If Ive said it once, Ive said it a thousand times here on ERV-- Scientists are wrong all the time. ALLLLLLLL the time. Its what we *do*. We make a hypothesis, design an experiment, collect data, and refine the hypothesis, because the original hypothesis was wrong.
Over and over and over and over and over. Less wrong to slightly less wrong, to slightly less wrong. But we are wrong all over the place.
Sometimes things go really wrong and we go from less wrong to more wrong.
Ideally one realizes this has occured before they publish their experiments/data/conclusions in a paper, but sometimes they dont, and papers have to be retracted. I think the general public might think retraction is a bigger deal than it really is, thanks to high-profile retractions in the case of fraud, but fraud and making a mistake are two vastly different creatures. Retraction after you realized you made a mistake is the right thing to do, as it contributes to the progress of science and prevents others from wasting time.
So that is what happened with Robert Silverman and his lab, and their contribution to the 2009 'XMRV-->CFS' paper in Science:
Partial Retraction
In our 23 October 2009 Report, "Detection of an infectious retrovirus, XMRV, in blood cells of patients with chronic fatigue syndrome," two of the coauthors, Silverman and Das Gupta, analyzed DNA samples from chronic fatigue syndrome (CFS) patients and healthy controls. A reexamination by Silverman and Das Gupta of the samples they used shows that some of the CFS peripheral blood mononuclear cell (PBMC) DNA preparations are contaminated with XMRV plasmid DNA.
It sucks, as in its pretty embarrassing, but other scientists cant laugh too hard at Silverman because due to the nature of our work, it could very well happen to them the next day. I literally dont know anyone that looks down on Silverman for what happened. I dont know of anyone Silverman attacked or degraded when they couldnt replicate his data. He just do what he do, like any other normal scientist, so the consensus opinion is pretty much what Myra McClure voiced herself:
Myra McClure of Imperial College London conducted a study in the UK last year that found no trace of the virus in people with CFS - one of almost a dozen to have done so since 2009. She applauds Silverman for the retraction. "Bob Silverman is a good scientist and an honourable one," she says. "I guess he can only retract the figures that he contributed to the original paper."
Actually, McClure also mentioned a second thing there, that needs to be discussed...
See, Silverman didnt just say "Hey, we messed up these figures. Im sorry. Here is what happened. But we stand behind the conclusions in this paper."
According to the WSJ, Silverman took his lab off the 'XMRV-->CFS' paper entirely. He cannot take down the entire paper-- he can only take his name/his lab off the paper.
To understand why that happened, what caused him to change his mind, we need to look at the science Silverman did to determine he was wrong--
Long-time readers of ERV and/or followers of the XMRV fiasco know that of the many criticisms of the XMRV work, one was that all of the sequences the Whittemore Peterson Institute uploaded to Genbank were identical.
They were not only identical to one another, they were identical to an infectious molecular clone of XMRV, VP62.
The WPI/Judys response to others pointing that out to her were:
1-- We promise for reals its not VP62!!
2-- There is, liek, TOTALLY a lot of sequence diversity! Theyre not identical! LOOK AT ALL THIS DIVERSITY!!!!!!
Problem #1 is Silverman sent the WPI VP62 plasmids in 2007 (before they 'found' XMRV in patient samples.
Problem #2 is that there is ZERO GODDAMN DIVERSITY in the sequences they uploaded to Genbank. YOU CAN SEE IT WITH YOUR OWN EYES.
But Mikovits was above those petty facts.
Luckily, Silverman wasnt.
To investigate whether the samples he got from the WPI were contaminated with VP62 plasmid, he looked for two things:
1-- The antibiotic resistance gene found in VP62. We grow more plasmids in bacteria. To select for the bacteria that have the plasmid we want, we give the plasmid an antibiotic resistance gene. You, nor any virus, let alone a retrovirus, dont contain any antibiotic resistance genes. If this gene is present, it indicated that plasmid contaminated the samples.
2-- The Promoter-XMRV junction. Lets say I want to grow up some HIV-1 from an infectious molecular clone. I chemically treat my plasmid, plop it onto some mammalian cells, and in a couple of days, there is TONS of HIV in the cell supernatant. That works because there is an artificial promoter in front of the HIV genome in my plasmid, in my case, the promoter from cytomegalovirus. CMVpromoter-->HIV genome does not exist in real life, anywhere. Its a lab trick. Likewise, CMVpromoter-->XMRV does not exist in real life. If you put one primer in CMV, and one primer in XMRV, and you get a product, that product indicats that plasmid contaminated the samples.
Silvermans lab found VP62 plasmid in their samples. Which means the positives Silvermans lab reported in 2009 were all because of plasmid contamination. The positive results were NOT the result of real infection.
Well, crap.
Again, not *that* big of a deal. Plasmids contaminate PCR reactions all the time. Coulda happened to anybody.
But... thats not really the end of it...
See, when you contaminate your reactions with plasmids, its either A) sporadic, or B) in every reaction. If plasmid was just 'around', you would have expected to see ~3 positives in the 15 CFS samples, and ~3 positives in the healthy controls. If plasmid got into, say, your molecular grade H2O, you would expect to have all samples positive, even your 'H2O only' control reaction.
That is not what happened.
Silverman only found VP62 in the CFS samples. Not the healthy controls.
And they detailed in this paper the *extreme* lengths they went to to avoid plasmid contamination. You know what I do to prevent contamination? I set up my PCR in one room, and add my template in the lab. Thats it. You know what they did?
In early 2009 we received PBMC DNA samples from CFS patients and healthy controls from the Whittemore Peterson Institute (WPI), Reno, Nevada. The PBMC DNA samples were taken directly to a clean room upon arrival and stored in a -20oC freezer in the same room. Precautions were taken to minimize the possibility of cross-contamination of the human samples with laboratory sources of XMRV DNA. In particular, neither plasmid XMRV VP62/pcDNA3.1(-) nor XMRV PCR products were ever taken into the clean room. Also, new pipetmans (Gilson) were purchased for exclusive use in the clean room and were never used elsewhere. At the entrance to the clean room there is a sticky pad on the floor and lab personnel must change lab coats upon entering and exiting the clean room. The clean room is locked when not in use. The PCR reaction mixtures that contained PBMC DNA were pipetted in an AirClean 600 PCR Work Station (ISC Bio Express) in the clean room. The PCR Work Station was purchased for use in the clean room and never used elsewhere. The single-round PCR on human DNA samples was performed in a BioRad PCR thermocycler, used exclusively for that purpose, in a separate room from the clean room. The PCR on the plasmid XMRV VP62/pcDNA3.1(-) was performed in yet another room in a different PCR thermocycler from the one used on patient DNA samples.
Uuuuuum... yeeeeeeah... I dont do that. And Ive never gotten contamination. They go super-neurotic and do get contamination?
Well, that would be possible if the source of the contaminant was one of the previously proposed mechanisms-- Mouse DNA is in PCR and reverse transcription reagents, its in Qiagen columns. MLVs of any stripe contaminate all kinds of cell lines as proviruses and exogenous viruses. These mechanisms would cause widespread contamination not matter how hard you tried to prevent it.
... But thats not what Silverman found.
He didnt find mouse ERVs.
He didnt find the same exogenous viral sequence over and over.
He didnt find the same XMRV provirus in every sample because of contaminating cell line DNA.
He unquestionably found VP62 plasmid in the samples he got from the WPI... and only in the CFS patient samples.
Meanwhile, at the WPI, they say they get FANTASTIC results with their assays. The 67% positive rate flew up to, what, 100% after the Science publication...
And yet, when WPI/Mikovits are given samples where they do not know beforehand who is 'supposed' to be positive and who is 'supposed' to be negative, they cannot differentiate between CFS/Healthy/Positive controls. 50:50, implying that half of the people they say are positive are really negative, and half of the people they say or negative are positive, or in other words, they have no idea what they are doing.
When samples are collected from 'XMRV positive' patients without any 'processing' at the WPI, the samples come up negative.
And yet the CFS samples shipped to Bob Silverman in 2009 were contaminated with XMRV PLASMID before his lab touched them, after WPI touched them, after Silverman gave them the VP62 plasmid.
Isnt that weird?
I think thats just weird.
I mean, how would you get weird results like that?
Thats just so weird!
Huh.
Well, I guess Silverman thought that was weird too, so he took his lab off the paper.
And lets just say, I dont think he did anything wrong. I think he did what any scientist would do, were they in his position. I think he actively recognized that something was 'weird' and investigated it, determined the root cause, and corrected the field.
That is how you make a mistake and correct it gracefully in science.
On the other hand, it is now less weird why the very first place Mikovits went after the first negative paper was 'FRAUD!! THEYRE ALL FRAUDS!!!!'
Quoting Jon Cohen and Martin Enserinks excellent article again:
Back in Reno, Mikovits and Lombardi began feeling besieged. "After the first negative study, it was a dog pile," Lombardi says. "Let's be honest: A number of people in the mainstream medical community heard chronic fatigue, and they rolled their eyes and laughed."The problem, as they saw it, was that nobody was following their recipe exactly.
Hmm. Yes, it does seem that others are missing a key ingredient to the WPIs 'recipe for success'.
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More like this
No doubt this is in someones lab notebook :p
PCR master mix:
H2O
Buffer
MgCl2
DNTPs
DNA
HiFi polymerase
Top secret PCR enhancer (VP62 plasmid)
Wow... Just. Wow. So Mikovits was right on one point after all; it wasn't contamination -.-;
So what do you think happens next? Any chance of WPI losing their grant from NIAID?
In archeology they call it salting a site, what do you call it in virology?
Nice post again, ERV.
Perhaps this is just me and my lack of experience of what's considered "normal" in this field, but what I do find the most intriguing is the following.
Mikovits touted at a conference the day after the partial retraction that she did the very same tests as Silverman had done and didn't find contamination. However, from that Retraction Watch article you've linked to, Science editor Bruce Alberts is quoted as saying:
Now why on earth would you not share that data? Oh, I can see why you wouldn't want to do that, but I mean why would you not do that if you're convinced you're right?
What are possible legitimate reasons for acting like this?
@ their non-contamination procedure: WTH. I didn't read the 2009 paper, but who would even do that? Just use filtered pipet tips (that's usually enough) and maybe fresh PCR regents and run negative control reactions. It's not like long DNA fragments would fly around in the air at high concentrations, lol.
Does it say anywere after how many cycles the Silverman lab could detect VP62? did they do qPCR?
JohnV: use NEBs stuff, then you don't have to add MgCl2 :P
In the last few days, Mikovits has been quoted in various media out lets as saying:
Mikovits continued to strike a defiant tone, insisting that XMRV had not been ruled out as a potential cause of CFS.
"Anyone who says this is a lab contaminant has drawn the wrong conclusion and has done a disservice to the public," she told the journal.
She vowed to continue working to prove that XMRV is a genuine virus and is present in CFS patients. "The virus is real," she told Science. "I have isolated it from patients. I know it's there."
"The conclusion of the Blood Working Group was that we don't have a reproducible assay to detect XMRVs in the blood -- not that they weren't in the patients at all."
She vowed to continue working to prove that XMRV is a genuine virus and is present in CFS patients. "The virus is real," she told Science. "I have isolated it from patients. I know it's an outbreak of XMRV.
But in another recent quote Mikovits stated:
Dr. Mikovits said she stood by the theory that there was a retrovirus associated with chronic-fatigue syndrome, though not necessarily XMRV. "We have to dig in to find the right viruses. We need to keep looking," she said.
Huh...a total 180?
Mikovits unwittingly or unknowingly just called herself a liar with that statement. It's all smoke and mirrors.
Then you have Gerwyn stating fiction as though it was scientific fact or a foregone scientific conclusion on http://treatingxmrv.blogspot.com/2011/09/when-going-gets-tough.html#com…. Unfortunately, who have a patient community that is given a false sense of hope. Sad...very sad and pathetic.
Can it get any weirder?
Can't understand why Ruscetti is committing career suicide unless he believes that a captain should go down with the ship.
It's funny this was published when it was. I'm making a new video about Watson comparing her against, say, Carolyn Porco. Can you guess a point that Porco points out over and over?
Errors happen. But a good scientist is one who when informed of the error takes steps to make the error public and retract it.
It's like truth and honesty are valued among scientists or something.
I want you all to know that we are proceeding with the Lipkin studies and now that we know the complete sequence of XMRV is not correct..and that VP-62 XMRV is not likely to be the XMRV in CFS patients..we are working to full length sequence the XMRV/HGRVs isolated in our patients.
Huh?
The results do not say that HGRVs are not in the blood (it) simply (says that they are) at levels too low to detect in the samples as they are saved in blood banks world-wide.
@ERV
Question for ERV. If Mikovits cannot find xmrv via pcr, culture or serology. It is stated that gammaretroviruses leave the blood and are thereafter only found in tissues and the antibody response disappears. What methodology can Mikovits employ given the above and what does Mikovits mean the xmrv sequence is not correct?
The reason Silverman went back and verified, then retracted the original results is simple. It's the same reason I would do it and probably the same reason any real scientist would; It sucks to do it, yes, but it sucks less than losing your credibility in the field of science where credibility is the most important thing one can have. My hat is off to you Dr. Silverman.
@FWD
If this virus truly leaves the blood after some time, it is impossible for Mikovits to detect it in (up to) 100% of her study cohorts. And yes, she did find 108 out of 108 CFS patients to be positive for this 'HGRV' for her latest 'cytokine study', as well as up to 99% (100 out of 101 patients) of the original Science cohort.
And this was all found through just looking in the blood of those patients. So no, this pathetic excuse does not even begin to make sense.
What makes this argument even more crazy is the fact that, in this latest study, Mikovits and Ruscetti together designated 11 out of those 15 "pedigreed negative controls" to be positive for 'HGRV' after blinding.
Again, this was found just through looking in the blood of those 15 controls. How can she even begin to explain when the virus often leaves the blood?
One of the weiredst aspects of this whole sick tale is the complete absence of anyone actually linking XMRV (or whatever version Mikovits is now chasing) with a clinical description of M.E/CFS. A defining characteristic of M.E/CFS across all the competing sets of diagnostic criteria is that there is a pronounced gender imbalance ranging 1:2 - 1:4 male/female. Without any viable hypothesis to explain why an infectious agent would preferentially cause chronic illness in women, trying to find an infectious cause lacks any logical basis . It's as though the virologists, having been set the task of finding the virus, never stopped to ask "does this make any sense ?" Of course there could be something paradigm busting to find, but how many $millions does Mikovits propose spending on what appears to be an unjustified search for unknown HGRVs ? If infection does have a role in M.E/CFS then it is only part of the story, and there are multiple known agencies which are already well associated with CFS type illnesses. Tracing out new phylogenies of HGRVs seems superfluous when good old EBV still demands attention as M.E/CFS coincident.
One major consideration, Silverman is an academic, presumably tenured. His career might take a damper for a couple of years due to this retraction (so I read it as "we got duped"), if Judy retracts she destroys the whole business model of the WPI and is out of a job by Wednesday, with a career so badly damaged she'll have trouble finding a job as a pharma rep.
RRM @ #10- Not only that, but for the Emory monkey model to be applicable, ie XMRV leaving the blood for tissue after a few weeks/months, then wouldn't that mean that most if not all of the patients in the Science study would have had to have been infected within a few weeks/months of their blood draw? Keep in mind these are long term sick patients from different parts of the country with blood draws most likely occuring at different points in time in different locations.
IVI @ #11- In my opinion, there are likely several different causes and/or subsets in ME/CFS, so while the well known gender difference in ME/CFS could be explained by the fact that other diseases such as MS, lupus and autoimmune diseases in general happen more often in women than men, a purely infectious agent would be entirely plausible for a subset (just in general, not really referring to the WPI/XMRV in particular).
Based on what I (think I) understand, the whole thing is just so freaking complicated- for instance there is the 'classical ME' cohort with sudden, flu-like onset, sore throat, swollen lymph nodes, neurological sequelae, etc, which we can call 'subtype A'.
Then there is the gradual onset group which don't have swollen lymph nodes, sore throat or neurological sequelae (not counting general cognitive dysfunction) but do have a progressive disease course, which we can call 'subtype B'.
Then there is the whole issue of post-viral fatigue syndrome(s), where any number of infectious agents have been shown to cause long term illness following the acute infection, ranging from West Nile virus, SARS, giardia lamblia, Q-fever, EBV, Ross-River virus, etc. Are each of these post-viral illnesses a shared post-viral autoimmune sequelae, ie 'subtype C', or is each one its own subset, ie 'subtypes C, D, E, F, G...?
The craziest thing is that out of all these illnesses, which currently go under (or rather are ignored under) the name 'ME/CFS', they probably stack up to be one of the largest sources of disability, doctors visits, healthcare usage, etc., yet are currently all but ignored by mainstream medicine as a whole.
PS- Just doing some googling for female/male ratio in post-polio syndrome, which I think occurs more frequently in women than men, and came across the following about mumps- "In addition, mumps continues to cause 10-20% of meningitis and meningoencephalitis cases in parts of the world where vaccines are not readily accessible. Males 16-21 years of age are at highest risk for developing this infection, with a 3:1 male/female ratio." So it appears that there can be male/female discrepancies in viral diseases even though this is opposite to what is seen in ME/CFS.
http://emedicine.medscape.com/article/1168529-overview
IVI - you're right. If you go beyond gender breakdown you'll find some other stunning common ground between the vast majority of CFSers. They're virtually all white, all from the developed world, all middle class, all with depression.
There is no virus on earth that's that picky
It's just a repeat of neurasthenia, glove paralysis, etc and the same goes for 'chronic' lyme, morgellons and fibromyalgia. Weird eh? Such a narrow demographic.
Somatisation disorders share that same demographic. How strange! There is no virus at work here, just lonely, depressed people turning their hatred inward because they feel admitting to being mentally ill is a weakness.
That's where she's headed anyway.
This may explain why Mikovits kept vehemently insisting that none of the labs that were getting negative results were following her protocol. It was because they were all skipping the step where she added the VP62 plasmids to the "+CFS" samples.
#12: "with a career so badly damaged she'll have trouble finding a job as a pharma rep."
Drug companies prefer to hire young, attractive women, recent college graduates, especially cheerleaders, to be drug reps. I don't think Judy fits the profile no matter what happens to WPI.
http://www.nytimes.com/2005/11/28/business/28cheer.html?pagewanted=all
#6, FWD:
The posted link
http://treatingxmrv.blogspot.com/2011/09/when-going-gets-tough.html#com….
shows some slide of JM and I was directly stuck with slide no. 3 'cause I saw this IP plot already in 2010 on JM poster in Prague at the "Centennial Retrovirus Meeting".
But, of course just a "small mistake" ;-) at 2010 the third lane is inscribed with a different sample/patient number.
A mistake here, a mistake there (single round PCR vs. nested PCR) makes up a fine Science pubilcation.
Btw., what a massive plasma virus load! Guess this is hard to reach even within chronical infected HIV patients and for sure never in HTLV infected individuals.
Thanks Abbie.
Strange to think that all the lengths Silverman went to in order to protect his samples were heralded at the time as further 'proof' that there was no contamination.
The only lay-person-patient criticism I have of Silverman (as well as all the others on that Lombardi paper), is the time it has taken to discover this truth. Even for science this seems to have taken forever.
And as for the sequences, well, that just beggars-belief it really does. How can such a thing be disputed for so long? Makes no sense to me.
I notice that Vipdx are now up and running as WPI Unevx: http://unevx.com/
Oh you can be 'tested' for all sorts. Though this hasn't changed: 'Human Gammaretorvirus serology assay: includes XMRV and related viruses: detects antibodies to HGRV'.
Only $65 for the test kit - dunno about the cost for the actual 'tests' themselves...
Funny they don't 'test' for VP62 or even have a statement about contamination somewhere...
'Choo Choo' Gravy train coming on through...
@John - agreed at this stage single causation across the global M.E/CFS affected population appears highly improbable. And of course a particular infective agent could be responsible for disease in a subset of patients, the problem was that Lombardi, Mikovits et al were not claiming a small subset were displaying XMRV presence, but that incedibly (as in unbelievable) XMRV was present in M.E/CFS patients at a rate 17 times that found in the healthy population.
The Mumps example is interesting because it shows something that might be expected in other gender differentiated infections - prominent symptomology of gender specific morphology - to date there appears no equivalent reports in M.E/CFS patients, the reported symptomology being highly consistent across age groups and gender. Mumps also shows how careful one has to be when dealing with headline statistics - while it's certainly true that historically late adolecent males were notably affected, this isn't evidence of preferential infection. Difference in male/female lifestyles mediating exposure seems likely as indicated in the age range infection rates given in this pape, Table 1: http://ajph.aphapublications.org/cgi/reprint/83/12/1717
Remember that Macaque study: http://jvi.asm.org/cgi/content/abstract/JVI.02411-10v1 ?
Just wondering if, well, as I believe you might have said at the time ERV, but in light of Sliverman's latest revelation, the results could have in anyway been generated by contaminated 'XMRV'/Whatever?
Or should this study also now be 'checked' for contaminants? What does a scientist do with his previous studies in light of this recent development? Does he go back over them all? Is he obliged to?
Just wondering...
@El Perro
I know it's difficult for you psych jocks to grasp ideas such as evidence and logical process, given that your business is largely based on (albeit very erudite) story telling - but please try and keep up with those of us who use science as a reference rather than 19thC phantasms of science.
There have been no large scale epidemiological studies of M.E/CFS based on a widely accepted case definition, so no one actually knows with any certainty who, in demographic terms, is affected by M.E/CFS. The Reeves' study, which used its own unique case definition, produced a prevalence rate in a demographically representative (US) population that would make an exclusivly white/middle class national patient population highly improbable. Ironicaly most M.E/CFS affected people see Reeves as hopelessly flawed both in methodology and and in conception, but one could hardly say Reeves was antithetical to a psychiatric paradigm. http://www.anapsid.org/cnd/diagnosis/cfscdc2004.html
M.E/CFS may for any all any of us know, be a disease that predominantly affects white middleclass people living in the developed world - but throwing around scientifically untestable classifications such as "somatisation" is no substitute for actual science. And actual science is something which psychiatry has consistently demonstrated it is incapable of doing without the assistance of other medical disciplines. If M.E/CFS patients don't want to be herded into the psychiatric stable, it's not because of any disdane for those who have a psychiatric diagnosis, it's because psychiatry is so god awful ineffective without the ivolvement of neurochemistry and neurosurgery, and to date no one has suggested M.E/CFS falls under the purpview of those disciplines. Why would any ill person want to be under the care of psychiatrist in those circumstances.
Abbie, anyway you can change something around these parts that we might be able to google +1 your articles?
Just to add to In Vitro's comments:
Even if we knew that CFS did concentrate in a specific social group, that wouldn't necessarily tell us anything. Look at what's happening with autism-spectrum diagnoses in specific regions/neighborhoods/social networks. Those diagnoses are probably of genuine disorders, even if their place on the spectrum is sometimes questionable.
Point is, you COULD have diagnoses of a non-psychogenic disease or diseases clustered in specific social groups. Nevertheless, I also agree with the sentiment that the stigma of mental illness among patients and the public needs to be dealt with, and I have little doubt that some cases of CFS are psychogenic.
@El Perro
Do some research before spouting your psych-based bullsh*t. The epidemiological research we do have, though not perfect, shows that ME/CFS is more common in lower socio-economic and non-white ethnic groups, as shown in the CDC community-based study that In Vitro Infidelium refers to and in a recent UK study.
http://www.biomedcentral.com/1741-7015/9/26
Another recent study showed that prevalence rates are comparable between the UK and Brazil, but in the latter, ignorance of the condition results in it going undiagnosed.
http://www.ncbi.nlm.nih.gov/pubmed/19182171
XMRV is dead, but no more dead than the outdated and proven wrong psych based theories on what is a serious neuro-immune disease. Stick to commenting on things that you know about, if that doesn't limit you too much.
"El Perro wrote - It's just a repeat of neurasthenia (...) Somatisation disorders share that same demographic. How strange! There is no virus at work here, just lonely, depressed people turning their hatred inward because they feel admitting to being mentally ill is a weakness"
Have you ever seen the medical test results from someone with CFS?
If you had to live with a disabling condition and no perspective of a cure in your lifetime, you would too develop a reactive depression as you lose your job, your livelihood and your social life.
Depression doesnt explain though why my biochemistry is abnormal, my MRIs show brain atrophy, my immune system is depleted and my adrenals don't function any longer.
As a psychologist with CFS myself, I know that neurastenia doesn't explain the above.. or do you really think it does?
@Cristina (26): I'm not going to defend El Perro's comment, but this "clinical findings disprove psychiatric causality" chestnut needs to die. Patients with pure depression show abnormal biochemistry, shifted immunological markers, and other "physical" pathologies too. In fact, there's quite a lot of overlap between the test results for depressed and CFS patients. That doesn't prove CFS is psychiatric, only that a wide range of things, including psychiatric disease, can cause the types of changes you point to.
What you're seeing is the body's "check engine" light: these changes say something's wrong, but provide no useful information about what it is. Could be a virus, could be psychiatric, could be an environmental toxin, could be an autoimmune disease, could be a whole bunch of factors that gang up and produce this outcome. If I were a gambling man, I'd put my money on the last one - it seems very likely to me that CFS will turn out to have a complex cause. But that's just a guess.
@Alan Dove
You make a good point that biomedical abnormalities are also seen in psychiatric disorders, but a key point to remember about ME/CFS is that a very many patients do not display any neuro-psychiatric symptoms, such as depression and anxiety, and those that do, do not recover when those issues are resolved. I think it's true that such factors can further aggravate the disease, but they do not cause it.
Of course there's also the very important issue of definition and diagnosis, and with the broad definition often used and the widespread ignorance of the disease among physicians, undoubtedly some patients with psychogenic illnesses get misdiagnosed as having ME/CFS, which doesn't serve their interest or that of real ME/CFS patients. Until an accurate diagnostic test becomes available, this will continue to be an issue, though it does seem that some progress is being made in that direction.
http://finance.yahoo.com/news/Hemispherx-Biopharma-Chronix-pz-257018906…
Anybody ever tell you that you have a wonderful blog?
OMFG....
i'm having one of those "light dawns over marblehead" moments.
anybody know anything about Judy's career before bartending and pretending to know what she is doing at WPI...?
was she ever competent in science?
ERV - the detail above about the lengths that Silverman went to in order to isolate and protect those samples - where might I find it?
It doesn't seem to be linked to anything I can see and I would like to read more about that part of the process.
Danke.
Well, the big-big question is now wether Silvermann still stands with his XMRV / PCa results?
@Camaro
Not likely, given that he also published a paper last week showing direct evidence of contamination in his PCa work.
http://jvi.asm.org/cgi/content/abstract/JVI.05624-11v1
Got somewhat overlooked with all the CFS/XMRV hoo-ha.
I know that one cannot really block someone who wants to commit suicide, but doing experiments on human is as far as they go:
http://treatingxmrv.blogspot.com/2011/09/reason-for-hope.html#comments
This is about the craziest thing I have ever seen.
I don't understand the jargon in that piece, Idonotremember, but, um, proof of concept is one person who stops responding to ATRs, but then adds another ATR and has some response? One person. One drug. One piece of sampling data. And it's therefore XMRV?
If my understanding here is a coarse grain model of what I'm reading, then I am, to put it mildly, dubious.
There you go, Jack:
http://www.sciencemag.org/content/suppl/2011/09/21/science.1212182.DC1/…
(registration required I think)
@Mary
Mikovits Bio
http://www.wpinstitute.org/about/about_execboard.html
Now they are going after Dr. Racaniello and his virology blog
http://treatingxmrv.blogspot.com/2011/09/ignobel-prize.html#comments
Yes-- Me, my mentor, my university and (humorously) surrounding universities have been harassed by those freaks because I have the audacity to write about XMRV.
Luckily, there is no university on the planet (well, in the US...) that has *any* interest in censoring/policing the free-speech rights of their students or faculty *shakes fist angrily at the Constitution*
Though frankly, Id rather have them harassing me (please, I grew up on 4chan) than the scientists who arent use to that kind of crap.
People really need to stop thinking that there are "psychological" and "physiological" disorders and that these are two different things that can be distinguished.
There is only the brain, and the brain only works because of physiology and physiology only happens via chemistry and physics.
The brain only works because there are control systems that maintain physiology in the state where it keeps everything working. If those control systems get screwed up, then physiology gets screwed up and the brain gets screwed up and the brain can't function the way it evolved to function.
The symptoms of the somatiform disorders are non-specific. They are like the non-specific symptoms that many disorders have; flu-like symptoms. Having flu-like symptoms doesn't mean you have the flu, what it means is that you have a constellation of symptoms that people also get when they have the flu. Those symptoms are not caused by the flu, they are caused by your body's response to the flu. Flu-like symptoms are caused by the various cytokines and other things that your body dumps into your blood stream to signal to the rest of your body that there is shit it does not want and needs to get rid of.
When people go on a cocaine binge for a week, what happens? They start to have itchy skin, get paranoid and have hallucinations and depressive symptoms. Why? Because the cocaine and cocaine withdrawal triggers many of the same stress response pathways that are triggered in other stress responses, including when you have flu-like symptoms. Opiate withdrawal is a specific cause of the non-specific flu-like symptoms.
You can induce flu-like symptoms by injecting people with things that trigger those symptoms. You can trigger flu-like symptoms by injecting people with flu vaccine. Flu vaccine doesn't cause flu because flu vaccine is dead flu virus particles. But those dead virus particles trigger the compensatory pathways that cause the body to produce the cytokines that do cause flu-like symptoms.
There are things that cause somatiform symptoms. Low nitric oxide causes somatiform symptoms. Many cytokines cause low NO, and especially in the brain because the brain is special and can't tolerate some of the other things the immune system does to get rid of shit it does not want.
Usually what triggers flu-like symptoms is some type of infection. If the infection is bacterial, there is something the body needs to do ASAP, that is crank the nitric oxide level in the body as high as it will go ASAP. Bacteria floating around in the blood stream are really bad. Bacteria attached somewhere in the vasculature as a biofilm is at least a couple of orders of magnitude worse. Bacteria in a biofilm are hundreds of times harder to kill than bacteria that are just floating around. That is why the body cranks the NO level as high as it will go, because high NO does inhibit bacteria from forming a biofilm. High NO does this not by killing the bacteria (which they would evolve to beat), but by triggering quorum sensing that makes them go planktonic or stay in a planktonic state.
This very high NO state is what is called 'sepsis' and 'septic shock'. It has a fatality rate of ~30% in previously healthy individuals. What people die from is from multiple organ failure. What happens is that the NO level is so high that mitochondria get turned off by blocking cytochrome c oxidase with NO so it can't reduce O2 to water. Mitochondria are also turned off on the front end by the high ATP level that NO regulates to happen. That high ATP level is produced by glycolysis, but glycolysis can't supply very much ATP, which is why the cytokines make you feel really tired, so you don't do anything to use up the tiny amounts of ATP that can be produced without mitochondria.
If you do stuff that uses up the ATP you are making from glycolysis, either by pushing through the fatigue, masking it with drugs, running out of glucose, or running out of muscle to turn to amino acids to make glucose (making enough glucose is why people in sepsis can lose 10 pounds of muscle in a day, they need the amino acids to make glucose to run glycolysis, the resulting lactate is turned to fat to get rid of it), then the ATP level falls. If the ATP level falls, then mitochondria turn on to keep the ATP level up. For mitochondria to turn on in a high NO environment, they have to get rid of the NO first. They do that by making superoxide. Mitochondria have an unlimited capacity to make superoxide. To try and turn on they will make superoxide until they do turn on, or until they die trying. That is what causes multiple organ failure, mitochondria trying to turn on but generating so much superoxide that they irreversibly turn off. Without mitochondria, your organs die and then you die.
However, neurons can't get ATP from glycolysis. Neurons have to use mitochondria. Mitochondria can't work in a high NO environment, so neurons need to destroy the NO before it gets inside. That is where the neuroinflammation that cytokines produce comes in. That neuroinflammation destroys the NO before it can get to the mitochondria in neurons so the mitochondria in neurons don't succumb to irreversible turnoff during sepsis.
The somatiform symptoms are all produced by inflammation in specific tissue compartments due to skewed control of the pro-inflammatory and anti-inflammatory cytokine balance. That imbalance can occur through a variety of triggers. Infection and sepsis can trigger it, physical trauma can trigger it, social stress can trigger it, exposure to certain chemicals can trigger it, certain drugs can trigger it.
The usual pro-inflammatory cytokines are the various interferons, TNF, and the other things that produce flu-like symptoms when they are administered. Chronic flu-like symptoms will produce chronic neurological symptoms like depression because the chronic flu-like symptoms include chronic neuroinflammation. Remember, the neuroinflammation is a necessary feature to protect neurons from too much NO during flu-like symptoms.
Nitric oxide is the major anti-inflammatory cytokine. It is not produced like the other cytokines, it is produced by iNOS which is induced, expressed, then generates as much NO as possible for a while and then the iNOS is degraded and the NO level falls. By that time either you have prevented the bacteria from attaching to your blood vessels and have survived or you didn't prevent that and you died.
If you survived because the bacteria were killed with antibiotics, your body can end up in a state it doesn't know how to deal with. The bacteria are gone, but it didn't get the âall clearâ signal to turn off the pro-inflammatory cytokines, so it keeps them on, just in case. The high NO from iNOS is gone, but the pro-inflammatory cytokines are not, so you have unbalanced inflammation and in the brain that causes chronic degeneration.
I'm going to have to spend some time on that comment by daedalus2u, because I have a strong suspicion that what you're saying matches up with my reckonings.
Abbie I'm sorry you get abuse from people re this stuff. I have ME/CFS, have had it for years & am so "sick" of being taken advantage of by charletons like the WPI. It's incredibly upsetting to realise how many people there are who just see people like me as an opportunity for making money. I'm grateful to you for pointing out how ridiculous they are being in a clear & concise manner.
What's worse is to realise that as daedalus2u says (if what I'm reading above is right) there is a reason behind the "CFS or ME" that so many people have been diagnosed with. That a doctor can diagnose CFS/ME & then leave it at that - not try to find out what is causing the symptoms (& I don't mean some magic retrovirus) - is cruel.
To me it seems apparent that some "CFS" sufferers have sleep apnoea. Some have uncontrolled diabetes. Some are anaemic. Some have an unrecognised disease (not unrecognisable, just unrecognised). And some even have depression. It completely sucks that it's ok for a doctor to diagnose CFS & then walk away.
So I'm sorry you get abuse 'cause honestly, someone has to point out to these "scientists" that their time would be better spent elsewhere if they are genuinely interested in helping me.
What's kind of weird though is that people think that CFSers are the mentally ill ones (& some of us most deinfitely are) and yet no-one has sectioned Judy Mikovits. Now there's a serious nutter.
Heaven preserve me from that kind of "help".
Anyway I don't have anything to say that's worthwhile reading except thanks a tonne. Thank you so very much.
I am very grateful to Dr D-J.
Grateful because I would have missed Prof Racaniello's podcast otherwise :)
Thanks for the links to that Silverman detail guys - very useful :)
I am not sure this was picked up before now - sorry if it has been - I am rather slow I am afraid ;)
'The source of the contamination is not known, but Clinic officials say it occurred outside their labs. '
http://blog.cleveland.com/metro/2011/09/cleveland_clinic_researchers_r…
Now I know it doesn't say that WPI/NCI were the source, but kind of makes you wonder what with:
'Intrigued by the RNase L link to XMRV, Mikovits and Lombardiâwho by then had joined WPI as wellâmet Silverman in October 2007 at a prostate cancer conference in Lake Tahoe, where they discussed the possible role of XMRV in CFS. Silverman was happy to collaborate and sent WPI a clone of the virus, known as VP62.'
http://www.sciencemag.org/content/333/6050/1694.full
I know. I know. All 'speculative' stuff but the sources are pretty reliable aren't they?
And on top of this we have of course the information above from Abbie that also demonstrates the extraordinary lengths that Silverman went to to ensure his samples were kept in as clean a condition as when he got them.
Judging by Racaniello's podcast and his following blog - the question also remains as to whether Science should retract the WHOLE bloody Lombardi Paper.
Oh and some darned published data from Knicker-fits would be just peachy right about now ;)
But as ever it is all those patients (well not that many) who 'tested positive for XMRV' that I feel sorry for.
Scientists should know better than to leave patients dangling. Where is the statement? The apology? The refund?
Or are all these patients now to receive a letter saying:
'Well yeah, you don't actually have XMRV but well you know how it goes, you might have something else but we just don't know what yet. Still donate to WPI and feel better.'?
What a bloody public health disaster!
OK now I am running on gas :)
I see Cohen has reconfirmed what he said in his article:
'WPI did use VP62, in contrast to claims posted here.'
Oh and also:
'XMRV is, without a doubt, dead. The viral sequence reported in Lombardi et al. is the result of a contaminant.
If other gammaretroviruses prove to have links to CFS/ME, they will not be the virus described first by Silverman as XMRV.
It's no more complicated than that, a point that John Coffin made clearly in his Ottawa debate with Judy Mikovits.
I think confusing XMRV with other possible viruses clouds the waters for everyone.'
http://news.sciencemag.org/scienceinsider/2011/09/insider-looking-out-h…
That's all folks!
Friend, you might want to check out this blog which has more discussion and links of the low NO hypothesis of CFS.
http://www.chronicfatiguetreatments.com/wordpress/treatments/chronic-fa…
This is not my normal NO blog, but I don't have much specifically on CFS except here.
OMG, again with the Nitric Oxide. Look, either publish a paper in a respected journal and show evidence of your purported NO-CFS connection or shut the hell up. A blog is not suitable replacement for reproducible data. Because what the CFS community needs right now is yet another dick giving them false hope based on some BS they've decided simply must be the correct answer without any sort of real data.
Yes poodle stomper, what the CFS community does not need are ignorant dicks trash talking research avenues they don't understand and which have not been investigated.
What the CFS community does need are plausible research avenues to be funded and investigated. Unfortunately getting such funding is easy for quacks who are willing to lie and cheat patients, it is not easy for people who are not quacks but don't have the charisma or the lack of scruples that quacks have.
I agree with you that a blog is not a replacement for data.
It looks like Deckoff-Jones (the former ER physician who put herself and her daughter on antiretrovirals based on "XMRV tests") is VERY unhappy with Dr. Racaniello, and wants the devoted readers of her blog to give him and the president of Columbia University a piece of their minds.
http://treatingxmrv.blogspot.com/2011/09/ignobel-prize.html
I cant decide if my favorite part of that post is DJ comparing herself to African Americans who lived in constant fear of lynching, or when she apologizes for that comparison, and compares herself to 6 million murdered Jews.
She is one classy, TOTALLY NOT CRAZY woman.
The CFS community likewise doesn't need someone with zero qualifications making absolute statements such a "The cause of CFS is low NO" as you have made in the past. You have no credible evidence to back up such a claim. You likewise have no qualifications to do any sort of clinical trials. Leave the science to the scientists rather than making unfounded claims.
...especially after you yourself stated:
but that's OK because...wait for it...wait for it...
Well sorry but anecdotes don't = data and a single anecdote is worth even less. At this point you sound just like the idiots selling their snake oil. Get some real data, publish it and get it reproduced, THEN make the claims.
Psst Poodle Stomper: daedalus2u has been on an NO kick for at least the past four years. He's all over SB, and whatever the topic is, he's all about the NO. I'm shocked when he posts without mentioning NO.
Yah, I know. It's just sad to me when people criticize others for unscientific behaviour and then do the same thing. =(
ERV - Looks like Prof Racaniello removed the offending T Shirt:
http://www.virology.ws/2011/09/29/admit-when-you-are-wrong/#comments
Thanks, Ed.
Haven't seen this paper yet. Well, at the beginning the Plos Path publication by Silvermann and DeRisi seems to be a solid scientific work - but in the end the number of cases XMRV+/R462Q-RR were based on PCR, so with 22Rv1 DNA and/or VP62 plasmid and/or murine DNA in the lab this is also now very questionable. That means retraction of that Nature Review will come up...?
I was under the impression that the insane methods they used to prevent contamination were used in the WPI and not by the Silverman group, because of the wording:
"In early 2009 we received PBMC DNA samples from CFS patients and healthy controls from the Whittemore Peterson Institute (WPI), Reno, Nevada. The PBMC DNA samples were taken directly to a clean room upon arrival and stored in a -20oC freezer in the same room. [...]"
Is my English too bad to understand that clearly? I thought this indicated that samples were taked from patients and controls at the WPI and then directly treated like described, without any shipping to another lab.
If this was done in the Silverman lab, I also have to be suspicious of his integrity and his not-knowledge that it was a contaminant.
Because if they thought it necessary to go to such lenghts instead of normal contamination prevention messures, they probably had some idea that there were more contamination issues in XRMV experiments than expected.
Take a look at the preceding sentence. "We received" from the WPI, means WPI sent them to another lab. Since the partial retraction covers Silverman and Das Gupta's results, it must be referring to their lab in Ohio.
Why would taking precautions against contamination issues make you suspect their integrity?
Yeah, the precautions, as worded, were taken by the Silverman group. It isn't so much indicative of being suspicious as it is wanting to make sure your data is reliable. =)
yes, but I thought the sentence meant that the Mikovits lab received the samples from another division of the WPI...
regarding the anti-contamination safety, it's a bit ambigious. Of course VP62 is everywhere in the Silverman lab, so they would have to take some preventions against such contamination. but normaly you clean your gear with 70% ethanol and use filtered tips and milliQ water and maybe work in a fume hood. You don't buy new pipets and work in a room almost suitable for immunesuppressed mice.
That they did that speaks to me that they probably had experience with XMRV-like sequences contaminating more samples than they should. If that is the case, they should have had a internal investigation to track down the source of those contaminations. This could have prevented their contaminated prostate cancer work and also, maybe, pervented to give Mikovits the idea that XRMV causes CFS.
But they didn't do the investigation, or at least they didn't report it.
This is of course just a hunch I have, and there can't be any evidence that they knew of the problem, but they should have.
@Mo #58 "and also, maybe, pervented to give Mikovits the idea that XRMV causes CFS."
There is, and never has been any reason to link XMRV (or any other retrovirus) with M.E/CFS. That the prostate work may be flawed is no basis to shift the blame from Lombardi et al for the absurdity of connecting XMRV with M.E/CFS. The whole thing was fool's errand, amounting to no more than a random fishing trip without any meaningful reference to the nature of the disease under investigation. The Science paper was published because the authors thought they'd got lucky - not because any evidence of disease process was discovered, and correlation (meaningless as it turned out) was taken as significance. Without the 70%correlation with M.E/CFS, there'd have been no story and the study would have been a mildly interesting paper in PloS1 or similar journal, the world would have moved on and somewhere down the line someone would have started asking questions about whether XMRV was a lab artifact or a genuine wild virus. No panic about infected blood supply and the redirection of the attention of public health officials, labs and resources to track down a hyped story based on a screw up.
@Mo
This might help. John Cohen addressing the VP62 'issue' and whether or not WPI had it. It seems Mikovits confirmed they did...
'You and other can keep repeating that VP62 was never in the WPI labs, but it does not change the facts, as described to me in detail by both Judy Mikovits and Robert Silverman.
I think the confusion may stem from a May 30 letter that Judy Mikovits sent to Bruce Alberts in which she writes:
"Neither 22Rv1 nor any of the cell lines reported to be contaminated with XMRV or cell lines growing the VP62 infectious molecularly cloned virus was in the laboratories where the patient cells were isolated."
(Judy Mikovits, by the way, not Science, gave me a copy of this letter.)
Note that this does not say anything about whether VP62 was at WPI, which Silverman told me he sent to WPI in March 2008.
Judy Mikovits said to me, "We had VP62 as a clone."
Whether VP62 at WPI could have contaminated patient samples is another question.
But I have told you my sources for the statement I made. Who are your sources?
Note, too, that in the partial retraction, supporting online material, it states in reference to Silverman's group at Cleveland Clinic: "In particular, neither plasmid XMRV VP62/pcDNA3.1(-) nor XMRV PCR products were ever taken into the clean room."
I also refer you to figure 3 in the original supplementary material for Lombardi et al., which adds more details about the use of VP62 for serology tests.'
http://news.sciencemag.org/scienceinsider/2011/09/insider-looking-out-h…
I think that will probably be his final words on the subject now. But them folk who persist with saying 'WPI never had VP62' need to wakey-uppy :)
Maybe he is very anal about contamination? I don't honestly know. I just know that the level of precautions taken here gives me a science-stiffy.
@ Jack,
I don't know it this was all directed to me, however, I'm not sure what you are getting at in most of your sencences. Maybe there are some quotation marks missing?
Mikovits got the idea of the XMRV -> CFS because RNAse L is expressed in prostate cancer (in which Silverman thought he had found XRMV) and in CFS patients, according to the Science editorial "False positive". But these are very, very, VERY shaky observations to base a hypothesis of an infectious agent upon.
For example, the human pancreas expresses many genes which have roles in neuro development. But this makes the structure and identity of the pancreas not in anyway related to the brain, the genes have independent roles in the funtion of the two organs. The name for the effect that genes have multiple independent roles in one organism is called 'pleiotropy', and there is much pleitropy in biology.
RNAse L could be expressed in CFS and prostate cancer for identical, similar, or independent causes.
A hypothesis for independent causes I can make up on the spot: RNAse L may be expressed in prostate cancer because cancers always have messed up gene regulation, and in CFS it may be expressed as a inducible gene to pathological stressors, which seem to exist in CFS patients on a chronic level (unspecific immuneresposne and all that).
This hypothesis is more likely than "XMRV/another gammaretrovirus did it", because independent causes are generally more likely than dependent causes, if we don't know much about the condition in the first place. Also, we know that XRMV is a contaminant now, gammaretroviruses generally don't infect humans (this was known long before) and it was convincingly shown that the WPI has no idea what it is doing.
@ Poodle Stomper:
:PPPPP
... And it makes me slightly suspicious, because I'm a lazy person and first try the easiest way to data and can manage contamination free work without doing that. Also I think minimalism is aesthetic. :-)
I'm sorry for the mistakes, i'm sure they make my post hard to read.
In reponse to El Perro (26/9/11). I have M.E. I am not depressed in the slightest. What is depressing is your ignorant attitude. It's amazing how many so-called 'intelligent' people can come up with the amazing (and very old and boring) theory that M.E. is depression.
I have met many people like you since I have been ill. At times, I wish that all I did have was depression. I would have no problem in admitting it to it and taking the treatment and getting on with my life.
El Perro, it's not that simple mate, so stop simplyfying it. Your opininon is plain wrong - I know because I have the illness and you don't know because quite simply, you don't have the illness.
Also, I'd rather be ill with M.E. than be a gigantic ignoramus like yourself. For me, there is hope that one day there will be treatment but for you and your scathing, dismissive attitude, there is clearly no hope.
Lay person here trying to understand this: "The conclusion of the Blood Working Group was that we don't have a reproducible assay to detect XMRVs in the blood -- not that they weren't in the patients at all." - Mikovitz
Is she saying that she accidently stumbled on the virus because of contamination? Thus, the blood cultures she was convinced were positives were really not, but the virus does exist? Huh?
It's actually a lot crazier. What's she saying is really this:
- Mikovits was sent the XMRV clone VP62 and some reagents by Silverman
- Using these tools, they detected a REAL retrovirus
- They later sequenced several ~300 bp parts of this REAL virus at WPI
- They sent the samples to Silverman
- He then contaminated these samples with VP62, and fully sequenced this contaminant over its ~8000 bp region
- Now, the "coincidence" is that these several 300bp WPI sequences are 99-100% identical to the corresponding region of Silverman's contaminant. What are the odds?
Of course, it makes much more sense that:
- Silverman sent VP62/reagents to WPI
- WPI contaminated their samples
- WPI later sequenced parts of this contaminant
- Silverman received contaminated samples
- He sequenced the same contaminant as WPI partially sequences, which is why they are the same sequences.