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Mikovits interview states the FDA will confirm WPI findings in a Sept publication

Discussion in 'Media, Interviews, Blogs, Talks, Events about XMRV' started by Stone, Aug 16, 2010.

  1. August59

    August59 Daughters High School Graduation

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    Andrea's blog says she is on Ampligen.
  2. alex3619

    alex3619 Senior Member

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    Hi anceindaze,

    There is a reason its called the central dogma I think, one lecture they tell you about it, next lecture they tell you it is wrong ... dogma in the old fashioned sense. RNA retroviruses are interesting beasts, as are RNA viruses themselves. One thing that gets lost is that RNA is bioactive, you don't need protein if you have the right RNA. Indeed, much of the human genome is DNA->RNA, it never goes any further. Last I was reading on this (eight years ago) some were questioning if most of the genome ever goes to protein. Of course, once you get protein you can cut and paste and modify and refold, so one DNA sequence can give rise to dozens of different proteins - another problem with the central dogma. It is hypothesised that RNA is the original DNA and protein, you don't need either except for the fact that RNA is biochemically unstable compared to DNA or protein, so it is hard to retain good mutations so they evolve slowly.

    My comment on mutation was from my pedantic geek biochemist side which rears up occasionally. My comp sci side uses a different definition for mutation yet again ... oh well. I once presented a paper on a specific use for genetic algorithms at an engineering conference in Dunedin, New Zealand. Not a good paper mind you, just an excuse for the uni to pay for me to travel overseas and get my PhD supervisor yet another co-authorship.

    Bye
    Alex

  3. alex3619

    alex3619 Senior Member

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    Hi,

    Which may have forced PNAS to release Alter prior to September, or lose the scoop.

    Bye
    Alex
  4. anciendaze

    anciendaze Senior Member

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    As a matter of fact, I ran across a piece by Francis Crick in which he admitted he didn't understand the precise meaning of dogma when he first used it. (You might say he is ''not into religion".) It simply turned out to be unusually appropriate for the way it has been used.

    Yes, the bulk of the genome is never transcribed to protein. Many sequences may have regulatory significance only. This is completely independent of whatever role endogenous retrovirus plays. From a pure biological research standpoint, independent of CFS/ME, XMRV is fascinating. It looks very much like a virus right at the point of switching from exogenous to endogenous, which would give exceptional insight into the way the human genome evolves through horizontal transmission of genetic information. You couldn't keep researchers away from this bug if you beat them with clubs.
  5. alex3619

    alex3619 Senior Member

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    :D
  6. anciendaze

    anciendaze Senior Member

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    Last time I checked on Gallia they were into division and parties tre bien, (though I suspect Italia has an edge in this regard.)

    I'll take another crack at explaining. Anyone who knows the subject well may want to hide their eyes. I got the idea from a statement by Judy Mikovits, though she is certainly not responsible for my interpretation.

    We are dealing with a virus which carries genetic information in RNA, and transforms this to DNA it can insert in cells. These genes then produce the proteins which form the components of the virus, other than RNA. This inserted DNA is called a provirus, even if it is just sitting there doing nothing.

    One discovery of the past year is that this proviral sequence is mutated by an enzyme named Apobec 3G, and possibly others. This appears to be a natural defense against retrovirus, though details remain to be worked out.

    As it happens, the mutated sequence is translated into precisely the same sequence of amino acids in a protein. This is part of a natural mechanism to limit damage to the cell's own DNA caused by random mutations by using redundant coding to produce the same amino acid from different nucleotide sequences in DNA. In one case the cell is mutating the provirus, to stop it from harming the cell. In another the cell is trying to protect its own genetic information from damage by random mutations. The virus is exploiting this to enhance its own survival. (The XMRV virus may be new, but the 'strategy' here looks old to me.)

    Since DNA PCR is extremely specific for particular sequences, any such change is likely to prevent detection of proviral DNA by that means. A provirus which lies in these living cells for long is likely to accumulate changes which make detection difficult, but the mechanism described above allows it to still produce a virus competent to infect other cells. (I need to mention that Apobec 3G has not been found in prostate cells, where detection should be easier.)

    I'm making a reasonable assumption that insertion of proviral DNA is most likely to happen when the cell is actively reproducing. Activating cells needed for a particular role in an immune response, and allowing a clone of them to grow, is the way the immune system takes really tiny signals from specific infections and amplifies them until the specific response is strong enough to defeat infection. (We don't even know how many different responses are possible. The number must be huge.)

    One point of contention between supporters of the XMRV hypothesis and deniers is the need for artificially stimulating (activating) immune system cells from blood before running tests. If the cells were already active, because of a natural response, there would be no need for this. If the cells were inactive, and any provirus in those cells was mutated, there wouldn't be anything for DNA PCR to find. If the cells were active, and the virus was inserting fresh proviral DNA, this material would not be mutated immediately, allowing time for detection. The time the provirus sits in a cell is important.

    What I'm proposing is that the decision to exclude people with signs of active viral infection, made far back in the history of some research groups, had the effect of excluding those who would show up with XMRV by DNA PCR on unactivated cells. When some of the same samples were tested by WPI, where the cells were activated, some tested positive.

    All the deniers used 'spiked' positive control samples in which a DNA plasmid (a simple loop of DNA not in a chromosome) was added to a known negative sample. (This was forced on them by the assumption there are no infected human subjects to provide positive controls.) Because this was outside the cells, it was not subject to mutation by Apobec 3G, or other cellular enzymes. This meant is was easy to pick up through DNA PCR, with or without activated cells.

    Does this make things clearer or murkier?
  7. shannah

    shannah Senior Member

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    Is there a link you can post to her blog?
  8. urbantravels

    urbantravels disjecta membra

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    Thanks anciendaze. I'm beginning to get the picture, although I'm going to have to go back to the books (and re-review Vincent Racaniello's Virology 101 lectures on viral pathogenesis) before it really starts to sink in.

    This is beginning to look like pretty huge stuff, not just for our poor afflicted selves, but for biomedical science.

    It'll be interesting to see how garbled all this gets in the popular press. A "stealth virus" - why, the scare headlines practically write themselves!
  9. urbantravels

    urbantravels disjecta membra

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    Ok, couple questions for anciendaze or alex or anybody who might be able to weigh in.

    First - we know the WPI picked "highly viremic" (I suppose one should properly say retroviremic) patients for the Science paper - and the deniers were biased toward picking people *without* "signs of active viral infection."

    Does anyone know exactly what signs we are talking about? What made some people look more "viremic" than others? Is it just the typical symptom set of sore throat/fever/swollen lymph nodes that "looks" like an active viral infection, or was it a matter of picking people who were more debilitated, i.e. housebound/bedbound? I'm assuming they would have excluded people with co-infections - or would they?

    Where does the relative absence or presence of specific *neurological* symptoms play into all this? Undoubtably the WPI picked some people with pretty serious neurological manifestations, and we know the CDC tends to consider neurological symptoms exclusionary for CFS.

    It would be awfully interesting to catch an XMRV infection in its initial stages, which I don't think anyone has done or tried to do yet. After all, if you have an acute flu-like onset, what reason would you have to think it's anything other than the flu? ... until you've gone through the long slow nightmare of it NOT GOING AWAY. Many people don't get a diagnosis for years. (And I can see many, many logistical obstacles to designing a study that would look at acute-onset viral symptoms and try to catch a few initial XMRV infections in there amidst all the regular influenzas. Hosptializations maybe? But how many people get hospitalized in the course of an acute onset of XMRV? Would an initial XMRV infection be more or less likely to cause serious complications than a flu?)

    Separate question from the above flurry of related questions.

    I can envision a scenario where the CDC et. al, the whole chorus of deniers (not just of XMRV but of the idea that there ever was a viral infection involved in CFS) are going to attempt to cover their exposed hindquarters with a lot of tsk-tsking about how of COURSE nobody would have been able to detect XMRV before, it is only now with our modern knowledge that it was detectable, what a shame it was *impossible* to detect any sign of a viral infection before 2009 or so.

    I can plausibly see the narrative developing that way. Not "there have been 25+ years of needless suffering and neglect of the disease because the early science got strangled in its cradle about 20 years ago by politics, egos, and institutional arrogance" - but "What a terrible pity that we could not detect and treat this awful disease before now. Of course we have been trying hard but it was just impossible to do. Hooray for modern medicine!"

    (And there will be concerted efforts to leave out of the public narrative any mention of 20+ years of sufferers being told it's all in their heads, and research dollars being diverted into attempts to prove what twisted individuals we all are.)

    I think this is where the real awareness challenge is going to lie. The XMRV science itself is undoubtably going to blow up big. I think most of us are pretty convinced at this point that the avalanche has been triggered on the scientific side and no "cover-up" of the science is going to be happening ... THIS time. But there may well be some very creative/selective re-writing of the history of how the disease has been treated.

    So, persons who actually know the science, riddle me this: If research into a viral cause of CFS *hadn't* been quashed back when Elaine DeFreitas's work was rubbed out, is there actually anything about the state of the science at the time that would have prevented researchers from detecting XMRV? Is there something about the state of the science *now* that made this the soonest possible time XMRV could have been detected?

    Because I strongly suspect that's going to be the cover story from now on.
  10. Mark

    Mark Acting CEO

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    Very good point, crucial question I agree. Perhaps the wider question really is: were DeFreitas' findings related to XMRV and other retroviral/MLV activity in ME/CFS patients.

    Apart from the fact that there may still be other unknown retroviruses involved and it could turn out that DeFreitas' work contained clues about them, the point I think is that XMRV detection itself is not necessarily the only and crucial way in which biological clues could be found, and it's not true that in the absence of XMRV-detection technology we knew nothing. In fact, one can now list all the studies that showed immune abormalities, that showed high viral load, and at least hinted at retroviral infection - studies that were only recently dismissed and now they too turn out to be highly significant - and say that those lines of inquiry were never fully investigated. So I think the thing is to point out that the technology of XMRV detection itself is not really the point regarding the failure to reproduce DeFreitas' work - she found clues to something, which are at the very least possible to have been relevant to XMRV, and that opportunity was lost, at great cost...how that happened does need to be explained...

    You kind of highlight how the media and public are about to start wandering down this road and asking themselves all these same questions...I think they may take some while to travel that road, it's a pretty incredible story...
  11. urbantravels

    urbantravels disjecta membra

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    The media is going to be monumentally confused about all this. And sensationalistic, Good Lord are they going to be sensationalistic.

    I think XMRV (ok, we'll all need a little while to switch to the new name) detection IS the point. Not that it should be - but that it is. I keep going back to that quote from Dr. Bell in Osler's Web: You can't talk business until you have the pathogen. (Actually he said "organism")

    The lack of the pathogen has always been the big escape hatch from treating this like a "real" disease.
  12. anciendaze

    anciendaze Senior Member

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    I'm going to take this in stages, after reminding people I am not an authority. What you get from me are the words I post, nothing else. I do not have any relevant degrees or certifications. These are the opinions of an affected individual. You are free to check them however you can.

    "Tender lymphadenopathy", meaning those swollen lymph nodes, has been on lists of symptoms since about day one. This has disappeared from recent CDC definitions, and what mention they've made of use of this, and similar signs, by others has been in the context of exclusion.

    Peterson and Cheney (who consulted the world expert on EBV) had used available tests for antibodies to EBV, and complete absence of those which hold the virus latent, as an indication of reactivated infection and immune dysfunction. This was misinterpreted to mean EBV was responsible. Recent CDC statements against testing immunological status are striking, considering the wealth of data currently available.

    To tell the truth, we still don't know what the CDC consider exclusionary. I will quote myself, (a vile habit,) from un-posted material.
    This takes us into a morass. They have made illness with unknown etiology, like MS, exclusionary for CFS diagnosis. Unfortunately, in the absence of clear lesions on MRI scans, MS is also a diagnosis of exclusion. The logical fallacy here is having two diagnoses of exclusion with the same symptoms.
    I'm going to cut off some of that question, because it is based on a false assumption. Earlier outbreaks with the same symptoms were not merely reported, but actively investigated with the technology available at the time. One particular outbreak, in Punta Gorda Florida, was investigated by a CDC Epidemic Investigation Service team which not only talked to doctors in the community, but went around knocking on doors to find the 50% of patients not reported by physicians. They wrote up their findings and published them in NEJM in April 1959. The same issue contains an investigation by Alexis Shelokov of an outbreak at Chestnut Lodge Hospital in Rockville, MD, as well as a survey article on prior outbreaks. The goal was that, when the next outbreak took place, investigators would be prepared to go in early and capture data which had eluded these investigators. All three people went on to distinguished careers, demonstrating they were not flakes. In this context, the squandered opportunities at Incline Village or Lyndonville are especially poignant.

    In response to the notorious 1970 paper attributing these outbreaks to 'mass hysteria', one investigator, David Poskanzer, wrote a very good letter to BMJ. He made the remarkable suggestion that instead of attributing the illness to psychoneurotic people, they might consider all psychoneurotic illness the result of residual deficits from infectious disease. This has been widely ignored.


    I'm going to trim some of these statements, not because I disagree, but because this post is already long.

    Here's the real kicker in that episode. Before she crashed and burned, Elaine DeFreitas had TEM micrographs showing more than one virus. The really interesting one for me was a C-type virus with a diameter of approximately 70 nanometers. This pretty well shouts retrovirus, and one expert who saw the pictures said so at the time. The whole series of pictures has not, to my knowledge, been published anywhere. What I would love to get my hands on is the picture showing a virion inside a mitochondrion. MuLV is known to infect mitochondria, and I don't think any other virus is known to do this. All by itself, the discovery of a retrovirus in human beings which infected mitochondria should have been a major result. Yes, it was possible; it was done.

    DeFreitas had a mess in the samples she was given, from patients with multiple infections, and she had teased out clues that a retrovirus was involved. She thought it was related to HTLV-1 or HTLV-2, but she stated it was neither of these. This didn't stop people from testing for those, and announcing they had shown her wrong. In terms of sensitivity and specificity, she was really pushing the envelope of the state of the art. It is not surprising others had trouble replicating, even if they tried.

    When Tom Folks was personally involved in the CFS work, he got preliminary results confirming DeFreitas. He had to go chasing a contamination problem, leaving Heneine, who "did not get along" with DeFreitas (extreme understatement) on CFS. The end result was that one lab got no response at all, while a different lab got response to every sample from any source. These conflicting results were taken to discredit DeFreitas. She never did finish her work, because Wistar management forced her out, hurricane Andrew hit Miami, and her health deteriorated. We don't know what might have happened if she had had support.

    We had another mess with a researcher (John Martin?) who found spuma virus apparently causing cytopathology, which is not characteristic of spuma virus. I suspect they were both seeing the recombination action of an "acutely transforming" virus shuffling genes. Historians will have to sort this out. I'm sure there are other episodes I know nothing about.

    How this plays out will be VERY interesting.
  13. urbantravels

    urbantravels disjecta membra

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    Were they actively investigated as soon as people went down sick - i.e. within 14 days of initial symptoms? That's the question I was getting at. I don't have a real sense of how often the "acute onset" makes people suspect anything other than the flu, or how often the first 14 days of infection are serious enough to warrant hospitalizations. (I didn't really have a well-defined acute onset period myself, but I had a "coming down with the flu" feeling for a number of weeks before I went down unrecoverably.)
  14. anciendaze

    anciendaze Senior Member

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    As I understand it, the investigators were on the ground while new cases were still turning up. By going door-to-door they found people who had not yet gone to a doctor. Unfortunately, this was before any human retrovirus had been identified. They were hoping whatever it was, and the mode of transmission, would be more evident early in an outbreak, and expected their work to bring in future investigators early, prepared and informed.

    Predicting things is uncertain, especially the future.
  15. urbantravels

    urbantravels disjecta membra

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    I don't suppose they saved any of that blood from those early outbreaks? Ha, I know I'm a dreamer...ever since learning from Prof. R. that they have identified HIV in blood that had been stored since 1959 and 1960, I have this fantasy that there are banked samples somewhere from early outbreaks of whateverthisthingis...

    And speaking of antiquarian zeal, where *are* Elaine DeFreitas' pictures? At Wistar?

    p.s. you just freaked me out by channeling my dad, who is an economist. I've been hearing him say "Making predictions is difficult, especially about the future" my WHOLE LIFE.
  16. anciendaze

    anciendaze Senior Member

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    I'm afraid that 1956 outbreak fell just below the threshold for storing samples. There are samples from the Lyndonville outbreak, and Dr. Bell is consultant in a study to examine them.
    Drs. Bell and Cheney should know.
    Have you ever been able to use the line on him from the joke about the economist who falls into a pit in the jungle. "No problem. Assume a ladder." ?
  17. John Leslie

    John Leslie

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    The Lo/Alter results have already been reported by Alter himself to confirm the WPI's finding that "XMRV and its variants" are in the blood of patients with chronic fatigue syndrome and healthy blood donors. Lo refers to these as "MLV-related virus gene sequences" in the title of his talk at the September conference. Therefore , the delay in publication has simply allowed the CDC to influence NIH officials to use its phony "CFS" definitions to hurt the patients. More importantly the delay (and internal review and study by the Reeves acolytes) has allowed all of the authors of the negative studies to prepare excuses as to why they couldn't find XMRV and its variants (MLV-related virus gene sequences). The WPI has publically advised every scientist that if you use the right primer sets (Lombardi) you will find more retrovirus. If as a "scientist" you only want to find the synthetic clone ("VP62") and use the wrong patient cohort, you can design a "study" to find nothing.
  18. JT1024

    JT1024 Senior Member

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    The statement I've bolded above just blew me away.....
  19. Cort

    Cort Phoenix Rising Founder

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    Htlv

    Yes, maybe she did find something but no one was able to reproduce what she did find using her techniques (or others). All they had to do was find the sequences - and a large number of people, including herself, weren't able to do that. Its too bad she didn't have more money - she clearly needed it - but she couldn't get grants except for the CAA - which, of course, didn't have much money. Maybe if she'd had more money things would have been different...but my guess is not.

    DeFreitas was unable to distinguish CFS patients from controls at the CDC using her test and that the following groups were also unable to distinguish CFS patients from control using DeFreitas work or were unable to find HTLV in CFS patients.


    • A lab licensed by Wistar (her funder) to produce a test
    • A lab in Texas that had been reporting near 100% accuracy until blinded tests were done at the CAA - their findings were described as resembling throwing darts a board
    • Dr. DeFreitas herself was unable to do that using patients of her own choosing from Dr. Bell's studies at the CAA (Hillary Johnson chose not to report this in Osler's Web. Dr. DeFreitas was given a final chance to show that she was right. Based on her findings about half the CFS patients and half the healthy controls had her virus.)
    • The Gow Group
    • A Japanese Group
    • the CDC twice
    • The National CFIDS Association about 10 years ago.
    • The WPI reported XMRV is not HTLV-like and that they found no evidence of HTLV viruses or viral sequences in their extensive pathogen arrays on CFS patients.

    Based on that I really don't think an HTLV-like virus is a possibility. Its a tough field! Her viral findings in multiple sclerosis didn't pan out either.
  20. Cort

    Cort Phoenix Rising Founder

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    Are you saying that the CDC is somehow influencing the NIH to use the empirical definition to find patients for its studies? What are you referring to? I don't get it?

    There are only a certain number of excuses for not getting a positive result - I doubt that anyone needs months to come up with them. the retesting also gave Alter the chance to build a stronger paper as well. Wanda Jones, of the CFSAC, wrote that the paper is much stronger because of the retesting....

    He and us may actually have come out on top. The CDC obviously did limited retesting, perhaps because they were so sure of themselves and their paper came out pretty quickly. Dr. Alter, it looks like, did alot of new testing - he could now, because of the time put in, have an absolutely unassailable paper. He may just be able to completely blow the CDC away now. ...:cool:

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