It was good to hear from “John” again in the comments this morning. My head has been so completely in the clinical world since I wrote that post, that it’s hard for me to come back to it. I’d rather step back and take a look at the big picture. I’m sorry if it’s too loose for you John. I’m a doctor again. I don’t have the time that I did to read the pure science in exquisite detail trying to divine the truth from little bits and pieces of incomplete information. Not my job. Thanks for the input though, and may you never need my services:). Fortunately, the patient community still has a few friends in the scientific world and we will continue to rely on them to help us. Dr. Mikovits and I continue to “translate” for one another.
DNA
Protein biosynthesis
Retrovirus
Mitochondria
Mitochondrial DNA
All organisms have a strategy for perpetuating themselves. Viruses are the simplest, carrying out their tasks by hi-jacking cellular machinery from the host. Retroviruses have a very efficient evolutionary strategy, inserting into the host genome. Simple animal retroviruses, in particular murine leukemia viruses, MLV’s or MuLV’s insert in places in the host DNA called CpG islands, start transcription sites, where they activate genes, presumably to create favorable conditions for them. They become endogenous when transmitted vertically. Endogenous means that the viral sequences are present in every cell in the body. Once endogenous, a retrovirus can be fully replicative or not. If not, it may still be able to generate viral proteins if activated, setting up a cycle of persistent immune activation as the body tries to deal with the foreign products. It may be measurable in the form of antibodies and sometimes antibodies are generated in response to self, producing the low level autoimmunity seen so commonly in this patient group.
The axiom we were taught that viruses don’t jump species turns out to be untrue. Simple animal retroviruses are infectious to human cells in tissue culture. Animal cells have been used to grow live attenuated virus since at least the early ’30s. The first paper reporting the use of yellow fever vaccine, attenuated in mice, was published in 1932. Vaccines were tested on nurses and doctors. The first outbreak of a disease similar to ours was at LA County Hospital in 1934. The first cases of autism were described in the early ’40s. Kanner’s earliest paper on “infantile autism” was published in 1946. It has been known for a very long time that there were animal retroviruses present in the cells used to produce vaccines, but the assumption was made that it was an insignificant risk compared to the good done by vaccinating.
In general, nature maintains a balance by killing off the weak organisms. There have probably always been a few ME patients, women with failure to thrive, “the vapors”, so the potential was there, the “jump” had already occurred, but then, we had to improve on Mother Nature. So we gave it an incredible leg up. Mainlined it into almost everybody. And not just one virus, but lots of them, some capable of recombining with each other, so that everybody’s infection is a little different. The result? An unbelievable increase in the incidence of all kinds of chronic diseases. Neuroimmune, autoimmune, genetic illness, cancer. It really hurts that I’m so old as to remember how different it was 35 years ago, when I was in medical school. I can actually remember being taught to do a review of systems when taking a history so as not to miss anything, generally expecting it to be negative. A negative review of systems is a relative rarity now, even in children.
Regardless of what is there precisely, with respect to viruses and pieces of viruses, there are generalizations that can be made about the common pathophysiology seen in animals and humans. In mice, similar viruses can produce neurodegeneration or cancer. The viruses that produce neurodegenerative disease cause inflammation, with vascular permeability in the central nervous system. Other MuLV’s cause lymphoproliferation and malignant transformation.
Take a look at the following table:
NIH publication. Increase in cancer incidence 1950-1989. Ries et al.
So where do the dots connect clinically for ME/CFS? Simply put…
1. Persistent immune activation due to foreign viral product fueling inflammation. This happens in HIV disease. The way their disease is playing out, with proper treatment, they die sooner of the usual things. That’s the way our disease plays out without treatment, since untreated the disease doesn’t kill you like HIV. Rather taking the more colorful symptoms out of it, the expectation is earlier onset of cardiovascular, neurodegenerative disease and cancer. Vascular permeability, as in the mouse models, fits. Leaky endothelial junctions in the brain, gut, elsewhere.
2. Symptoms consistent with inflammation in the brainstem and other structures in the CNS. In particular, most of the “mysterious” symptoms of the illness, that have confounded doctors for so long, can be tied anatomically to a strip of dorsal brainstem, which is housed in a tight bony canal and sensitive to any swelling. Structures in close proximity include the cranial nerve nuclei, carrying all the senses above the neck, the spinothalmic tract, carrying sensory information from below the neck to the brain, including pain and temperature sense, the reticular formation, controlling sleep and arousal, and relay nuclei for the autonomic nervous system, regulating all the involuntary functions of the body, including vascular stability and endocrine control. Nuclei in the brainstem are responsible for the production of neurotransmitters, norepinephrine (the locus coeruleus), serotonin (the raph nuclei), and dopamine (the substantia nigra), so dysfunction affects everything which is experiential. There is also a venous plexus that would be subject to compression, consistent with the recent findings that venous insufficiency, poor drainage, is common. The feeling of “brain swelling” that many report is probably accurate, like all the “crazy” sensations that patients describe. Structures in close anatomic proximity to this strip of tissue are the cerebellar peduncles, the amygdala, hippocampus and pituitary.
3. Gene activation. In addition to making viral proteins or particles, simple animal retroviruses turn on genes, which may be clinically important, depending upon the functional integrity of the gene in question. Certain genetic disorders, such as Marfan’s and Ehlers Danlos, and certain autoimmune disorders, such as Hashimoto’s thyroiditis and Sjogren’s, are certainly over-expressed in the patient group. Methylation is necessary for proviral latency and it is clear that many of us have genetic methylation defects. However, it’s not as simple as methylating, as it isn’t desirable to induce latency in tumor suppressor genes.
4. Lymphocyte abnormalities, proliferation, depletion, dysfunction. Currently a focus of my reading, including clonal expansion. Rather than butcher it, I’m going to hold off on this one for now.
5. Mitochondrial dysfunction. The mitochondria are the energy factories of cells. ATP, the energy currency of the body, is produced from glucose in an oxygen dependent chemical reaction. Aerobic metabolism is much more efficient than anaerobic metabolism, to which the body must convert when not enough oxygen is present. Oxygen gets into mitochondria by diffusion along a pressure gradient, needing to cross the mitochondrial membrane. The internal mitochondrial membrane contains phospholipids called cardiolipins, and anticardiolipins turn up on the list of associated auto-antibodies seen in ME/CFS. MtDNA (mitochondrial DNA) is a circular chromosome which is inherited from the mother, unlike the nuclear chromosomes which come from both parents, so mtDNA is not subject to genetic recombination. Maternal inheritance certainly fits the epidemiological picture. MtDNA maintains genetic integrity, so it would be a safe place for a retrovirus to stow aboard.
Andrew Mason MD, from the University of Alberta, has been publishing on a human beta retrovirus associated with PBC (Primary Biliary Cirrhosis). It is similar to MMTV (mouse mammary tumor virus), which was known as the “milk factor” before anybody knew what a retrovirus was. PBC is associated with an AMA (anti-mitochondrial antibody). In the following papers, he makes his argument for an HBRV (human beta retrovirus) and it all looks pretty congruent with our HGRV hypothesis, including his rationale for the use of antiretrovirals.
- Detection of retroviral antibodies in primary biliary cirrhosis and other idiopathic biliary disorders. Mason/Garry
- Retroviruses in autoimmune liver disease: genetic or environmental agents? Mason/Garry
- Reverse transcriptase activity in patients with primary biliary cirrhosis and other autoimmune liver disorders. McDermid/Mason
- Mouse mammary tumor virus in anti-mitochondrial antibody producing mouse models. Zhang/Mason
- Human Betaretrovirus Infection Is Detected In PBC Patients Biliary Epithelium And Triggers The Mitochondrial Phenotype Of PBC. Wang/Mason
- The evidence supports a viral aetiology for primary biliary cirrhosis. Mason
An excerpt from the last paper:
HBRV and the mitochondrial phenotype
Arguably, any causative agent linked to PBC should be associated with the aberrant expression of pyruvate dehydrogenase (PDC)-E2 on the cell surface of biliary epithelium and in lymphoid tis- sue, a highly specific PBC phenotype that is thought to lead to the formation of AMA. In vivo, HBRV is detected in PBC patient’s cells with aberrant PDC-E2 expression. In vitro, homogenized PBC patients’ lymph nodes, the conditioned supernatants containing HBRV and even pure MMTV have all been shown to trigger the mitochondrial phenotype in healthy biliary epithelium, whereas control lymph node homogenates and other viruses do not. Importantly, no in vivo patient data exist to link the mitochondrial phenotype with either bacteria or xenobiotics; indeed the idea of molecular mimicry has been circulating for over 50 years and never proven.
Of interest, betaretroviral infection has also been linked to the mitochondrial phenotype in several immunodeficient mouse models that spontaneously express AMA. For example, MMTV p27 capsid and gp52 envelope proteins have been detected in lymphoid tissues and biliary epithelium that also express aber- rant PDC-E2. Furthermore, we have found that the development of AMA mirrors anti-MMTV production. Indeed, MMTV has been shown to be central in triggering viral cholangitis in the NOD.c3c4 mouse model of PBC, as highly active antiretroviral therapy and MMTV neutralizing antibodies abrogate cholangitis. Of interest, NOD.c3c4 mice treated with lamivudine and zidovudine (Combivir) develop viral resistance with mutations in the YMDD region of the reverse transcriptase gene, similar to muta- tions found in hepatitis B virus or HIV occurring as a result of antiviral therapy.
Translational studies
Using the NOD.c3c4 mouse model with MMTV infection, how- ever, we have found that highly active antiretroviral therapy with Truvada and Kaletra is efficacious without the development of resistance. Recently, the same combination has been reported to normalize hepatic biochemistry in a PBC patient with HIV and HBRV co-infection. Accordingly, a randomized controlled trial with Truvada and Kaletra is planned to treat patients with PBC who are unresponsive to ursodeoxycholicacid (UDCA). Indeed, it is notable that clinical trials ultimately led to the recognition that H. pylori infection caused peptic ulcer disease and the proof that a viral association with PBC may be resolved in a similar fashion.
In summary, there are converging data to suggest a mechanistic link of betaretrovirus infection with the mitochondrial phenotype of PBC in co-culture studies and in a mouse model. However, we still lack firm patient data linking virus with disease. Accordingly, before we can endorse the argument that the evidence supports a viral aetiology for primary biliary cirrhosis, further studies will be required to definitively demonstrate integrations sites in diseased biliary epithelium and the serological reactivity to HBRV in the majority of patients with PBC.
>A reflection on HIV/AIDS research after 25 years
Robert C Gallo
"A problem then occurred that enormously hindered our work over the coming years. One of our culture samples became contaminated with virus sent to us by Luc Montagnier. At first we stubbornly refused to believe that this was possible, because the strain of HIV from Paris had different characteristics in cell culture. However, this has now been clarified [16,17]. Montagnier had unknowingly sent us a very different strain of HIV that grows well in cell lines. This strain contaminated his culture of LAV before it contaminated one of ours."
>Dear John/etc:
You did get personally insulting. You also said what I wrote lacked logic without pointing out any specifics. If this was a formal debate, you would have lost a bunch of points.
Again you digress about things like I.Singh and this is far from the main issue. If you noticed, I just repeated the exact adjective that you used to characterize any discussion of motives behind what we perceive as unfortunate politics. If I have been unfair to Dr. Singh, I should apologize but the situation is more complicated than that.
The main issue is that there is a retrovirus killing us and we really don't care what its initials are. I assume you read the posts of people who have improved with ARVs and the recent post of a patient with ME whose partner developed ME. We need larger trials obviously to see who the best candidates for treatment would be and what the best treatments would be. Unfortunately, your focusing on sequences rather than the larger clinical picture is typical and has ended research funding and set us back at least two years.
If I understood you correctly, you are open to the concept that we are infected with a murine-leukemia related virus. I am pleased by this. Did you have a better identity for these organisms? Please teach us if so. I am glad that you accept that further research on HGRVs and ME and cancer is indicated. We are quite concerned about this and rightfully so. At this point, I am not on any team but I have faith in Dr. Mikovits' direction of research. It would be welcome for you to put your energy into positive research also.
Michael Snyderman, MD
>"I am going to start deleting gratuitously insulting comments. Nobody needs the stress."
Are you going to be deleting insulting comments in general? Or just ones directed at yourself and Dr Snyderman?
>@ Dr. Snyderman
First, I am not the same person as "John" if that is what you are implying. In contrast to many people posting on several sites using several pseudonyms, all of my posts on this matter have been under the name of 'RRM'.
Second, I did point out what I thought was specifically illogical about what you had posted. It is right after the colon that follows "logic". I think I have made clear why the statement that:
"[…]there is enough sequence diversity in the different strains of this MLRV to make the contamination theory of little importance."
…is illogical: it completely negates the fact that with significant sequence diversity you would expect all of the labs to find this significant diversity within their samples.
And why wouldn't I be open to the concept of severely affected people being infected with viruses? I am, but I must say that I find the MLV-related virus link to be very unlikely, to the point of finding the 1,5M being spent on the Lipkin study a waste of money IF the upcoming Blood Working Group results turn out to be negative. However, like I said before, I am open to being proved wrong.
Finally, I am happy for you to be feeling better. However, I do not think it is helpful to rely on anecdotal reports, especially with a disease like this. I am not a clinician nor a psychiatrist, but I would suggest that it is just as easy for "opponents" of the biomedical model to conclude that your story proves them right as it is for you. It is exactly for reasons like this why science does not progress in this way. If you are keen on doing positive research that will be able to actually help patients, I would suggest that you design a study that eliminates possible bias.
>One of my comments was deleted because I have no respect for RRM. So anon August 16, 2011 1:44 PM you are wrong.
>Why would a scientist expect to discover a virus anew with unvalidated assays even if there were more sequence diversity then you believe there is?
Again, you make no attempt to back up your remark that you "find the MLV-related virus link to be very unlikely". Try looking at the evidence, not the opinions that claim to be based on evidence.
HIV relied on anecdotal reports in the early days. Perhaps if your life was on the line you wouldn't be so quick to ignore what is the humane thing to do.
>Blogger has a spam filter which is beyond my contol and it cannot be disabled. I put the held comments through a couple times a day. If I delete something it shows as deleted by the administrator. I do not moderate the comments, except for limiting repetitive comments by two of our contributors.
Jamie
>Samual Wales, at least one paper reported finding just the opposite in regards to different numbers of patients vs. controls being positive, namely that the samples from healthy controls were positive much more often than the samples from CFS patients. This is why no studies on the subject will likely be published unless cases and controls are collected at the very same time, at the same place, collected and prepared by the same people using the same equipment, reagents, etc. None of the positive studies have taken this level of care as it was not known at the time such practices were so critical- "Oakes et al found that 53% (19/36) of the healthy volunteers and 1.8% (2/112) of the CFS patients, yielded PCR products when using XMRV gag primers, but no positive amplification was observed when using qPCR with pol primers."*
*Shixing Tang and Indira K. Hewlett Testing Strategies for Detection of Xenotropic Murine Leukemia Virus Related Virus (XMRV) Infection
http://www.hindawi.com/journals/av/aip/281425.pdf
>It has been known for decades that care is required in a lab to stop contamination. It has been known that MLVs were also a major problem in this regard.
The assay used in Oakes could also detect mouse viruses, so they cannot conclude it was not mouse contamination. Patients were also not of the same cohort as Lombardi et al.
"…used the nested PCR assay for XMRV gag sequences mentioned above, which also detects many endogenous MLV proviruses, as described [1]. "
>@Anonymous August 16, 2011 10:33 AM
"Yes, they did replicate. But you have no interest in how any of this works or what has happened. For whatever reason you".
You are wrong on both occasions. No they didn't exactly replicate the methodology of the original HIV finding and yes, I do have an interest in how any of this works.
The fact that no one can provide me with a citation that shows an exact replication study in the field, rather shows that your dictionary definition of "replication" does not have a historical precedent in the history of virology and is therefore incorrect.
Please prove me wrong. I am not being sarcastic. What should I offer for you to provide me with a proper citation of a 'proper' replication attempt?
@Anonymous August 16, 2011 2:17 PM
"This is why no studies on the subject will likely be published unless cases and controls are collected at the very same time, at the same place, collected and prepared by the same people using the same equipment, reagents, etc. None of the positive studies have taken this level of care as it was not known at the time such practices were so critica."
This is exactly true.
You cannot blame Lombardi et al. at all (sorry for that lousy pun) for not taking this into account, but given what we know now, any future studies should make sure that patients and controls are handled in exactly the same manner. From start to finish.
That is exactly why any skeptical proponent of the HGRV-ME/CFS association should take the results of the Blood Working Group as well as Lipkin's results very seriously.
>You missed the post where I said the French provided a positive to Gallo. HTLV was replication.
Lipkin and the BWG are only single studies and anything can go wrong before or after sample are in labs.
>Anon @ 3:18pm- The point wasn't what the Oakes study detected or where the contamination came from, the point of my post was in response to a previous post asking why patient samples were positive at a much higher rate than controls in the positive studies. As the Oakes study shows, just the opposite can and does occur as well.
>"That is exactly why any skeptical proponent of the HGRV-ME/CFS association should take the results of the Blood Working Group as well as Lipkin's results very seriously."
Oops, it slipped out…the hidden agenda Dr. Snyderman was asking for.
Actually, the last thing a wise "skeptical proponent of the HGRV-ME/CFS association" would want to do is put their faith in a government-backed study.
>The Oakes study is so bizarre in its results that one would suspect they actually reversed the samples by mistake. Duh! But that's different from contamination. It was probably just a major screwup. It could have been worse. They could have charged a few hundred patients for a test that had never ever found XMRV in anyone. That has been done, you know.
"The point wasn't what the Oakes study detected or where the contamination came from, the point of my post was in response to a previous post asking why patient samples were positive at a much higher rate than controls in the positive studies. As the Oakes study shows, just the opposite can and does occur as well."
>@ Anonymous August 16, 2011 4:54 PM
"You missed the post where I said the French provided a positive to Gallo. HTLV was replication."
No, I didn't. Providing a positive does not mean the study in question is a replication study. Quite to the contrary, actually: when a validation study would use a (supposed) positive of the study it was trying to validate, it would essentially end trying to be a replication study, as this wasn't part of the original study's methodology either.
Remember, Montagnier's study could not calibrate its assays/methods to a known positive from an earleir study (as there simply was not yet such a study). Any study that would exactly try to replicate Montagnier's study should have calibrated its assays/methods in the same way as Montagnier did for it to be a exact replication.
With "HTLV" I think you might have missed the post where I explained that you should provide proper references. I can guess that you would actually mean "HTLV-1", but there was never any exact replication attempt (in the sense that patients and advocates are demandig here) in that field either.
The reason for that is not that all retrovirologists are lousy scientists, but rather that the definition that has been applied here is not the standard in the field. Of course, you could still argue that this new standard is better and should be applied, but please do not assert that retrovirologists are suddenly diverting from their usual methodology, but because it simply isn't so.
>@ anonymous August 16, 2011 7:47 PM
"Oops, it slipped out…the hidden agenda Dr. Snyderman was asking for."
Are you honestly trying to argue here or are you just trying to somehow "trap" me with a play on words?
Nothing slipped out. I carefully explained how both the BWG and Lipkin studies have a better experimental design than the Lombardi and Lo studies (which wasn't their fault at all by the way). That is why these results are important. While I think it's honest to state that you wouldn't trust any goverment funded study, why would you trust ANY study then? Surely the government can meddle with studies that they have't funded just as easily?
Now, if you are really not trusting any government sponsored XMRV study, you should really take this up with the WPI. First, they entered both (costly) studies and agreed on their study designs. Second (and this is more important), the WPI could have done another study instead that would eliminate all of the problems without any government intervention pretty easily.
But instead you argue that WPI and Lo/Alter have entered a 1.5M study that will take 1.5 more years (it was announced in september 2010) of your and every patient's life and is taking quite a lot of the WPI's resources, but is not to be trusted.
>@RRM
If you understood this you would realise that with HIV they used a clinical positive to validate their assays. The only way, other than through replication, that you can reliable and scientifically conclude that an assay would work. You misread the post.
Montagnier discovered HIV. As Lombardi found HGRVs in blood. So it is for other labs to then replicate or clinically validate their assays.
With HTLV, Gallo and the Japanese worked together on a paper to prove they had detected the same virus. In that paper they used the same methods. Up until that point Gallo produced several papers on HTLV without the need of others to produce confirmatory papers. The Japanese had something similar. That joint paper used the same methods on both findings to prove they were the same virus.
http://www.science-connections.com/books/moderntrends/trends5/003-Mechanism_of/389-Transmission_of.pdf
What do you mean by usual methodology? There is no usual methodology.
"Oops, it slipped out…the hidden agenda Dr. Snyderman was asking for."
People wanting to turn the BWG and Lipkin study in what they could never be – definitive. Remember that is not how science works and that mistakes can happen before panels get to the labs and after they leave the lab. Everyone is acutely aware of that.
>@ anonymous August 17, 2011 3:54 AM
You are right: no study is ever defenitive. This goes for the Lipkin, Blood Working Group and the failed validation studies as well as for the Lombardi and Lo studies.
But just like no one can positively prove that I don't have HIV only in my little toe (or some other potential reservoir), at or just below the limit of detection and in a unknown strain undetectable by current assays, there is a limit to what the scientific community will investigate on HGRV's too, with its limited resources.
When the Lipkin and the BWG studies turn up negative for WPI and Lo, Science (the magazine) will most likely retract the Lombardi paper and most retrovirologists will stop doing research on the association of XMRV/MLV-like viruses with ME/CFS. That is just the reality of the situation.
Of course, even then, the WPI (or other labs) remain free to keep investigating the supposed association and will thus be able to prove us all wrong with a watertight study. When they are actually right and their methods continue to get better over time, they (or someone else) will surely do this (if they are right). Luckily, in all of science, the (moral, honor and financial) incentive for individual scientists around the world to report great new findings that would help a lot of sick people is immense.
Therefore, there is nothing wrong with other scientists "abandoning" research and diverting their attention to fields that they feel show greater promise.
And fair enough about the Gallo paper. But then I am still forced to conclude that no one is apparently able to provide me to two papers of which one is the exact replication of the other?
With "usual methodology" I meant "the methodology that is mostly used within a given field to validate a principle finding".
And I would venture to guess that most previous findings in this field have been validated through methodology that is very much like the validation attempts that were done in the case of XMRV/MLV-like viruses.
I have seen many patients confused about the (essential) difference between "calibrating an assay to a known positive in a validation study" and "calibrating an assay to a known positive after a finding is already validated through other means". The first a no-go really (it is in fact self-contradictory) while the latter is accepted practise.
[By the way, there is actually no mention in Gallo's paper that Gallo actually used the Montagnier samples to "clinically validate" or to calibrate his assays to, but I don't think it is important here]
>The scientific community includes all those labs who have published on detecting human gammas in several diseases. It includes everyone who has presented evidence at conferences. The community is split between those who have no problem replicating and validating, and those who are choosing not to follow the scientific method.
Science will more likely retract Paprtoka et al. as that paper left out information that will prevent testing of that hypothesis through replication. I know it upsets you, but this is fact. Replication is a fundamental of science. As I said, with HIV they used clinical positives and it was proven this was the case when the science was investigated and the two viruses were the same one, from the same patient. Another scientific fundamental you would reject. I am not surprised. HGRVs have been validated by multiple labs and methods. There is no excuse for them to avoid doing this.
"With "usual methodology" I meant "the methodology that is mostly used within a given field to validate a principle finding"."
There is no such thing with a novel virus or new discovery, nor with other viruses that change.
>@ Anonymous
By your own defintion of "replication", none of the positive studies have actually "replicated" the original study, or have even come close. By your own admission, Alter/Lo and Hanson failed to follow "the scientific method". As the positive studies that were published or presented at conference thus far have done methodologically essentially the same as the negative studies (perform similar but certainly not the exact same experiments), it rather proves that your definitions of "replication" and "scientific method" are off.
I have no emotions whatsoever regarding studies that Science will or will not retract. As far as I can see, Paprotka et al. performed a couple of eloquent experiments that provided convincing evidence that the strain that we know as XMRV is most likely a lab artifact. Most scientists that spoke out about this issue agree with that conclusion, and I remember even Harvey Alter agreeing that the reported findings were "very convincing" indeed.
Now, if you or scientists in the field think to have spotted any fundamental flaws in the study's methodology, I am sure this information has been sent to the proper people and proper action is sure to follow by the editors of the journal. I eagerly await the outcome.
If "replication is fundamental of science" in the way you envision it, can you please provide me with a single study in the field of virology that supports this notion? The fact that, after repeated inquiry, you are unable to do so is pretty telling with regard to the existence of such studies.
The ironic thing about the Gallo study is that it rather shows the dangers of importing samples from another lab into your own lab (while of course that doesn't mean that it should not be done). While I never disputed the fact that Gallo did use samples from Montagnier (this has been well reported and I have already commented on this on other blogs), I dispute the notion that he actually used them to tweak his assays for calibration.
Of course, you (or anyone else) could easily put me to silence by quoting the part from the Gallo paper(s) that would prove me wrong. Remember, I can't prove a negative like this, while all it takes for you is a simple, single quote from the paper (or even some other relibaly source).
I have absolutely no idea what you are trying to say with that last sentence, as there MUST logically be a "methodology that is mostly used within a given field to validate a principle finding". One methodology (1. exact to the letter replication, 2. calibration through samples from the earlier study, 3. validation through using one's own methods, or 4. some other methodology) surely HAS to be the most widely used in the field (in the absence of ties).
Now, I can get you citations from papers which use the most commonly used methodology according to me (no. 3) if you want. How many would suffice to make you reconsider your position? I will gladly reconsider my position if you (or ayone else) can give me just one example of no. 1. Simply because, like you said, science isn't absolute and everybody should be open to the possibility of being wrong.
>"In May 1983, doctors at the Institute Pasteur in France reported that they had isolated a new virus, which they suggested might be the cause of AIDS.50 Little notice was taken of this announcement at the time, but a sample of the virus was sent to the CDC.51 A few months later the virus was named lymphadenopathy-associated virus or LAV, patents were applied for, and a sample of LAV was sent to the National Cancer Institute.52"
http://www.avert.org/aids-history-86.htm
>That quote doesn't even begin to prove that Gallo (or anybody else) "calibrated his assays" to the sample that was sent by Montagnier (this aside from the fact that a site like that (that is not targeted to scientific readers) can not be considered to be a reliable sourse for showing the exact methodology of a study).
I sincerely thank you for actively trying, though.
>@RRM
Lo/Alter and Hanson have all detected HGRVs. They don't need to replicate when they have found them already. If they hadn't they would then need to replicate before making any claims about HGRVs not being present in people with ME. They looked at the methodology in Lombardi and lowered the annealing temperature as they did. Hanson has reported that a 1% drop in temp is the difference between detecting and not detecting HGRVs. Others have used temperatures way above those groups.
Paprotka et al. used a RT-PCR. Pathak stated this at CROI. The results from this are in the paper, the assay details are not.
Ironically, HIV shows you could contamination and it still be a human retrovirus and that the results still stand. Whereas there is no evidence of contamination in the labs you wish to cast aspersions on.
Scientists don't swap samples to have them sit in their office for nothing. You really are not interested in facts.
>"…it is highly implausible that HIV-1 Lai/LAV and HIV-1 Lai/IIIB were derived independently from two different individuals."
http://www.nature.com/nature/journal/v363/n6428/pdf/363466a0.pdf
HIV-1 Lai/LAV is LAV from the Pasteur Institute
HIV-1 Lai/IIIB is from the LTCB of the NCI.
"In July, the Pasteur Institute sent a sample of LAV to Gallo. Another sample of LAV was sent in September, and by December, Gallo’s lab was successfully cultivating LAV."
"Dr. Gallo stood before the press conference at the National Cancer Institute to announce that he had discovered the virus. What he neglected to mention was that Montagnier had also identified what turned out to be the same virus. The two institutes had previously shared samples; they agreed to publish together and even make a joint announcement. But when the press got wind of the news, the NCI felt compelled to proceed without the French.
“If I could relive those days, I wish they had been at the press conference,” Gallo said. “I was a little swept away.”
At the press conference, Gallo showed pictures of HTLV-III. But it didn’t look anything like HTLV-1 or HTLV-2, and it was hard to see how they could be of the same family. As it turned out, the picture of HTLV-3 was actually a picture of the LAV virus sent to Gallo by Montagnier.
The cause of AIDS had been discovered by Gallo. Or was it?
The French didn’t think so. The picture of Gallo’s HTLV-3 was indisputably a picture of Montagnier’s LAV virus."
http://www.dallasvoice.com/who-discovered-hiv-gallo-montagnier-or-both-1021402.html
>I want to thank you for a most perceptive post, Dr. Deckoff-Jones. I've been needing to read something like this for a long time. My poor synapses aren't firing so well now and having it laid out so clearly and concisely helps a great deal.
>As Gerwyn previously stated on another blog:
"Sadly i must state that the design of the study is hopelessly inadequate.The cytokine profile demonstrated upon examination of patients supplied by Dr Klimas and Dr Bateman to trials are at complete odds with the cytokine profiles demonstrated in the recent study by Mikovits et al which exist in xmrv positive patients.One must remember that CFS is a metaphor and not an objective diagnosis.The cytokine profile demonstrated by the patients of Klimas and bateman is suggestive of a herpes virus infection and or the effects of prolonged elevation of stress hormones.The cytokine profile of XMRV positive patients resembles that of patients with a disease caused by HTLV1.This is a TH17 bias.The raised Il-2 levels found in xmrv positive patients indicate a chronically activated immune system which is the same picture which results from a HIV infection.Unless some form of objectively measureable inclusion and exclusion criteria are developed then the heterodgeneity of the study population will lead to yet more confusion.To restore the balance and exclude bias then the patients treated by Drs Bell and Chaney must be added.Their patients have been shown to contain a hgrv positive population and the patients of Levine bateman and klimas have not.To eliminate potential bias from different diagnostic criteria then the design needs to be ammended in the way I suggest
Otherwise we will have the argument that the latter doctors dont treat the same patients.
If on the other hand their patients do not test postive but the patients of Drs. Cheney, Bell and Komaroff do then the argument is over they do treat patients that are objectively different. We can then also demonstrate that methodology is crucial in detecting HGRVs.
As the study stands those answers are unobtainable."
Cheney patients in particular have several compelling biomarkers diagnostic for M.E. The question is, why weren't these other patient groups included, since they tend to be the sickest? Smells like a rat (er, wild mouse). I'm not sure the Lipkin studies will prove definitive for anything.
>@ Anonymous
"Scientists don't swap samples to have them sit in their office for nothing. You really are not interested in facts."
I read that as "no, there is no indication in the published literature that Gallo (or anyone else in the history of virology) actually used the samples of the study he was trying to validate, to calbrate his assays to. Makes perfect sense too, by the way.
"Lo/Alter and Hanson have all detected HGRVs. They don't need to replicate when they have found them already."
Thus, if they hadn't found anything, they would be bad scientists by not copying the eaxt same methodology, but because they did find something, their methodology was great?
This makes absolutely no sense with regard to sound scientific methodology. What should these scientists have done if they hadn't found anything with their "non-replication" methodology? Pull the plug and not try to publicize their results?
"As Gerwyn previously stated on another blog"
The argument employed by this Gerwyn is (again) wrong. The WPI have been heavily involved with the cohort selection of the Lipkin study. Even if some of the clinicians involved (e.g. Klimas) would select TOTALLY the wrong patients, there would be no problem at all. The samples from the involved clinicians don't just get "thrown together". Every clinician represents a cohort that is pretty close to the size of the Lo study! Thus, even if just one of the clinicians involved selects the proper set of patients and the WPI will reliably identify these, it will be regarded as confirming the Lombardi finding and that XMRV is indeed infecting humans. And even better, the clinicians who selected the "wrong" patients will be exposed. What more can you ask for from a single study?
Furthermore, as both the clinicians from the Lombardi and Lo studies are involved as selecting patients for this study, there should be no worries at all that there will be more than enough "proper" patients selected to validate the initial findings.
Please also note that the above arguments would not address BWG negative results, as they involve patients that are pedigreed as positive by WPI beforehand.
Finally, the WPI DID NOT use the mentioned cytokine profiles paterns for patient selection in Lombardi et al. Therefore, it is rather bizarre for a person who insists on exact replication of the Science study on occasions that don't involve the WPI, to insist that patient selection should be done different from the Lombardi study when the WPI themselves ARE involved.
It thus seems a rather desperate attempt to explain away a possible negative result beforehand (as is always possible).
>The majority of the samples they used were from the databank maintained in Reno, plus samples sent from the aforementioned physicians, among others. Most would have had this particular and peculiar cytokine profile. Regardless, even if XMRV is a contaminant, the blood is a bad place to look for this virus by PCR, the serology studies are more compelling, and there was certainly a reaction to some type of retrovirus. I hardly think it matters if it's XMRV or another XMLV.
>Not to mention the pictures of budding virions.
>By the way, I am not the same anon that you have been preoccupied with.
>@RRM
I provided the evidence that Gallo used the positive sample from the French in the post above Andrea Pring's. Everyone can see you have ignore it.
"Thus, if they hadn't found anything, they would be bad scientists by not copying the eaxt same methodology, but because they did find something, their methodology was great?"
Yes, because that is how you test a hypothesis.
"This makes absolutely no sense with regard to sound scientific methodology. What should these scientists have done if they hadn't found anything with their "non-replication" methodology? Pull the plug and not try to publicize their results?"
Non-replication is not replication. They have to attempt to then replicate. If they are not willing to follow the scientific method, no they should not puiblish and no journal should let them.
Answering your remark to someone else, Lo and Lombardi are not selecting patients for the Lipkin study. 6 clinicians are.
>Unless Gerwyn has brought in new evidence on the subject, the last (and only) evidence I remember him referring to about his infamous 'chronic stress' cytokine profile was that it was complete bullshit and that he totally misread the conclusions of one single paper.
As I remember, Gerwyn's assessment that other CFS physicians choose a patient cohort with cytokine profiles which resembles a chronic stress state was based on one single paper that he completely misread the results of. The paper in question was on the topic of patients with depression vs. healthy controls who undertook an exercise challenge. The results of this paper were that both patients with depression AND the healthy controls had slightly elevated IL-10 after the exercise challenge. However the IL-10 in both groups quickly returned to normal in both groups and did not remain elevated for several days as it did in the Light's gene expression study, which found that IL-10 gene expression levels did differentiate CFS patients vs. controls.
So basically as far as I understand, Gerwyn is saying that a single paper on patients with depression vs. healthy controls, which could not differentiate depressed patients from the healthy controls using measurements of IL-10, somehow means that papers which can differentiate CFS patients from healthy controls based on IL-10 gene expression mean that raised gene expression of IL-10 in CFS patients somehow equals a cytokine profile of depression, which makes no sense.
In short, the vast majority of Gerwyn's analyses that I have seen suck big time donkey dong and I think that the people who rely on him without questioning for his 'scientific analysis', and who parrot his comments all over the net, are going to be fairly disappointed when they finally realize that he has very little clue as to what he's talking about.
>@Anonymous
I have never stated that Lo and/or Lombardi were actually selecting patients. I stated that they were "HEAVILY INVOLVED" with cohort selection. If you read closely, you can plainly read that I stated several times that multiple clinicians were actually doing the selection of patients. It were the participating labs that suggested to Lipkin which clinicians were to be asked for patient selection however, which is why you won't see Reeves or Wessely on that list.
Thank you for stating that Lo/Alter should not have publicized their results if they were negative, as this invalidates your whole argument: most if not all studies are conducted on the basis that results will get published no matter what the results, this to avoid what in science is known as "publication bias". Therefore, a study that is designed to only get published when its results are positive will never get funded and therefore, the idea that validation studies have only to be exact replication studies when the results are negative is patently untrue.
@Anonymous (the other one ;-) )
I actually agree that the serology results should give confidence if you believe the results to be right. However, that is just one more reason to trust the results of the BWG and Lipkin studies, whatever the outcome: in both studies, the labs are free to test for serology too.
Therefore, if no one can relibaly discriminate between supposed positives and supposed negatives, there is not much chance that blood collection/processing is a major issue, as then you would have to argue that not only did the virus disappear somehow before the blood arrived at the WPI/Ruscetti, but the antibodies also disappeared from the blood. Like Ilsa Lund said in Casbablanca, it is indeed a crazy world and anything can happen, but that would certainly seem highly unlikely to me.
So yes, every study in the world is "just" one study, but I think the combination of these two studies leave very little room for experimental error. Of course, one could always assert a vast conspiracy of some kind, but that would really equally apply to every replication study by any third party too.
>I will say that we CFS patients need to remember all the other stuff going on outside of all this infighting, such as the MRC's 'Expert Group' funding ME/CFS proposals-
"The Medical Research Council (MRC) recently launched a call for proposals to support high quality, innovative research to increase the current knowledge base of CFS/ME and draw in expertise and resource from related fields. Applications were required to address the mechanisms underlying chronic changes related to CFS/ME particularly focusing on one or more of the following areas: autonomic dysfunction, cognitive symptoms, fatigue, immune dysregulation, pain and sleep disorders. The application deadline was 7 June and up to £1.5 million will be made available to support research proposals; the MRC expects to announce any awards towards the end of the year."*
Notice the language used-
1. "Applications were required to address the mechanisms underlying chronic changes related to CFS/ME"- "Chronic changes related to CFS/ME"? What the hell is that? That is the result of some fancy weasel wording which avoids saying underlying pathology in ME/CFS, since the psychs on the panel believe that there is no underlying pathophysiology in ME/CFS.
2. "autonomic dysfunction, cognitive symptoms, fatigue, immune dysregulation, pain and sleep disorders"- Notice as well how 'cognitive symptoms' is used instead of cognitive dysfunction, as well as the emphasis on 'fatigue' in the absense of post-exertional malaise. They've left this one wide open for applications on psychosocial bullshit.
I think we CFS patients are in danger of fighting over who misplaced the mantle clock in the middle of our house being robbed.
* http://www.mrc.ac.uk/Ourresearch/ResearchInitiatives/CFSME/index.htm#P49_3252
>@ RRM
Good to see you posting again.
I fear there will always be an audience for the same circulatory arguments to be 'debated'.
I can't help but notice that some ardent proponents seem to have been 'repositioning' themselves over recent months in case BWG and Lipkin produce 'negative' results.
Nobody seems concerned that Lipkin will not be 'replicating' the methodology of the original Lombardi paper. I do find that odd.
I mean if it was good enough then, why not now? Isn't that what has been demanded? 'REPLICATION!'
>@RRM
Some of the clinicians in the Lipkin study are known to have mixed cohorts. The immune profiles they have produce prove this, as they do resemble herpes infection or stress. Therefore it is easy to hypothesis that the number of positives that will appear in that cohort will be much less than with a CCC cohort.
"Thank you for stating that Lo/Alter should not have publicized their results if they were negative, as this invalidates your whole argument: most if not all studies are conducted on the basis that results will get published no matter what the results, this to avoid what in science is known as "publication bias"."
Scientist should not be seeking to publish any old tat and neither should a journal. Once replication of methodology is done it is appropriate to publish. At that point it does not matter what the results are, as the investigation would have been scientific. This is again not happening in the Lipkin study. If that study was organized correctly, each lab would also be using the methods of the other.
>@Anon August 17, 2011 11:11 AM
Do you have a quote where anyone has only talked about IL-10?
Klimas and Bateman are known to use mixed cohorts. The definitions (Fukuda) employed prove this, as does the immune profile. The WPI's specific HGRV and CCC cohort looks entirely different, in fact very similar to MS. They cannot be the same patients.
>@Anonymous August 16, 2011 6:51 AM
" ERV has no background in MLV, or in HTLV, another human retrovirus with a very low or seemingly absent mutation rate.
Her ideas do not fit the scientific knowledge on retroviruses."
Nothing could be further from the truth. Maybe if you read her science blogs, ERV does HIV-1 research, you could learn something on retroviruses.
Abbie clearly explains the mutation rate in XMRV in her blogs:
http://scienceblogs.com/erv/2011/07/xmrv_evilution_its_more_than_j.php
http://scienceblogs.com/erv/2011/01/xmrv_and_occams_razor.php
The WPI will have every chance in the current Phase III to replicate their study.
>… if the samples aren't tainted away from a true M.E. cohort. The serology studies are interesting, but, unlike other illnesses, chronically ill M.E. patients even seem to lose some of their humoral immunity after a lengthy period of illness. Nonetheless, a contaminant isn't going to evoke an antibody response. I think Mikovitz found something and was diligent in her approach, but it may not necessarily be XMRV. But many people are being helped by anti-retroviral treatments, both conventional and unconventional, and some have shown evidence of severe immune depletion, despite the more widely accepted chronic immune activation or immune exhaustion, at early points in their illness, suggestive of some type of retrovirus. The politics of this are just sad. And that Cheney, Bell, and other significant cohorts were left out just begs the question, do they really want to find anything? They should all be on the same page.
>HIV is nothing like HTLV or HGRVs. Her blogs are full of misleading statements and ignorance around retrovirology. Don't forget she is also a student. Her ideas on mutation and variants are at odds with the published literature on retroviruses.
>Like I explained, in the Lipkin study there is not much to worry about "mixed cohorts" from one, two, or even five clinicians. Lipkin will of course be looking at results collectively, but he will also evaluate each clinician's cohort seperately from the other clinicians' cohorts.
One other thing that people seem to be forgetting: Lipkin is using duplicates for each sample. Thus, even in the very unlikely event that ALL of the clinicians are providing labs with "just tired" people, the (supposed) background levels of HGRV's should be enough for these scientists to at least prove part of their case (that HGRV's are "out there"), which will mean a whole lot of new research.
Thus, based on "cohort reasoning", there is really not much to worry about. Only if ALL of the participating clinicians provide labs with the wrong samples AND if ALL of the participating clinicians manage to not pick ANY healthy persons infected, there would be a serious "HGRV's are unreasonably being buried" problem. Outside of some conspiracy, I estimate the chances of this happening as about 1 in a googolplex.
@Anonymous August 17, 2011 3:04 PM
"… if the samples aren't tainted away from a true M.E. cohort. "
You are simply wrong. You were attaching this to the comment of a previous poster, but he/she was talking about Phase III of the Blood Working Group. There are no cohort issues in Phase III. The WPI and Lo have picked 30 patients that were pedigreed as being positive for XMRV/MLV-like viruses by them and they (and others) have retested these in blinded fashion. Therefore, there is no question that the *right* patients were selected for this study whatsoever..
@Firestarter
Thanks and I agree with you.
There is one problem however: if the upcoming BWG/Lipkin results are not at all confirmatory of the WPI and/or Lo findings, I expect (F.) Ruscetti and/or Alter to "concede".
While "proponents" of the WPI's findings have had no problem throwing everybody including Ila Singh under the bus thus far to save the hypothesis, I feel that Alter and/or Ruscetti leaving camp will be much harder to deal with in terms of reducing cognitive dissonance.
>A mixed cohort will include patients with fatigue of a psychological origin and idiopathic chronic fatigue, not CCC. That is a big problem. And what if the CDC get all the positives? Their blood tests have already been shown not to work. Background level won't make it an association by the way.
The Lipkin study should be getting all the labs to also use the methods of the other labs. Without that this study is useless.
>That's what I'm trying to say…
M.E. patients have several distinct diagnostic signatures. Judy knows this, as do others. They should be culling patients only with those patterns, not doing some Raggedy-Ann mix and match bs that will provide even less clarity.
The CDC? Please. Anyone but them. They blew it 20 years ago and we've being living hell on Earth as a result.
>There is no evidence that ME patients have different immune profiles.
There are researchers who use a non existent grouping called CFS and who have produced different profiles (like herpes and stress) each time they have a new set of patients. But they cannot be called ME or ME/cfs patients.
>PLEASE SIGN KHALY'S PETITION: Patients against the nomination of Suzanne Vernon to the CFSAC
There are 121 signatures so far, but more would be very helpful. Thanks.
http://www.change.org/petitions/patients-against-the-nomination-of-dr-suzanne-vernon-to-the-cfsac?utm_medium=facebook&utm_source=share_petition&utm_term=own_wall
>RRM wrote: "…there is nothing wrong with other scientists "abandoning" research and diverting their attention to fields that they feel show greater promise."
A field like, say, genetics? It is interesting that an international team led by the Fred Hutchinson Cancer Research Center (with whom A. Dusty Miller and his colleague Ramon R. Mendoza are associated) recently published this paper:
http://www.sciencenewsline.com/medicine/2011081622370010.html?continue=y
A genetic etiology for prostate cancer (and ME/CFS) would be incompatible with a retoviral etiology, no?
>Thanks for the studies on possible retroviral association with PBC. It appears that retroviruses are going to be the new frontier in medicine. I am so glad they are already on to a trial on PBC with antiretroviral medication.
If only we could get the politics out of ME, we could have trials too and find out for sure if antiretroviral medication is useful in ME. After all, that is only humane after all these decades. Trials are voluntary and the naysayers are not being forced to try anything. I just don't understand why they can't let others freely choose their treatment.
Or maybe I can. It seems as if they are afraid of the outcome.
Thanks, Dr. Jamie
Sincerely, Ann
>I don't know how they can play these silly games whilst people die. How many friends and family members will be lost?
>Thanks for this post. Also I have to say that it is actually heartening to see contributors to the comments arguing so passionately! It gives me hope even though they may not feel it themselves! Robust, intellectual debate produces good science surely. Alas I cannot contribute on a scientific level. Thanks for your efforts, I can see points on both sides. Carry on people, my 12 year old girl needs some results! ; )
>deltaretroviruses and gammaretrovirus display almost no sequence variation yet are not contaminants but deadly pathogens.They propagate by clonal expansion and are transmitted via breast milk saliva and direct blood contact.
PCR analysis of oxidised DNA is difficult and very often impossible.The reason is that oxidatively modified DNA leads to stalling of taq polymerase.Oxidative stress leads to oxidative lesions in DNA.Patients with ME display high levels of oxidative stress.Gammaretrovirus DNA will almost certainly contain oxidative lesions.Armed with this knowledge using a synthetic clone to optimise a PCR reaction is childish.One must use clinical isolates or a PCR assay preoptimised to detect a clinical isolate.The HIV assays have been preoptimised the ones failing to locate a gammaretrovirus have not been
Science has been defined as a belief in the ignorance of experts.The level of ignorance displayed by self proclaimed experts like Coffin and Towers is frankly astounding