The Race to Retract Lombardi 2009...

[currer]

The following article is an excellent analysis of how intimidation and misrepresentation in scientific disputes can be used by supporters of the dominant theory to undermine a challenger.

Because these techniques themselves violate expectation of the norms of scientific debate, various subterfuges are employed to conceal bias

A fascinating read and very relevant to this debate.

http://www.bmartin.cc/pubs/10sac.html

 

[jace]

Hi Esther,

jace - I don't mean to come across as condemning of you for posting what you believe to be valuable information, but I really don't understand how you can say that Gerwyn's statements have always held up so far. What about the claims that were being put forth about the identical images Mikovits used to illustrate different results?

I can say it, because it is true for me. I have not seen Gerwyn post that the images were identical. If you can provide me with a link that proves otherwise, then I will acknowledge that in this case he was wrong.

 

[Sam Carter]

With Silvermans retraction of his sequences from the Lombardi 2009 Science paper, the people running the 0/0 studies have huge problems.

I think it would be news to Bob Silverman to hear that he had retracted his *sequences*. Also, I would suggest that it is somewhat disingenuous to argue that the people running the 0/0 studies are the ones with huge problems.

The VP-62 sequence is now known not to correspond to the gammaretroviruses detected by Lombardi et al. It is also known that Silverman's primers are capable of detecting the VP-62 plasmid and NOT capable of detecting the gammaretroviruses which exist in the Lombardi CFS patients.

The gammaretroviruses detected by Lombardi et al -- the ones that are *definitely not* XMRV/VP62 -- have they been sequenced? Has the sequence data been added to GenBank? Without these data is it possible to say with such confidence that Lombardi's HGRVs are not XMRV? Of the two gag sequences detected by the WPI in the BWG, one differed from VP62 by two bases whilst the other was identical.

The WPI and NCI tried to use Silverman's primers on the patients who tested positive for their nested PCRs, but could detect nothing. A great number of the 0/0 studies used Silverman's primers alone or in combination and thus their negative findings are invalid.

I listed in a previous post[*] some of the research groups who have looked for related murine retroviruses in their patient cohorts (ie. they have not confined their search to XMRV/VP62) and still found nothing. Are their negative findings also vitiated?

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.

No one is attacking the slide -- the slide is safe! People are asking questions about the *labels* -- the multiple labels -- accompanying the slide. It may be true that 5-azacytidine enables the detection of an otherwise occult retrovirus, but the experiment illustrated by the slide (whichever version of the labels you choose) does not show this.

So what, says a chorus of voices - well, the virus or viruses are integrated into G-C rich areas called CpG islands. These are extremely difficult if not impossible to amplify using standard PCR approaches.

Dr Mikovits, Dr Lo and Dr Hanson have all been able to detect XMRV/murine-related-viral-sequences using standard PCR.

Any PCR which has been adjusted to detect the VP-62 clone in a spiked sample would not have a prayer of detecting a human MLV related gammaretrovirus integrated into such a region even if the virus did have the same sequence as VP-62 which it or they do not.

Thus the combination of Silvermans retraction and the discovery that demethylation can activate the virus or viruses in question completely invalidates ALL the negative 0/0 studies

It's possible that all the 0/0 studies are invalid but the chain of reasoning presented above does not make it so.

Stoye, Coffin and ERV and their ilk must get Lombardi retracted at all costs before the scientific community as a whole realize that.

Their ilk being: Knox K, Carrigan D, Simmons G, Teque F, Zhou Y, Hackett J Jr, Qiu X, Luk KC, Schochetman G, Knox A, Kogelnik AM, Levy JA., Shin CH, Bateman L, Schlaberg R, Bunker AM, Leonard CJ, Hughen RW, Light AR, Light KC, Singh IR.,Lintas C, Guidi F, Manzi B, Mancini A, Curatolo P, Persico AM.

If new data emerge, say from the Lipkin study, to support an association between HGRVs and ME I will not find it at all difficult to adjust my sceptical position. I would hope the OP(s) will also be able to review their beliefs such that they are in accordance with the world as it is and not the world as they wish it to be.


[*] forums.phoenixrising.me/showthread.php?13830-The-real-story-about-XMRV-coming-out-today&p=211078&viewfull=1#post211078

 

[Angela Kennedy]

The quote I supplied was not written by Abbie Smith. There has been independent support on different websites that what Gerwyn has stated is erroneous.

Ah- I see. It wasn't Abbie Smith. Ok. It was because you were responding to Firestormm's comment that it looked to me as if you were quoting Abbie Smith.

Nevertheless, 'independent support on different websites', while sounding authorititive, cannot constitute adequate empirical evidence either. I'm wagering these are 'aggy anons' from blogs and Bad Science type forums, and that is an educated guess on my part, sadly, as this is the usual phenomenon. My comments about the prejudicial value judgements and how that renders them unreliable witnesses still stands.

 

[Angela Kennedy]

Sorry, Angela, but your misrepresentation of what I was saying is so total that I am unable to respond.

This is why I post so rarely - I simply don't have the energy to respond to this kind of twisting of my words.

It's fascinating how the journal "Science" was bandied about in 2009 as some worthy purveyor of scientific truth - when it was suggesting CFS might be associated with a retrovirus. Now that same journal is guilty of all manner of conspiracy and underhand dealings ( if you listen to the BS artists ) because it's done what most retrovirologists have done : decided the XMRV story, in light of subsequent data, doesn't stack up. That's science in action for you....

P.S. There are indeed a lot of "non-scientific" factors at play in science, as Esther12 suggested. "Plastic Fantastic" by Eugenie Reich - documenting one of the biggest scientific frauds of all time - shows how commercial and academic pressures can combine with good intentions, good people, and some dodgy characters to produce a huge scientific mess. ( That's not a plug, BTW )

KFG, I didn't bandy the Science article around at all. Many people were careful, like me. I think you tend to make some very prejudicial descriptions of this community, so that they are unfairly constructed as 'anti-science', and that worries me. I was merely showing you where your logic was leading.

 

[jace]

Hi Sam,

I think it would be news to Bob Silverman to hear that he had retracted his *sequences*. Also, I would suggest that it is somewhat disingenuous to argue that the people running the 0/0 studies are the ones with huge problems.

Silverman has retracted 3 strains, the VP62 plasmid contamination. It transpires that VP62 does not exist in nature. The sample portions retained by the WPI and NCI have subsequently been tested, and proved not to contain the VP62 clone. The WPI and the NCI had, up until BWGIII, not had VP62 or the 22rv1 cell line in their labs. Silverman's prostate cancer sequences still stand. No one else has looked for HGRVs. They used VP62 or had not validated their assays.

The gammaretroviruses detected by Lombardi et al -- the ones that are *definitely not* XMRV/VP62 -- have they been sequenced? Has the sequence data been added to GenBank? Without these data is it possible to say with such confidence that Lombardi's HGRVs are not XMRV? Of the two gag sequences detected by the WPI in the BWG, one differed from VP62 by two bases whilst the other was identical

The WPI and NCI have sequences in the genbank, including new ones. So does Lo et al. For Lo and the WPI, it's been a damned if you do and damned if you don't situation. Sequences have been criticised for being too close, and therefore 'contamination' and conversely for being too different, even though sequence homology is greater than that found in the various strains of HIV.

I listed in a previous post some of the research groups who have looked for related murine retroviruses in their patient cohorts (ie. they have not confined their search to XMRV/VP62) and still found nothing. Are their negative findings also vitiated?

I hope you don't mind, instead of the asterisk to a footnote with the link, I've made the words "previous post" into a live link.

You are referring to Knox et al, Shin et al (the Singh paper), Erlwein et al (McClure)(2011), Lintas 2011 (Autism autopsy), O for goodness' sake Satterfield et al, O no not the first Erlwein (McClure) paper, and that's it. Well, Satterfield and Erlwein 2010 have both been exposed for the shoddy work they were. The McClure study was completed in weeks, and peer reviewed in days. I attach a critique of Erlwein 2011, Satterfield et al, and Annette Whittemore's response to the Science expression of concern.

No one is attacking the slide -- the slide is safe! People are asking questions about the *labels* -- the multiple labels -- accompanying the slide. It may be true that 5-azacytidine enables the detection of an otherwise occult retrovirus, but the experiment illustrated by the slide (whichever version of the labels you choose) does not show this.

Labelling to protect patient identities is routine. This is what occurred in the Science paper. The non-reporting of AZA is not germane to the paper, which was edited down some 40% in the peer review process. John Coffin was one of the peer reviewers and he had access to all date from Lombardi et al. He was also in the audience at CFSAC in October 2009 when the use of AZA on those two patient samples were discused. Frank Ruscetti mistakenly introduced the wrong slide into his PowerPoint presentation in Ottawa at the IAME/CFS meeting recently.

Dr Mikovits, Dr Lo and Dr Hanson have all been able to detect XMRV/murine-related-viral-sequences using standard PCR.

Oh boy. Standard PCR? Really? I think not. Annealing temperatures, buffers, so many details need adjusting. I attach yet another pdf explaining more.

Silverman retracted his PCR and his sequencing, which das Gupta admits was done in error, hence any negative study looking for gammaretroviruses in ME populations are now completely invalid. All optimised their PCRs to detect the VP62 clone in spiked samples using high stringency conditions and thus were only capable of detecting the VP62 sequences. Hence all the 0/0 studies must be retracted.

 

[RustyJ]

Hi Sam,

Silverman retracted his PCR and his sequencing, which das Gupta admits was done in error, hence any negative study looking for gammaretroviruses in ME populations are now completely invalid. All optimised their PCRs to detect the VP62 clone in spiked samples using high stringency conditions and thus were only capable of detecting the VP62 sequences. Hence all the 0/0 studies must be retracted.

You are right Jace. After Silverman's outing, I can't understand why the negative studies are still being referred to as supportive of the anti HGRV case. What most of them looked for is a contaminant, a lab artifact, using assays optimized to VP62.

Far from closing down the XMRV, the negative studes, post Silverman, only closed themselves down. Hopefully, sooner or later the science will catch up, if there's any integrity left.

At the moment it is pretty much Lo and Mikovits (plus Hansen, unpublished?) for HGRVs, none against. The case for HGRVs in ME is actually stronger now.

 

[Esther12]

I can say it, because it is true for me. I have not seen Gerwyn post that the images were identical. If you can provide me with a link that proves otherwise, then I will acknowledge that in this case he was wrong.

From what I saw, V99 was posting on behalf of Gerwyn, and started by claiming that the images were not the same. Then it was claimed ERV had manipulated the images to make them look the same. Then is was claimed that results to different tests with the same results should have all of the same artefacts, and be visually identical. This was in the ME/CFS thread about 'ERV is quitting virology' thread. All the stories were absurd to anyone who had even a passing knowledge of the relevant science. It was a transparent fumbling around, and looking for excuses to explain away an inconvenient fact.

I do not understand many of Gerwyn's arguments, and it's easy to assume that is because I am lacking in sufficient knowledge to do so (or just that the grammar is often rather poor) - but when arguments that I do understand are made, they're pretty consistently poor. Gerwyn is either a maverick genius, whose understanding of virolgy/spot-the-difference/PCR is so vastly superior to the rest of humanity that it looks to other scientists as if Gerwyn is just confused and wrong.... or Gerwyn is just confused and wrong.

 

[Esther12]

You are right Jace. After Silverman's outing, I can't understand why the negative studies are still being referred to as supportive of the anti HGRV case. What most of them looked for is a contaminant, a lab artifact, using assays optimized to VP62.

Far from closing down the XMRV, the negative studes, post Silverman, only closed themselves down. Hopefully, sooner or later the science will catch up, if there's any integrity left.

At the moment it is pretty much Lo and Mikovits (plus Hansen, unpublished?) for HGRVs, none against. The case for HGRVs in ME is actually stronger now.

Lo/Alter were looking for XMRV, and managed to find quite different viruses. The WPI sequences loaded up to genbank are not so radically different from VP62 that other scientists have decided it would be impossible to find them using a test for VP62, but so similar that most think it adds weight to the claim that this is a contaminant, rather than a naturally occurring virus.

If there is now new evidence of an association between CFS and a virus which could not be detected by tests designed for XMRV, then a paper on this needs to be published, because the evidence for this is not in the Science paper.

 

[Firestormm]

I think you will also find that those sequences uploaded by WPI to Genbank were authored by Lombardi himself and not Mikovits. IF there is anything to her latest theories then it would be interesting to not only see a published paper but also to see these sequences.

 

[RustyJ]

Lo/Alter were looking for XMRV, and managed to find quite different viruses. The WPI sequences loaded up to genbank are not so radically different from VP62 that other scientists have decided it would be impossible to find them using a test for VP62, but so similar that most think it adds weight to the claim that this is a contaminant, rather than a naturally occurring virus.

If there is now new evidence of an association between CFS and a virus which could not be detected by tests designed for XMRV, then a paper on this needs to be published, because the evidence for this is not in the Science paper.

Even if this was a valid argument, which it is not (as far as I know only partial sequences have been loaded up by WPI), then why has not anyone tried to replicate Lo's findings?
Lo still found gammas in ME patients, so they are still there. Noone has attempted to negate Lo's findings. I know why the book is being closed on XMRV, but why is it being closed on HGRVs.

No matter which way you look at it, there is still a retrovirus (s) very much like that identified by Mikovits being found in patients, much less than in controls which suggests association at the very least.

 

[Firestormm]

Morning Rusty,

You see this is where I don't understand. You said 'there is still a retrovirus (s) very much like that identified by Mikovits being found in patients, much less than in controls which suggests association at the very least'.

The sequences from Lo et al (and I am pretty fogged up this morning) were criticised if I recall. Something about the collection dates being so far apart and the sequences being the same i.e. they hadn't changed?

I was reading about this only recently and I will try to find it again and repost if you like or post a link.

N.B. My point about Lombardi being the one sequencing the WPI strains was to suggest - just to throw it in the mix - that along with all the debate about whether or not those tests that were sold to patients are worth the paper the results were printed on - and with Lombardi now in Mikovits' former position - well will he become the scapegoat for those who think the former director did no wrong? Just a thought as we perhaps head towards a full retraction.

 

[Esther12]

Even if this was a valid argument, which it is not (as far as I know only partial sequences have been loaded up by WPI), then why has not anyone tried to replicate Lo's findings?
Lo still found gammas in ME patients, so they are still there. Noone has attempted to negate Lo's findings. I know why the book is being closed on XMRV, but why is it being closed on HGRVs.

No matter which way you look at it, there is still a retrovirus (s) very much like that identified by Mikovits being found in patients, much less than in controls which suggests association at the very least.

All of the negative studies since Lo/Alter have also been looking for these sequences. And Lo/Alter found them by looking for XMRV, with authors of earlier negative studies saying that they should have been able to find those sequences were they there.

Singh didn't just forget about the Lo/Alter paper when she was doing her study!

We've have two papers which have found positive results in CFS patients, but for what could be two different types of contamination. We've also had a lot of negative studies, one of which was finding more positives in controls than patients because contamination is such a difficult problem to address.

We've also now had the BWG, with Mikovits, Ruscetti and Lo/Alter being unable to distinguish between samples from patients who previously tested positive and healthy controls who previously tested negative when under blinded conditions.

No matter which way you look at it, it's not looking good for the claim that Mikovits has a blood test which is able to score substantially more positive results for samples from CFS patients than healthy controls when under properly blinded conditions. That part of her paper has now been retracted does not strengthen her case, or invalidate all of the negative papers which we have so far seen.

 

[RustyJ]

Morning Rusty,

You see this is where I don't understand. You said 'there is still a retrovirus (s) very much like that identified by Mikovits being found in patients, much less than in controls which suggests association at the very least'.

The sequences from Lo et al (and I am pretty fogged up this morning) were criticised if I recall. Something about the collection dates being so far apart and the sequences being the same i.e. they hadn't changed?

I was reading about this only recently and I will try to find it again and repost if you like or post a link.

N.B. My point about Lombardi being the one sequencing the WPI strains was to suggest - just to throw it in the mix - that along with all the debate about whether or not those tests that were sold to patients are worth the paper the results were printed on - and with Lombardi now in Mikovits' former position - well will he become the scapegoat for those who think the former director did no wrong? Just a thought as we perhaps head towards a full retraction.

Hi Firestormm. I have not seen anything to negate Lo's findings, but would be interested to see information to the contrary.

Re the testing. I don't know whether there are false postives or false negatives in VIPdx assays. The BWG did not determine that. Not even sure which assays Mikovits was upset about - the ones used by VIpdx in the BWG or the ones being used for normal testing. Also it does not have to be that a decision by WPI not to offer HGRV testing has anything to do with their validity. There does seem that the WPI has made a corporate decision to shift away from HGRVs altogether, irrespective of whether they exist or not, at least in the short term. This may have to do with ownership of patents, or it may be due to external pressure.

Furthermore, the issue of validation of assays used in commercial agencies on behalf of the WPI have little to do with the Lombadi Science paper as such. As I see it, commercial assays are very much reliant on turnaround times and cost expedients and are not the same as lab testing. Without any inside information, I suggest that Mikovits has grounds to not to be very happy with the commercial decisions made by WPI, irrespective of whether the hand was Lombardi or Whittemore. It also seems to me that Mikovits has acted with integrity by choosing not to go along wih those commercial decisions (if these are indeed the reasons for her leaving).

 

[Firestormm]

Since Silverman (but also BWG) the focus shifted to the commercial and laboratory research testing ability at WPI and their wholly-owned VIPdx. For a long time the WPI and Mikovits were saying that the same methods used in Lombardi were also used in the commercial testing.

Since the issue of her being fired - this has become more acute with Mikovits saying she was concerned that the testing done by VIPdx was not the same as that done in her laboratory, and perhaps not even the same as that done in Lombardi et al.

Trouble is.... nobody suggested any of this prior to Silverman's retraction and the BWG results. And we have yet to hear anything from Annette or Lombardi about what it was they were doing at VIPdx and/or whether people who paid their money now have a case for compensation.

Of course partly this stems - once again - from the fact that the only one doing any talking is Mikovits (well initially via Deckoff-Jones I suppose). However, from the facebook comments on the WPI site and elsewhere there seems to be a lot of concern about those tests - not that this wasn't voiced by others outside of the company of course many times.

NB I will look up that stuff on the Alter Lo sequencing. Give me a wee while.

 

[Esther12]

Also - it's Mikovits's name on the BWG paper, not Lombardi's.

I don't know why some people seem to be acting like the poor BWG results had nothing to do with Mikovits's testing techniques. Apparently Lo/Alter had been using the techniques explained by Mikovits, and Ruscetti had worked closely with her too - none of them had anything like consistent results.

 

[RustyJ]

Lo/Alter were looking for XMRV, and managed to find quite different viruses. The WPI sequences loaded up to genbank are not so radically different from VP62 that other scientists have decided it would be impossible to find them using a test for VP62, but so similar that most think it adds weight to the claim that this is a contaminant, rather than a naturally occurring virus.

If there is now new evidence of an association between CFS and a virus which could not be detected by tests designed for XMRV, then a paper on this needs to be published, because the evidence for this is not in the Science paper.

All of the negative studies since Lo/Alter have also been looking for these sequences. And Lo/Alter found them by looking for XMRV, with authors of earlier negative studies saying that they should have been able to find those sequences were they there.

Singh didn't just forget about the Lo/Alter paper when she was doing her study!

We've have two papers which have found positive results in CFS patients, but for what could be two different types of contamination. We've also had a lot of negative studies, one of which was finding more positives in controls than patients because contamination is such a difficult problem to address.

We've also now had the BWG, with Mikovits, Ruscetti and Lo/Alter being unable to distinguish between samples from patients who previously tested positive and healthy controls who previously tested negative when under blinded conditions.

No matter which way you look at it, it's not looking good for the claim that Mikovits has a blood test which is able to score substantially more positive results for samples from CFS patients than healthy controls when under properly blinded conditions. That part of her paper has now been retracted does not strengthen her case, or invalidate all of the negative papers which we have so far seen.

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.

 

[Esther12]

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.

'Human Gamma Retro Viruses' is a new term which has not been widely accepted within the scientific community. I'm not sure if there's been a single published paper on them. I don't know when, if ever, the term should be used.

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

At an earlier conference Coffin said we should not yet talk viruses yet, but only of sequences. I'm not too sure as to what terminology is best, and tend to try to adopt that which is being used by whomever I am talking to - either way, it is possible that the Lo/Alter findings were the result of contamination.

re Singh not looking specifically for the sequences found by Lo/Alter:

After not finding XMRV using qPCR, serological, and viral culture assays, the authors used the nested PCR assay described by Lo et al. Although positives were observed, they were not consistent between different assays. This led the authors to look for contamination in their PCR reagents. After examination of each component, they found that two different versions of Taq polymerase, the enzyme used in PCR assays, contained trace amounts of mouse DNA.

Given the care with which these numerous assays were developed and conducted, it is possible to conclude with great certainty that the patient samples examined in this study do not contain XMRV DNA or antibodies to the virus. Its not clear why the 14 patients resampled from the original Lombardi et al. study were negative for XMRV in this new study. The authors suggest one possibility: presence of trace amounts of mouse DNA in the Taq polymerase enzymes used in these previous studies. I believe that it is important to determine the source of XMRV in samples that have been previously tested positive for viral nucleic acid or antibodies. Without this information, questions about the involvement of XMRV in CFS will continue to linger in the minds of many non-scientists.

http://www.virology.ws/2011/05/04/ila-singh-finds-no-xmrv-in-patients-with-chronic-fatigue-syndrome/

 

[ukxmrv]

'Human Gamma Retro Viruses' is a new term which has not been widely accepted within the scientific community. I'm not sure if there's been a single published paper on them. I don't know when, if ever, the term should be used.

They do have to start somewhere with a name. Look at HIV, called LAV, HTLV and so on.

Other scientists publish papers with tentative names and papers with names not used before and before agreement.

Dr Mikovits is just doing what others before have done.

 

[Esther12]

They do have to start somewhere with a name. Look at HIV, called LAV, HTLV and so on.

Other scientists publish papers with tentative names and papers with names not used before and before agreement.

Dr Mikovits is just doing what others before have done.

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.