    link #2- http://treatingxmrv.blogspot.com/2011/03/year-of-antiretroviral-therapy.html
    relevant excerpt from link #2 in regards to link #1-”Frankly, I was expecting that people far more knowledgeable than I would punch holes in what I’d written. But it has now been read by thousands of people including a bunch of virologists and although some found it inflammatory, nobody has yet taken exception with the science.”

    I’ve tried, any other takers?

  73. #73 daedalus2u
    March 13, 2011

    John, it is impossible to use facts and logic to argue someone out of a position they didn’t use facts and logic to adopt.

  74. #74 Charl
    March 18, 2011

    Silverman’s lab are still putting out abstracts suggesting they think XMRV has a role in prostate cancer: http://download.journals.elsevierhealth.com/pdfs/journals/0022-5347/PIIS0022534711006203.pdf

    XMRV in prostate samples (embedded in formalin), but no sequenced integration sites, by the look of things: http://download.journals.elsevierhealth.com/pdfs/journals/0022-5347/PIIS0022534711016181.pdf

  75. #75 RRM
    March 18, 2011

    To be fair, that abstract was probably submitted some time ago.

    I a very recent Chicago Tribune article, Silverman was quoted as follows:

    “I am concerned about lab contamination, despite our best efforts to avoid it,” Silverman wrote in an e-mail, adding that similar cell lines “are in many, many labs around the world. Contamination could come from any one of a number of different sites.”

    ..and…

    “22RV1 cells were once previously (more than a year earlier) grown in my lab but were being stored in a liquid nitrogen freezer at the time, and not the same freezer used to store prostate tissues,” Silverman wrote in an e-mail. “At the time it was unknown that 22RV1 cells were infected with XMRV.”

    Source: http://www.chicagotribune.com/health/ct-met-chronic-fatigue-xmrv-20110317,0,6116823.story?page=1

  76. #76 caught XMRV in 2010
    March 25, 2011

    Brain Demyelination/lesions AIDS Yes ME/CFS Yes

    Chronic sore throat Flu like illness AIDS yes ME/CFS yes

    Swollen lymph nodes AIDS yes ME/CFS Yes

    Cognitive problems AIDS yes ME/CFS yes

    Skin Problems AIDS yes ME/CFS yes

    IBS and other stomach problems AIDS yes ME/CFS Yes

    Cancer/Leukimia/Lymphoma AIDS yes ME/CFS Yes

    Weird tumor
    spleen,liver,brain,testicular AIDS yes ME/CFS yes

    Heart Failure AIDS yes ME/CFS yes

    Many active viruses AIDS yes ME/CFS yes

    White thrush AIDS yes ME/CFS yes

    Swollen tongue with teethmarks around it AIDS yes ME/CFS yes

    Fatigue AIDS yes ME/CFS yes

    Seizures AIDS yes ME/CFS yes

    How blind and gullible do you have to be, to not be able to see that ME/CFS is also caused by an HIV like virus? ME/CFS is caused by a retrovirus, we have known this since the early 80s when ME/CFS brain MRIs were taken and they looked exactly like AIDS patients, in the early 90s De Freitas found a retrovirus in the blood of ME/CFS patients and the CDC didn’t even bother paying attention to her, now the WPI has found the XMRV virus which is a retrovirus which was suspected all along and people still can’t admit that ME/CFS is caused by just that.,

    How blind and dumb are you?

    How can you tell me that is all in my head ?when two of my friends that have HIV have the very same health problems that I do but they do much much better then me because they have meds and I don’t.

    hey let me come to you and infect you, if you are 100% sure that XMRV does not exist let me come to you and infect you with my XMRV, if you don’t get sick then i will definitely call myself crazy and hopefully my brain demyelination will go away, if you get sick then you can come back to this blog and tell people how fucked up your health is and how the doctors think you are just a quack.

    if you have the balls to call me crazy have also the balls to actually get a shot of my blood or have unprotected sex with me,do something useful for this world show us that u can get infected with XMRV and not have any health problems..

    please reply to me don’t be a coward i’ll come to you anywhere you are, i live in Chicago flights at ohare are very cheap to any part of the country..

    In the mean time while i wait for your reply and see you pussy out, i will wait to get somebody else infected(4 people so far and counting) and i will wait for another two weeks to go donate more blood and more plasma.

  77. #77 NJ
    March 25, 2011

    caught @ 76:

    How can you tell me that is all in my head ?

    All I can do is tell you what’s not in your head.

  78. #78 heidi
    April 24, 2011

    I am so confused…After reading all of this I have come to the conclusion that even under the simplest of explanations, unless I am sporing multiple Phds. I will never grapple all of this.

  79. #79 Prometheus
    April 25, 2011

    caught XMRV in 2010@#76

    “if you have the balls to call me crazy have also the balls to actually get a shot of my blood or have unprotected sex with me,do something useful for this world show us that u can get infected with XMRV and not have any health problems..”

    Based on this remark I imagine the “balls” located on either side of the nasal bones are sufficient both in perception and the provision of a safe distance to pronounce you not merely crazy but of the batshit variety.

    At what point did we vest iconic in disease to the point that we have venereal disease fabulists doing a buck and wing into full blown delusions of medical grandeur?

    Delusions should be fun. This is why I accuse the psychiatric community of having done the dear Karl Friedrich Hieronymus, Freiherr von Münchhausen a terribly disservice.

    For future reference could you people come up with something that at least captures the panache of an imagined Dauphin or garden variety snake pit messiah.

    Shall we have a contest?

    Examples:

    I would have finished graduate school but for;

    the radioactive spider bite.

    the golden tablets.

    the gypsy curse.

  80. #80 Richard Jefferys
    May 4, 2011

    http://jvi.asm.org/cgi/content/abstract/JVI.00693-11v1

    JVI Accepts, published online ahead of print on 4 May 2011
    J. Virol. doi:10.1128/JVI.00693-11

    Absence of XMRV and other MLV-related viruses in patients with Chronic Fatigue Syndrome

    Clifford H. Shin1, Lucinda Bateman2, Robert Schlaberg1, Ashley M. Bunker3, Christopher J. Leonard1, Ronald W. Hughen4, Alan R. Light4, Kathleen C. Light4, and Ila R. Singh1

    1 Department of Pathology, University of Utah, Salt lake City, Utah, 84112
    2 Fatigue Consultation Clinic, Salt Lake City, Utah, 84102
    3 ARUP Laboratories, Salt Lake City, Utah, 84108
    4 Department of Anesthesiology, University of Utah, Salt Lake City, Utah, 84112

    Corresponding author: Mailing address: Emma Eccles Jones Medical Research Building, Department of Pathology, 15 North Medical Drive East, Suite #2100, Salt Lake City, UT 84112, Phone: (801) 213-3737, Fax: (801) 585-7376

    ABSTRACT
    Chronic fatigue syndrome (CFS) is a multi-system disorder characterized by prolonged and severe fatigue that is not relieved by rest. Attempts to treat CFS have been largely ineffective primarily because the etiology of the disorder is unknown. Recently CFS has been associated with xenotropic murine leukemia virus-related virus (XMRV) as well as other murine leukemia virus (MLV)-related viruses, though not all studies have found these associations. We collected blood samples from 100 CFS patients and 200 self-reported healthy volunteers from the same geographical area. We analyzed these in a blinded manner using molecular, serological and viral replication assays. We also analyzed samples from patients in the original study that reported XMRV in CFS. We did not find XMRV or related MLVs, either as viral sequences or infectious virus, nor did we find antibodies to these viruses in any of the patient samples, including those from the original study. We show that at least some of the discrepancy with previous studies is due to the presence of trace amounts of mouse DNA in the Taq polymerase enzymes used in these previous studies. Our findings do not support an association between CFS and MLV-related viruses including XMRV and off-label use of antiretrovirals for the treatment of CFS does not seem justified at present.

  81. #81 ERV
    May 4, 2011

    Ill put a post up on it tomorrow, Richard :) Thanks for the heads up, I dont really PubMed XMRV anymore…

  82. #82 RRM
    October 5, 2011

    Err..Richard/Abby, that’s just the “old” Singh study (Shin et al.) that was apparently released *way* ahead of print…

  83. #83 JKR
    December 23, 2011

    #76, caught XMRV in 2010

    Wow.

    1) I understand you are envious of your friends who are doing better than you because they have medication for their illness and you don’t, but that attitude is incredibly immature. Do you intend to go through your entire life saying: “it’s unfair, you have X,Y,Z, but I got squat?” That’s not going to help you.

    2) what bothered me immeasurably more is your callous attitude for the well being of others. If you feel victimized because others don’t seem to sympathize or understand or immediately kowtow to your perspective, then threatening to infect people you hope to persuade isn’t going to help your cause. And if your anger stems from the fact that you have decided those here are never going to rally to your cause, you made certain of that by threatening.

    3) If you really are certain that you DO have XMRV, and that it really is the true cause of all your miseries, then may I ask you politely to not go around donating blood and more plasma for the sake of spreading it to others? It is an unethical, immoral, dishonorable attitude. No matter how unfair life has been to you, I can’t believe you’ve gone around deliberately wishing/causing misery on people (4 so far and counting?)

    As a scientist, but more importantly as a human being, I’m appalled by your irresponsible and petty behavior. It’s making me sick to my core.