• Welcome to Phoenix Rising!

    Created in 2008, Phoenix Rising is the largest and oldest forum dedicated to furthering the understanding of, and finding treatments for, complex chronic illnesses such as chronic fatigue syndrome (ME/CFS), fibromyalgia, long COVID, postural orthostatic tachycardia syndrome (POTS), mast cell activation syndrome (MCAS), and allied diseases.

    To become a member, simply click the Register button at the top right.

Negative XMRV CFS study with Ila Singh's name on it (University of Utah)

Angela Kennedy

Senior Member
Messages
1,026
Location
Essex, UK
That is not what Alex's argument amounted to. Alex amplified points about falsifiability of hypothesis - not about whether 'findings' are provable. What Alex defined as the Lombardi Hypothesis was tht which is implied in the introduction to the science paper: The recent discovery of a gammaretrovirus, xenotropic murine leukemia virusrelated virus (XMRV), in the tumor tissue of a subset of prostate cancer patients prompted us to test whether XMRV might be associated with CFS.

When it comes to real world phenomena - then evidence is required and 'proof' of evidence has to be demonstrated if others are to accept the reality of the claimed phenomena; in science the requirement (the source of 'proof') is that the results of experiment should be reproducable. To argue that only by an absolute strict adherence to a single protocol can a result be reproduced requires an extraordinary explanation of why a result can only be achieved by that strict adherence. In the absence of a sustainable argument for the need for a wholly undeviating replication of Lombardi et al, then simply saying that all those studies which fail to reproduce the Lombardi results are 'bad science' is absurd. It maybe that the Lipkin and BWG studies will demonstrate that XMRV, as a non contaminant, can be detected in blood, and is indeed present in some people with a diagnosis of M.E/CFS - and that will indeed provide a 'proof' of the phenomenon that Lombardi et al claimed to have observed. Conversley even if neither the Lipkin nor the BWG studies find XMRV in the blood of people with an M.E/CFS diagnosis, then the Lombardi Hypothesis will remain unfalsified because that hypothesis (as defined by Alex) is not reliant on XMRV being identified in the blood of M.E/CFS diagnosed people.

It is preposterous to suggest that technological applications and medical interventions do not require 'proof' - is there anyone reading this forum who would approve of CBT/GET treatments on the basis that the hypothesis that "CBT/GET helps some people with M.E/CFS" has not been falsified ? Somehow I don't think so, and that what would be expected is some very strong proof/evidence that CBT/GET actually does help people with M.E/CFS, before anyoe reading this forum would take part in CBT/GET. Hypothesis of disease association or causation may not of itself demand 'proof' but the application of technology in achieving a test of a hypothesis does require proof of adequate function - in the XMRV case, if the technology of observation is shown to be vulnerable to error, then validation of that technology is required - that is, the technology has to be 'prooved' as sound.

IVI

IVI, the fact you are using the word 'proof' now in parentheses indicates you understand that use of the word previously was problematic, so I'm pleased about that.

Alex appears to have been using the Popperian context of falsifiability and disproving in the way I said, so I stand by that.

What I think you have a problem understanding is that many people here are not latching onto the WPI as proven until otherwise disproven. What many people want to see is the science pan out until the WPI's claims are correctly disproven, or until enough evidence accrues to enable a reasonable prediction it is correct, and that XMRV is most likely to cause ME/CFS, in which case the possibility of treatment then becomes available.

To take your CBT/GET example. IF there was plausible evidence that CBT/GET helps anybody with ME/CFS, people would be taking up that offer. They could not expect 'proof'. The incoherence and implausibility of the claims, followed by the poor empirical adequacy, that CBT/GET helps people with ME/CFS (actual ME/CFS now- not metaphorical fatigue!) is what makes people not want CBT/GET.

Your use of the word proof is not correct because you've been misrepresenting (miscontruing, probably) what many - possibly most- people in this community know about science, the issue of CBT/GET and about the whole saga of XMRV. You think they're all emotionally supporting XMRV- which they are not. This may be because of the way the community is being misrepresented by her majesty ERV and the Bad Science mob. ERV believes its her job to educate the plebs that XMRV has nothing to do with ME/CFS - her attendance on the BS forum shows this- which makes her an idiot and unable to grasp the scientific process.

The ME/CFS community is mostly waiting for the science to pan out- free from politics- and for good science to prevail. If they don't like psychogenic explanations, it's because they are implausible- products of badly done 'science'.

But none of this can adequately be explained by claiming 'proof' is needed. Most people in this community have become only too aware of the problems of that word when applied to the scientific process.
 

Navid

Senior Member
Messages
564
Also ppl have tried GET/CBT and either not been helped or had their conditions worsen under GET.....ppl are ready to try just about anything if there is even the slimmest chance it will help....CBT/GET has proven itself useless in fighting ME/CFS.....not the point of your discussion but the reality of treatment options....and what ppl will try.
 

Bob

Senior Member
Messages
16,455
Location
England (south coast)
I thougth this was very interesting in Cort's Buzz entry of 16th April...
It would be interesting to understand it all better:


http://phoenixrising.me/?p=5568

Exact Replication? Dr. Singh reported in her paper that she replicated the methods of the Lombardi paper but there were differences. I asked if she was could be getting different results because of small differences in preparation and testing?

She stated

We used a total of 9-12 assays on each sample to look for XMRV. Some were new assays that we developed and these assays are far more sensitive than any of the assays where sensitivity data is shown. Others were a replication of assays performed in Lombardi et al or Lo et al. The viral culture was done exactly as explained by Dr. Ruscetti.

And then explained one difference that she felt was missing in both the Lombardi and Lo studies which meant the studies were prone to contamination; ie there was one part of those studies that she felt compelled not to replicate.

The nested PCR was done as described in Lo et al, with one small modification. We used the dUTP-UNG system to prevent contamination of our lab with PCR products.

Since nested PCRs involve opening of tubes containing a PCR product, the danger of this product contaminating other equipment, reagents and samples in the lab is very real. Once contamination has occurred, it is very difficult to get rid of it. Any reputable lab that uses PCR as a test on clinical samples, uses dUTP-UNG. It has been shown to not affect the PCR itself, and to provide a very real safeguard against contamination.

I do not know why Lo et al or Lombardi et al used a process prone to contamination like the nested PCR, and then did not use the dUTP-UNG system (youll have to ask them). But I could not risk contaminating my lab with PCR amplicons then every subsequent test we did would be suspect.
 

Bob

Senior Member
Messages
16,455
Location
England (south coast)
Wouldnt the type of contamination described by Dr. Singh cause the same risk of contamination for controls as well as patient samples?

One would have thought so... Singh considered this and commented that she thought it was likely due to the amount of handling that each sample received... That the patient samples would have been handled more than the control samples... But this seems like a rather weak argument to me, especially as the WPI say that have tested, retested, and retested again for contamination... I imagine that the WPI put negative control samples through their equipment and through the complete testing procedures, to see if the controls will pick up any XMRV contamination. That seems like an obvious basic thing to do.
 

Cort

Phoenix Rising Founder
Replication Needed - Racaniello on The Singh Study

Racaniello believes a 'broader replication study' is needed and thinks there's a limit to how much exact replication is needed.. (but where to draw the line????:confused::confused::confused:)

http://www.sun-sentinel.com/health/ct-health-chat-viruses,0,3358676.htmlstory

Do you consider the Shin/Singh study to be a validation replication of the Lombardi/Mikovits study?
12:52

Vincent Racaniello: It's not a replication because it's not the exact study. But Singh used the same techniques. I understand the limitations and I agree that a broader replication study is needed.
12:53

Trine Tsouderos: There is this idea out there in some patient forums that if you don't replicate a study down to the smallest detail - same lot number on the test tubes, same everything - that it is not a true replication of the study. I don't think this is what scientists mean when they talk about replication...true?
12:54

Vincent Racaniello: If you hold to that description, then no study is ever replicated. For example, you cannot replicate the physical location of the study, which in some cases might have an influence. You have to work within the limitations of reason.
 

liquid sky

Senior Member
Messages
371
Racaniello uses a completely ridiculous argument saying, "you cannot replicate the physical location of the study." He knows what constitutes a true replication study and it does not involve using your own newly constructed tests that have not been proven to find xmrv in any person.

These 0/0 studies are getting really old, a constant shell game. Do these people want to find it?
 

Jemal

Senior Member
Messages
1,031
Racaniello uses a completely ridiculous argument saying, "you cannot replicate the physical location of the study." He knows what constitutes a true replication study and it does not involve using your own newly constructed tests that have not been proven to find xmrv in any person.

These 0/0 studies are getting really old, a constant shell game. Do these people want to find it?

I do think many of these scientists want to find it... but they want to use their own methods or old methods. And that's the problem. One thing I have learned is that many of these scientists have egos and they want to make discoveries for themselves, not always build on what others have already found.
 

Bob

Senior Member
Messages
16,455
Location
England (south coast)
I agree with Racaniello that an exact replication study is not practical.

There are so many variables at play that it is impossible to replicate everything.

For example, if a near-replication study was carried out, that had nearly everything identical to the WPI's preferred procedures, and we all agreed that it was a good study, but then it came up negative, then I'm sure that we'd all be looking for the one small thing that they didn't quite get exactly right.
But all our hopes would have rested on that one replication study. I don't think it would be helpful.

I think that, instead, it will be the evolving wider body of research that gives us a broader picture of the facts, and a better knowledge about XMRV. It's a very slow process, but we are slowly developing a picture about XMRV. It's just not happening as fast as we'd like it to.

As an example of the evolving developments, the CDC now appear to accept that XMRV is a wild human virus, which they are now able to detect in some prostate cancer patients. They also acknowledge that they aren't able to detect XMRV in the blood of prostate cancer patients due to the low copy numbers. This came about because they did their own research, and not a replication study.

But anyway, we also have the best possible replication studies approaching... The WPI and Lo are participating in the Lipkin study, which will effectively be two exact replication studies.
 

liquid sky

Senior Member
Messages
371
I'm looking forward to those studies too, Bob. It is a shame that egos get in the way of science. Two years may not seem like a long time to a healthy person, but there are a lot of really sick people trying to hang on through this process.

There are some good conferences coming up. I hope we will get more info from these. Some of the titles appear to show progress. I am interested in the one where they will release the results of the study on Rituxan in PwME.

I do think looking for xmrv in ME needs to move into tissues also. The fact that they can find it in prostate tissue, but not blood shows that would be a logical progression.
 

Sean

Senior Member
Messages
7,378
As an example of the evolving developments, the CDC now appear to accept that XMRV is a wild human virus, which they are now able to detect in some prostate cancer patients. They also acknowledge that they aren't able to detect XMRV in the blood of prostate cancer patients due to the low copy numbers.

This is an important point.
 

free at last

Senior Member
Messages
697
This observation is very important, and backs up the monkey studies lack of detection in blood. theres only one problem. JM found it in the blood rather easily compared to what we learned with the monkeys. and what the CDC are learning. If that anomaly could be explained well, then im sure the 0/0 studies really could be missing this virus. But how to explain that anamoly ? it seems a rather difficult stretch. Anyone have any ideas ? I know JM talked about testing certain times of the day. because sometimes the virus showed up, sometimes it didnt. But of course all the 0/0 studies would be unlikely to miss ALL THOSE TIMES surely ? It has to be something else doesnt it ?
 
Messages
34
Location
Belgium
Hi,

I was with KDM yesterday, and he's coping with the same problem. All of his blood samples are sent to VIP in the US for XMRV testing, and still quite a few come back negative (serology and culture), although the cytokine, chemokine profiles give a pretty good indication of XMRV being present. That's why he has started taking stomach biopsy's, which then turn out to be positive for XMRV in 70% of all samples. So the step to tissue samples has been made, and turns out to be more reliable then blood.
Just wanted to let you guy's know. Also he'll be making a statement about this tomorrow at the conference.

Regards,
K.
 

Enid

Senior Member
Messages
3,309
Location
UK
Looking forward to that K - hoping the Conference will resolve the detection problems found all over.
 

ukxmrv

Senior Member
Messages
4,413
Location
London
Free at last,

One of the blood working group reports showed that it was the testing day after blood collection that seemed to be important. It was the 2nd day (I think) that showed the positive results. Yes, the 0/0 studies if they all started testing on day 1 then it could explain the difference.

IKKE, I'm off to the conference tomorrow and looking forward to hearing the news. As I remember KDM was freezing his blood samples and sending them in batches to VIP dx?
 

Bob

Senior Member
Messages
16,455
Location
England (south coast)
Hi,

I was with KDM yesterday, and he's coping with the same problem. All of his blood samples are sent to VIP in the US for XMRV testing, and still quite a few come back negative (serology and culture), although the cytokine, chemokine profiles give a pretty good indication of XMRV being present. That's why he has started taking stomach biopsy's, which then turn out to be positive for XMRV in 70% of all samples. So the step to tissue samples has been made, and turns out to be more reliable then blood.
Just wanted to let you guy's know. Also he'll be making a statement about this tomorrow at the conference.

Regards,
K.

That's very interesting...
By 'KDM', you mean Kenny De Meulier?
 

acer2000

Senior Member
Messages
818
I agree with Racaniello that an exact replication study is not practical.

There are so many variables at play that it is impossible to replicate everything.

I actually have the exact opposite opinion. Its often easier to replicate someone else's work exactly than to come up with your own methods. Thats why its so annoying that it hasn't been done.

If there weren't any discrepancies between the results, it would be one thing. But there are. Which makes reducing the number of variables changed from the original study to "none" - and then moving forward the only real way to figure out what is going on.
 

Cort

Phoenix Rising Founder
This observation is very important, and backs up the monkey studies lack of detection in blood. theres only one problem. JM found it in the blood rather easily compared to what we learned with the monkeys. and what the CDC are learning. If that anomaly could be explained well, then im sure the 0/0 studies really could be missing this virus. But how to explain that anamoly ? it seems a rather difficult stretch. Anyone have any ideas ? I know JM talked about testing certain times of the day. because sometimes the virus showed up, sometimes it didnt. But of course all the 0/0 studies would be unlikely to miss ALL THOSE TIMES surely ? It has to be something else doesnt it ?
]

If it comes down to you have to test for it at certain times of the day....actually it will never come down to that point...there's no virus that you have to come in at 8 am in morning or you won't find it type of thing. PCR tests are so sensitive they can find ANYTHING.....

It was readily found in the blood in the Lombardi study and it needs to be found in the blood in the others before the scientific community really digs anywhere else I imagine.
 

Cort

Phoenix Rising Founder
I actually have the exact opposite opinion. Its often easier to replicate someone else's work exactly than to come up with your own methods. Thats why its so annoying that it hasn't been done.

If there weren't any discrepancies between the results, it would be one thing. But there are. Which makes reducing the number of variables changed from the original study to "none" - and then moving forward the only real way to figure out what is going on.

I think that's where we are and you're right they would have saved alot of time and money if they had tried to really replicate it from the beginning. I think that they thought they would validate it quickly using other means and the field would move on. So now they are finally replicating just about everything. Too bad it took so long....