XMRV testing PART 2: Blood doesn't come cheap (the butchers bill)

[jace]

This is the next part of the story that was started on this thread.
Copied from http://me-advocacy.com/Blood_does_not_come_cheap.html

Why did the BWG not publish the REDLABS testing for the BWG and were the XMRV tests sold to patients clinically validated? What evidence do we have? And, what did Mikovits and Max find and why was she fired?

In Part one I presented information about the clinical validation and licensing of the XMRV tests sold by REDLABS to patients (1). Part two begins with Phase III of the Blood working group (BWG), publication on those results on the 22nd of September 2011, returns to the tests sold by REDLABS and finally ends with the firing of Dr Judy Mikovits on the 29th September 2011.

Part two of my presentation is quite long, but I would urge everyone to read it.

[Note: REDLABS is not R.E.D. Laboratories in Belgium. The Belgium lab is not related to this presentation]

​

PART 2: Blood doesn't come cheap (the butchers bill)

The results of the BWG were on the surface, a mess (2). Too few people had been tested and the results were scattered amongst patients, controls and labs. Dr Ruscetti openly said he disagreed with the interpretation of the results (3) and in contrast others have continued to find the ME retroviruses (4,5,6). Later a closer inspection of the BWG paper had revealed a catalogue of flaws that rendered the results void. These were the main issues.

• All the assays in the Blood working group used VP62 to optimise their assays, but this strain has never been detected in a human by any lab so it should not have been used.
• Controls had not been pre-screened by all labs using all methods.
• Only the three lab technician control samples were screened with all methods prior to blinding.
• None of the 12 control peripheral blood mononuclear cells (PBMCs) were screened prior to blinding. This is the most sensitive assay, so none of the controls have been recorded as negative before blinding.
• No preservative or Trizol was used for storage of the PBMCs during processing. This would have degraded the RNA and defeated Dr Mikovits test.
• Patients were taking medications that could produce false negatives.
• A portion of collection tubes had been in the CDC lab with 22Rv1 cells.
• The time allotted for serology and culturing was massively reduced from what had been used in Lombardi et al.
• The WPI was not given the opportunity to complete virus culture testing. Although there were samples provided to several commercial companies who had been added to the study.
• The amount of blood draw was too little.
• The NCI-Ruscetti did no PCR and the WPI no serology.
• Only 14 CFS patients were tested, and 15 controls.
• Only 6 patients had been tested in Lombardi et al.
• The positive serology results from Dr Ruscetti, the NCI co-author of Lombardi et al. (2009), must also be accepted as evidence of a retroviral infection, as the test has only ever been shown to react to exogenous MLVs.
• The WPI/Mikovits and NCI/Ruscetti have never had an assay capable of detecting MRVs in plasma or whole blood.

Seven days after the publication of the BWG results, on Thursday 29th September 2011, Annette Whittemore summarily fired Dr Mikovits, while she stood outside her rented home in Nevada, and closed down the Whittemore Peterson Institute (WPI) research program (7,8). This was kept from patients until Dr Jamie Deckoff-Jones revealed the shocking news on the following Monday, in what was a blog intended to share her opinion of the BWG results (8). As Dr Deckoff-Jones explained, testing for the BWG had been split between the Mikovits research lab and the commercial lab where Dr Vincent Lombardi was given responsibility for overseeing XMRV testing.


“In terms of the BWG: I was told that the BWG specimens were being run in both the WPI research lab and the VIP Dx clinical lab. Though the labs were kept separate, and cooperation between the two labs was already very troubled, Dr. Mikovits believed that VIP Dx would succeed, and everything would be doubly validated.”
(Dr Jamie Deckoff –Jones, MD, Square One, X Rx, 3 October 2011) (8)


This was a surprise, for Dr Mikovits had no authority or oversight over any activity taking place in the clinical lab (AKA commercial lab, REDLABS trading as VIP Dx). Why then was the commercial lab conducting testing for the BWG study? Why had the NIH allowed REDLABS, an independent company with a vested interest, to take part in the BWG? Did REDLABS hope to clinically validate their tests? Had Dr Mikovits wanted them to use this opportunity to clinically validate their tests?


Mikovits has stated that she had requested for the best part of two years to see the evidence for REDLABS tests sold to patients (7), was this why she wanted REDLABS included in the BWG study, if she did want them included? Dr Deckoff-Jones stated that Dr Mikovits believed they would succeed. An opportunity to have several labs confirming the existence of the ME retroviruses may have been Dr Mikovits reason for wanting REDLABS inclusion in the study. Alternatively the BWG may have wanted another lab to take part to take the number of labs participating to an even ten.

Within days of the Dr Deckoff-Jones article appearing, the WPI had hurriedly arranged for Annette Whittemore to answer questions on the WPI Facebook page, under the page name 'Whittemore Peterson Institute', with Kellen Jones-Monick and Andrea Whittemore moderating (9). Much was said in the exchanges that followed, but perhaps the most significant comment related to the REDLABS tests and the BWG.


“Whittemore Peterson Institute
Many of you have questions regarding the blood working group. The purpose of this phase of the BWG study was to determine if current assays could reproducibly detect XMRV/MLV in blood samples. "They concluded that these results indicate that current assays do not reproducibly detect XMRV/MLV in blood samples and that blood donor screening is not warranted."
It is important to note that the results reported in the blood working were not based on the testing methods that are used in the clinical laboratory.”
(Annette Whittemore, WPI Q & A, 7th October 2011) (9)


If the results in the Blood working group were not the tests used by REDLABS, what happened to the results produced by the REDLABS group led by Dr Lombardi? Why were the results of the commercial lab not published? This was the chance to validate the commercial tests in the eyes of the world. Why was publication of the REDLABS results avoided? What was wrong? Dr Mikovits was quoted as having said that the REDLABS (trading as VIP Dx) tests were not reproducible in the BWG.


“Then, when the BWG results were finally made public on September 22, Dr. Mikovits was quoted as saying, “VIPdx lab will NOT continue XMRV-testing because it hasn’t been shown to be reproducible in [the] BloodWorkingGroup”. Shortly after she said this, cooperation between the two labs ceased completely and the research lab was closed. Why?

It is important to know that Dr. Mikovits stands by her work at the WPI research lab, which is all she can vouch for. She cannot account for what happened at VIP Dx. It was in a different location, under different leadership: Dr. Lombardi was in charge at VIP Dx.”
(Dr Jamie Deckoff –Jones, MD, Square One, X Rx, 3 October 2011) (8)


The results from REDLABS must have therefore been uncoded and known to all the participating labs and the authorities. Dr Lombardi's name is also not on the BWG paper (2), but his team clearly participated. So how could testing performed at REDLABS for the BWG, that was shown to not be "reproducible", have vanished?

The aim of Phase III of the BWG was to assess clinical sensitivity and specificity of the assays (10), was this anything to do with the failure to report the REDLABS data? These are serious questions that demand the truth, the whole truth and nothing but the truth from Annette Whittemore, the management team of WPI, Dr Lombardi, the man in control of REDLABS, Harvey Whittemore, and the organisers of the BWG.

It is also peculiar that the BWG had ever portrayed Phase III as being capable of clinical validation when only 45 clinical samples in total were to be screened (10), and only 30 were in fact screened (2). True clinical validation would require hundreds of samples (11). Therefore none of the tests from the others participating labs could have been said to be clinically validated, but did any of the members of the BWG see any clinical validation data for the tests used by REDLABS?

Regardless of how REDLABS (trading as VIP Dx) came to be conducting tests for the BWG, by July 2011 Dr Mikovits had expected REDLABS to stop selling tests to patients.


“In the summer of 2011, Mikovits and her young lab assistant, Max Pfost, began poring through their notebooks, trying to find where such a contaminant might have entered their process.

In July, she says, she found it—an entry from March 2009 indicating that a culture of the XMRV virus had been placed into the same incubator with the rest of the lab’s blood samples. Mikovits says she was out of town the day this occurred.

In July 2011 she told Harvey Whittemore of the potential contamination, she says, and expected that the VIP Dx lab would cease testing patients for the XMRV virus. “I just kept saying, stop it, stop it, stop it. We have to sort this out,” Mikovits says. According to Mikovits, the testing did not stop. And after a tense summer, she was fired in September.”

(Casey Schwartz, The Daily Beast, 23 July 2011) (12)


As recounted in her interview with Casey Schwartz of The Daily Beast, Dr Mikovits and lab assistant Max Pfost had discovered a potential source of contamination, but what samples could have been contaminated? How did it relate to REDLABS? And why did Harvey Whittemore ignore her advice that testing be stopped at REDLABS?

In addition, Dr Mikovits had also said that she had no confidence in Dr Lombardi’s ability to carry out testing and that he had been unwilling to take her direction as Research Director (7). Therefore again we must ask why the NIH had invited REDLABS, an independent company with a vested interest, to take part in the BWG? Had Dr Mikovits objected to their participation or ask for their inclusion?

Annette Whittemore had, during the Facebook Q & A, stated that REDLABS (trading as VIP Dx) were offering clinically validated tests.


“Regarding XMRV testing at VIP Dx. All tests offered by VIP Dx laboratory are clinically validated. If you have further questions about the tests please send your questions to info@VIPdx”

(Annette Whittemore, WPI Q & A, 7th October 2011) (9)


Yet, by the 7th October 2011 when this statement was made, REDLABS were no longer selling XMRV tests to patients, so this comment cannot relate to those tests. They had in fact stopped offering clinical tests by the 6th June that year, but were continuing to test samples for XMRV they had already received payment for (13). The question therefore remains, were the XMRV tests sold by REDLABS clinically validated?

As of June 6, 2011, VIP Dx will no longer be accepting samples for any clinical tests.

If you are interested in the specialty clinical testing once offered by VIP Dx, please visit the website of UNEVX at www.unevx.com.

If you currently have tests pending with VIP Dx, those tests will be completed and reported by VIP Dx according to the current testing and reporting schedule.

If you have any questions regarding tests that you have pending at VIP Dx, please contact customer service at 775-351-1890 or info@vipdx.com (info@vipdx.com).

(VIP Dx statement, 6 June 2011) (13)

What had prompted them to stop offering commercial testing for XMRV at REDLABS? Had they found anything was wrong with their tests? If they did find the tests were wrong, how were they wrong and when did they discover this? They had stopped offering the tests before Dr Mikovits says she found evidence of a potential contaminant (12) and it was before the results of Phase III of the Blood working group were known, as samples had only been distributed to the participating labs for that study sometime around the middle of May 2011 (14) and results were not known until sometime after August 4th, as that same week Dr. Michael P. Busch, director of the Blood Systems Research Institute, had started to break the codes for the Phase III study of the BWG (15). Patients were also being directed to a separate clinical laboratory, UNEVX, for specialty clinical testing once offered by REDLABS (13). REDLABS were also happy to continue testing those samples that they had received payment for (13).


PATIENT INVESTIGATIONS

After the Q & A with Annette Whittemore on the WPI Facebook page (9), some patients took up her offer to email questions to Marguerite Ross about the REDLABS XMRV tests. Marguerite Ross is the Director of Marketing & Client Relations for REDLABS and the separate lab called UNEVX (16). The following response was included in one particular email exchange with a patient who was trying to discover if the tests sold were clinically validated.


“The protocols used by Unevx and/or VIP Dx are proprietary.”

(EMAIL: Marguerite Ross, October 2011)


The patients then asked Marguerite Ross to provide the full details of the test, such as the reagents and cycling conditions, so that they could compare them to the methods used in Lombardi et al. (2009). The following short response was received from Marguerite Ross.


“NO.”

(EMAIL: Marguerite Ross, October 2011)


Marguerite Ross was also unable to confirm the tests currently in use at REDLABS were clinically validated. If the tests were those used in Lombardi et al. (2009), then those tests are in the public domain and cannot be a commercial secret (17,18). If the tests are different, then questions about evidence for clinical validation still remain. Concern was further increased by a comment by an unnamed WPI representative on their Facebook page on the 14 October 2011, under a statement from Dr Vincent Lombardi.


“Andy thank you for your kind words of support for the Whittemore Peterson Institute. As we understand it VIPdx is no longer offering XMRV testing due to recent developments. The clinical laboratory of WPI has also decided not to begin testing. There is a misconception regarding what a clinically validated test is. In order for a test to be clinically validated its performance characteristics are determined regarding precision,linearity, and interference. Therefore, a clinically validated test can in fact be validated with plasmid,or recombinant construct or even an actual virus such as 22Rv1. We have high regards for the Miller lab. If you have futher questions please contact Vincent Lombardi Interim Research Director at the WPI and please say hello to Dr. Miller.”

(Whittemore Peterson Institute comment on Facebook, 14 October 2011) (19)


The method described above by the WPI would not even be suitable for determining analytical sensitivity let alone clinical sensitivity. Guidance from the FDA for the manufacture of HIV tests (11) states that for validating analytical sensitivity a dilution series of at least 10 distinct HIV positive clinical specimens from different individuals should be tested. Clinical sensitivity and specificity testing needs at least 200 clinical positives. Tests to determine analytical specificity for diagnostic purposes should be validated by testing a minimum of 500 blood or plasma donors. In short, a laboratory would not be given a license to test for HIV without providing data regarding analytical sensitivity and specificity and crucially clinical (sometimes called diagnostic) sensitivity and specificity. It is possible to determine the theoretical limit of detection using a plasmid or a virus in a cell line, but that is only a preliminary step in the journey towards clinical validation.

If the REDLABS (trading as VIP Dx) tests were validated according to the methods outlined in that statement (19), then the tests were not in fact clinically validated. Without establishing the clinical sensitivity the tests are not clinically validated. Based on this communication by the WPI (19), REDLABS (trading as VIP Dx), a company wholly controlled by Harvey Whittemore (20), may well have sold XMRV diagnostic tests to patients that had not been clinically validated.

Dr Mikovits has always been adamant that in her research lab 22Rv1 cells had never been present, and was clearly under the impression they have never been in the State of Nevada (21,22). Dr Mikovits lab had also continued to test for contamination at every stage (17) and so was not concerned by Dr Coffin and Dr Pathak’s suggestion that 22Rv1 could have accounted for the positive results in her research (23). Therefore why was WPI now under the impression that the use of 22Rv1, which is not a patient sample, could be used as a positive control? Why were the WPI, with Dr Lombardi now as their Director of Basic Research (24), happy to say that a plasmid, which would not replicate the conditions of an integrated virus, could be used to clinically validate a test?

Another patient, Mr Chris Douglas, who had been a part of the WPI’s UK research study and had sent his own samples to REDLABS for testing, took the matter further and managed to uncover several more troubling pieces of information, which were recorded this year in his blog for ‘CFS United’.


“Next, I contacted the State of Nevada Health Board Bureau of Health care Quality and Compliance which also handles Clinical Laboratory Improvement Amendments (CLIA).

During the ensuing correspondence, and contrary to VIPdx’s statement to me, it emerged that “Vincent Lombardi is not the laboratory director, nor has he served in that regulatory capacity” and “they took this off their website today, it is incorrect.”

[The regulatory Laboratory Director (i.e. the person who represents the lab for regulatory purposes) was/is Sanford Barsky who, in February 2012, CFS Chroniclesfound to be accused of scientific fraud.”


XMRV testing is for both the culture and the serology tests…” and that “…ALL of the tests we run are validated and inspected by the State of Nevada,”

I asked to see the “validation data”, requested details about “the State of Nevada” and reiterated my question about why a “clinically validated” test (or tests) was withdrawn.

VIPdx replied that “The State does not “hold” this information. It is a proprietary record of the laboratory. They inspect but do not keep our records. Our validation records and test protocols are proprietary intellectual property of the laboratory.”

Again, I requested “more tangible evidence of the scientific validity of the two XMRV tests” and an explanation of how they “…have been validated, particularly given that there was no previously established benchmark against which to compare them.

I received no further replies from VIPdx.”

(Chris Douglas, CFS United, 30 April 2012) (25)


Although the Nevada Health Board was correct to say to Mr Douglas that Dr Lombardi had no regulatory capacity as the laboratory director at REDLABS, he was given regulatory control of providing technical assistance and oversight of their XMRV testing on behalf of WPIs interests (26). Therefore he should be able to answer questions regarding the validation status of the tests sold to patients and used in the blood study. So why is Dr Lombardi silent on these matters?

Once again REDLABS (trading as VIP Dx) have told a patient that their tests are proprietary (25), but if they are, they cannot be the tests use in Lombardi et al. (17) for which details are published and in the public domain. REDLABS have also said that the Nevada Health Board inspect but do not keep their records (25). So what records has the Nevada Health Board kept regarding the tests sold by REDLABS? And does REDLABS have any record that would show the tests they have been using were clinically validated? Have they in fact ever provided the Nevada Health Board with records to prove they have clinically validated their XMRV tests? Is anyone at the Nevada Health Board even qualified to determine if these tests were clinically validated? Who actually gave approval? Could the Governor of Nevada grant a licence? Did the Governor of Nevada ever receive a phone call from Harvey Whittemore or any of his associates about these tests?


QUESTIONS FOR WPI AND THE BWG

These events raise some very serious questions regarding the licensing of the XMRV tests and those responsible for their performance at REDLABS, namely Dr Lombardi, his bosses and the State of Nevada Health Board Bureau of Health care Quality. They also raise hard questions for the WPI and those in charge of the BWG, regarding the missing tests performed by REDLABS for that study. Namely, why were the results of Phase III testing at REDLABS not included in the published BWG study and were the tests at REDLABS clinically validated? To sell tests to patients you have to clinically validate a test before it is licensed. Is there therefore any connection between the failure to report testing results in the BWG and the absence of publicly available clinical validation data for the REDLABS tests? Why has nobody connected to REDLABS been able to confirm that the REDLABS (trading as VIP Dx) tests had been clinically validated?

Why did the BWG allow a commercial lab to have any influence over scientific research into a retroviral association with ME anyway? Did Dr Mikovits want REDLABS to perform testing for the BWG or did she not want REDLABS to not take part? The extent of REDLABS involvement in the BWG must now be fully disclosed and open to scrutiny by the public. The public also has a right to know if REDLABS had anything to do with the collection processing or prescreening of the patient and control samples for the BWG. If someone did not want the REDLABS test results published, then it would be disturbing if that same lab had been responsible for any of those stages considering the flaws that have been discovered in the published paper.

An explanation for the involvement of Abbott laboratories (molecular and diagnostic labs), another company with several patents for XMRV tests, and the involvement of the company Gen-Probe, also need to be given by the BWG (2,27,28,29,30,31). Who decided that at the last minute that commercial companies, who had not participated in the first two stage of the BWG, would be allowed to participate in testing for Phase III? Is there any way that these patents could make money if the human infection was said to not exist?


THE DAILY BEAST INTERVIEW
Answers to these questions became even more paramount to patients interests after Casey Schwartz of The Daily Beast interviewed Dr Mikovits last month (12).


“In the summer of 2011, Mikovits and her young lab assistant, Max Pfost, began poring through their notebooks, trying to find where such a contaminant might have entered their process.

In July, she says, she found it—an entry from March 2009 indicating that a culture of the XMRV virus had been placed into the same incubator with the rest of the lab’s blood samples. Mikovits says she was out of town the day this occurred.

In July 2011 she told Harvey Whittemore of the potential contamination, she says, and expected that the VIP Dx lab would cease testing patients for the XMRV virus. “I just kept saying, stop it, stop it, stop it. We have to sort this out,” Mikovits says. According to Mikovits, the testing did not stop. And after a tense summer, she was fired in September.”

(Casey Schwartz, The Daily Beast, 23 July 2011) (12)


Why would an entry in a notebook from March 2009 relate to the XMRV tests sold by REDLABS to patients? Does the entry in the notebook and the XMRV tests sold to patients relate to Harvey Whittemore not taking Dr Mikovits advice to stop selling tests? Was there any connection therefore between Dr Mikovits sacking, the issue of Dr Mikovit's notebooks, this entry in a notebook from March 2009, and the XMRV tests sold by REDLABS?

There is no longer a criminal investigation into the notebooks (32), so why do the police continue to hold them? (12) Should Dr Mikovits notebooks not be given back into Dr Mikovits possession so that she can continue her research? Dr Mikovits was the principle investigator and was responsible for protecting that research and the notebooks. So on who's behalf are the police keeping these notebooks?

Max Pfost had also phoned Dr Mikovits the day after she was fired and told her that her work at WPI had been rifled through (12). Had someone been looking for the notebook from March 2009? Did this person not know where Dr Mikovits kept her research notebooks? Did they take any notebooks? Who had made the entry in that notebook? This was after the majority of the experiments for Lombardi et al. had been done, so what samples for what research had been infected? What happened to the XMRV culture and where did it come from? If the placing of an XMRV culture with patient samples was a deliberate act, what had been the motive for potentially contaminating the samples? Had Dr Mikovits and Max Pfost therefore discovered evidence of a potential crime and or the identity of the person who contaminated patient samples with XMRV infected cells?


‎Dennis Jones, lawyer for Judy Mikovits, also said the reason she was fired by the institute was because she “discovered a series of improper, unethical and possibly illegal acts” by the Whittemores and their lab director.

For those reasons, Jones said, Washoe District Judge Brent Adams’ rulings should be thrown out."

(Martha Bellisle, Reno Gazette-Journal, 23 April 2012) (33)


Annette Whittemore during the Q & A with patients on the 7th October 2011 had made the following comment regarding the research notebooks when asked if she would be giving them back to Dr Mikovits.


Whittemore Peterson Institute
Joan Clarksdale: We have offered Judy access to any necessary materials she needs to answer the concerns of the journal Science. WPI is not in possession of Judy's notebooks.

(Annette Whittemore, WPI Q & A, 7th October 2011) (34)


Whittemore Peterson Institute
Dr.Mikovits took her notebooks out of her office.

(Annette Whittemore, WPI Q & A, 7th October 2011) (35)


Yet in Max Pfosts first affidavit taken by a WPI employee, Kellen Monick, Max claims he took notebooks from WPI on the 30th October (day after Dr Mikovits was fired), but that Dr Mikovits flew back to Reno on the 16th October to retrieve the notebooks (36). So why had Annette Whittemore on the 7th October, when Max is claiming he had the notebooks, claimed Dr Mikovits took her notebooks out of her office? Who had witnessed this event?

The offer of access to any necessary materials also seems strange if Annette thought Dr Mikovits she had taken the research notebooks and that WPI owned them. Why give her access? What necessary materials were they offering?

It had been claimed that Dr Mikovits was fired because she had taken cell lines that belong to Dr Lombardi (7). Dr Lombardi however was responsible for XMRV testing at REDLABS (trading at VIP Dx), but that lab is located on Fox Avenue several miles from WPI research lab, which is located on the University of Nevada campus in Reno (37,38). Soon after Dr Mikovits was fired patients were also reporting that when they had phoned REDLABS (trading as VIP Dx), using the VIP Dx phone number, 775-351-1890, that was associated with the Fox Avenue address for VIP Dx (37), to ask questions about the clinical validation evidence for the XMRV tests they had been selling, that the phone was being answer by UNEVX (39,40).


WPI is not responding to patients regarding the validity of the VIPdx tests. They are sidestepping these questions. They are telling patients to contact VIPdx and when you call VIPdx guess who answers? UNEVX. They are telling patients that neither they or UNEVX are responsible for answering the questions. This is a mis-representation. If UNEVX is aswering the phone for VIPdx they should answer the question. All this is being done to confuse the patients that had their testing done at VIPdx. Why won’t they answer these patients who have paid for the testing? Call VIP at (775) 351-1890 and see who answers. Bye the way here is the info on who is the Director for both business entities:
Marguerite Ross, Director Marketing & Client Relations VIP Dx
Marguerite Ross, Director Marketing & Client Relations UNEVX Clinical Laboratory

(Rios, Let No Man Cast Asunder…., Sciencevsantiscience, 9 October 2011) (39)


UNEVX is a separate company to REDLABS (trading as VIP Dx) that is wholly controlled by Annette Whitemore (42). Also, like REDLABS several of the same people are affiliated to UNEVX. Sanford H Barsky is the UNEVX Laboratory Medical Director, Marguerite Ross, is the Director of Client Relations, and Dr Vincent C Lombardi is the Director of Operations (41). UNEVX were also for a time offering XMRV tests (43), but had by 4th October 2011 stopped offering these tests (7). In addition Dr Lombardi had also put out a statement on behalf of REDLABS (trading as VIP Dx) on the 14 October 2011 on the VIP Dx website (44), and UNEVX also filed articles of incorporation on the 6/2/2010 (42,45). Therefore both labs were in operation simultaneously, using the same personnel and contact details.

Max Pfost had said that the cell lines had been delivered to the WPI lab from Japan, and were addressed to Dr Lombardi (36). Why would Dr Lombardi order cell lines and have them sent to Dr Mikovits research lab at WPI? Why would he be doing any work that Dr Mikovits would not be aware of, and when he was only a Director of Basic Research? REDLABS (trading as VIP Dx) was also not a research lab. So why would Dr Lombardi have needed to order cell lines? Were these cell lines not already available at either the WPI research lab or REDLABS?

It is now time for all of those involved to answer all these questions. If the tests sold by REDLABS (trading as VIP Dx) and UNEVX have not been clinically validated then all money collected for those tests should be immediately returned to patients, as you cannot license a test unless it is clinically validated. To assist in this the BWG should immediately release all testing data produced by REDLABS (trading as VIP Dx) for the Phase III study. The cost to the health of the ME population and the wider public is at stake and any delay is an unacceptable risk.


REFERENCES

1. Anonymous. 8 August 2011. XMRV testing: The REDLABS, trading as VIP Dx, WPI connection. PART 1: AN XMRV TEST FOR SALE. 8 August 2012. http://me-advocacy.com/XMRV_testing_REDLABS.html
2. Simmons et al. 2011. Failure to Confirm XMRV/MLVs in the Blood of Patients with Chronic Fatigue Syndrome: A Multi-Laboratory Study. Science. 334 (6057), 814-817. http://www.sciencemag.org/content/334/6057/814
3. Jon Cohen and Martin Enserink. 23 September 2011. False Positive. Science. 333, 1694-1701. http://www.sciencemag.org/content/333/6050/1694.full.pdf?sid=17d901ca-6d08-4081-9697-120a2e2f1aa8
4. Lo et al. 2010. Detection of MLV-related virus gene sequences in blood of patients with chronic fatigue syndrome and healthy blood donors. PNAS. 107 (36), 15874-15879. http://www.pnas.org/content/early/2010/08/16/1006901107.abstract
5. Lee et al. 2012. Sensitivity of PCR Assays for Murine Gammaretroviruses and Mouse Contamination in Human Blood Samples. PLoS ONE. 7 (5), e37482. http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037482
6. Paolucci et al. 2012. Xenotropic and polytropic murine leukemia virus-related sequences are not detected in the majority of patients with chronic fatigue syndrome. New Microbiol. 35 (3), 341-344. http://www.newmicrobiologica.org/PUB/allegati_pdf/2012/3/341.pdf
7. Jon Cohen. 4 October 2011. Chronic Fatigue Syndrome Researcher Fired Amidst New Controversy. Science Insider. http://news.sciencemag.org/sciencei...l?rss=1&utm_source=dlvr.it&utm_medium=twitter
8. Dr Jamie Deckoff-Jones MD. 3 October 2011. Square One. X Rx. http://www.x-rx.net/blog/2011/10/square-one.html
9. Annette Whittemore. 7 October 2011. Q & A on WPI Facebook page. https://www.facebook.com/note.php?note_id=10150346044661797
10. Slides presented by the Blood XMRV working group. 7-8 September 2010. 1st XMRV conference. Bethesda, USA. http://regist2.virology-education.com/1XMRV/docs/30_Simmons.pdf
11. FDA.1999. Guidance for Industry: In the Manufacture and Clinical Evaluation of In Vitro Tests to Detect Nucleic Acid Sequences of Human Immunodeficiency Viruses Types 1 and 2.http://www.fda.gov/biologicsbloodva...toryinformation/guidances/blood/ucm077067.htm
12. Casey Schwartz. 23 July 2012. How Research into Chronic Fatigue Syndrome Turned into an Ugly Fight. The Daily Beast.http://www.thedailybeast.com/articl...tigue-syndrome-turned-into-an-ugly-fight.html
13. REDLABS (trading as VIP Dx) no longer accepting samples for clinical tests. 6 June 2011. www.vipdx.com. http://www.mecfsforums.com/index.php/topic,7746.0.html
14. Slides: Results of the Blood XMRV Scientific Research Working Group Study. 14 October 2011. CFIDS Association webinar. http://www.cfids.org/xmrv/srwg-webinar-oct2011.pdf
15. Mindy Kitei. 4 August 2011. Breaking the codes. CFS Central. http://www.cfscentral.com/2011/08/breaking-codes.html
16. Marguerite Ross profile on LinkedIn. (Access date 13 August 2011) http://www.linkedin.com/pub/marguerite-ross/5/707/804
17. Lombardi et al. 2009. Detection of an Infectious Retrovirus, XMRV, in Blood Cells of Patients with Chronic Fatigue Syndrome. 326, (5952), 585-589.http://www.sciencemag.org/content/326/5952/585
18. Mikovits invented WPI patent. 2010. (WO2010148323) DIAGNOSIS AND TREATMENT OF DISEASES OR DISORDERS ASSOCIATED WITH XENOTROPIC MURINE LEUKEMIA VIRUS-RELATED VIRUS. http://patentscope.wipo.int/search/...NE+DISEASE"&sortOption=Pub+Date+Desc&maxRec=2
19. Comment by the WPI on the WPI Facebook page under a statement from Dr Vincent Lomardi. 14 October 2011. https://www.facebook.com/notes/xmrv...onger-offering-xmrv-testing/10150356171906797
20. Harvey Whittemore, REDLABS USA INC. http://nvsos.gov/sosentitysearch/CorpDetails.aspx?lx8nvq=3HqeF%2fFCg2b8fQKoG
21. Dr Judy Mikovits. 29 March 2011. Webinar: Disease Associations of XMRV and MLV-Related Viruses. Pathogens in the Blood Supply. The New York Academy of Sciences. http://www.nyas.org/Events/Detail.aspx?cid=0918b8d8-9a46-4334-b194-23ade9c2a7aa
22. Dr Judy Mikovits. 29 March 2011. Webinar: Disease Associations of XMRV and MLV-Related Viruses. Pathogens in the Blood Supply. The New York Academy of Sciences. 1min 19sec.http://www.mecfsforums.com/wiki/22Rv1_&_Du145_cell_lines
23. Pathak et al. 1 March 2011. Paper # 91LB. MRV Probably Originated through Recombination between 2 Endogenous Murine Retroviruses during in vivo Passage of a Human Prostate Cancer Xenograft. CROI. http://www.retroconference.org/2011/Abstracts/42508.htm
24. WPI press release stating that Dr Mikovits was now the Director of Translational Research and Dr Lombardi was now the Director of Basic Research. 24 March 2011. WPI. http://www.wpinstitute.org/news/docs/DirTransRes.pdf
25. Mr Chris Douglas. 30 April 2011. Misopathy Over Disclosure–Proof of VIPdx Test Validity Still Not Forthcoming. CFS United.http://cfsuntied.com/blog2/2012/04/...of-vipdx-test-validity-still-not-forthcoming/
26. Frankie Vigil, R&R Partners for Whittemore Peterson Institute.14 January 2010. WPI. http://wpinstitute.org/news/docs/WPI_pressrel_011410.pdf
27. Abbott laboratories XMRV patent. (EP2448960) MARKERS OF XMRV INFECTION AND USES THEREOF http://patentscope.wipo.int/search/...revFilter=&sortOption=Pub+Date+Desc&maxRec=21
28. Abbott laboratories XMRV patent. (EP2449381) MARKERS OF XMRV INFECTION AND USES THEREOF http://patentscope.wipo.int/search/...revFilter=&sortOption=Pub+Date+Desc&maxRec=21
29. Abbott laboratories XMRV patent. (WO2012024518) MOLECULAR DETECTION OF XMRV INFECTION http://patentscope.wipo.int/search/...revFilter=&sortOption=Pub+Date+Desc&maxRec=21
30. Abbott laboratories XMRV patent. (WO2012024513) MOLECULAR DETECTION OF XMRV INFECTION http://patentscope.wipo.int/search/...revFilter=&sortOption=Pub+Date+Desc&maxRec=21
31. GenProbe Incorporated XMRV patent. (WO2012030856) COMPOSITIONS, METHODS AND REACTION MIXTURES FOR THE DETECTION OF XENOTROPIC MURINE LEUKEMIA VIRUS-RELATED VIRUS http://patentscope.wipo.int/search/...revFilter=&sortOption=Pub+Date+Desc&maxRec=21
32. Ewan Callaway. 14 January 2012. Criminal case against chronic fatigue syndromeresearcher dropped. Nature News blogs.http://blogs.nature.com/news/2012/0...onic-fatigue-syndrome-researcher-dropped.html
33. Martha Bellisle. 23 April 2012. Fired Whittemore Peterson Institute researcher claims justice system flawed. Reno Gazette-Journal. www.rgj.com. http://www.rgj.com/article/20120423...itute-researcher-claims-justice-system-flawed
34. Annette Whittemore is happy to answer your questions. 7 October 2011. Mecfsforums. Page 4.http://www.mecfsforums.com/index.php/topic,9825.45.html
35. Annette Whittemore is happy to answer your questions. 7 October 2011. Mecfsforums. Page 6.http://www.mecfsforums.com/index.php/topic,9825.75.html
36. Exhibit 1: Affidavit of Max Pfost. 16 November 2011. WPI. http://www.wpinstitute.org/news/docs/Exh1-ReplyISOMotionforPreliminaryInjunction.pdf
37. Address of VIP Dx. http://laikaspoetnik.files.wordpress.com/2010/04/test_rqn_feb_2010.pdf
38. Address of the WPI. http://www.wpinstitute.org/about/about_contact.html
39. Rios. 9 October 2011. Let No Man Cast Asunder…., Sciencevsantiscience.http://sciencevsantiscience.wordpress.com/2011/10/09/let-no-man-cast-asunder/
40. Robyn. 9 October 2011. Marguerite Ross refused to confirm tests used in ViP Dx are Lombardi et. Mecfsforums. Reply 36.http://www.mecfsforums.com/index.php/topic,9839.msg117196.html#msg117196
41. Main staff members of UNEVX. http://unevx.com/about/
42. Annette Whittemore, UNEVX Inc. http://nvsos.gov/SOSEntitySearch/CorpDetails.aspx?lx8nvq=BlnqHf7ro%2b%2bx6x%2fFy72jGQ%3d%3d&nt7=0
43. Jeannette (Sick and Tired). 17 August 2011. UNEVX’s XMRV test takes longer than initially announced. ThoughtsaboutME.comhttp://thoughtsaboutme.com/2011/08/17/unevxs-xmrv-test-takes-longer-than-initially-announced/
44. Statement of Vincent Lombardi, Phd, Clinical Lab Director, VIP Dx, 14 October 2011. http://niceguidelines.blogspot.co.uk/2011/10/statement-by-vincent-lombardi.html
45. UNEVX inc. Articles of incorporations file date. http://nvsos.gov/sosentitysearch/co...o%2b%2bx6x%2fFy72jGQ%3d%3d&CorpName=UNEVX+INC.

To quote Cort xx dig deeper - http://www.dailystrength.org/c/Chronic_Fatigue_Syndrome/forum/14148241-latest-whittemoremikovitz

 

[In Vitro Infidelium]

More confusion based on leaps of logic from unreliable and/or second hand sources. The only source for the claim that VIPdx did testing for the BWG study comes from Deckoff-Jones who had nothing to do with laboratory work either at the WPI or VIPdx, and it's not even clear from the quote what it is that Deckoff-Jones is referring to.

Far from being a mess as claimed above, the BWG study succeeded in dragging scientific data (requires registration)out of what was otherwise a hopeless situation. If Mikovits, Lombardi and Ruscetti hadn't been so attached to their original conclusions but had re-examined their positions following the lack of independent repliction studies, they could have held the laurels for identifying a very significant problem of scientific testing - the capacity for novel contamination of common laboratory reagents. As it is they were left stranded by the BWG results.

IVI

 

[asleep]

Far from being a mess as claimed above, the BWG study succeeded in dragging scientific data (requires registration)out of what was otherwise a hopeless situation. If Mikovits, Lombardi and Ruscetti hadn't been so attached to their original conclusions but had re-examined their positions following the lack of independent repliction studies, they could have held the laurels for identifying a very significant problem of scientific testing - the capacity for novel contamination of common laboratory reagents. As it is they were left stranded by the BWG results.

Sorry I have to completely disagree with you. The BWG failed to meet its primary goal, which was to elucidate the impact and role of collection and processing on viral detection. If done well, this could have provided clarity to a messy situation where numerous uncontrolled variables across prior publications had made it impossible to identify the true reason for disparate results. Instead, they added to the confusion by conducting an experiment that introduced yet more novel variables in the areas of collection, processing, control determination, blinding, and coding. Upon their discordant findings, there was no attempt to determine what had been found in the positives, nor any attempt to identify the purported contamination. They instead chose to speculatively assume that the results were due to contamination without properly ruling out alternative explanations. This is the essence of flawed science.

From an empirical standpoint, the BWG was a mess of confounding factors topped with a baseless, unsubstantiated conclusion. From a narrative standpoint, though, it is denialist gold.

 

[In Vitro Infidelium]

Sorry I have to completely disagree with you. The BWG failed to meet its primary goal, which was to elucidate the impact and role of collection and processing on viral detection. If done well, this could have provided clarity to a messy situation where numerous uncontrolled variables across prior publications had made it impossible to identify the true reason for disparate results. .

What disparate results ? - no reproducibility of the results of the original study has ever been demonstrated. The is Lombardi et al 2009 - and then there is everything else, which includes the BWG.

Instead, they added to the confusion by conducting an experiment that introduced yet more novel variables in the areas of collection, processing, control determination, blinding, and coding.

Reproducibility isn't demonstrated by mere copying of what was done previously.

Upon their discordant findings, there was no attempt to determine what had been found in the positives, nor any attempt to identify the purported contamination.

Discordant with what ? You mean there was a range of data ? And just how do you propose to find "what had been found in the positives" ? Your assumption is that there was something there, rather than the result being artefacts of the processing .Why would anyone spend time chasing down a possible mirage when reproducibility has not been demonstrated in any other study ?

They instead chose to speculatively assume that the results were due to contamination without properly ruling out alternative explanations. This is the essence of flawed science.

There are an infinite number (albeit mostly highly improbable) alternate expalantions, which is why science doesn't operate on a Sherlock Holmes paradigm. The results of the original study turned out to lack reproducibility - doing a post mortem on a study lacking lacking reproducibility rarely forms part of the scientific process, everyone just moves on.

From an empirical standpoint, the BWG was a mess of confounding factors topped with a baseless, unsubstantiated conclusion. From a narrative standpoint, though, it is denialist gold.

And the denialists includes the whole of science, given that not a single competent criticism of the BWG has been made by anyone ? Disagreeing with me is irrelevent - you appear to disagree with the whole process of science, which rather fundamentally questions what basis you might be using judging flawed and unflawed science.

IVI

 

[asleep]

What disparate results ? - no reproducibility of the results of the original study has ever been demonstrated. The is Lombardi et al 2009 - and then there is everything else, which includes the BWG.

The primary question is whether there exists an infectious HGRV. Questions of disease association and furthermore causality are downstream of this primary question (though they can be precluded by it). However, if even a single genuine infection is proven, then these downstream questions become serious business and methodological insufficiencies as well as cavalier claims that such an infection is "harmless" or "non-pathogenic" become ethically liable.

The "nothing to see here" camp universally contends that the answer to this primary question is "no such human virus exists because all positive results are due to contamination," thereby making the downstream questions moot. The BWG and the 0/0 studies are held up as evidence of this positive claim that no such virus exists. I assume you would support these contentions that all positive results to date are contamination, though perhaps you have a more nuanced position than that.

The reason I make this distinction between questions is because it is crucial in understanding the burden of proof needed to reasonably support different claims.

If we look at the primary question of HGRV existence in isolation (which is reasonable since that is where the anti-HGRV crowd has chosen to stake its claim), there is a great deal of evidence spanning multiple diseases (PC, ME, possibly BPH and others), multiple methods (PCR, IHC, serology, culture), and multiple studies (Lombardi, Lo, Hanson, Paolucci, the Lithuanian sequence, Grossberg's MLV-like virus, numerous negative studies that found sporadic evidence) that supports a genuine HGRV. From the standpoint of this primary question, some apparent discrepancies (sequence variation) actually form secondary evidence of a real virus.

As for evidence against the existence of such a virus, there are the negative studies (absence of evidence, which is indirect to this question), studies with confirmed contamination (again, indirect evidence as contamination in one instance doesn't imply contamination in general), the BWG (the internal discordance provides evidence against disease association but not necessarily against the existence of a virus), and a hypothetical source for a very narrow range of potentially contaminating sequences. All of this is only indirect evidence that fails to adequately support of the generic, positive appeal to contamination in all instances. There is no direct evidence of contamination in Lombardi, Lo, Hanson, Paolucci and the positive PC studies.

In essence, the claim that all positive results to date are due to contamination is a strong positive claim requiring direct evidence. However, those arguing this point are attempting to transform indirect or equivocal evidence into direct evidence by treating contamination as a de facto null hypothesis, whereby failure of data prove or support HGRV existence, by default, means it can be treated as supporting contamination. This is a subtle and insidious form of confirmation bias. That this has become the apparent modus operandi of the virology doesn't make it rational or scientific, merely faith-based and ritualistic.

Furthermore, we have seen a conflating of this primary question with downstream questions in a way that places an unreasonably disproportionate burden of proof on RV proponents. Your claim above that the evidence base consists of Lombardi vs everything else utilizes this conflation to artificially gerrymander evidence. For example, given the failure to isolate a contamination source, the positives in the BWG are equivocal to the existence of an HGRV and could possibly reflect a genuinely infectious HGRV, just as they could reflect contamination. However, by conflating the question of HGRV existence with disease association, and imposing the implicit demand that evidence must somehow support both in order to be counted as supporting the former alone, this study is subtly and irrationally reclassified as negative on the simple question of existence. Likewise with other pieces of evidence, where a perpetually shifting mixture of secondary issues (semantics about sequence variability and virus names, differing disease associations, etc) is used to improperly reclassify evidence that is positive or equivocal to the question of existence.

It's a bit like arguing that a forest doesn't exist after removing all trees from consideration on the grounds that each tree on its own doesn't prove that a forest exists.

Reproducibility isn't demonstrated by mere copying of what was done previously.

I didn't say anything about reproducibility. The issue is controlling for all your variables (which involves understanding what needs to be controlled and how to do so) so that logical conclusions can be reached. The BWG didn't do this, in fact it went the opposite direction which greatly hampers the ability to draw substantiated conclusions from it.

It's also a bit of a double standard that you would consider the BWG, despite its novel differences to Lomardi, to be a valid test of reproducibility while simultaneously discounting Lo, Hanson, and other positive studies as confirmation of reproducibility because of their differences.

Discordant with what ? You mean there was a range of data ? And just how do you propose to find "what had been found in the positives" ? Your assumption is that there was something there, rather than the result being artefacts of the processing .Why would anyone spend time chasing down a possible mirage when reproducibility has not been demonstrated in any other study ?

I meant internally discordant. There are a number of things they could and should have done to get to the bottom of this. They could have redone subsets of experiments to try to pinpoint sources contamination rather than just assuming its existence. They could have had Ruscetti redo some cultures so that they could isolate and sequence some of his positives. Or they could have designed a study that wasn't a mess of uncontrolled variables.

Again, your appeal to "reproducibility" here is ambiguous. You are ignoring a great deal of evidence, including the fact that the positives themselves from this study (in the absence of direct evidence of contamination) could possibly represent a reproduction of evidence for HGRV existence.

There are an infinite number (albeit mostly highly improbable) alternate expalantions, which is why science doesn't operate on a Sherlock Holmes paradigm. The results of the original study turned out to lack reproducibility - doing a post mortem on a study lacking lacking reproducibility rarely forms part of the scientific process, everyone just moves on.

In the context of such an uncontrolled experiment, contamination is simply one of these myriad explanations. Claiming that it is the most probable, and therefore that it can be assumed to be the correct explanation without direct evidence, is just run-of-the-mill confirmation bias.

And the denialists includes the whole of science, given that not a single competent criticism of the BWG has been made by anyone ? Disagreeing with me is irrelevent - you appear to disagree with the whole process of science, which rather fundamentally questions what basis you might be using judging flawed and unflawed science.

I believe I've been very painstakingly elucidating the empirical flaws in the BWG design as well as the illogical use of evidence by those who argue against HGRV existence. I am, after all, not the one appealing to scientific convention (the use of assumptions of contamination as a null hypothesis; the failure to control for variables; the avoidance of post-mortem work) to justify the failure of the scientific community to abide by its own purported principles of scientific inquiry.

Also, it seems a bit presumptive to position yourself as sole arbiter of competence when it comes to criticisms of the BWG. Nor do I understand how you've determined the stance of "the whole of science" on these issues.

 

[Firestormm]

I do not recall that the BWG was looking for 'HGRV existence'. It was looking for whatever it was that Mikovits et al. allegedly discovered in patient's blood. They were involved. They couldn't reproduce their results either. They deemed their finding 'XMRV'. It wasn't there. You and others seem to have expected BWG to have trawled a rather large net.

From my own - albeit limited understanding - it doesn't work that way in science - Lombardi et al. established a claim and that claim was investigated in a blinded methodical way. The association they purported to find so relatively easily and in such high concentrations - could not be substantiated.

If other studies produce results similar to the Lombardi paper that purport to have discovered an association - with something else - another strain - and it was considered significant - that would likewise be investigated. Assuming now of course - in the case of MRVs - they had a solid paper with which to back their claims.

Lipkin for example is attempting to discover if there is indeed the XMRV from Lombardi and the MLV implicated by Lo. It would help of course if all those you are claiming to have reported positively - would have sequenced their findings. Not all have done that I understand.

But Lipkin - as BWG - will do what they can with the evidence they have and that includes properly blinding samples, paying great attention to collection and processing methods, and checking as best they are able for contamination. Indeed I would imagine those involved in the Lipkin Study will pay very close attention - perhaps the closest yet - to checking for contamination and will try to ensure that any source is traced.

As patients we - understandably perhaps - expect 'science' to dot every i and cross every t. To explain every single thing we consider important and even things we don't. But again it doesn't always work like that. It can't.

We sometimes seem to approach these things with a preconceived notion that 'there must be something there and they aren't looking hard enough' or 'they have an agenda not to reveal the truth'. Not always but when it comes to possible retroviral theories and following the publication of Lombardi - this does seems to be the case more often than not on forums especially.

I sometimes feel like asking, if the people who feel published papers are not concluding the 'right' things/whatever whether they have ever engaged with the scientists who publish them (in a courteous way of course) instead of posting things like that at the top of this thread?

 

[In Vitro Infidelium]

The primary question is whether there exists an infectious HGRV. Questions of disease association and furthermore causality are downstream of this primary question (though they can be precluded by it). However, if even a single genuine infection is proven, then these downstream questions become serious business and methodological insufficiencies as well as cavalier claims that such an infection is "harmless" or "non-pathogenic" become ethically liable.

The "nothing to see here" camp universally contends that the answer to this primary question is "no such human virus exists because all positive results are due to contamination," thereby making the downstream questions moot. The BWG and the 0/0 studies are held up as evidence of this positive claim that no such virus exists. I assume you would support these contentions that all positive results to date are contamination, though perhaps you have a more nuanced position than that.

The reason I make this distinction between questions is because it is crucial in understanding the burden of proof needed to reasonably support different claims.

If we look at the primary question of HGRV existence in isolation (which is reasonable since that is where the anti-HGRV crowd has chosen to stake its claim), there is a great deal of evidence spanning multiple diseases (PC, ME, possibly BPH and others), multiple methods (PCR, IHC, serology, culture), and multiple studies (Lombardi, Lo, Hanson, Paolucci, the Lithuanian sequence, Grossberg's MLV-like virus, numerous negative studies that found sporadic evidence) that supports a genuine HGRV. From the standpoint of this primary question, some apparent discrepancies (sequence variation) actually form secondary evidence of a real virus.

As for evidence against the existence of such a virus, there are the negative studies (absence of evidence, which is indirect to this question), studies with confirmed contamination (again, indirect evidence as contamination in one instance doesn't imply contamination in general), the BWG (the internal discordance provides evidence against disease association but not necessarily against the existence of a virus), and a hypothetical source for a very narrow range of potentially contaminating sequences. All of this is only indirect evidence that fails to adequately support of the generic, positive appeal to contamination in all instances. There is no direct evidence of contamination in Lombardi, Lo, Hanson, Paolucci and the positive PC studies.

In essence, the claim that all positive results to date are due to contamination is a strong positive claim requiring direct evidence. However, those arguing this point are attempting to transform indirect or equivocal evidence into direct evidence by treating contamination as a de facto null hypothesis, whereby failure of data prove or support HGRV existence, by default, means it can be treated as supporting contamination. This is a subtle and insidious form of confirmation bias. That this has become the apparent modus operandi of the virology doesn't make it rational or scientific, merely faith-based and ritualistic.

Furthermore, we have seen a conflating of this primary question with downstream questions in a way that places an unreasonably disproportionate burden of proof on RV proponents. Your claim above that the evidence base consists of Lombardi vs everything else utilizes this conflation to artificially gerrymander evidence. For example, given the failure to isolate a contamination source, the positives in the BWG are equivocal to the existence of an HGRV and could possibly reflect a genuinely infectious HGRV, just as they could reflect contamination. However, by conflating the question of HGRV existence with disease association, and imposing the implicit demand that evidence must somehow support both in order to be counted as supporting the former alone, this study is subtly and irrationally reclassified as negative on the simple question of existence. Likewise with other pieces of evidence, where a perpetually shifting mixture of secondary issues (semantics about sequence variability and virus names, differing disease associations, etc) is used to improperly reclassify evidence that is positive or equivocal to the question of existence.

It's a bit like arguing that a forest doesn't exist after removing all trees from consideration on the grounds that each tree on its own doesn't prove that a forest exists.



I didn't say anything about reproducibility. The issue is controlling for all your variables (which involves understanding what needs to be controlled and how to do so) so that logical conclusions can be reached. The BWG didn't do this, in fact it went the opposite direction which greatly hampers the ability to draw substantiated conclusions from it.

It's also a bit of a double standard that you would consider the BWG, despite its novel differences to Lomardi, to be a valid test of reproducibility while simultaneously discounting Lo, Hanson, and other positive studies as confirmation of reproducibility because of their differences.



I meant internally discordant. There are a number of things they could and should have done to get to the bottom of this. They could have redone subsets of experiments to try to pinpoint sources contamination rather than just assuming its existence. They could have had Ruscetti redo some cultures so that they could isolate and sequence some of his positives. Or they could have designed a study that wasn't a mess of uncontrolled variables.

Again, your appeal to "reproducibility" here is ambiguous. You are ignoring a great deal of evidence, including the fact that the positives themselves from this study (in the absence of direct evidence of contamination) could possibly represent a reproduction of evidence for HGRV existence.



In the context of such an uncontrolled experiment, contamination is simply one of these myriad explanations. Claiming that it is the most probable, and therefore that it can be assumed to be the correct explanation without direct evidence, is just run-of-the-mill confirmation bias.

I believe I've been very painstakingly elucidating the empirical flaws in the BWG design as well as the illogical use of evidence by those who argue against HGRV existence. I am, after all, not the one appealing to scientific convention (the use of assumptions of contamination as a null hypothesis; the failure to control for variables; the avoidance of post-mortem work) to justify the failure of the scientific community to abide by its own purported principles of scientific inquiry.

Also, it seems a bit presumptive to position yourself as sole arbiter of competence when it comes to criticisms of the BWG. Nor do I understand how you've determined the stance of "the whole of science" on these issues.

I appreciate the fullness of your response, but it doesn't seem in anyway related to how 'science' is currently 'transacted', and that you are reprising critique of science as a whole, in a sort of a Kuhn/Popper digression when the bulk of biochemistry operates in assuredly Popperian terms. Sure the critique of science is fine, but it doesn't have much releveance to how things happen at 'the coal face'. Though you do seem to misapply your accusation of confirmation bias, and not to grasp the vital significance of reproducibility - the Lo&Alter, Paolucci, and Hanson studies did not reproduce what was claimed in Lombardi et al 2009. You may wish that 'science' would operate differently but given the deep philosophical, not to mention profound funding, issues that would required to be addressed to effect the kind you appear to envisage, I really can't see how in any practical terms that can affect M.E/CFS research, which needs to happen within the world as it is, not as we would wish it to be.

IVI

 

[natasa778]

I appreciate the fullness of your response, but it doesn't seem in anyway related to how 'science' is currently 'transacted', and that you are reprising critique of science as a whole, in a sort of a Kuhn/Popper digression when the bulk of biochemistry operates in assuredly Popperian terms. Sure the critique of science is fine, but it doesn't have much releveance to how things happen at 'the coal face'. Though you do seem to misapply your accusation of confirmation bias, and not to grasp the vital significance of reproducibility - the Lo&Alter, Paolucci, and Hanson studies did not reproduce what was claimed in Lombardi et al 2009. You may wish that 'science' would operate differently but given the deep philosophical, not to mention profound funding, issues that would required to be addressed to effect the kind you appear to envisage, I really can't see how in any practical terms that can affect M.E/CFS research, which needs to happen within the world as it is, not as we would wish it to be.

IVI

You have completely bypassed all of the important issues raised by asleep. Not seeing the forest from the trees, which you all conveniently chopped down

 

[In Vitro Infidelium]

You have completely bypassed all of the important issues raised by asleep. Not seeing the forest from the trees, which you all conveniently chopped down

Who all ?

There maybe 'issues' which you consider important, but if the discussion is about a particular study (as opposed to a general critique of 'science'), then the only pertinent issues are those relative to the way that science is conducted as is presently accepted by its practitioners and commissioners (funders). You are free to want, and to argue for something different but that tells us nothing about the merits of Lombardi et al 2009 and the failure of all other studies to show the results of Lombardi et al 2009 are reproducible, nor is it likely to persuade any scientist that doing things differently, but in some (unspecifed) way more comprehensively, would produce a more informative result.

IVI

 

[Adamskitutu]

She meant you conveniently chopped all the trees down. It's a metaphor. Are we to resort to correcting grammar and syntax now?

And yes - we ARE all free to criticise scientists and their foibles under the mantle of 'science'. Also on the list of people it is ok to criticise: priests, rabbis, politicians, teachers, bus drivers, hairdressers, nutritionists, cooks, lawyers, nurses. All experts in their field. All accountable for their mistakes in one way or another.

 

[In Vitro Infidelium]

She meant you conveniently chopped all the trees down. It's a metaphor. Are we to resort to correcting grammar and syntax now?

Thank you for presenting an alternate syntax, though I think my original reading makes more sense since it follows more directly the repeat of the metaphor as used first in a prior post. No doubt the poster to whom I posed the question will answer in due course to clarify what was intended.

And yes - we ARE all free to criticise scientists and their foibles under the mantle of 'science'. Also on the list of people it is ok to criticise: priests, rabbis, politicians, teachers, bus drivers, hairdressers, nutritionists, cooks, lawyers, nurses. All experts in their field. All accountable for their mistakes in one way or another.

That may be true but certainly doesn't relate to any point I made which was about the critique of science, not criticism of individuals - the comparable conditions would be Christianity, Judaism, Politics, Education, Public Transport, Hairdressing, Nutrition, Cooking, the Law, and Nursing. A major advantage of considering the 'field' and not the 'players' is that it greatly helps avoid getting lost in the ad hominem fallacy.

IVI

 

[natasa778]

She meant you conveniently chopped all the trees down. It's a metaphor.

Finally. Thank you! Sheesh

(this is NOT a personal attack at lumberjacks, who I hope are not covered under special moderating rules )

 

[August59]

All I can say is that all of this is in the past and in so many very unfortunate to a lot of and in a lot of different ways. The only thing that truly matters is what happens next! I have high hopes and very much confidence that Dr. Lipkin and associates will sort all of this out in the most professional manner. His teams results may not answer all questions and I suspect answering these questions are not a direct concern of his.

He is not going to let that paper be released until every reporting entity has presented data that is precisely documented and presents no bias whatsoever. Considering all the information that has surfaced lately, I speak for myself in that having Dr. Lipkin at the helm of this upcoming paper is surely a blessing to the current state of affairs.

I thank Jace for compiling all of this information and as always when we continue to get more and more information about a subject that is highly charged as this is, it tends to escalate the highly charged opinions of the people getting it. I am in no way intending to trivialize this situation because it is a cluster ^#*%. I really feel for all the people that paid to have these test done and waited patiently for months for an answer. Then to find out that there answer might not be worth the paper it is printed on, but then again it might be.

I don't like to see people on the forum get wound up so tight that they sometime get personal in some of their highly charged statements. I do not know what went on in this thread because i just came on here and it had all been deleted by then.

One thing is for sure, none of us need anymore added stress put on us. I truly do not think that there is a single person on this whole forum that does not want every other person on here to be cured of this freakin life robbing disease. I know I would really like to see every one of you cured tomorrow (tonight!!!).

I am anxious and am really looking forward to the studies we are getting from this point on, but at the same time very cautios as I am sure we all are. All of the wrong, confusing, contradicting negative information in the past will just have to stay there. I'm to dizzy to keep turning around and looking at it. It is not anything new that we get information of this type, It has happened several times over the last decade or longer and unfortunately it will probably happen again, but I sure hope not.

Here is to hoping everyone has a great day!
Jerry

 

[Adamskitutu]

Thank you for presenting an alternate syntax, though I think my original reading makes more sense since it follows more directly the repeat of the metaphor as used first in a prior post. No doubt the poster to whom I posed the question will answer in due course to clarify what was intended.



That may be true but certainly doesn't relate to any point I made which was about the critique of science, not criticism of individuals - the comparable conditions would be Christianity, Judaism, Politics, Education, Public Transport, Hairdressing, Nutrition, Cooking, the Law, and Nursing. A major advantag of considering the 'field' and not the 'players' is that it greatly helps avoid getting lost in the ad hominem fallacy.

IVI

Actually it is the people 'doing' the professions who are the ones accountable here. That includes science. Science is often wrongly seen as a 'pure' venture - but scientists are humans who do not act rationally and methodically all the time (sometimes not often at all), whose actions are therefore not above scrutiny, and who are therefore accountable to others. If they get it wrong - people are free to call them out on it, and sometimes get things changed. You are wrongly arguing for science by 'insider consensus' as if scientists can never be accountable for their mistakes or misdemeanours, that the best the rabble can hope for is for a scientist to deign to change their minds entirely of their own free will, like little gods (ironically), but that can only happen if people maintain a deferent posture and 'inside' voices. You maintain it is so, and that is one of your main answers to anybody's counterarguments to your beliefs, but you are wrong.

 

[In Vitro Infidelium]

Actually it is the people 'doing' the professions who are the ones accountable here. That includes science. Science is often wrongly seen as a 'pure' venture - but scientists are humans who do not act rationally and methodically all the time (sometimes not often at all), whose actions are therefore not above scrutiny, and who are therefore accountable to others. If they get it wrong - people are free to call them out on it, and sometimes get things changed. You are wrongly arguing for science by 'insider consensus' as if scientists can never be accountable for their mistakes or misdemeanours, that the best the rabble can hope for is for a scientist to deign to change their minds entirely of their own free will, like little gods (ironically), but that can only happen if people maintain a deferent posture and 'inside' voices. You maintain it is so, and that is one of your main answers to anybody's counterarguments to your beliefs, but you are wrong.

I'm unclear who is being addressed - none of this charactisation that is address as 'you' -has any resemblence to the attitudes I hold, and more significantly doesn't relate to anything I've written on this thread. My understanding from what you have written is that (as with what I understand to be Asleep's position) your concern is with 'science' as you believe it should be (and you may right to want change),however that concern is with a broad cultural issue, while the point I addressed was about a single study. Selecting a single study which happens to have results which you don't agree with and then using a broad cultural critique to question that study is clearly a fallacious form of argument - the broad cultural critique would apply to all science as practiced under the terms you disagree with, which would include Lo&Alter, Paolucci, and Hanson, as well as Lombardi et al 2009.

In any event, perhaps we could see an end to structuring the argument around who does and who does not believe 'what', and focus on what people write and take that as being the substance rather than what is imputed, implied or ascribed to someone by others.

IVI

 

[lansbergen]

none of this charactisation that is address as 'you' -has any resemblence to the attitudes I hold,

I disagree and washing your hands of does not help.

 

[asleep]

My understanding from what you have written is that (as with what I understand to be Asleep's position) your concern is with 'science' as you believe it should be (and you may right to want change),however that concern is with a broad cultural issue, while the point I addressed was about a single study. Selecting a single study which happens to have results which you don't agree with and then using a broad cultural critique to question that study is clearly a fallacious form of argument - the broad cultural critique would apply to all science as practiced under the terms you disagree with, which would include Lo&Alter, Paolucci, and Hanson, as well as Lombardi et al 2009.

I am by no means making a "broad cultural critique." I am concretely describing how the claim that "all HGRV evidence to date is due to contamination" is logically and empirically unsubstantiated, and furthermore how rhetorical sleight of hand (conflating questions, substituting assumptions for the null hypothesis) is being used to distract from this chasm between evidence and conclusion. Even in the context of the BWG, while there is some indirect evidence of contamination, there is no direct evidence that could be used to support the positive claim that every single positive found in the study is the result of contamination. What is being perpetrated is "contamination until proven otherwise" while logically it should be "unknown until proven to be contamination, infection, or something else." (I'm using the word "prove" loosely here to mean essentially "empirically supported.")

I am well aware of the realities and limitations of real-world science. The point is that these limitations must be acknowledged as such when and where they contribute to unsubstantiated conclusions, especially when they require the substitution of assumption for missing data. However, you seem to be arguing that the existence of these limitations means we can alter the essence of what empirical rationality demands in order to accommodate them. If, e.g., virology were conducted by having John Coffin consult his magic eight ball, the reality of this situation doesn't miraculously make the conclusions rationally sound. Yet this seems to be what you would suggest: truth defined by convention, not truth defined by reason.

The fact that so many virologists are reaching the "everything is contamination" conclusion on the basis of so much assumption, while steadfastly refusing to acknowledge the role or even existence of this assumption, is why many people have become suspicious. Such conspicuous professional disingenuousness is unacceptable when so much is on the line.

 

[Firestormm]

Hi Asleep,

"all HGRV evidence to date is due to contamination"

Who said that?

 

[Mula]

I do not recall that the BWG was looking for 'HGRV existence'. It was looking for whatever it was that Mikovits et al. allegedly discovered in patient's blood. They were involved. They couldn't reproduce their results either. They deemed their finding 'XMRV'. It wasn't there. You and others seem to have expected BWG to have trawled a rather large net.

From my own - albeit limited understanding - it doesn't work that way in science - Lombardi et al. established a claim and that claim was investigated in a blinded methodical way. The association they purported to find so relatively easily and in such high concentrations - could not be substantiated.

If other studies produce results similar to the Lombardi paper that purport to have discovered an association - with something else - another strain - and it was considered significant - that would likewise be investigated. Assuming now of course - in the case of MRVs - they had a solid paper with which to back their claims.

Lipkin for example is attempting to discover if there is indeed the XMRV from Lombardi and the MLV implicated by Lo. It would help of course if all those you are claiming to have reported positively - would have sequenced their findings. Not all have done that I understand.

But Lipkin - as BWG - will do what they can with the evidence they have and that includes properly blinding samples, paying great attention to collection and processing methods, and checking as best they are able for contamination. Indeed I would imagine those involved in the Lipkin Study will pay very close attention - perhaps the closest yet - to checking for contamination and will try to ensure that any source is traced.

As patients we - understandably perhaps - expect 'science' to dot every i and cross every t. To explain every single thing we consider important and even things we don't. But again it doesn't always work like that. It can't.

We sometimes seem to approach these things with a preconceived notion that 'there must be something there and they aren't looking hard enough' or 'they have an agenda not to reveal the truth'. Not always but when it comes to possible retroviral theories and following the publication of Lombardi - this does seems to be the case more often than not on forums especially.

I sometimes feel like asking, if the people who feel published papers are not concluding the 'right' things/whatever whether they have ever engaged with the scientists who publish them (in a courteous way of course) instead of posting things like that at the top of this thread?

The blood working group was established to create blood screening assays using the sample types that blood specimen repositories store, or this was the intention with the initial stages. The great majority of repositories store serum, but whole blood and plasma are also common. Prevalence, transfusion transmission and so on were to be determined in later stages. The Lombardi paper tested different sample types and matrices to the types stored in repositories. Far from this being a failure of their methods it was a failure to create an assay able to screen the blood supply as none of these new tests were found to be reproducible, or if you like able to consistently detect virus. This term could be mistaken for relating to the existence of the virus but in reality it is how consistent an assays performance is.

 

[Adamskitutu]

I'm unclear who is being addressed - none of this charactisation that is address as 'you' -has any resemblence to the attitudes I hold, and more significantly doesn't relate to anything I've written on this thread. My understanding from what you have written is that (as with what I understand to be Asleep's position) your concern is with 'science' as you believe it should be (and you may right to want change),however that concern is with a broad cultural issue, while the point I addressed was about a single study. Selecting a single study which happens to have results which you don't agree with and then using a broad cultural critique to question that study is clearly a fallacious form of argument - the broad cultural critique would apply to all science as practiced under the terms you disagree with, which would include Lo&Alter, Paolucci, and Hanson, as well as Lombardi et al 2009.

In any event, perhaps we could see an end to structuring the argument around who does and who does not believe 'what', and focus on what people write and take that as being the substance rather than what is imputed, implied or ascribed to someone by others.

IVI

'Broad cultural issue' or not - it is nevertheless relevant to this thread - because you are using a broad cultural issue to argue against people critiquing the science on this issue, including the 'single study' here. The parameters of this particular discussion were introduced by you - I am merely responding to your own argument. My argument is therefore not fallacious. But your retort above was. You backtracked on your own argument in order to try to win the point against my objection.