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Dec 26, 2011               

me+ME: Sorting through some evidence about dr. Mikovits


Abbie Smith had better get her parents to cough up money for her oncoming legal woes. A grad student from some bogus Kansas university can damage the reputation and career of a world renowned researcher? WHO was Abbie Smith's so-called "source"? Since Smith is not a journalist she should be required to tell her source.
Good luck finding a job if you do complete your degree.
-- Sharon Stapleton

It is hard to believe that a man is telling the truth when you know that you would lie if you were in his place.
-- H.L. Mencken


      1. Introduction
      2. Backgrounds
      3. Sorting through some evidence about dr. Mikovits

1. Introduction

I have divided the earlier version of Nederlog of December 26 - Boxing Day - in (i) a boxing part about the Bobbean horrors that intelligent readers of the Phoenix Rising forums have to suffer a lot from, willy nilly, for this freaky horror may pop up everywhere, in any discussion that promises to be possibly rational, by educated persons, and (ii) the present part about some evidence in case of dr. Mikovits.

So... having considered the horror of anonymous nitwits who make any rational discussion by rational people on forums for patients with ME/CFS effectively impossible, and who also make the reading of such forums a daily exercise in nausea control, let me turn to the case of dr. Mikovits and the hunting for the XMRV-snark that has turned out to be a HGRV-bogus.

2. Backgrounds

To start with my own Nederlog on the withdrawal

- me+ME: Science withdraws 2009 XMRV-paper

Here the reader can find seven links, of which the first listed there, by Jon Cohen in Science, is best and contains the most information:

- In a Rare Move, Science Without Authors' Consent Retracts
  Paper That Tied Mouse Virus to Chronic Fatigue Syndrome

There also was a good article by David Tuller in the NYT:

        - Fatigue Syndrome Study Is Retracted by Journal

And there is an issue in Abbie Smith's series on XMRV and CFS:

- XMRV and chronic fatigue syndrome: RETRACTED

She in turn links to another good Jon Cohen article, namely that of October 4:

- Chronic Fatigue Syndrome Researcher Fired
   Amidst New Controversy

This I will consider below, but while Science did report well on the subject, so did Nature, and here is a list of Ewen Callaway's articles on it all from 2011, but in the order published and with dates and titles:

- Mar 14: Fighting for a cause
- Oct  5:  Integrity issue follows fired researcher
- Nov 21:
Researcher arrested over missing lab notebooks
- Nov 22:
Researcher confesses to stealing lab notebooks
- Nov 29: Embattled scientist in theft probe
- Dec 15: Chronic fatigue syndrome scientist
              finds a temporary home

Taken together, the links in this section provide a fair summary of dr. Mikovits's case, although something is still missing that those interested in detective novels or criminal cases should not miss. I provide a link to a Nederlog of mine

- ME: WPI vs Mikovits - documents in the case

and from thence links to four pdf's produce by the WPI (Whittemore Peterson Institute, whence dr. Mikovits was fired on September 29). The first is by the lawyers for the WPI, the other three are sworn statements. All is from the court case WPI vs Mikovits, about the disappeared lab books and other materials, and it reads like a crime novel:   [*]

- Reply To Opposition To Motion For Preliminary Injunction
- Exhibit 1: Affidavit of Max Pfost
- Exhibit 2: Affidavit of Max Pfost
- Exhibit 3: Affidavit of Amanda McKenzie 

3. Sorting through some evidence about dr. Mikovits

Now let me consider six consecutive paragraphs from Jon Cohen's

- Chronic Fatigue Syndrome Researcher Fired
   Amidst New Controversy

that gives the clearest explanation of the matters I'm concerned with in one place. I start with noting that it is from October 4 last, and that I quote by indenting:

Then on 29 September, Mikovits was fired from her job as research director of the Whittemore Peterson Institute for Neuro-Immune Disease (WPI), a private organization in Reno, Nevada, devoted to CFS research and treatment. Both Mikovits and WPI's CEO, Annette Whittemore, say the firing was not related to the XMRV theory's demise.

That seems true, though the reason given around that time by the WPI seems also not to have been the full truth, which seems to be that dr. Mikovits had "misappopriated" cell lines addressed and sent to dr. Lombardi. See

- me+ME: More on St. Judy

Also the 29th of September is the day when dr. Mikovits and her personal assistent Max Pfost decided, after dr. Mikovits had been fired, that Max Pfost should steal the lab-books, notebooks and some flash drives from the WPI, using the keys of the former, as also was done in the morning of September 30:

- Exhibit 1: Affidavit of Max Pfost

To continue with Jon Cohen's article:

The very next day, a graduate student who writes a snarky blog that has been highly critical of Mikovits and the XMRV theory raised questions about whether a figure in Lombardi et al. had been misrepresented. Science Executive Editor Monica Bradford said in a statement that the journal is investigating the allegation. "As is our policy in cases of alleged figure manipulation, we follow up with the research authors as soon as our own review of the allegation is complete," said Bradford. "Science takes all such matters seriously and seeks to respond thoroughly and efficiently."

Actually the relevant blog is here, including pictures and 1122 comments:

- ERV's blog # 29 on XMRV and CFS ("magic trick")

This ended 10 weeks later with Science's chief-editor retracting the whole article. I do in fact have the pdf for that, but can't find it on line on the moment, but as Abbie Smith also reported

- Bulk of the letter is up at Retraction Watch!

To continue quoting Jon Cohen's October 4 article:

The furor revolves around an image—the bottom half of Figure 2C in Lombardi et al.—that shows XMRV proteins in CFS patients but not healthy controls. In her blog known as ERV (endogenous retroviruses), Abbie Smith on 30 September noted the striking similarities between Figure 2C and a slide Mikovits presented at a CFS meeting in Ottawa, Canada, on 23 September. Smith, who is working on her doctoral dissertation at the University of Oklahoma, Oklahoma City, and studies HIV, wrote that an anonymous tipster had pointed out to her that the two images looked identical but had different patient numbers and experimental conditions. Smith questioned whether this was a simple mistake or an attempt to recycle old data to make a new argument.

At the time, this led to a lot of denials by V99 and Gerwyn and others of the group of those who just KNOW it takes only a brainfogged non-scientist, or some sociology lecturer, to KNOW what is true about ME/CFS:

The Ottawa slide supported Mikovits's contention that even if XMRV could not be detected in CFS patients, other gammaretroviruses still lurked in their chromosomes. Mikovits described how she had treated cells from two CFS patients with a chemical, 5-azacytidine, that takes methyl groups off DNA. This procedure prods cells that harbor latent versions of retroviruses to produce them, and the image on the slide showed the resultant proteins in what's known as a Western blot gel. In Lombardi et al. what appears to be the same image shows "XMRV proteins" and makes no mention of 5-azacytidine use.

The first major difficulty with this is is that the same slide - as meanwhile, in spite of V99 et al's many denials, seems accepted by anyone halfway sane or better - cannot support two different interpretations, "proving" ocularly in September 2009 to the reviewers of Science that there is XMRV in patients, and "proving" ocularly in September 2011 to a mostly lay audience in Canada that other gammaretroviruses could be found in ME/CFS-patients' blood.

Of course, for dr. Mikovits this was a way of trying to cope with the quite epic fail of her group in the BWG-study, summarized here

- XMRV Webinar Links & Other XMRV Updates

in which it was shown, with her and Ruscetti's signatures next to 23 others, that she could not distinguish blood with XMRV from blood without XMRV beyond chance level, if the samples were blinded: "Really" - her story runs - "there is no XMRV in the blood of ME/CFS-patients, for this indeed is a lab contaminination, as the BWG showed, but there is something there: Look at my pictures!" (I do not quote, but sketch dr. Mikovits argument.)

But then the same slide cannot bear two conflicting interpretations, and in fact there is a logically more simple explanation than that dr. Mikovits and her group had found evidence of not "XMRV" but of "HGRV" in 2009:

Dr. Mikovits, or someone else in her group, had added 5-azacytidine, and not to prod HGRV to appear, as was claimed in 2011, but to prod the referees of Science into a conviction - by ocular "proof" - that dr. Mikovits and her group had found "XMRV", in 2009.

As it happens, this was clearly explained on Phoenix Rising on October 6:

- Why does 5AZA matter?

to which I returned in my long sum-up of October 8 of exactly two years of hunting for the snark, that turned out to be a bogus:

- me+ME: Two years of XMRV + recent personal e-mails

The second major difficulty, logically speaking, is that dr. Mikovits's move - "no, it actually isn't XMRV: it's HGRV!" - is a typical fallacy known as ad hoc or as the No True Scotsman fallacy when faced with a counterexample.

The Scotsman got involved thus: If someone has a theory that all Scotsmen are drunks, and someone names a Scot who isn't, that person gets fallaciously rebutted that it cannot be a true Scotsman, then, simply because all Scotsmen - the true ones - are drunks. Similarly, dr. Mikovits's line of reasoning was that the Lombardi et al paper does not prove that XMRV can be found in the blood of ME/CFS-patients, for this is not a proper Scot: The true Scot she and her group found was HGRV.

The third major difficulty with the whole fallacious line of reasoning is that in any case the work done by the BWG shows that it is most improbable that dr. Mikovits can distinguish either in the blood of patients: The first not, because it is a lab-contaminant, as she meanwhile agrees; the second not, because she never showed she could, and the whole idea of HGRV is an ad hoc construction without any proven reality. (*)

I turn again to Jon Cohen's article:

Mikovits's collaborator, Francis Ruscetti of the National Cancer Institute (NCI) in Frederick, Maryland, who ran all of the Western blots, confirms that the Ottawa slide uses the same image that appears in Lombardi et al. Ruscetti and Mikovits, in a joint e-mail to Science for this article, said many patients and their doctor, Daniel Peterson (who since has had a falling out with WPI), knew the original coded numbers, so the researchers changed them for the Science publication to "protect the patient privacy." Ruscetti says it was a mistake for Mikovits to have used the original patient codes in Ottawa. "We were under so much pressure, we missed it," says Ruscetti.

The first statement contradicted tales from V99 and/or Gerwyn, who have insisted for a most irrationally long time that the gels Abbie Smith did her magic trick with were not identical; and then that the same gels must have been stolen if identical (presumably because meanwhile dr. Mikovits stood accused of having stolen things, and True Believers' minds work this way), which at least V99 seems to believe to this day.

The second statement is very strange, for it suggests that dr. Peterson deserves to be misled and lied to: Why could he not be simply informed, also in 2009, of the findings, and asked not to tell the patients? Is it not more likely that he simply knows too much about ME/CFS to be taken in if supplied with all relevant information? And indeed, dr. Peterson has since 2010 disbelieved the XMRV-story, while dr. Mikovits may have known enough of her own colleague at WPI to have known he probably would disbelieve her. Which explains also why he was not informed in 2009, originally, and for a long time.

As to the third statement, dr. Ruscetti is probably right that dr. Mikovits made a mistake - but then there is this problem, for which I return to Jon Cohen's text:

As far as the use of 5-azacytidine, Ruscetti and Mikovits stressed in their e-mail that "there was no attempt in the original paper to hide anything." They say for the purposes of Lombardi et al., the use of 5-azacytidine was not germane: They were simply trying to demonstrate that CFS patients had viral proteins not seen in controls. By the time of the Ottawa meeting, they say they realized that this experiment did not in fact show XMRV but proteins from a broader family of gammaretroviruses.

The last part is again the ad hoc fallacy considered above - which logically implies the two in fact agree that the 2009 paper was mistaken: It did not establish evidence that XMRV was correlated to ME/CFS. (For it undubitably proved the presence of a true Scotsman, pardon, HGRV, they want it to be believed, ad hoc.)

The first part seems false: It seems most retrovirologists are agreed that if Science's reviewers would have known that Lombardi et al had used 5-azacytidine, then they would not have accepted the paper, which in turn would not have started quite a few retrovirologist on a hunt for the XMRV-snark, while they should have looked for a HGRV-bogus, or some kind of fraud, possibly well intended.

Indeed, the last possibility seems one of the two most likely hypothetical explanations:

Hypothesis 0: Some of he authors of Lombardi et all believed they had found something real in the blood of patients with ME/CFS, namely XMRV, but because they found it themselves difficult to establish, they decided to add a primer to a test which would make it appear to be there - after which, they hoped, in this hypothetical explanation, colleagues would help finding more of it, since they had found it also (not knowing at the time it was a lab-contaminant).

The other most likely hypothetical explanation is a bit more cynical:

Hypothesis 1: Some of the authors of Lombardi et all decided to add a primer to a test which would make it appear they had found XMRV - after which, they hoped, in this hypothetical explanation, they could keep the story going for quite a while, and cash in on XMRV-related tests and patents, meanwhile maintaining that real science is difficult and uncertain, while they themselves meant extra-ordinarily well, and patients should support and believe them.

I admit to being a bad, elderly and cynical person, who has read too much history to believe in a majority of intelligent and honest rational men and women, which may be the reason that I incline to the last explanation, that also has the merits of being logically simple while explaining much. ("You have been had! LOL!") (**)

Either hypothetical explanation is a LOT more credible - it seems to me - than the one dr. Mikovits, V99, Gerwyn, Bob and Angela tout:

Hypothesis 2: That the dear sainted one, while failing to find XMRV, quite unbeknown to her planet-sized brain, in fact established the presence of HGRV.

For that's rather a bit too much like Harold Camping's repeated warnings of the coming of the apocalyps, including his (ad hoc, post hoc) original calculating mistake. See also

- Cognitive Dissonance
- When Prophecy Fails
- Pseudoscience

- Unfulfilled religious predictions

[- Breaking News: PR-F: XMRV: Lo et al paper retracted by author]
 - Virology Blog: Authors retract paper on detection of murine leukemia
   virus-releated sequences in CFS patients ]

(*) It still is logically possible that there is a virus involved in ME/CFS and indeed also possible that dr. Lipkin may find it, using the new NGR-sequencing technique. I don't know, but having fallen ill, like my ex, with EBV, in January 1979 and never having gotten better, my first guess must be EBV, and my second some flue-like virus that manages to upset and indeed bug the process of recuperation from disease in some people, possible for a genetical reason. See my Nederlog from March:

    - me+ME: Some speculations around ME and XMRV - part I

Warning on Phoenix Rising links on my site (and others):

Phoenix Rising changed the internetname of its forums this year, for which reason links to these forums from before the summer of 2011 fail, at least for me and from my sites. (I may try to repair this later, and will remark upon this when I have.)

(**) That ill people may have been had is a distinct possibility, but whatever is the truth, I do believe most authors of Lombardi et al meant well, and did not know about manipulation of the data, if indeed this happened.

Corrections, if any are necessary, have to be made later. 
-- Dec 27, 2011: I have split the original Nederlog of Dec 26 into
two parts, and made a few other changes, mostly to make a clean
break between satire and exposition.
[*] Dec 28, 2011: I found yesterday that the materials the WPI had on its site
about the civil courtcase against dr. Mikovits have disappeared from the WPI-site.
Since I had them downloaded - status 22 and 23 nov 2011 - I put them on my
site and relinked to have the evidence available.


As to ME/CFS (that I prefer to call ME):
1.  Anthony Komaroff Ten discoveries about the biology of CFS (pdf)
3.  Hillary Johnson The Why
4.  Consensus of M.D.s Canadian Consensus Government Report on ME (pdf)
5.  Eleanor Stein Clinical Guidelines for Psychiatrists (pdf)
6.  William Clifford The Ethics of Belief
7.  Paul Lutus

Is Psychology a Science?

8.  Malcolm Hooper Magical Medicine (pdf)
 Maarten Maartensz
ME in Amsterdam - surviving in Amsterdam with ME (Dutch)
 Maarten Maartensz Myalgic Encephalomyelitis

Short descriptions of the above:                

1. Ten reasons why ME/CFS is a real disease by a professor of medicine of Harvard.
2. Long essay by a professor emeritus of medical chemistry about maltreatment of ME.
3. Explanation of what's happening around ME by an investigative journalist.
4. Report to Canadian Government on ME, by many medical experts.
5. Advice to psychiatrist by a psychiatrist who understands ME is an organic disease
6. English mathematical genius on one's responsibilities in the matter of one's beliefs:

7. A space- and computer-scientist takes a look at psychology.
8. Malcolm Hooper puts things together status 2010.
9. I tell my story of surviving (so far) in Amsterdam/ with ME.
10. The directory on my site about ME.

See also: ME -Documentation and ME - Resources
The last has many files, all on my site to keep them accessible.

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