The Race to Retract Lombardi 2009...

[ukxmrv]

Sure - but given the uncertain status of the term, and understanding of what different findings represent, I don't think that I can be fairly criticised for my own shifting use of terminology.

I wasn't doing that Esther. It is fair to point out that the different terms can mean different things. Go back on the last few replies people have made to you.

 

[ukxmrv]

The sequences/viruses found by Lo/Alter, which have been described as HGRVs, could be the result of contamination.

]

Anything in any research paper could be the result of contamination. If you read "and the band plays on" you will read accounts of how Gallo claimed that the French finding of what went on to be called HIV was contamination. He did this repeatedly.

Alter has spoken about the safeguards he used against contamination. He appears very open minded and eager to get some answers. However, he has not found any contamination and his paper has not been retracted. It is rarely criticised.

If you keep thinking of the "what if's but no evidence for it", you should be able to think of equal arguments along the opposing lines as well.

 

[Andrew]

I've been trying to read this and can't remember who said what. Also, I might be confused. But here are some things that came to mind.

1. If the Singh study found something in tissue other than blood, but did not find it in blood, one possibility is the immune systems clears the blood. This process has already been demonstrated in the monkey studies.

2. The negative studies are not "wrong" because they found nothing. They were searching for XMRV, which is the rv discovered and named by Silverman and claimed by the Lombardi study to be in CFS.

3. If memory serves me, there was a follow up to alter/lo that found something wrong with one of the reagents. I wish I could remember his name now. I think he's in California, and made some snide remark about science wasting money on this.

One thing that gives me some hope: I don't think this contamination revelation will stop rv research dead in its tracks. I'm also glad this came out before Montoya ran his tests. Now he can adjust them. But it does put more pressure on anyone saying they are finding something. It better be fairly easy to replicate, or people are not going to be as willing to consider it a possibility.

 

[Esther12]

I wasn't doing that Esther. It is fair to point out that the different terms can mean different things. Go back on the last few replies people have made to you.

I was originally replying to Rusty's comment, and did not mean to imply that you were criticising me for my use of terminology:

Esther, your earlier post seemed to suggest Lo/Alter did find gammas, but too diferent to bear any relation to those found by Mikovits. When I pointed out that that may not be so, your second post then suggested that Lo did not find gammas. Which is it? Not that it matters, Singh and the other negatives were not using assays optimized to look for anything other than VP62 or very close relatives.

The only difference between my posts was the use of terminology.

re the possibility of contamination: the failure of Mikovits/Ruscetti/Lo/Alter to distinguish between samples from previously positive patients and previously negative controls, combined with the string of negative papers, combined with the realisation that the sequences from the original Science paper were contamination, all point towards the likelihood of contamination/error. Even if the two positive papers were both the result of contamination, it is quite possible that this could never be conclusively proven - with the Lipkin study there is one more chance for those who had found positives to perform their testing under independently blinded conditions - if that comes up negative too, I think that the evidence that the two positive papers were a result of error/contamination will be overwhelming.

As you say, any positive study may be the result of contamination. We all knew that when the Science paper first came out.

 

[ukxmrv]

re the possibility of contamination: the failure of Mikovits/Ruscetti/Lo/Alter to distinguish between samples from previously positive patients and previously negative controls, combined with the string of negative papers, combined with the realisation that the sequences from the original Science paper were contamination, all point towards the likelihood of contamination/error. Even if the two positive papers were both the result of contamination, it is quite possible that this could never be conclusively proven - with the Lipkin study there is one more chance for those who had found positives to perform their testing under independently blinded conditions - if that comes up negative too, I think that the evidence that the two positive papers were a result of error/contamination will be overwhelming.

It's your opinion. Not a scientific argument.

Adding up things that are negative in your estimation doesn't prove any point.

If they had added up all the failed attempts to find HIV/AIDS and stopped at some point then it could have been argued in exactly the same way.

HIV could not have been conclusively disproved as well.

The BWG was never designed to see if any lab could distinguish controls from positive patients. It was designed to see if a test could be found to work under bulk conditions - it failed and the disgrace is that we do not have a test.

These are feelings that you have and it's not proof or even an argument. It's an explanation for your own feelings. All fine and good but not proof of anything other than what influences you to think a way.

 

[Esther12]

The BWG was never designed to see if any lab could distinguish controls from positive patients. It was designed to see if a test could be found to work under bulk conditions - it failed and the disgrace is that we do not have a test.

Why do you think that?

This is what it said their aims were:

The Blood XMRV Scientific Research Working Group was formed to facilitate collaborative studies into the impact of XMRV in blood donors. Studies will evaluate XMRV detection assays in terms of sensitivity, specificity and reproducibility; assess performance on specimens represented in existing blood donor repositories, and determine the prevalence of XMRV in donors.

http://www.retrovirology.com/content/8/S1/A231/abstract

Labs were able to do whatever testing they thought would be most effective. They wanted to find out if there was reason to think that there was a detectable retrovirus circulating in the blood supplies, not just if there was quick and easy testing for it. If there was evidence of a detectable retrovirus circulating in the blood supplies, then this would be an emergency for which the development of mass testing would become a priority.

It makes no sense to assume that the BWG are uninterested in a retrovirus unless there's already a suitable process for bulk testing. They would have to be complete morons to operate in that way, and I see no reason to assume that they are.

 

[Firestormm]

Here is the full paper: Failure to Confirm XMRV/MLVs in the Blood of Patients with Chronic Fatigue Syndrome: A Multi-Laboratory Study from Simmonds Mikovits et al.View attachment science.1213841.full.pdf

 

[ukxmrv]

Why do you think that?

This is what it said their aims were:



http://www.retrovirology.com/content/8/S1/A231/abstract

Labs were able to do whatever testing they thought would be most effective. They wanted to find out if there was reason to think that there was a detectable retrovirus circulating in the blood supplies, not just if there was quick and easy testing for it. If there was evidence of a detectable retrovirus circulating in the blood supplies, then this would be an emergency for which the development of mass testing would become a priority.

It makes no sense to assume that the BWG are uninterested in a retrovirus unless there's already a suitable process for bulk testing. They would have to be complete morons to operate in that way, and I see no reason to assume that they are.

That's just your interpretation. It doesn't say anywhere in there that this was a test of a lab being able to find XMRV in a sample and that it is the same as the Science paper. You are reading more into that paragraph and adding your spin to it.

The paragraph you quoted says blood donors - not in a population or even in people with CFS. It's a very selective and exclusive quote.

Have a look at how the processing was done. If it was intended to test a particular lab (as in the Science paper) then the processing would be done from start to finish in the same way.

Have you read the paper and understand that the processing wasn't done in the same way?

You are taking a process that was out of the control of the WPI, acknowledging that they could have some control on one part and then declaring it the same - when it isn't.

When it boils down to it there is still no way of testing the blood donors for the HGRV's found in the Science paper and Alter/Lo - so the process failed.

The BWG was never a contest to see if the WPI could find HGRV's in the blood of patients as per the Science paper.

 

[Firestormm]

Sorry I meant to quote the following from the paper I attached above:

'We report here the results of a comprehensive study where multiple laboratories analyzed the same blood samples for XMRV/P-MLV. These blood samples, which were drawn from persons who were previously reported to be XMRV- (2) [Lombardi et al 2009] or P-MLV-positive (4) [Lo et al. 2010] and from blood donors who previously tested negative for XMRV, were aliquoted into replicate tubes and assembled into coded panels together with replicates of experimentally prepared positive control samples.

The testing was performed fully blinded to remove bias. These samples were tested by nine laboratories using highly sensitive and previously validated nucleic acid, serological and culture assays (tables S1 to S5) for XMRV and other MLVs (16).

The two laboratories that had previously found an association for the MLVs with CFS participated in this study (2, 4). All nine laboratories used XMRV/P-MLV nucleic acid amplification testing (NAT), serological and/or culture assays of their own choosing which were incorporated into parallel or serial testing algorithms to generate final results. The majority of laboratories included assays to detect murine DNA contamination either on all samples or on all NAT positive samples...'

'A total of eleven NAT, five serology and three culture assays were performed on the samples (17). The WPI laboratory did not report culture assay results because their
target cells had become contaminated with mycoplasma. Other than this, all sites reported results on all distributed and coded sample aliquots to the central laboratory. The results were then decoded and compiled into analysis datasets specific to the panels.'

'Altogether, 15 XMRV/P-MLV cohort subjects were represented in this study, the maximum number of subjects who could be recruited by the cohort investigators (2, 4) [Lombardi et al. and Lo et al.].'

Anyway, the full paper isn't to difficult to read or too long for that matter. Bottom line is that all samples came from WPI and Lo et al. and they provided the best that they could find and in the best (and only) quantity they could find i.e. 15 patients (which raises more issues personally). All methods were run as best they could. And they still couldn't find anything - despite these patients being positive previously.

One can't even argue with the results really. All authors signed off on the conclusion. They couldn't find XMRV/MLVs despite the best attempts of ALL the labs. OK you could say that the contamination problem at WPI was an issue - mycoplasma - but that's a stretch as is the 'revelation' that a couple of patients were on medication. I repeat - the WPI and Lo provided the positive patients. Did they sabotage the results? [Joke].

Not a single author has raised any question about the validity of this research. I mean there is that Webinair thing on Friday - you could ask a question.

 

[Esther12]

That's just your interpretation. It doesn't say anywhere in there that this was a test of a lab being able to find XMRV in a sample and that it is the same as the Science paper. You are reading more into that paragraph and adding your spin to it.

The paragraph you quoted says blood donors - not in a population or even in people with CFS. It's a very selective and exclusive quote.

I provided the link for you to check the context. Right the quote I provided says blood donors.

Studies will evaluate XMRV detection assays in terms of sensitivity, specificity and reproducibility; assess performance on specimens represented in existing blood donor repositories, and determine the prevalence of XMRV in donors.

So they were evaluating XMRV detection assays in terms of sensitivity, specificity and reproducibility - they did that by taking samples from those who had previously tested positive, samples from those who had previously tested negative, blinding the samples and sending them to be tested by the different labs. They were doing this is order to be able to check the safety of blood supplies, and the prevalence of XMRV in donors. They found that none of the tests were reproducible, and that rendered questions of sensitivity and specificity somewhat moot.

I don't understand why you think this:

The BWG was never designed to see if any lab could distinguish controls from positive patients. It was designed to see if a test could be found to work under bulk conditions - it failed and the disgrace is that we do not have a test.

I've not seen anything from the BWG which would support this.

This is from the conclusion of the BWG paper, with Mikovit's name on it, endorsing its contents.

In summary, our study demonstrates that no XMRV/PMLV
assay in any of the nine participating laboratories could
reproducibly detect XMRV/P-MLV in fifteen subjects
(fourteen with CFS) who had previously been reported as
XMRV/P-MLV-infected usually at multiple time points and
Downloaded from www.sciencemag.org on September 28, 2011
/ www.sciencexpress.org / 22 September 2011 / Page 4 / 10.1126/science.1213841
often by multiple assays (2, 4). The two laboratories (WPI
and NCI/Ruscetti labs) that reported positive results in this
study reported similar rates of reactivity among XMRV/PMLV
subjects and known negative control donor samples.
The results from both laboratories were inconsistent when
their assays were performed in parallel on replicate sample
aliquots derived from individual subject specimens. There
was also no agreement of reactivity when comparing results
between these two laboratories for the 30 blinded XMRV/PMLV
cohorts and control samples. In contrast, assays
developed by FDA (Lo and Hewlett), CDC, NCI/DRP,
Abbott Diagnostics, Abbott Molecular and Gen-Probe, all of
which have been designed to detect XMRV and relevant
MLVs with high sensitivity and specificity, failed to detect
evidence of viral infection in any of the previously positive
subjects, including CFS patients, or negative control
specimens represented in the study.

Have a look at how the processing was done. If it was intended to test a particular lab (as in the Science paper) then the processing would be done from start to finish in the same way.

Have you read the paper and understand that the processing wasn't done in the same way?

You are taking a process that was out of the control of the WPI, acknowledging that they could have some control on one part and then declaring it the same - when it isn't.

When it boils down to it there is still no way of testing the blood donors for the HGRV's found in the Science paper and Alter/Lo - so the process failed.

The BWG was never a contest to see if the WPI could find HGRV's in the blood of patients as per the Science paper.

The BWG was designed to test the sensitivity, specificity and reproducibility of the available assays for XMRV from the most prominent labs responsible for them. We have no specific reason to think that the processing of samples would have prevented detection, and no reason to believe that Mikovits had requested a different approach was taken during the planning stage. The BWG wanted to create the conditions for the most accurate testing possible, and tinkered with collection procedures during the last phase of testing to try to do this.

If it turns out that XMRV/HGRV is circulating in the blood supply, and Mikovits had a successful test for it but the BWG somehow stopped from working, then heads will roll. Everyone involved would have been working very hard to avoid that outcome, and I've not seen any good reason to think that they failed. I don't understand why you think that this was only about testing under bulk conditions - I've not seen any reason to believe this is true.

 

[Firestormm]

O dear did we cross-post Esther? Sorry about that

 

[Esther12]

Not a single author has raised any question about the validity of this research. I mean there is that Webinair thing on Friday - you could ask a question.

Your post has turned much of my own in to an echo. Curses - I was typing that for ages. I'm off to veg out.

 

[Esther12]

O dear did we cross-post Esther? Sorry about that

Twice now. Ridiculous.

 

[dannybex]

The slide being so viciously attacked demonstrates that the viruses are normally in a latent state which is maintained by methylation of the provirus. If one removes the methyl groups as shown by the experiment in the slide and the virus becomes active.

Doesn't this suggest (if these retroviruses play a role) that Rich Van Konynenburg is on track with his partial methylation cycle block hypothesis?

d.

 

[ukxmrv]

There's nothing there to support your assumptions Esther, where is it?

The BWG does not say that this was a test to see if XMRV/HGRV's could be found using the same conditions as the original papers.

When you say "I can see nothing" what I hear is "I cannot prove my assumptions".

If the BWG merely wanted to replicate the Science paper or the Alter/Lo paper then they would have provided the same conditions right from the choice of blood tubes and control of all the process in the labs.

They didn't do this. This is no test.

Have a look at history and how the blood banks in the 80's refused to listen to the doctors over the HIV virus. They were pretty vicious then.

I'm not saying that there is any conspiracy here. It may be that the conditions were never going to work. I'd like to see a proper post-mortem by all the parties explaining exactly what went wrong. I have no idea why it didn't work. Dr Mikovits spoke briefly at the IiMe conference about her concerns on their blood tubes and contents. She said that they were asked to develop tests under those conditions and that it was not the blood tubes/contents they would have used.

The end result is that we don't have a test for HGRV's in the blood supply (bad) but at the same time to claim that the results have any bearing on Lombardi et al and Alter/Lo is just a feeling and a theory. Also to claim that it was designed to have a bearing on these papers isn't supported by your postings from the papers.

 

[currer]

I always understood the BWG was to test rapid throughput tests specifically for bloodbank use.

I dont think it was concentrating on the kind of analysis required for research on a novel retrovirus.

I do not think we can draw any firm conclusions as to why the results were so inconsistent and we should be wary of making assumptions based on the information available at the moment.

 

[RustyJ]

Doesn't this suggest (if these retroviruses play a role) that Rich Van Konynenburg is on track with his partial methylation cycle block hypothesis?

d.

This was on my mind also, Danny. I was too scared to display my ignorance to ask. Maybe different meanings of the word methylation (and I do not fully understand even RK's meaning), but if someone has a clue about this I would love to know?

 

[citybug]

I think the best thing is for everyone to read all the papers themselves. Even though I am not a scientist I could read in their study and video presentation that Lo created new primers to use for his nested PCR. This was the first study that did anything original and they found similar percentages in patients and controls to the other studies. The small study in Spain also found that, and also the study of respiratory infections in Germany in transplant patients.

At all the conferences including the first intl xmrv conference Mikovits and Ruscetti have been saying Not PCR, Not PCR! use culture. Their second published paper (I meant the Addendum in Virulence Sept/Oct 2010 has same name as Science paper http://www.landesbioscience.com/journals/virulence/article/12486/ ) said culture was most reliable then serology. In the lab and studies they used several methods, and repeat blood draws to get all the positives. So mycoplasm ruining their cultures is a major problem with the BWG study. BWG and Lipkin comparison to me aren't research studies at all in terms of spending any money on researching ME/CFS. They are contests for who has the most commercial test so far, can the CDC get back in the game?, when we already know nobody has published anything about an efficient test. Hopefully Lipkin's study of tissues will find more but it doesn't start for a while.

Retracting the Silverman slide is great, because all the researchers were latching onto that single round PCR that Mikovits and Ruscetti said did not work for the average patient. At the time they thought it was only the sickest of the sick. The only papers besides Alter and Lo that seemed to try to find something were Singh and Levy. I hope Singh is finishing the random autopsy study she mentioned on twiv using her expertise with tissue and wish she would look at patient tissues.

The main thing is to find out if we have retroviruses. Anyone doing research could have asked WPI about the methods for the slide in question. It's probably printed somewhere. Dr. Mikovits usually confirms what Gerwyn says about science. V99 was wrong about whether the slide was different but anyone could make up their own mind about that. I think there was previous mention of changing the patient ID numbers, maybe in the early prohealth video presentation (which was half transcribed). About believing all the scientists who know all about PCR, I wonder if they read all the papers involved and MLV literature themselves? Most of the studies try one method which they find does not work. They don't try looking another way.

One of the biggest criticisms from the beginning by the science community is that WPI offered the test. From the patients point of view, we wanted it, even if it was experimental, and we knew there were many delays in Lombardi's lab figuring it out, and they dropped PCR very early. Scientists should appreciate that she has been against it from the start. I hope the Lombardi and Mikovits papers are in the library here for patients.

 

[gu3vara]

This was on my mind also, Danny. I was too scared to display my ignorance to ask. Maybe different meanings of the word methylation (and I do not fully understand even RK's meaning), but if someone has a clue about this I would love to know?

Anybody asked Rich about it? think he would be interested to look at it.

 

[justinreilly]

Why anyone would listen to people who were claiming the slides were not the same, despite now having this confirmed by Drs Mikovits and Ruscetti, is totally beyond me.

"Credibility" is not easily won in science. That's why it's not a good idea to listen to non-scientists who have clearly been shown to be talking utter nonsense about the work of actual professional scientists.

There are few skills more valuable than being able to spot an apparently convincing BS artist. Unfortunately, the ME/CFS arena has quite a few of them.

As regards this thread : if what little remains of Lombardi et al is retracted, it will be for 100% scientific reasons.

No conspiracies. No politics. Just data.

I agree that I have seen some comments by pwME on the science blogs comments that are not carefully worded enough. People then point out these mistakes and it makes our advocacy look that much less credible. I ask people who post to look over what they read to see if there's anything in there that's suseptible to a (semi-valid or valid) attack.

KFG, it certainly seems to me that many of the scientists involved in this debate are somewhat biased and overreach in their press releases. I don't think that's a conspiracy, but it is caused or aggravated by the conspiracy and fraud that Wessely, CDC, NIH etc have been doing forever in ME research.

Why don't they just change the title to "[preliminary] evidence of HGRV infection in pwME" or whatever title the data support. I agree that without sequencing of the HGRVs the paper doesn't tell us as much, but it still contains valuable, scientifically valid information. Why retract it then? It seems there is only calls for paper retraction when there is fraud. So why retract Lombardi when there are no calls to retract all hundreds of fraudulent papers and book chapters on ME by Wessely et al.? There is certainly bias against bona fide ME research and this is an example of it.