Nederlog

 

December 22, 2010

 

ME+me: XMRV=contamination?



I continue being not well, and otherwise also as before, so I cannot do much. Today I take up the theme of the last time, also summarized in the title. And I assume you mostly remember what I said the last time for which also see, and especially the first, because it is brief, clear and to the point

Sections:

1. Lipkin and Mikovits
2. Pinching an ME Association
3. Racaniello and Klein
4. Lies, deception and ME

The issue, then, is whether the positive XMRV-findings are due to lab contamination:

1. Lipkin and Mikovits

I wrote the last time that I was interested in Dr. Lipkin's statement, and it was made the same day, is to be found on PR-F, and is eminently rational and addresses the papers in Retrovirology, the claim that it is la contamination, directly:

These papers emphasize the pitfalls of molecular assays and raise concerns. Nonetheless, it is premature to rule out XMRV or related viruses as factors in prostate cancer or CFS. Links have also been made based on serology and the presence of viral proteins as well as of viral sequences. Thus, we still need appropriately powered, rigorous blinded studies of well characterized patients and controls. One such study is underway under the auspices of the National Institutes Health.
Ian

W. Ian Lipkin, MD
John Snow Professor of Epidemiology and Director
Center for Infection and Immunity
Mailman School of Public Health

Professor of Pathology and Neurology
College of Physicians & Surgeons
Columbia University
722 West 168th Street, 17th Floor

And here is Dr. Mikovits, likewise eminently rational and addressing points raised in the fresh "it is lab contamination" publications:

The Lombardi et al. and Lo et al. studies were done using four different methods of detection. They were not simply PCR experiments, as were the studies by McClure et al. and others who have recently reported their difficulties with contamination. Experienced researchers such as Mikovits, Lombardi, Lo and their collaborators understand the limitations of PCR technology, especially the possibility of sample contamination. As a result, we and Lo et al. conducted rigorous studies to prevent and rule out any possibility that the results reported were from contamination.

In addition to the use of PCR methodology, the Lombardi team used two other scientific techniques to determine whether, in fact, we had found new retroviruses in human blood samples. We identified a human antibody response to a gamma retroviral infection and we demonstrated that live gamma retrovirus isolated from human blood could infect human cells in culture. These scientific findings cannot be explained by contamination with mouse cells, mouse DNA or XMRV-related virus-contaminated human tumor cells. No mouse cell lines and none of the human cell lines reported today by Hue et al. to contain XMRV were ever cultured in the WPI lab where our PCR experiments were performed.

Humans cannot make antibodies to viruses related to murine leukemia viruses unless they have been exposed to virus proteins. Therefore, recent publications regarding PCR contamination do not change the conclusions of the Lombardi et al. and Lo et al. studies that concluded that patients with ME/CFS are infected with human gammaretroviruses. We have never claimed that CFS was caused by XMRV, only that CFS patients possess antibodies to XMRV related proteins and harbor infectious XMRV, which integrates into human chromosomes and thus is a human infection of as yet unknown pathogenic potential "The coauthors stand by the conclusions of Lombardi et al. Nothing that has been published to date refutes our data."

Judy A. Mikovits

Both responses are from December 20. Nevertheless...

2. Pinching an ME Association

Something that calls itself "Professor Anthony J Pinching" - never heard of it - in liege with no less than the worthies of the ME-association, that supposedly is on the side of patients with ME, and not on the side of pseudoscientists the next day, December 21, published the following, that I quote in full in blue. You find Pinching's disgraceful phony baloney under the link. I quote it in blue with my comments in black in between:


XMRV update: comment from Professor Tony Pinching

December 21, 2010

Since the original study suggesting a possible link between CFS/ME and the XMRV retrovirus, there have been six published reports from reputable groups in three continents that have failed to find evidence of this virus. These studies have used appropriate techniques in well characterised CFS/ME patients.

I have no evidence of that - "appropriate techniques" and "well characterised CFS/ME patients" - and dislike claims presented at science that are mere opinion without any proof. Also, Cort Johnson printed a list on Phoenix Rising that showed that in fact only few samples were investigated:

"I just looked at the Hue paper: this is what they looked at

  • CFS - 2 full-length samples
  • pol sequences from prostate cancer - 6
  • sequence from 22Rv1 cell line - 1
  • endogenous MLV sequences - 46
  • DG 75 complete genome sequence - 1
  • full length MLV sequences from VP 62 - 28
  • murine C retrovirus - 1
  • MLV complete genome sequence - 1
  • Moloney MLV - 1
  • AKV MLV - 1

So there were only two XMRV CFS samples - not alot!"

One study found evidence of two different retroviruses, the significance of which is unclear.

Four very recent further studies (two of them including as author one of the original commentators on the first report) have provided strong evidence to suggest that laboratory and/or reagent contamination are the likely explanation for the original findings.

Well... no: I reject "strong evidence". That's again mere opinion without argument and manipulative when addressed to a public of non-scientists.

The current view of informed observers

And yet more manipulative propaganda talk, this informed observer concludes: Professor Pinching, who are you being paid by? Who are you really serving while pretending to be serving science, truth and patients with ME?!

is that the research evidence does not support the idea that XMRV or other retroviruses have a role in the causation or manifestations of CFS/ME.

False. Some research evidence does, other research evidence doesn't.

Why are you misrepresenting, Pinching?

This type of virus is especially liable to be found as a result of inadvertent laboratory contamination,

Unfounded: "especially liable ". And why not say simply: We - Greg Towers, Tony Pinching etc. - claim that doctors Lo, Alter and Mikovits are incompetent if not liars?!

and there is now direct evidence to support this explanation.

So let's be straight: there was no direct evidence before, right?!

There is an ongoing study in which samples from the same patients are sent to multiple laboratories, and this together with the latest reports may conclude the matter.

I take it this refers to Lipkin's research, who did have this plan. And his statement is printed above, and whatever the truth, Lipkin is a name in medical science, Pinching merely a non-entity, a cipher.

There is currently no basis for using tests or treatment based on the initial findings in clinical practise.

False: The Lombardi and Lo/Alter-papers give evidence for trying out such treatments. Pinching may disagree - God knows on what rational knowledge, for that he does not deign to give - but he may not misrepresent, and does.

I find that extremely dishonest, worrisome and despicable - and see my Feynman vs Wessely for my reasons why: Pinching, it may be safely concluded, is yet another Cargo Cult pseudo-scientist, if not an out and out betrayer of patients.

The original findings raised high expectations, but the hopes now seem to have been dashed.

Manipulative language, and as so much manipulative language without clear referents while oozing innuendo: whose "high expectations", and whose "hopes"?! And why the manipulative "seem"? (In any case, speaking for myself: I just don't know whether XMRV is involved in ME, and nobody does, at this point in time - and again I am not precisely madly happy about the possibility of having XMRV: It's not a pleasant prospect if true, in my estimate.)

We have been here many times before.

Pinching certainly has not been there any time before as a patient. And I dislike this phonyness, and besides do not consider myself in his class, nor him in my class.

Professor Greg Towers, an author of one of the recent studies comments appropriately in a press release. Our conclusion is quite simple: XMRV is not the cause of chronic fatigue syndrome.

Well, that is false. And it is intentional lying if made into a press release or published comment by a supposed medical scientist: The conclusion they are at most entitled to is that there is some new evidence that XMRV may be detected due to lab contamination. But in fact that has possibility has been known from the beginning. And there has been no scientific discussion, while the papers referred to are pre-published.

So messrs. Towers and Pinching are misrepresenting and deceiving the public - whatever the real facts of the matter, that they have as little definite knowledge of as anyone else.

All our evidence

False and misleading: "All" the evidence Pinching - pretends to - believe; not all evidence in all scientific journals, for both Lombardi et al. and Lo and Alter et al. present contrary evidence.

So why does Pinching lie? In whose pay is he?

shows that the sequences from the virus genome in cell culture have contaminated human chronic fatigue syndrome and prostate cancer samples.

Again, Pinching phony baloney: be honest and say clearly that Lo, Alter and Mikovits are incompetent if not liars, for that is what it comes down to, also what with "All our evidence". Tell the world that you, Tony Pinching, knows what the truth is, and a man like Alter compared with you a fool if not a liar. For that's what your doing, phony Tony - except that you lack the balls to be forthrigth.

It is vital to understand that we are not saying chronic fatigue syndrome does not have a virus cause we cannot answer that yet but we know it is not this virus causing it.

If so, Pinching is a liar or an incompetent, for he knows no such thing. Neither do I, nor do I know its denial, but I am not lying.

Indeed, it's an interesting question why Pynching and Towers and indeed Wessely and McClure overplay their hands so much, scientifically and logically speaking, and do so especially in especially prepared press releases.

The answer is, no doubt, for the most part that they are not real scienists but pomo propagandists for their own interest-groups of pseudo-scientists making money from patients and health-insurance by pseudo-science, lies and deceptions, for money. See:
McCulloch vs. Wessely.

The main benefit of the episode has been an increased awareness of the need for more substantial understanding of the biological basis for CFS/ME,

Mother Hubbard's Soft Soaping exemplified.

and for better tests and treatments.

O the lovely hypocrisy! May I conclude this also covers the NICE treatments and tests, and the Wesselyan tests and treatments?! I may, mayn't I? And these are all without any biological basis, right?! And nevertheless imposed as if they were science on patients?! What happened to science, medicine and morals in England?!

For the CFS/ME community,

I am not a community. I am an individual.

the strong health warning must be not to rush to embrace new research findings until they have been confirmed.

Well, WTF are you liar or nitwit sending press releases or pretentious professorial comments into the world for? And whence this condescending BS about what I should and should not feel or think?

Professor Anthony J Pinching

Note to self if ever I come to England:

Clearly this creature is not a medical person equipped with a rational mind and moral conscience. Beware!

What I also question having arrived here is the morality and/or brains of the medical advisor of the ME Association:

Chas, what do you have between your ears? You do not need to believe in XMRV as a possible cause for ME .... but since when is it fit for a patients organization to publish execrable baloney like the above stupid shite - if you excuse me - as if it could possibly make scientific sense, and is not an out and out piece of lying propaganda for the Wesselytes?!

In support of this there is the following, again by medical doctors very much more prominent and well-known than either Pinching or Shepherd:

3. Racaniello and Klein

Meanwhile, a prominent retrovirologist, professor Vincent Racaniello, has insisted yesterday that he is not convinced xmrv is the result of lab contamination, but at the moment I can't get his site. The link is here:

And the text is this - quite courageous also:

Yesterday the Chicago Tribune published my reaction to the four papers on the retrovirus XMRV published this week in the journal Retrovirology. I was quoted as saying These four papers are probably the beginning of the end of XMRV and CFS. I wish to retract this statement and explain my reasons for doing so.

Early Monday a reporter for the Chicago Tribune, Trine Tsouderos, sent an email asking for my thoughts on four XMRV papers that had just been released (paper one, two, three, four). I read all four papers and decided that they raised serious concerns about the role of XMRV in human disease. Specifically, the four papers demonstrated different ways that assays for XMRV could be subject to contamination with murine viral sequences. I wrote an email to Ms. Tsouderos outlining my summary of the papers, and later that day her article was published. My statement was reproduced exactly from the email I had sent her, so I was not misquoted.

I then set out to write about the papers for my blog about viruses. I read the papers over again, and began checking XMRV sequences in Genbank. I also began an email correspondence with authors of three of the four papers, and spoke with my virology colleagues here at Columbia. As a consequence of this additional research I decided that my initial impression of the papers was incorrect, which is evident in my post entitled Is XMRV a laboratory contaminant?. Almost immediately after publishing the piece readers began to ask why my comments to the Chicago Tribune had such a different tone. I concluded that a retraction and explanation were necessary.

Upon re-reading three of the four Retrovirology papers it became clear to me that they show that identification of XMRV can be fraught with contamination problems, but they do not imply that previously published studies are compromised by these findings. Clearly any new studies done on XMRV should keep in mind the potential for contamination from PCR kits and murine nucleic acids.

I was initially more troubled by the fourth paper by Hue and colleagues. There are four major findings in this paper (gag PCR primers are not specific for XMRV; the virus is present in 5 human tumor cell lines; two XMRV isolates are nearly identical to a virus from the human prostate cell line and also contain an insertion from the murine retrovirus MoMLV; and there is more nucleotide diversity in viral sequences from 22Rv1 cells than in all the patient XMRV sequences). The fact that two XMRV isolates seem to be laboratory contaminants judged by the presence of MoMLV sequences was initially unsettling until it became clear that other XMRV isolates do not have this insertion. That leaves the fourth finding that XMRV from 22Rv1 cells appears ancestral to, and more diverse than, all the human XMRV sequences. I decided that this result was less troublesome than I had originally believed, in part because it is not clear that the differences among the 22Rv1 viruses did not arise during PCR amplification.

My conclusion is that these four papers point out how identification of XMRV from human specimens can be complicated by contamination, but they do not mean that previous studies were compromised. They serve as an important reminder that future experiments to identify XMRV need to be appropriately controlled to ensure that the results are not compromised by contamination.

In other words, these four papers are NOT the beginning of the end of XMRV and CFS. Rather, research on the role of this virus in human disease must proceed, with large, case-controlled epidemiological studies, as suggested by others.

I would like to apologize to anyone who was offended, angered, or disappointed in any way by my statement to the Chicago Tribune. It is my goal to educate the public about virology, and clearly I did not do that very well.

There are at least two lessons that you can take away from this incident. First, that I make mistakes, and that Im willing to admit it. Everyone does, including scientists. Second, if I had difficulties interpreting these papers, how would non-scientists fare?

And professor Klein, from the Cleveland Clinic, protested as follows, also yesterday

We have reported XMRV integration in fresh frozen prostate tissue taken directly from patients at radical prostatectomy that has never been put in tissue culture and believe this is solid evidence of authentic human infection. See Dong et al PNAS 2007 and Kim et al. J Virol 2008

Again, this is no proof positive that none of the positive findings of xmrv can be caused by lab contamination, but it is proof positive that persons like Pinching and Towers lie and deceive, and do so knowingly, for else they were not professors:  They systematically and on purpose give one side of the argument only, and pretend the other does not exist.

That is not science, that is propaganda, and it is very immoral dirty playing when done by nominal "medical scientists" or nominal "advocates" for patients with ME.

4. Lies, deception and ME

Meanwhile... one of the things I have learned over the past year is that the main reason why there is now for decades no real scientific progress in the study of the cause(s) of ME/CFS is that several groups of pseudo-scientists, working in coordination since over two decades - namely in and around the CDC in the US: Reeves, Jones, and in various British universities: Wessely, White, Chalder, Sharpe, and governmental institutions and in the Radboud Universiteit in Nijmegen, Holland: Bleijenberg and Van der Meer - have given up science if they ever were real scientists, and instead further the interests of their professions or health-insurors or the state that has to pick up part of the medical bills by doing pseudo-science that is in fact directed at and meant for the media, parliamentarians and bureaucrats and ngo's to get their egoistic ways.

This gets very nauseating to me, also because these are crafty, degenerate, immoral and also, especially in England, powerful and dangerous liars and deceivers:

Whereas some real scientists try to do real science in the interests of patients who are really ill, there is a socially and institutionally more powerful group of pseudo-scientists who in fact are playing the media and doing politics rather than science, while pretending to do the best and to do "evidence based science".

All the evidence have found over the past 15 months is that they are pseudo-scientific liars and deceivers, blocking the way of rational inquiry and reasonable help. And this judgment of mine is not a subjective but a logically highly informed one: What I get from pseudo-scientists in the name of "evidence based science" was invariably rhetorics plus methodological deception.


P.S. Let me again repeat what I said or suggested above: I have no strong beliefs about the relation between XMRV and ME either way, basically because I know nothing about virology, and I just don't know whether XMRV is involved in ME, and nobody does know, at this point in time - and also I am not precisely madly happy about the possibility of having XMRV: It's not a pleasant prospect if true, in my estimate, and there are less worrisome possible scientific bio-medical explanations for ME/CFS.

Meanwhile, a logically relevant fact that I did not mention sofar is this: The American medical doctor Deckoff-Jones and her daughter, both with ME/CFS since many years, and also another American medical doctor, are doing quite well now since quite a few months on medicines suggested by HIV-research, and based on the relations between XMRV and HIV, that both are retroviruses.

But yes... it is difficult to appraise this other than as 'interesting anecdotical evidence', and in the end I just don't know about the relation between XMRV and ME, and so far nobody knows, and all who say they know and are medical scientists are incompetent or liars - and I do know when I am lied to, when I am propagandized, when frauds present pseudo-science as "evidence-based science", when an argument is logically or mathematically valid or not, and what does make fundamental sense in real science, for I am a psychologist and had hoped to be a philosopher of science and mathematical logician if I had not fallen ill.

And to the best of my knowledge professors Pinching and Towers, whose stuff on the papers in Retrovirology I have read, lie knowingly and indeed as if they are trained well in doing so. I do not extend this to the papers in to be published in Retrovirology: These have to be decently discussed in a rational scientific way, instead of abused while they are not even published properly yet, to make propaganda to the media in the way of Pinching and Towers.

But the abuse Pinching and Towers made of this, specifically in their lies and deceptions directed at the media, is frightful and sickening, and should be sufficient reason for the professional bodies of these gentlemen to take steps against them.

Corrections to the above text will have to be made later in view of my health.
-- 23 december 2010: Some typos have been corrected.

P.P.S. It may be I have to stop Nederlog for a while. The reason is that I am physically not well at all. I don't know yet, but if there is no Nederlog, now you know the reason.


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

1. Anthony Komaroff

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 (many 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)

Short descriptions:

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:
   "it is wrong always, everywhere, and for anyone, to believe anything upon
     insufficient evidence
".
7. A space- and computer-scientist takes a look at psychology.
8. Malcolm Hooper puts things together status 2010.
 


    "Ah me! alas, pain, pain ever, forever!

No change, no pause, no hope! Yet I endure.
I ask the Earth, have not the mountains felt?
I ask yon Heaven, the all-beholding Sun,
Has it not seen? The Sea, in storm or calm,
Heaven's ever-changing Shadow, spread below,
Have its deaf waves not heard my agony?
Ah me! alas, pain, pain ever, forever!
"
     - (Shelley, "Prometheus Unbound") 


    "It was from this time that I developed my way of judging the Chinese by dividing them into two kinds: one humane and one not. "
     - (Jung Chang)

 


See also: ME -Documentation and ME - Resources


Maarten Maartensz

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