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Jun 1, 2011                              

me+ME: More on XMRV and Science

    
     "A wise man proportions his belief to the evidence."
    
    (David Hume, An Enquiry Concerning Human
      Understanding
)

This continues yesterday's
that was triggered by an article in the Wall Street Journal by Ms Amy Dockser Marcus with the title:
Ms Amy Dockser Marcus's article was triggered by a decision of the editors of Science to try to move dr. Mikovits and her co-authors to retract the study that was published originally in Science in October 2009, that also triggered quite a few other responses, that I will not consider all - and then I am speaking of those I read or glanced through, and not of those that did not reach my attention at all.

Let me start with a few links with brief comments on what they are and link to - and also mention before going on that I presuppose that you have read some about both ME/CFS and XMRV (see nr [1] of the above two links, for example), for else what follows is hard to follow - and I use the original titles of the texts I give links for, but of course the numbering is mine:
I have listed them mostly for documentary purposes, and have myself downloaded all of this, but should remark that at present I can't find [6] where I found it.

Also, I want to quote and remark some, but not about all, and start with remarking that my own position is in item [1] and the links provided there, and that in the text that follows I presuppose the first three items linked above as known.

To item [4] then, by Jamie Deckoff-Jones MD, who is ill with ME/CFS since a long time, like her daughter, and presently working for the Whittemore Peterson Institute, but speaking only for herself on her blog.

I quote by indenting:

Here is Dr. Mikovits' response to the EEC, link, Annette Whittemore's response, link, and the response of the WPI's Clinical Advisory Board, link, sent to Science over the weekend.

The timing of the EEC seems "premature", to put it mildly, with Dr. Lipkin's and Dr. Maldarelli's findings still pending. There is nothing new in either paper that should have precipitated this.

I quite agree - and I also suppose my own degree of belief in XMRV as the cause for ME/CFS is less than that of Ms Deckoff-Jones. Then again, it is a possible cause; it has not been refuted as a possible cause; and I am thankful that Ms Deckoff-Jones, who is an MD, experiments with anti-retrovirals on herself, since she is a medical doctor; knows about both the risks and her own illness; and this kind of experimentation, that indeed is not free from risks,  is one way to find more knowledge and a possible cure, if not for all then for some.

Now to a rather different matter, that I myself have briefly touched upon here, in March:
namely the relation between Dr. Peterson, Dr. Mikovits and the WPI:

I receive many questions about why Dr. Peterson is no longer working with the WPI, which I have generally tried not to answer, because I wasn't there. But, as of today, I think it safe to say that not only is he not working with us, the people he is collaborating with seem intent on destroying the institute that bears his name. I am in the middle of it, and it is unfathomable to me. I have never met Dr. Peterson, but here is my best guess, as the one following in the wake of this attempt to destroy the institute. It has to be all about intellectual property, and revenge. Nothing else makes sense. Why would he provide already tested specimens to Konstance Knox, who has a vendetta against the WPI? Knox worked as a consultant for VIP Dx and left under "difficult circumstances" related to her business practices. Science should have been aware of this history and made a serious inquiry of it. They were alerted to it, but proceeded to publish this morning anyway.

Ms Knox is an author of one of the recent negative papers - meaning in the present text: A paper that reports it couldn't find XMRV in patients with ME/CFS, that also suggests that "therefore" those who found it had a contaminated laboratory - and I did not know of the above, apart from what is in link [8].

I have myself only read the abstract of the paper by Ms Knox et.al., and here is Ms Deckoff-Jones take of it:

Taking the sordid details out of it, the Knox paper is yet another entirely negative paper where they proved they couldn't find it in anyone. Again, there was no real attempt to replicate Lombardi et al, only the innuendo that it was somehow disproved by this paper, by virtue of it being Peterson who provided the specimens. How could Science, a premier journal, publish such shoddy work, sloppier than the Singh paper, though with the same logical fallacy? It can't be both a contaminant and not there at the same time. Which is it? The totality of the evidence says neither. Why is no one asking the real question? How is it that VIP Dx finds approximately 4 out of 10 patients positive, not zero and not 100%? How do you explain contaminating only some of the specimens in the same run?

These are fair and good questions, but I can suggest some answers (without any certainty):

Those who insist it is a contaminant will insist it is there, but only because of contamination. This is difficult to prove and difficult to disprove, and Dr. Lipkin's study is the only one with a design fit to base rational conclusions on.

Meanwhile, one of the things that struck me is that if it is a contaminant, then why is it not present in other labs? Note that if it is a contaminant, 5 or 6 US laboratories, mostly with an excellent reputation, were contaminated - whereas researchers and "researchers" who found nothing generally have far less of a reputation in virology than those who did find XMRV, and should be at least as likely to have a contaminated laboratory as the others.

Then again, I can offer a fairly clear answer to the last question in Ms Deckoff-Jones's last quote: By assuming it is a chance process - but then again, I agree with Ms Deckoff-Jones that claiming it's contamination when it's found, and claiming it must be excellent science if it is not found, is not science but propaganda: At least give me a rational reason why the laboratories that did not find it did not find it because of some contamination, if those laboratories that did find it did find it because of some contamination.


Next paragraph:

And why do all of these scientists feel compelled to practice medicine without licenses? When Konstance Knox gets sick from the infectious contaminants in her lab, shall the doctors remind her that she said to the press that patients shouldn't have the right to try antiretroviral drugs for the viruses that she is too incompetent to find (or wasn't really trying to find in the first place)?

Ms Deckoff-Jones here protests against Ms Knox's insistence (and that of other as well, who are research scientists rather than medical doctors, like Ms Deckoff-Jones is) that one should not use anti-retroviral drugs against ME/CFS, as does Ms Deckoff-Jones, who is an MD, and who has ME/CFS.

Indeed, it is easy to prescribe to others if you don't suffer as they do, and easy to bear the pain and misery of someone other than yourself with stoic indifference. As for me: If Ms Deckoff-Jones, an MD with ME/CFS, is willing to experiment with anti-retrovirals, I can only praise her courage, while insisting that someone in her position is justified to take such a risk, if she feels her condition merits it.

In the next paragraph Ms Deckoff-Jones poses an interesting question:

Why would anyone want to make XMRV go away, when there's so much smoke?

One logical possible answer, that is unlikely testable before 2071 A.D., when the secret state papers on ME/CFS may be released, if the grandchildren of Wessely can't block it then, is that XMRV is a lab-created entity that escaped in the 1970ies, and that was, alas, created as part of secret defense work in England and the US, aimed at creating a sort of biological neutron-bomb: A disease that can lame a whole civil population, without killing them outright, and that may be curable if you know the state secret of what precisely caused it.

This same hypothesis would explain why none other than the British military expert on torture and interrogation - namely that all-too-human professor Wessely - might have been so deeply involved in spreading rumours it is not a virus and "therefore" 'must be'  insanity, neurasthenia, hysterics, somatoforming and/or psychogenic dysfunctional belief systems, if you believe him (which requires a much lower IQ than I have, I warrant you).

The problem is that all the good evidence for this that might be found is a British state secret (and perhaps a US one as well) until 2071 at the soonest (when I will be a mere 121: Secrets worth keeping secret for 60 years must be pretty awesome secrets, one must assume, in a supposedly free country, ruled by impartial and objective laws and courts.)

In any case: XMRV is too dangerous in principle to human beings not to thoroughly research, and any government which tries to block research into it is suspect - but indeed yes: suspicion is no proof, and proof is very unlikely, until professor Wessely is into his 115th year of life, and ready to cackle "who laughs last laughs best", before taking his private lethal draught kindly supplied by HM Secret Service.

Ms Deckoff-Jones final words in her blog are

Today is 600 days since Lombardi et al was published. It is shameful. Please express your outrage to Science.

And while I can understand her anger, I disagree with this: If it makes any difference, it most likely will make a negative difference, and I don't think the editors of Science are malicious or incompetent, while I do believe that they are probably doing and saying what they think is the right thing, while also attempting to protect or salvage their own reputation.

I turn to item [5], by Ms Lopato and Ms Cortez, that starts thus, with a fair enough summary:

A 2009 study on chronic fatigue syndrome that led to a ban on blood donations from sufferers of the disease may have been spoiled by laboratory mistakes, according to the science magazine that published the research.

While the study linked the syndrome to the mouse virus XMRV, at least 10 trials since then haven’t been able to duplicate the results, the journal Science said in an editorial published today. New research also indicates the blood samples used in 2009 likely were contaminated with the virus in the lab, Science said.

The article summarizes more in a journalistically adequate way that I here suppose mostly known to my readers and skip, to turn to this on Dr. Lipkin:

The study of 150 patients with chronic fatigue syndrome and another 150 healthy volunteers should be complete by early 2012, said Ian Lipkin, a professor of epidemiology at Columbia University in New York, who is leading the effort. Until the research is complete, it’s too soon to know whether there is a link between a virus and chronic fatigue, he said.

“Calls to retract the paper at this point are premature,” said Lipkin, director of Columbia’s Center for Infection and Immunity, in a telephone interview. “We need to let this study take its course, look at the data in a coherent fashion and figure out what it tells us.” While interesting, “the publications don’t dissuade us from continuing our work.”

Quite so.

A little further on, Ms Lopato and Ms Cortez come to one of the authors of a negative study:

Scientists led by Jay Levy, a professor of medicine at the University of California, San Francisco, said in a study today that the link was probably because chemicals and cell lines used in the lab where it was detected were contaminated with XMRV.

Levy’s group examined 61 patients with chronic fatigue syndrome, 43 of whom had been previously reported as infected with XMRV. Using a similar procedure to the original paper, the scientists tested the blood. They didn’t find any evidence of XMRV or any other mouse-related virus.

In addition, the Levy study demonstrated that human serum quickly kills the virus, making an infection unlikely.

My problem with this, indeed having known of XMRV now for some 600 days, is that while I am not claiming professor Levy is incompetent or partial or prejudiced (he does seem an associate of Dr. Peterson), I find it quite difficult to apportion degrees of belief, having heard meanwhile so much about contamination:

For example, how can I know, or rationally believe, that professor Levy's negative findings were not caused by some contamination, faulty glass ware, improper test-tubes, or somehow infected medical robots? And similarly, how can I know, or rationally believe, that professor Levy's claim - or more exactly: Ms Lopato and Ms Cortez's claim that
"the Levy study demonstrated that human serum quickly kills the virus, making an infection unlikely.": What was present or absent in his retorts, labs, robots etc.?

Now I am myself quite willing to suppose that professor Levy has rational answers to these questions - but my logical point is that I don't have them, and I haven't read them either, whereas I have meanwhile read quite a lot about contaminations and "contaminations" so called, that apparently can explain any result in any which way some researcher in virology finds convenient, or is convinced is true, or probable, or serves his or her interests best.

And while I am far more optimistic about virology as a science than about psychiatry as a science, this is again why I like the design of Dr. Lipkin's study, both logically and ethically speaking, which has the only design fit to base rational and empirically properly based conclusions on - in principle - that this or that lab did in fact make mistakes, wittingly or unwittingly, and by doing or leaving undone what, precisely.

Finally, to turn to item [6], which is Annette Whittemore's spirited defense of the WPI in a letter to the Editors of Science - and I will quote just two bits, of which the following is the first:

Your conclusions as to why you are issueing this EEC [= "Editorial Expression of Concern" - MM] are based on "at least 10 studies conducted by other investigators and published elsewhere [that] have reported a failure to detect XMRV in independent populations of CFS patients." Not one of 10 referenced studies challenging the results of our research can ethically claim to be a replication study using the methods, processes or materials of Lombardi et al. The only claim that any of the previously published studies are even partial replications of the Lombardi study is limited to the Lo, Alter study. This study confirmed the findings of a retroviral association to those with CFS, as did the Lombardi study. The negative studies are PCR centric and have many flaws. For your use, I have attached a very simple exhibit reviewing the methods used in several studies as a tool to compare these studies to the Lombardi study. I want to assure you that there is no data to suggest that our research results are invalid.

The exhibit Ms Whittemore mentions is quite interesting, but I won't include it i.a. because I have to copy by typing, since the pdf is an image rather than text, and the exhibit is fairly large as well. But it is a good and interesting comparison, that's also quite relevant.

Then to Konstance Knox, principal author of a negative study that the Science editors seem to have found convincing, and also the subject of complaints by Ms. Deckoff-Jones, that I quoted above. Here is Annette Whittemore on the same subject:

As to the second report referenced by you, authored by K. Knox et. al., I am obligated to report that the first author, dr. Konstance Knox, is not unbiased, impartial, or independent with respect to the WPI. She and her laboratory, Wisconsin Viral Research Group, were former contractors and left under difficult circumstances. Her conduct was the subject of an internal review of serious matters related to ethical violations; misuse of proprietary information; improper use, retention and destruction of patient samples and data; and disagreements over the ownership of intellectual property.
 
Well... this is fairly strong stuff, that is hard to judge for outsiders. But from the face of it, it seems as if Ms Knox may have had her own reasons not to want to find any XMRV or perhaps to settle scores with the WPI somehow.

However that may be, I think Dr. Lipkin is right: To insist that Lombardi et.al. should withdraw their paper is premature, if only because the dangers involved in XMRV ought to be researched properly, and not finished by unproved and unprovable aspersions of laboratory contamination.

And if laboratory contamination is a factor at all, which it well may be, then that should be properly investigated, because as the situation is presently, it seems one can get around the results of any virological research, if one finds the results inconvenient, namely by setting up a rumour of 'it's lab-contamination, stupid!'

That is not scientific procedure - and I can do myself quite the same for any negative study, if I felt thus inclined.

So let's see what Dr. Lipkin's study brings, and then try to decide on the basis of those results whatever really happened around XMRV.

Also, since this does involve rather a lot of money of US taxpayers, let me remind the scientists involved that they are, ethically speaking, responsible to the US citizens in the first place, namely to try to guarantee that the blood in US bloodbanks, that any US citizen may need at any moment given an accident, is not contaminated with dangerous retroviruses, or if it is, what can be rationally and reasonably done about this.



P.S. Corrections, if any are necessary, have to be made later.


                              As to ME/CFS (that I prefer to call ME):

1.  Anthony Komarof Ten discoveries about the biology of CFS (pdf)
2.  Malcolm Hooper THE MENTAL HEALTH MOVEMENT: 
PERSECUTION OF PATIENTS?
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)
9.
 Maarten Maartensz
ME in Amsterdam - surviving in Amsterdam with ME (Dutch)
10.
 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.


Maarten Maartensz (M.A. psy, B.A. phi)
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