Some answers…

Although the personal questions in the comments of the last blog were asked very rudely, I will try to answer them anyway. I have represented myself as an open book, and I truly am, even though it gets me in trouble, as witnessed by the tone of the questions. Most of this has been said before, but things have changed, and perhaps it needs to be said again, from our current vantage point. So, I’ll give it a go.
I am not trying to persuade anyone to take anything. I share my reasoning, with references, within the limits of my writing ability. I intentionally report before I know the outcome so that it won’t be seen as my pushing a particular protocol. I am in the same boat as everyone else. I don’t know what to do to fix it. I don’t believe that anyone else does either. Arv’s are only one of the treatments I have written about here. I am sharing my thoughts and experiences in real time. 
This is a blog. Opinion. If you read it carefully, there are inconsistencies. I even reserve the right to change my opinion from time to time. I try to summarize occasionally, but yes, a “casual” reader might come away with something I didn’t intend. I am not sure what to do about that. I cannot recapitulate the entire blog each time I write. It is an ongoing discussion, not “the truth” at a moment in time. Almost everybody gets that, I think.
I am endlessly surprised that my opinions are so controversial and can evoke such ire. Most of it seems common sense to me. It is incredible, and very telling, that there are actually people that want to restrict my freedom of speech! Why does anyone care if others find my musings useful? I am not telling anyone else what to think. I have said repeatedly that I could be wrong about anything. If I were to say nothing until everything is scientifically validated and I was positive, I would never say anything at all. I am learning as I go, as is everyone. For some peculiar reason, I seem to need to write, and some people find it helpful. The blog is the best I can do, with the limited energy and time I have left, and I am grateful for it. When Ali suggested I write a blog, I didn’t know what a blog was:). The patients who comment and write are very sophisticated and opinionated all on their own, not needing me to tell them what to think. They ask for my thoughts so they can put the information into their own equations, not take it as some kind of truth written in stone. The reflex to restrict what I say so that the poor gullible patients won’t hear it is patronizing. And to the conventional physicians who might be reading, why the sudden concern for our well being? There are many useless things that you are willing to prescribe that are much more dangerous than arv’s.
I have never claimed to be anywhere near “well” and I have said all along that there were confounders with respect to our treatment with arv’s. As noted in the comments, gamma retroviruses replicate by clonal expansion, so we need specific drugs, but transcription of viral proteins and the assembly of new viral particles may be involved in pathogenesis, if the hypothesis is correct. I am endlessly reevaluating everything with new information as it becomes available. I am not in fact a “true believer”. I would love to hear any alternative hypothesis that fits close to as well. Anything at all that might suggest a direction to turn for efficacious treatment. I am dismayed that we are back to having an idiopathic immune disorder, albeit repackaged to sound like good news. Redefining it as a syndrome, yet again. 
There is no way to know if arv’s are helping us at this time, as I have said several times. I expected viral load measures and other ways to monitor that didn’t pan out. I did monitor several likely parameters which showed trends, but not convincingly enough to be useful. There are specimens sitting at the WPI that might contain valuable information. I certainly hoped it would be less ambiguous than it turned out to be. But there are others that experienced what we did, apparent cause and effect improvement from starting arv’s (often after an initial mild symptom flare). Some of them have written on this blog. I am NOT saying anyone should take arv’s, and never have, only that they shouldn’t be forbidden. The main problem I have recommending it as an option now, is that because it isn’t being studied, anyone starting will likely find themselves where we are, not knowing what to do for the long haul, and no help coming anytime soon. I actually think it is probably mostly a moot point now; the forces against have essentially won, shut it down for all practical purposes. The important thing isn’t really even arv’s, which at best only help incompletely, but our inability to get any help at all due to the attitude displayed in the reaction we have seen to the idea.
There are many drugs that are used because they work, even though the mechanism is unknown. One would think that for a debilitating disease which affects millions of people, for which there is no meaningful treatment, somebody would want to find out if that might be the case here. The usual way that happens is somebody has a good case, publishes it and then it gets studied. I have reported our experience. The burden of proof is not on me. What if it was a serendipitous discovery for the wrong reasons? The reaction of the medical community to trying arv’s is irrational, as the reactions of the medical community often are, especially when it comes to anything to do with this disease. The reaction of the scientific community is a joke, with no basis for an opinion at all; practicing medicine without a license, understanding nothing of the disease about which they are so opinionated.
Take a look at this paper: Zidovudine in primary Sjögren’s syndrome. Steinfeld. Rheumatology (Oxford). 1999 Sep;38(9):814-7. Did everyone get up in arms about this small clinical trial? Were the authors discredited for trying it? It doesn’t look like anyone followed up on it.
I have shared many personal details here, both physical and emotional. I have been very forthcoming, approaching undressing in public at times, so it is strange to be accused of “hiding”. The problem is that my sharing a list of symptoms that are “better” than before isn’t terribly illuminating, since some things are better or gone and some things aren’t. I even have a couple of new things. Like most ME/CFS patients, my condition changes from day to day and tweeting my moment to moment condition would benefit no one. However, I will try to define the big things. 
The most tangible thing that happened to me, seemingly from arv’s, was the near resolution of my chronic malaise. I had it much of the time for 15 years. It went away shortly after starting AZT/Isentress and I almost never have it now. So 90% of the time before, 10% or less now. That alone was life changing for me. 
My down periods used to last for 5 days to a week at a time, and now, rarely more than part of a day. The worst moments happen less often.
When I started arv’s, I never slept more than two hours without awakening, and I didn’t dream at all. I now often sleep all night with one or two awakenings and I dream normally. My day to day wellness is linked to the quality of my sleep in a chicken or egg fashion, so this improvement is key. 
Painless migraines (scintillating scotoma without headache) and hypertensive crises are much reduced in frequency.
Another “big thing” that happened: I experienced a definite decrease in my peripheral neuropathy pain at one point early into arv’s. However, trying to explain one’s pain to anyone else is an exercise in futility. The pain I have now is worse than pain that almost drove me insane at the beginning of my illness, but my coping skills are very different. Still when the reduction happened, it seemed definite. I am not pain free, but my pain is quite tolerable and does not require pain medicine. Others have also reported less pain on arv’s. Again, I am reporting, not selling. For everyone who thinks they were helped, somebody else thinks they weren’t, but the risks of trying it are pretty minimal with proper monitoring.
I acknowledge that it is possible that all these things happened in spite of, and not because of, arv’s. 

A big disappointment for me has been that the abnormal response to big time stressors remains, though it may be attenuated. Impossible to tell.

As for my daily functioning? I am able to work long days, most days, electronically (phone, Skype, email). I don’t have brain fog, but do sometimes have more symptoms after mental exertion. I am limited physically, more so in Santa Fe than Hawaii. I can climb a couple of flights of stairs with some dyspnea, more if needed, if I go slowly. I can usually walk several blocks, but might have some mild PEM if I overdo it, though my exercise tolerance is very variable. I don’t need handicap parking. I have no difficulty lifting groceries, etc. Resistance exercise is easier than anything aerobic. Swimming is easier than walking. Standing still is the hardest. The most physically challenging thing I have to do is negotiating airports and I use the airport wheelchair service for that. Gentle yoga is helpful. Pretty much all of the above is better than before I started arv’s, though as a commenter said, and, as I have said all along, other things happened too, before, during and after. Also my illness historically follows my state of mind (knowing full well how unPC it is to say that out loud). I am also much more tolerant of symptoms than I used to be, and not a very compliant patient, more confounders. 

I can only work part-time face to face, a couple of hours at a time, but I’m OK for many successive days. I could fake it for longer hours than that, but don’t want to do that. My patients travel a long way to see me, and I want it to be useful and special. I am seeing new patients for 4-5 hours on two different days, which is working out well for all concerned. It is a unique, collaborative endeavor. Sick doctor and sick patient. I am limited, but can function fairly reliably, though there are days when it’s tough; however, there are more days when it isn’t. 
When I started arv’s, I was unable to speak on the phone, because of auditory processing disturbance. I also had to lie down most of the day, only sitting or standing for a very short time, and I now sit up most of the day. Standing is more difficult some days than others, but there is never a time when I can’t if I need to; that was not always true. 
So huge functional change in the last 20 months on arv’s, but improvement started about 6 months before that, with cessation of Lyme and symptom-based treatment. From housebound to functional, but not at all “well”. I have written about the reasons why I abandoned the use of rating scales to evaluate our experiment and don’t want to rehash it again. It is sad that it’s all we have. I am collecting them on my patients, but don’t expect them to be as useful as patients’ subjective reports. Yes, I do believe what my patients tell me.
My illness certainly isn’t gone, though it has lifted, lessened, but it is a relapsing, remitting illness all on its own, making it extremely difficult to assess cause and effect. I have said this over and over again. I am fully aware that many ineffective or harmful treatments have been perpetuated because of this feature of the illness (see my prior blog entries about Lyme Disease treatment). Whenever anyone gets better, they think it’s because of whatever they were doing at the time. I received an email recently from a patient who was housebound for fourteen years and suddenly improved enough to get a life, having changed nothing. I was of course influenced by the fact that there were two of us sharing the same experience; Ali and I had similar experiences with respect to the timing of improvement, though she had no side effects and I did experience a flare of symptoms initially. And for the record, neither of us has a history of placebo responses. 
Ali went uphill during her first 6 months or so on arv’s, but had more therapeutic interventions concurrently than I did. The goal was always to get her better, not demonstrate something scientific to others. Her treatments did not prevent her crash when she tried to engage life again a year ago. She is doing well again now, but it is impossible to say if this level of wellness is the same, above or below her last remission. The “crash” didn’t become as serious as prior crashes have been for her. The important thing to her now, I think, is that she is better at this moment, and seems still to be slowly improving. Will it last? She is savoring it while it does.
My baseline was better prior to the events of early July than it is now, though I am not “crashed”. I have been under a great deal of stress, though I am hoping things will calm down a little now, so I can regain what I have lost. There is no way to know if I tolerated the crisis better than I would have without arv’s. I suffered the kinds of losses and persistent stress that have historically set me back in a major way. I stopped Isentress a while back, and am worse. Cause and effect? Who knows, but I don’t want to stay on monotherapy and am afraid to stop Viread, since a couple of patients who were forced to go off have lost gains. I may go back on Isentress. Also thinking about Lexiva (see Li on the sidebar).
I have received several demands for an apology from me to Dr. Peterson. As I said when I mentioned his name for the first time, I have never met him. Making enemies was never my intention, just the inevitable consequence of stating one’s opinions openly and publicly in such a contentious arena. My frustration feels overwhelming sometimes and it comes out in my writing. I hear from patients that love Dr. Peterson, and that does make a difference to me, but it still seems inconceivable that he abandoned the pursuit of a retroviral etiology when he jettisoned the WPI, knowing what he knows about the science and the disease. His teaming up with Konstance Knox to sink the WPI still seems really sleazy to me and his claim that it was to protect patients disingenuous. He could not have known there were problems with the VIP Dx test, or questions of contamination, at the time that he left, so how could he have been “right”. His agenda appears to go beyond figuring out how to treat the disease and help patients. I am not saying that I know precisely what that agenda is. It would seem that everyone who was involved with the WPI was hurt, likely including Dr. Peterson. I only wish that he hadn’t thrown the baby out with the bath water. 
I regret any pain that I have caused, but some truths are painful. For me, it is painful to acknowledge how few friends there are worth having in the medical or scientific communities. My referral list for mainland doctors is a very short list. When I think back over the people I have mentioned by name in an angry or personal way, it is a select few that had it coming. My lack of professional decorum, or whatever you want to call it, comes from outrage, and mostly justified. I challenge anyone who has been sick with this disease for any length of time to write their truth and not say some angry things. My writing is also full of hope for the future. It’s just that it is the hope of learning to live well with the disease, rather than to truly vanquish it any time soon.
I really think many have too much confidence in “science”, especially retrovirology, which seems to have an unusual number of landmines scattered across its landscape. Even if Dr. Lipkin were to say tomorrow that he agrees that there are gamma retroviruses infecting ME/CFS patients, it will be a long time before that translates into specific treatment. Compassionate use of existing drugs should be tried and available, especially for the sickest patients. There are possibilities besides arv’s. Lenolidamide? Pentoxyfyllin? Nexavir? Existing drugs. What others? I recently heard of a big time response to Copaxone. Is anyone looking in a systematic way? Really looking? Why does it feel almost subversive to talk about it? The idea that these patients should, or can, wait is indecent. Again, I am not trying to convince anyone to do anything other than consider my ideas. I continue to write because some find it helpful, and I have made many friends, but I have made enemies too, and that gives me pause. I do grow weary of the personal attacks, on top of everything else that has happened recently. I need to focus on my patients, but want to continue to reach out to readers; there is so little information with respect to how and what to consider for treatment in the here and now. Five or ten more years is too late for many of us. 
OK. Now I have some actual work to do:).
Aloha,
Jamie 
Today’s song: Can’t Find My Way Home 
Did you like this? Share it:

164 thoughts on “Some answers…

  1. >Jason,

    My samples are being analyzed by laboratories in California and Alberta for deep sequencing and integration. We hope to prove within the next couple of weeks that I do indeed have a unique HGRV and then I expect you and the virologists that you mention to go back to the drawing board and work with us. More patients need to be studied and we need more effective treatments.

    All of us must do good deeds during our lifetime. My chance came when I got CFS and then leukemia at age 65. We have high hopes and depend on you and your colleagues to further our research, not write it off.

    Michael Snyderman,MD

    Dr.Shechtman's situation is similar to that of Drs. Ruscetti and Mikovits. It is quoted below.

    When Israeli scientist Dan Shechtman said he stumbled upon a new crystalline chemical structure that seemed to violate the laws of nature, colleagues mocked him, insulted him and exiled him from his research group. After years in the scientific wilderness, though, he was proved right. And Wednesday, he received the ultimate vindication: the Nobel Prize in chemistry. The lesson? "A good scientist is a humble and listening scientist and not one that is sure 100 percent in what he read in the textbooks," Shechtman said. The shy, 70-year-old Shechtman said he never doubted his findings and considered himself merely the latest in a long line of scientists who advanced their fields by challenging the conventional wisdom and were shunned by the establishment because of it.

  2. >Jason,

    I'm sending your "souless freak" comment to the President of Columbia University, so he can see how inappropriately you are behaving on the internet. Calling a sick patient names in front of thousands of other people. And misspelled too. I'm sure he'll like that. Dr. Goff will get a copy also.

    Maybe some sensitivity training is in order for your entire department, which seems incredibly removed from the real world.

    So far, you have said nothing of substance, except why you think Mikovits is a fraud, that you don't like me and didn't like it that I think a few of your superiors have behaved badly. You take exception that I think it's an infectious disease. And I'm misleading poor, dumb patients who can't think for themselves.

    I doubt that you are really Jason Rodriguez, more likely a troll, since you are such a complete stereotype. Jason might have engaged in the scientific discussion, not just flinging infantile invectives. You never said why you think I'm wrong about HGRV's, when you agree that deep sequencing is needed to answer the question. Have you even read my blog? Or are you so put off by the arv discussion that you can't see beyond it to the underlying hypothesis, which is about what is there, instead of what isn't.

    Dr. Goff can sort it out and the real Jason Rodriguez can clear it up if he wants to. But if you are Jason, since you've worked with "XMRV", aren't you the least bit concerned for yourself or your family? Your new baby? If you're so sure it isn't a problem, and not infectious to humans, would you drink it? Inject it into yourself? Are you at all worried about vaccinating your baby, given what you know about how those vaccines are produced? Or are you so sure that all those autism moms are crazy too, and don't really know when their kids got sick. It's very easy to say, this could never happen to me, but it could happen to anyone, though I really do pray that you don't learn about it first hand. I don't wish anyone harm, not even Darth Vader.

    Jamie

  3. >@Jason

    AZA was not german to the Lombardi paper. John Coffin saw all the originally data from Lombardi et al. also had the slide in question for the best part of 6 months and was in the audience where the use of AZA on PCR negative patients in Lombardi et al. was discussed 2 years ago.

    Hiding the identity of patients is an ethical issue and is standard practice

    The sensitivity of the PCR assay used in Paprotka was not determined. It was only shown capable of detecting 2000 copies per 100 cells.

    http://app2.capitalreach.com/esp1204/servlet/tc?c=10164&cn=retro&s=20445&&dp=player.jsp&e=13725&mediaType=podiumVideo

    First to educate yourself on what has occurred in Paprotka et al. (2011) watch this video of Vinay Pathak at CROI talking about that paper. His talk begins at 1 hour 49 mins.

    There he states that the only assay used on the later xenografts was an reverse transcriptase assay on RNA.

    http://www.sciencemag.org/content/early/2011/05/31/science.1205292.short

    Now read the paper. Where are the details of the different cycling conditions and other variables for that RT-PCR assay? That's right, they are not included in the paper. Who reviewed that paper?

    Paprotka should be retracted. It is impossible to replicate. There is no evidence the patient was not infected and no evidence of a retrovirus having been created during passage through mice.

  4. >Message from Dr. Mikovits:

    Message from Judy Mikovits re- WPI research programme UK and Ireland;

    To UK/Ireland and all others in the Mikovits Research studies:

    I am writing this note today to reassure everyone who consented into the Research program of the WPI including but not limited to the 5 year R01 pathophysiology of ME/CFS, that as Principal investigator, I have the legal right to continue that research at another institution and to take with me the samples and materials and supplies purchased for the sole purpose of that research. Since the sudden closing of the WPI research program on September 30th, I have been in active discussion with several institutions who are enthusiastic about the opportunity to participate with me in this important research. I strongly encourage you to voice your support by emailing me at jamikovits@gmail.com. As you know, your consent form stated that you could withdraw from these studies at any time. The funding agencies need to know that you will withdraw your consent if the research is not done under my direction and thus two years of precious samples and resources will be wasted. Emails from participants in support of me continuing my research will greatly help me. I deeply appreciate not only your participation in my research but also your ecards, emails, encouragement and most importantly your trust in my integrity during this difficult time.

    Judy

  5. >"I'm sending your "souless freak" comment to the President of Columbia University, so he can see how inappropriately you are behaving on the internet. Calling a sick patient names in front of thousands of other people. And misspelled too. I'm sure he'll like that. Dr. Goff will get a copy also."

    I'll admit it, my spelling and writing skills do need some work :)

    And don't forget Jamie, I never called you a soulless freak. I'm simply stating that you continuously lash out at the scientific community stating they don't care about CFS patients, just the viruses in their test tube. This ticks me off and I'm gladly calling you out on it. Here is my quote:

    "Of course this makes us look like souless freaks that don't give a damn about people that suffer with CFS."

    Notice that I said US which refers to researchers.

    Your whole post above shows how defensive you are when someone comes on your blog and disagrees with you. Loudly.

    I hope the patients reading your blog read your post and see how you can lash out without compassion.

    The only thing you are right about is explaining my position more throughly. I'll give you that. You are correct, and I need to do this but need some time to go through the data and make ACCURATE interpretations of the data. The only thing I can state is what has not been proven yet, an infectious agent as a cause of CFS/ME.

    Go ahead and send letters to Lee and Dr. Goff. What I do after I get home from work is my business and not Columbia's. Especially when it's on the internet and anyone can post how they feel. Even you.

    Jason

  6. >@Jason

    Why are you not questioning how it is ok for an entire assay to be left out of Paprotka et a?

  7. >"But no toxic chemicals were ever detected in the ventilation system or water pipes or anywhere else."

    ————————————-

    Perhaps they didn't try hard enough.

  8. >Jason, you tactic of making out that people are attacking all researchers, rather than a handful of researchers having their work questioned for its rigour, is more than obvious. There are plenty of scientists who are unhappy with the behaviour of those who are wrongly equating an assay that can easily detect a free floating clone, never once found in nature (VP62), to one that can detect an integrated provirus with an affinity for CpG island. Standard PCR will not work on such viruses.

  9. >"Now read the paper. Where are the details of the different cycling conditions and other variables for that RT-PCR assay? That's right, they are not included in the paper. Who reviewed that paper?"

    Ugh…

    You have to read the supplemental data of the paper for the details:

    "To specifically quantify XMRV env
    sequences, primers 3f (5’‐CTTTCCCTAAACTATATTTTGACTTGTGTG‐3’; 600 nM final
    concentration) and 8r (5’‐CTGGATGCTACCGGAGCCC‐3’; 800 nM final concentration), probe
    5’FAM‐ATACTGTATTAACAGGGTGTGGAGGGCCGA‐TAM‐3’ (800 nM final concentration), and 2X
    Light Cycler 480 Probes Master (1X final concentration; Roche Diagnostics) were used in a 25 l
    reaction volume.    Cycling conditions using the LightCycler 480 Roche instrument (Roche
    Diagnostics) were 95 °C for 30 sec followed by 50 cycles at 95 °C for 15 sec and 63 °C for 55 sec.  "

    Great description eh? I could do this today and repeat there data if I had the reagents.

    "The sensitivity of the PCR assay used in Paprotka was not determined. It was only shown capable of detecting 2000 copies per 100 cells."

    I know this will be hard to swallow but sensitivity is a moot point in an experiment like this. To do a real time qPCR experiment you need three things. 1) a standard curve (they have this). 2) a negative control (they have this. 3) a positive control (they also have this). The sensitivity is implied in the standard curve that they construct which does not have to be published. This is quite a different scenario from patient samples. In this case there is no true positive control and sensitivity becomes more of an issue. I hope this description helps.

    Is there anything else that claims the need for retraction of the Paprotka paper?

    Jason

  10. >"Why are you not questioning how it is ok for an entire assay to be left out of Paprotka et a?"

    Which assay? I'm still confused here – maybe I'm missing something. I just answered a question about the "missing details of an RT-PCR" experiment above.

    Jason

  11. >@Jason

    You have just given the details for the quantitative real-time PCR assay. There are no details for a reverse transcriptase PCR assay in Paprotka et al.

    The PCR assay is not quantitative. This was the assay on which the results were based. That could only detect 2000 copies per 100 cells. It was not sensitive enough for the early xenografts.

    3 assays were used in Paprotka. One has been omitted.

    Have you watched the video yet?

    Paprotka et al. should be retracted.

  12. >"Jason, you tactic of making out that people are attacking all researchers, rather than a handful of researchers having their work questioned for its rigour, is more than obvious. "

    No, not that people are attacking all researchers. Specifically, that Jamie is attacking researchers. This isn't right.

    Jason

  13. >@Jason, Jamie has done so such thing. She has rightly pointed out the badly conducted studies of some researchers.

    Have you watched the video where Vinay Pathak states that a reverse transcriptase PCR assay was used on RNA for the later xenografts in Paprotka et al.? That assay is not in the paper. Paprotka et al. should be retracted.

    http://app2.capitalreach.com/esp1204/servlet/tc?c=10164&cn=retro&s=20445&&dp=player.jsp&e=13725&mediaType=podiumVideo
    1 hour 49 mins.

  14. >Jason,

    As a CFS patient who has followed this whole debacle closely from start to finish, I would like to thank you for your work in this field and for caring enough to write to this community on this blog.

    Scientists are not the enemy.

    The vast majority of patients do not believe that they are, and do not agree with the author of this blog or her followers about almost _anything_. They just aren't making as much noise, at this particular moment.

    It's become abundantly clear that looking at MLV's is going in the wrong direction. Wasting any more money on that would be a mistake.

    Eventually, researchers are going to figure this out. It may even be easier than people think.

    It's time to put the MLV's aside and move on. Otherwise we're never going to get anywhere in finding out what's really going on.

    Thanks again for your comments here.

  15. >From you, Jason:
    "The souless freak comment, albiet a bit harsh, was directed at the writer of this blog."

    You are completely incorrect that I don't like it when people disagree with me. If you look at the comments on this post, you will see people who disagree with me, but thank me for writing. If there was no disagreement, what would be the point of writing? We are all learning. Trying to make it different with new information. I was actually happy when you showed up, and thought we might even be making progress the other day. The song I was going to send you was Bonnie Raitt, Meet Me Half Way:

    http://www.amazon.com/Meet-Me-Halfway/dp/B000TDB5DE/ref=sr_1_sc_2?ie=UTF8&qid=1318347841&sr=8-2-spell

    I know that you don't understand where I/we are coming from. How could you? I didn't attack all scientists. I attacked a few (3?), who have shown remarkable lack of compassion, shooting their mouths off about things of which they know nothing, in ways that will harm the patient community over the long run. Dr. Coffin was initially very interested in the findings of the Science paper. That means that he understood the concepts underlying the work to be sound. So even if XMRV, or VP62, didn't pan out, what happened to the concept? Don't throw the baby out with the bath water. The baby is our lives.

    You have stumbled into a discussion about retroviruses that is not academic. I understand that for you, it is abstract. I value your perspective, though I think you are extremely naive. I would ask that you learn from us as well.

    Jamie

  16. >"There are no details for a reverse transcriptase PCR assay in Paprotka et al."

    OK, so let me clear something for everyone in general, including you. A reverse transcriptase PCR is used specifically to convert RNA to DNA. This DNA (cDNA) is then used to for whatever PCR experiments you want to do.

    The authors only worked with DNA, not RNA. They isolated genomic DNA samples from mice and human tissues and then did a real time PCR assay.

    Sorry to say but all of the experiments seem to be accurately described. They didn't leave anything out.

    Yes, I have watched the video and seen another presentation at another conference from a different author of the paper. If they didn't show a slide from about a figure from their paper, so what? Its published already, they don't need to show every piece of data in a talk.

    "The PCR assay is not quantitative. This was the assay on which the results were based. That could only detect 2000 copies per 100 cells. It was not sensitive enough for the early xenografts."

    Yes it is. qPCR assays are always quantitative and they state this by saying they made a standard curve. And I agree with you sensitivity is something up for debate.

    But retraction? Really? I really don't get your claims for retraction. They are not lying to you, just showing what they got as their result.

    Jason

  17. >All 00 papers have been discredited now that there is proof the HGRVs discovered in Lombardi et al. are not VP62. VP62 does not exist. The PCR primers Silverman used are also discredited as those never worked for Frank Ruscetti or Judy Mikovits.

    There are 2 positive papers.

    John Coffin saw all the originally data from Lombardi et al. also had the slide in question for the best part of 6 months and was in the audience where the use of AZA on PCR negative patients in Lombardi et al. was discussed 2 years ago.

    Hiding the identity of patients is an ethical issue and is standard practice

    So why did Coffin and Pathak fail to name the RT-PCR assay, which is a more sensitive assay then the standard PCR used on the early xenografts, in their paper Paprotka et al.?

  18. >@Jason

    "The authors only worked with DNA, not RNA. They isolated genomic DNA samples from mice and human tissues and then did a real time PCR assay."

    Incorrect!

    Read the paper.

    "Yes, I have watched the video and seen another presentation at another conference from a different author of the paper. If they didn't show a slide from about a figure from their paper, so what? Its published already, they don't need to show every piece of data in a talk."

    Vinay Pathak showed the slide from the paper for the later xenografts and stated they used an RT-PCR assay on RNA. An entire assay is missing from the paper!

    "Yes it is. qPCR assays are always quantitative and they state this by saying they made a standard curve. And I agree with you sensitivity is something up for debate."

    The quantitative real-time PCR assay was discarded after its sensitivity was determined when it detected XMRV in the early xenografts – that invalidates the paper already. The results however were based on the PCR assay and the undisclosed reverse transcriptase PCR assay.

    Paprotka et al.s should be retracted.

  19. >@ Jason, in hope that you will look at yourself.

    Help us. We could use your expertise. We know what we don't know. The saddest thing that was lost at the WPI was the opportunity for translational research. You have a piece of the puzzle. I have a piece of the puzzle. We need to meet in the middle.

    Jamie

    From my email last night:

    What I'm wondering is why this guy is taking everything so personally. The second thing I'm wondering is why all the ad hominem attacks on you. The other thing I notice is the horrible energy of it in general. I don't know how you may relate to airy fairy stuff but in my world this guy is doing psychic attack in a big way. The way to tell that is if you feel drained and sick if you encounter his stuff. I certainly do and I'm only a bystander.

    What strikes me is that it is really over the top in relation to what's being addressed. It seems that the idea is to evoke a response more to what's behind the words than what's in them. It's all pretty ugly. If you turn the emotional soundtrack off while reading the words it doesn't add up. It also doesn't add up to the context of what he's supposedly responding to.

    So much of this feels like being abused and then being beaten for saying "ouch". Or, god forbid, responding to the abusers as a reasonable adult, as you are. Bullies and evil do not like to have a light shone on them, they do not like to be seen, and the lights are coming up. I used the word "evil" quite consciously. Here's another quote for you: Sin is the denial of the right to thrive. Covers a lot of bases, that.

  20. >"Have you watched the video where Vinay Pathak states that a reverse transcriptase PCR assay was used on RNA for the later xenografts in Paprotka et al.? That assay is not in the paper. Paprotka et al. should be retracted."

    He also stated the total RNA was contaminated with gDNA in his preps. I'm glad they didn't include this in the paper!!! This would have made their results meaningless. Again, they only showed data from genomic DNA samples, not RNA. Showing RNA is unnecessary since they are looking at an integrated virus in genomic DNA. I'm sorry to disappoint you and disagree with you, but there really is no subterfuge here.

    Jason

  21. >""The authors only worked with DNA, not RNA. They isolated genomic DNA samples from mice and human tissues and then did a real time PCR assay."

    Incorrect!

    Read the paper."

    Ok, show me where they isolated RNA and did a reverse transcription of RNA. I'm all ears. Copy and paste. Please prove me wrong.

    "Vinay Pathak showed the slide from the paper for the later xenografts and stated they used an RT-PCR assay on RNA. An entire assay is missing from the paper!"

    They willingly omitted the experiment because it was contaminated with genomic DNA. You really want someone to publish meaningless results with contaminated samples?

    Your call for retraction is really unfounded and I think you missing my point. I'm sorry if I haven't my position clear.

    Jason

  22. >@Jason

    "He also stated the total RNA was contaminated with gDNA in his preps. I'm glad they didn't include this in the paper!!! This would have made their results meaningless. Again, they only showed data from genomic DNA samples, not RNA. Showing RNA is unnecessary since they are looking at an integrated virus in genomic DNA. I'm sorry to disappoint you and disagree with you, but there really is no subterfuge here."

    They also never performed the STR analysis on the later xenografts. So they were never proven to be from the same patient as the earlier and never shown to not be contaminated with another cell line.

    You are totally wrong about the RNA. Read the supporting material. Vinay Pathak could not have said it any more clearly. They used reverse transcriptase PCR on RNA.

  23. >"What I'm wondering is why this guy is taking everything so personally."

    I'm not taking everything personally. I'm taking what specifically you say against honest and hard-working researchers personally.

    Of course I take it personally. Your attacks on the integrity of my colleagues is akin to attacks on family. I take it even more personally when those attacks are unfounded.

    Oh yes and the whole "Some infectious agent causes CFS" stance. But to clear Jamie, I don't hate your opinion. I value it. I'm even open to the possibility of an infectious agent (and believe its a possibility). What i dislike is they way state it as if its fact and truth.

    With this post I am signing off for the day. I have to yet to get into lab and start my experiments for the day.

    Cheers all!

    Jason

  24. >@Jason

    Paprotka et al. omitted use of a third assay. Do you not agree that paper must be retracted?

  25. >I think you've made a great decision about sharing your experiences. As you say, people have a mind of their own. Whatever other patients do with their doctor is their responsibility. I applaude you for that.

    At the same time I think it's a bit of a paradox to use rather harsh language at other, whether it be the lyme community or the retrovirologists – and expect to be treated respectfully yourself. If you use harsh language at one group, it doesn't excuse the t-shirt prank. Two wrongs…

    I know everyone who you've been in direct contact with have not benefited from antibiotics used against CLD (chronic lyme disease). But around me, it's a different story entirely. I wouldn't be able to write if it wasn't for the antibiotics. And I relapse pretty quickly when off. I am very open to the fact that it might be other things than killing lyme which makes me better. But I don't think doctors who truly have an altruistic approach, such as several so called 'LLMDs' I've been in touch with should be used such langauge against. Disagree with them, yes, but it should have been done in a lot more respectfully way than the previous blog entries, and coffin should never have got the 'Darth Vader' stamp.

  26. >Jason must have now read Paprotka et al. watched the video and cannot deny the paper should be retracted by Science.

  27. >John Coffin saw all the originally data from Lombardi et al. also had the slide in question for the best part of 6 months and was in the audience where the use of AZA on PCR negative patients in Lombardi et al. was discussed 2 years ago.

    Hiding the identity of patients is an ethical issue and is standard practice

    So why did Coffin and Pathak fail to name the RT-PCR assay, which is a more sensitive assay then the standard PCR used on the early xenografts, in their paper Paprotka et al.?

  28. >"You are totally wrong about the RNA. Read the supporting material. Vinay Pathak could not have said it any more clearly. They used reverse transcriptase PCR on RNA."

    You are correct. I stand corrected. Apologies on my missing this.

    HOWEVER, it is still moot and I'm glad they did not put it as a main figure in the paper. They state:

    "The late passage xenograft samples were total RNA from which genomic DNA was not completely removed, and as a result contained variable levels of genomic DNA"

    They even comment on this in the main body of paper and acknowledge that supp figure S3 might provide a contaminating background signal:

    "The detec- tion of low levels of XMRV env sequence in the early xenografts (Fig. 1C) can be attributed to the PreXMRV-1 proviruses present in the contami- nating mouse DNA"

    Again I don't see the call for retraction. The were completely honest.

    Ok, I'm really signing off – I need to get to work!

    Jason

  29. >Really cold, Jason. Which is how I ended the first round of email I did with Professor Racaniello back when I started arv's. I wrote to him to share, wanting his opinion about why the drugs might or might not work. Instead, I got a response of the 'you're dumb' variety, arv's are forbidden to patients until we scientists say. We'll let you know in a couple of years. The really sad thing about the tee-shirt is, he didn't even get how awful it was. And personally, I'll never get over that he got it from the CAA.

    Jamie

  30. >From page 10 of the Supplemental Online Material for Paprotka et al: "Total RNA from the 2152 xenograft was converted to cDNA using either randomprimers or XMRV specific primers, while total nucleic acid from 2524, 2272 and 2274 was directly used for PCR." Not sure why they did RT only on 2152 but not on the others.

    Also from many previous posts on this blog and elsewhere, there seems to be quite a lot of focus on the lack of using Trizol as a PBMC "preservative" during collection in the BWG studies. I can't find any references for using Trizol as a PBMC preservative. Are they talking about "triazole" instead of "trizol"? Trizol would nuke the cells, which is what you don't want to happen if you're trying to culture them, right?

    And did Lo and Alter also use 5-AZA in their work like Lombardi et al. is now assumed to have done? And if CpG island integration makes PCR
    impossible, and whatever Lo and Alter found is a new HGRV that integrates into CpG islands, how did they detect it without trouble? (At least it looks like the PCR conditions were not excessively vigourous from what I was able to tell.) So they may have used 5-AZA, deciding like Lomardi et al. did that is was "not germane"?

  31. >Anon 10:27 AM,

    Thank you for writing. I hear you. The Darth Vader metaphor was over the top. But it was set up that way. Darth used the Joan of Arc metaphor. He knew he was going up against the patient community when he showed up. My understanding is he didn't even really bother to put up much of a fight. Just, "I'm right, you're wrong."; I wasn't there, but that's how it was described to me by several people. He was asking for it.

    I suppose I say things in an over the top way sometimes to be heard. Also, if I'm completely honest, to entertain a little at the expense of people who are hurting us. We've been so powerless for so long, that it's wonderful to have a voice. But you are right, an eye for an eye, isn't what I'm after.

    As for antibiotics. I realize that antibiotics are necessary for recovery for some patients, whether that has anything to do with Bb or not. I know that some patients need to be maintained on antibiotics to hold on to a remission. I also realize that no matter how many times I say that, people will think I'm against the use of antibiotics for ME/CFS/Lyme (which I believe to be the same diseases, despite the recent paper from Fallon's lab), but I am not. I will prescribe antibiotics, but not indiscriminately, like our LLMD did, and still does. My beef is with ILADS. Patients are being harmed. Antibiotics are very hard on the gut and gut health is crucial to the organism. The evidence is all over my mail.

    Jamie

  32. >Coffin has known about AZA for years. AZA was used by Frank Ruscetti on his western blots. No serology was performed in Lombardi et al.

    Trizol would not nuke the virus, but without it the WPI's assays would be defeated.

    Standard PCR will not work on CpG islands. That is why the WPI and NCI adjusted their variables appropriately, i.e. lower annealing temperatures, as did Lo et al. No other papers have done this.

    Cells 2152 are the cells that were used to create 22Rv1. As that link to the early xenografts is totally discredited, Paprtoka et al. cannot have made claims about the origin of XMRV.

  33. >more @ Anon 10:27 AM,

    When I started this blog I was so sick that I was coming from a place of nothing to lose, nothing to hide. It became my habit to write openly, things that a 'normal' person wouldn't say in public. Many disenfranchised people liked it, so I was encouraged in my misbehavior, if that's what it was. I've been propelled by the anger of others, in addition to my own. But anger shuts people down, and we do need to keep the lines of communication open.

    Mahalo for saying it in a constructive way,
    Jamie

  34. >Anonymous@October 11, 2011 10:58 AM said: "Standard PCR will not work on CpG islands. That is why the WPI and NCI adjusted their variables appropriately, i.e. lower annealing temperatures, as did Lo et al. No other papers have done this."

    Still confused here, sorry. If they lowered the annealing temperatures, wouldn't that reduce the stringency of priming? And reduced stringency would result in higher probabilities of non-specific amplification, wouldn't it? And then they went and did 80 rounds of PCR, with reduced primer stringency?

    Why didn't Lo and Alter use 5-AZA like Lomardi et al. did? If they didn't, and got acceptable results, how come Lombardi et al. deemed it necessary, if not germane?

    I am still not understanding this, perhaps the poster Jason or another scientifically-trained individual could enlighten.

  35. >AZA was used by Frank Ruscetti on his western blots. That has nothing to do with the nested RT-PCR assay used by Lombardi et al. No serology was performed in Lo et al.

  36. >The simple answer to a none scientist is that Lombardi et al. and Lo et al. altered their PCR variables to detect such viruses. The other groups did not.

  37. >John Coffin saw all the originally data from Lombardi et al. also had the slide in question for the best part of 6 months and was in the audience where the use of AZA on PCR negative patients in Lombardi et al. was discussed 2 years ago.

    Hiding the identity of patients is an ethical issue and is standard practice

    So why did Coffin and Pathak fail to name the RT-PCR assay, which is a more sensitive assay then the standard PCR used on the early xenografts, in their paper Paprotka et al.?

  38. >A statement has been made about the lack of epidemiologic data supporting an infectious etiology for CFS. We have an open survey that does appear to show a prevalence of CFS in partners that is at least a 100x higher than published prevalences.

    I contacted epidemiologists and asked them to help us and no one was interested. We have no money but what we have are people with ME/CFS who have experience with epidemiology software and data entry. The problem is everyone is ill and this will take a while but it will get done.

    Michael Snyderman, MD

  39. >Hi,

    Anon 10:27 AM again.

    "He was asking for it."
    To quote some brilliant words from yourself "an eye for an eye…"

    Why do I care?
    Because I don't want the debate climate to slide the wrong way. I don't want honest researchers to back off because of ad hominems or worse…

    "I also realize that no matter how many times I say that, people will think I'm against the use of antibiotics for ME/CFS/Lyme (which I believe to be the same diseases, despite the recent paper from Fallon's lab), but I am not."

    I am glad you are not (against abx use)! If you are referring to Fallon's "Distinct cerebrospinal fluid proteomes […]" than I agree with you. I think the fundamental question which wasn't, but should have been asked was "How would the CFS patients samples look, if they had went through an antibiotic course before testing [just like the others had done!]".

    "I will prescribe antibiotics, but not indiscriminately, like our LLMD did, and still does. My beef is with ILADS. Patients are being harmed. Antibiotics are very hard on the gut and gut health is crucial to the organism."

    A lot can be said about the ILADS (!), but what I react to is _how_ it's being said. Like you say, sometimes you are over the top, and I interpret that as the top being the boarder of decent tones in debate. Although both the retrovirologists and the ILADS may be terribly wrong in much they both do and say, feeding the "ad hominem beast" doesn't help us ;-)

    Now I am sure I come across as all negative, and that's really unfair to you. Because I think you've done (and do!) a brave act by sticking your neck out for the CFS community, and I agree, people have tried to chop at it… It's not good, and I truly appreciate your effort for us all. :-)

  40. >Wow, Jason.

    When invited in this commentary (argument?) to get in the lab and do some work on this, you cited being too busy with your new family etc.
    Fair enough.

    But somehow there is unlimited time to elaborate here in great detail your views, peppered with snarky comments and expressions of frustration at how ignorant we all are.

    No one can know yet who is "right", and some of the players in this whole game may or may not be ignorant, may or may not be able to
    understand science, may or may not even be who they claim to be.
    (I am always amazed how online people are so willing o accept someone's stated credentials.)

    Whoever you are, and whatever you do for a living, and whatever is your understanding of the science of today (science being a dynamic, continually-changing participatory process of reaching consensus about our collective perception of reality)….. PLEASE try to remember that you are speaking to live human beings who are CHRONICALLY ILL.

    Please reach into the possibly atrophied part of your being wherein dwells empathy and imagine what it is like to live years, decades, feeling ill every day–losing your job, your entire life savings, your standard of living and then standard of care; your hobbies, joys, friends, and social network; your independence, your sense of identity, your familiar ways of contributing to the world and those around you; your ability to think straight with any consistency, your physical and mental stamina, your
    eyesight, your thermoregulation, your autonomic nervous system's coherence—do you start to see what I'm getting at here?

    This is a group of people that needs–no, DEMANDS–that EVERY area of research that can be explored be explored, and no longer ignored as it has been for decades. If there is even a shadow of possibility that any one angle if research may shed light in breaking this thing open, it needs to be pursued.

    You are addressing a bunch of people who don't get to enjoy a lively career any more, the joys of a new family, the simple joys of life.

    So now, Mr. Busy, Mr. JudgyPants, take a moment to appreciate really deeply what you have, because none of us gets to have it any more;
    and try addressing us with that in mind, whether you are a researcher or a troll or somewhere in between.

  41. >Anon 12:00 PM,

    Yes, it is hard being judged by anonymous people. I do my best to be fair, in the face of what I see as unbelievable abuse of our patient community. I have very strong emotions often when I write. Patients have been surprised when they meet me that I'm warmer than they expected, from the blog persona. I guess I'm in mother bear mode often times when the muse strikes.

    It is amazing to me, that in the face of an awful lot of evidence to the contrary, ILADS still does not recognize that they are treating ME/CFS. Some of their patients are antibiotic responsive for sure, but so what? It's like one group of AIDS doctors treating a single opportunistic infection and ignoring all the others. They aren't even aware of the immune dysfunction that they are dealing with. It's all kill, kill, kill. No attention to terrible collateral damage. It's insanity. But see? I've done it again. They. I am not attacking all doctors who try to treat Lyme when I say that. ILADS guidelines, and a few doctors who perpetuate erroneous conclusions to the detriment of patients, despite the time test. Dr. Bransfield wrote to me that their guidelines were going to be revised, over a year ago, I believe. I haven't looked in some time, but I think the old ridiculous guidelines are still extant. I still hear all the same old stuff from patients. I took years of combination antibiotics, and I'm worse than when I started. My doctor said it was a good thing that I got worse, but I'm still not better. And yes, I hear from people who are better too. More who were harmed, but I acknowledge that may be selection bias. People who get better, often don't stick around to tell us about it.

    Anyway, I'm going to go lick my wounds, have a 3rd cup of coffee and go to work. Incredibly grateful that I can say that.

    Jamie

  42. >So, somebody fact-check me: Lo and Alter discovered a novel class of HGRVs using RT-PCR, but did no serology. Lombardi et al. discovered the same novel class of HGRVs using serology, but have no PCR results (retracted due to contamination). What was discovered is NOT XMRV, but a different class of novel HGRVs altogether? Is this correct?

    Meanwhile, Paprotka et al. claim that XMRV is a laboratory artifact. Various blog posters claim that it should be retracted. Perhaps it should,
    but if Alter, Lo and Lombardi discovered novel HGRVs that are NOT XMRV, how is Paprotka et al. germane? If Paprotka et al. is retracted, how does that answer the criticisms of the Alter, Lo and Lombardi work? Could not XMRV arisen as per Paprotka et al., and could not Alter, Lo and Lombardi et al. still have discovered a novel class of HGRVs? Why are they mutually exclusive?

    You retrovirologists sure do know how to throw a party.

  43. >A few comments:

    1) Jamie applaud you for stating that emotions of dealing with this horrible affliction can make you see things in sort-of one-sided manner. At least that's message that I got. I totally understand this position since I suffer from a non-related illness that has no cure or a known cause (Meniere's disease) and the frustration that can ensue from this. If something upsets you from a researcher I can understand you get upset. No problems here.

    However, you must be extra vigilant with your emotions since you sit at the interface between science, medicine, and the lay public. You must and should be truly objective on the science and not let you emotions get the best of you. Take the higher road so to speak.

    I admit in my responses that your attacks on my colleagues drove my emotions the same way.

    2) The Paptroka paper.

    It is my FIRM position that this paper should not be retracted. It is seminal in showing the origin of XMRV, and from a scientific perspective, a very well put together paper.

    Also, I can't find my other post on this but someone up top posted there is RT assays on RNA in the paper. I denied this.

    Well, after looking at the paper again (this what happens when feeding a two year old skimming articles) I was wrong and there is an RT assay on RNA in the supplemental figure. However, I disagree with some posters that this is cause for retraction.

    "Vinay Pathak showed the slide from the paper for the later xenografts and stated they used an RT-PCR assay on RNA. An entire assay is missing from the paper!"

    And rightfully so!! I would omit the data as well since they clearly admit their samples were contaminated with genomic DNA:

    "The detec- tion of low levels of XMRV env sequence in the early xenografts (Fig. 1C) can be attributed to the PreXMRV-1 proviruses present in the contami- nating mouse DNA."

    I wouldn't want to publish a sequence of the virus from contaminating DNA either and is why it is not described in the paper. As a matter of fact, if they did this and then claimed it to be something else (sounds familiar?) then this would be fraud.

    "The quantitative real-time PCR assay was discarded after its sensitivity was determined when it detected XMRV in the early xenografts – that invalidates the paper already. The results however were based on the PCR assay and the undisclosed reverse transcriptase PCR assay."

    This is just not true. The quantitation is not discarded, its plain to see in figure 1C. Also, the conclusions were based totally on sequencing genomic DNA which is evident from the three samples they tested with PCR and not an RT assay:

    "while total nucleic acid from 2524, 2272 and 2274 was directly used for PCR" – from the supplemental text.

    3) My own posts.

    I do apologize for not answering everyone's questions and criticisms from the comments on this blog post. I have to pick and choose unfortunately. As it is, I'll be getting home tonight at 11pm since I haven't started my own real time qPCR experiments. I simply have no time. I know this is a lame excuse but its the truth.

    I would love to explain further my views and my ideas from the literature, but this will have to wait. Maybe when I'm up at 3am feeding my daughter… ;)

    "PLEASE try to remember that you are speaking to live human beings who are CHRONICALLY ILL."

    To anyone who thinks that I have no compassion for your suffering or what you've been through you flat wrong and the SOLE reason for me even going head to head against Jamie. The CFS/ME patients deserve to know the truth, but unfortunately the truth is unknown. To state otherwise is not an accurate representation of the science and not fair to patients. I hope this is clear to everyone.

    Cheers,

    Jason

  44. >@ AnonymousNonRetrovirologist said…

    Lombardi et al. discovered HGRVs using multiple methods, including serology, culture and RT-PCR. Lo et al. confirmed the finding using RT-PCR. Lo et al. did no serology. None of these viruses are VP62/XMRV. HGRVs are yet to be fully sequenced, some may also have a xenotropic host range like VP62/XMRV, but they are not VP62/XMRV. Xenotropic is the largest host range of MLVs.

    There are no other papers on HGRVs but those two, as the other papers used VP62, which does not exist and is not the viruses found to be associated with ME/CFS. Any paper that used Silverman's primers can also no longer be included as that was VP62 plasmid contamination that was in Silvermans labs and has been shown to have not been contaminating the WPI and NCI samples. The VP62 plasmid has never been in the WPI or NCI/Ruscetti labs.

    Paprotka et al. is a separate paper that should be retracted for omitting use of a third assay. Coffin's paper is relevant as XMRV in prostate cancer still holds as a finding. Coffin would like Lombardi et al. to be retracted. Paprotka et al. is being used to push Science into a retraction, when there is no reason for such a step to be taken, when that paper cannot be about HGRVs and when that paper HAS failed to include details of the 3rd assay. Coffin has also known for 2 years that AZA was used by Frank Ruscetti, he has seen all the Lombardi data and had access to the slide. He was also in the audience at the CFSAC in 2009 when the use of AZA in Lombardi et al. was discussed.

  45. >Weird… Jamie, your spam filter must be catching my posts because I can not see the, after I posted them. I posted twice.

    Jason

  46. >@Jason

    Do you not agree John Coffins paper Paprotka et al. should be retracted for omitting the description of the third assay.

  47. >They are there now, Jason. I hate Blogger's spam filter. I have never needed it in 4000 comments. Have thought about moving the blog, but so much trouble…

    Jamie

Comments are closed.