Dr Singh Talks on her CFS XMRV study and the WPI's Response

[RedRuth]

Congratulations on completely misunderstanding my post! Anyway as I pointed out Dr Singh explains this very well

Control populations were often small, with as few as 43 in one study (25), and patient and control samples were often collected at different times, sometimes several years apart (11), leaving open the possibility that patient samples might have been handled more, and thus possibly contaminated more easily, than control samples. Additionally, in all except a subset of samples from one study (12), the identity of the samples was not hidden from the investigators.

She also explains why the nested PCR at the WPI is probably contaminated, using the wrong methodology.

Contamination in labs is very, very common, actually; despite our best efforts, there's rogue DNA all over our labs and the products we use, and when it happens in experiments we just shrug it off - even if it's contamination with a novel human retrovirus that was created in the lab and has spread unintentionally through an unknown process.

Contamination of PCR is very common, by it's nature it's very easy to contaminate, I'm not really sure what you're complaining about. Recombinant retroviruses are a worry as I've already said but if the WPI findings are the result of contamination, as seems increasing likely then it means that XMRV infection is not correlated with ME. That's what I meant by does it matter where the contamination came from.

 

[RedRuth]

Dr. Singh still believes in her XMRV and cancer research and stands by her earlier results (she detected XMRV in people with prostate cancer). At least she said so right after the XMRV and ME/CFS study she did. She's in a weird position...

That's kind of beside the point though with respect to ME and XMRV, this paper is a big blow to the theory that there's a correlation between XMRV and ME.

 

[RedRuth]

It has also been reported that some of the groups that found XMRV at first didn't find it and only after consulting with the WPI were ableo to find it.

Dr. Singh did consult with them and used the same culturing protocol. When she says ..........and patient and control samples were often collected at different times, sometimes several years apart (11) she's referring to the Lo study that's why it's referenced. (12) is the Lomabardi study.

 

[Jemal]

That's kind of beside the point though with respect to ME and XMRV, this paper is a big blow to the theory that there's a correlation between XMRV and ME.

Well, if XMRV is contamination, then it should also be contamination in her prostate cancer research, should it not? According to the contaminists, Singh should not be finding any XMRV, because it's contamination. That she still says: "Hey, I stand by my results of finding XMRV in prostate cancer." means she still thinks this is a real virus, infecting people (so it's outside the lab) and maybe causing cancer.

 

[asleep]

Congratulations on completely misunderstanding my post! Anyway as I pointed out Dr Singh explains this very well

Control populations were often small, with as few as 43 in one study (25), and patient and control samples were often collected at different times, sometimes several years apart (11), leaving open the possibility that patient samples might have been handled more, and thus possibly contaminated more easily, than control samples. Additionally, in all except a subset of samples from one study (12), the identity of the samples was not hidden from the investigators.

She also explains why the nested PCR at the WPI is probably contaminated, using the wrong methodology.

Contamination in labs is very, very common, actually; despite our best efforts, there's rogue DNA all over our labs and the products we use, and when it happens in experiments we just shrug it off - even if it's contamination with a novel human retrovirus that was created in the lab and has spread unintentionally through an unknown process.

Contamination of PCR is very common, by it's nature it's very easy to contaminate, I'm not really sure what you're complaining about. Recombinant retroviruses are a worry as I've already said but if the WPI findings are the result of contamination, as seems increasing likely then it means that XMRV infection is not correlated with ME. That's what I meant by does it matter where the contamination came from.

Actually, RedRuth, I think Mark understood your post perfectly well. He was addressing the attitude that comprises the core of your position: a palpable antipathy toward open, honest, fully evidence-based reasoning. Instead you are engaging in selective use of evidence and biased supposition to stuff the gaps. This stuffing of the (self-selected) gaps with plausibility instead of evidence is classic pseudoskepticism.

You are also trying to argue using a rhetorical device that I would call "semantic ratcheting," whereby the case for relative certainty of some assumed (not evidenced) conclusion is built by subtle and successive use of increasingly stronger adjectives. It is like the rhetorical version of the frog in boiling water. For example, person A claims that it's possible that gravity could cease tomorrow (which is vacuously true given the fundamental uncertainty of everything in science). Person B then quotes them and says it is probable that this will happen. Person C continues on with it being likely, etc, until we arrive at indisputable. I have taken the liberty of bolding your usage of this device above in transferring a vacuous point (the possibility of contamination) into a truth of such apparent certainty that it can be assumed without investigation. This is neither science nor skepticism.

To be honest RedRuth, it has been apparent to me since you first started commenting here that you were not interested in honest discussion, but rather in trumpeting anti-XMRV talking points, rationalizing bad science, and engaging in biased dissembling. Despite that, I am impressed with how extremely patient a number of posters here have been.

 

[RedRuth]

I think there are two contamination arguments
1. XMRV isn't an infectious Human virus, it's only present in cell lines.
2. XMRV may be present in prostate cancer tissue but the studies finding XMRV in the blood of ME sufferers are the result of contamination.

I don't think anyone is arguing that XMRV isn't a real virus.

 

[RedRuth]

until we arrive at indisputable.

You seem to have forgotten to bold the part where I say this. Why is that? Also, my words that you've bolded DON'T refer to the passage you've bolded words in, I'm referring to her comments on the PCR NOT the handling of the samples. So your analogy fails all round.

 

[Jemal]

I think there are two contamination arguments
1. XMRV isn't an infectious Human virus, it's only present in cell lines.
2. XMRV may be present in prostate cancer tissue but the studies finding XMRV in the blood of ME sufferers are the result of contamination.

I don't think anyone is arguing that XMRV isn't a real virus.

The most vocal and prominent contaminists are shooting for 1, that's for sure.
Also I don't believe argument #2 is feasible... but I am tired of these discussions. The fact is we need more research, not less, like some of the contaminists are pushing for. There's too many arrogant researchers.

 

[asleep]

You seem to have forgotten to bold the part where I say this. Why is that? Also, my words that you've bolded DON'T refer to the passage you've bolded words in, I'm referring to her comments on the PCR NOT the handling of the samples. So your analogy fails all round.

It's all part of the same tenuous patchworked argument you are making for contamination. You seem to have no issue weaving together disparate lines of evidence (handling vs inherent PCR vulnerability) into a single unitary thrust when it suits you, only to balk with dismay when this conflation is questioned. Or put another way, that the possible handling issue in Lo et al cannot explain the differing positive rates in cases vs controls in Lombardi et al is a distinction you seem to have willfully glossed over in making your case. Until, of course, it becomes convenient to point out that they are, in fact, incompatible pieces of evidence.

As for the "indisputable" issue, the theoretical description of the device was meant to be explanatory and was therefore a bit hyperbolic. However, despite that, your conclusion ("That's what I meant by does it matter where the contamination came from") quite clearly implies that the matter of contamination is certain and/or indisputable to the point of not needing any investigation. I didn't bold this part because it's difficult to bold an implication.

 

[RedRuth]

It's all part of the same tenuous patchworked argument you are making for contamination.

In other words your analogy was totally inaccurate, I was listing Dr. Singh's points and there was no handling vs inherent PCR vulnerability it was sample handling AND PCR methodology.

and was therefore a bit hyperbolic.

In other words, wrong. I'm very careful not to say anything of the sort.

 

[RedRuth]

Actually I agree with you about more research and arrogant scientists.

EDIT: Scientists are only Human and sometimes egos get in the way, Coffin and Muikovits are classic examples of feuding scientists. However, science is self correcting in the end and a consensus will emerge, it did with HIV, H. pylori and transposons.

 

[markmc20001]

I would like to see a legitimate consensus this time around. Not some false illusion of consensus created with the corporate controlled media and pseudoskepticism.

 

[redo]

Detecting retroviral sequences in chronic fatigue syndrome.
Singh IR. 2010
Abstract
XMRV or xenotropic murine leukemia virus-related retrovirus, a recently discovered retrovirus, has been linked to both prostate cancer and chronic fatigue syndrome (CFS). Recently, the teams of Drs. Shyh-Ching Lo and Harvey Alter discovered the presence of sequences closely related to XMRV in the blood of 86.5% of patients with CFS [1]. These findings are important because since the initial discovery of XMRV in CFS, several studies have failed to find XMRV in specimens collected from CFS patients. While the current study also did not find XMRV in CFS, Lo et al. did detect sequences that belong to polytropic mouse endogenous retroviruses (PMV), which share considerable similarity with XMRV. Criteria for future studies that will help bring greater clarity to the issue of retroviral sequences in CFS are proposed below.

Does anyone know if it's being done some follow up research on that, and what exactly PMVs role is? (if it's known)

 

[barbc56]

In the introduction to their paper, published in the Journal of Virology, the authors note other problems with many of the studies of XMRV in CFS patients:

Too small control populations

Patient and control samples collected at different times

Investigators generally not blinded to sample identity

PCR assays that rely on conservation of viral sequence mainly used

Limits of detection, reproducibility, and precision of assays unknown

Controls for each step that would identify analysis not done

Insufficient numbers of negative controls included

No study included positive samples from the original 2009 patient cohort of Lombardi et al.

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