Ruscetti Acknowledges Reuse of WB Image

[ukxmrv]

Lee,

What exactly is your friend angry about right now and why?

I have ME and I'm angry at the Silverman contamination and all the wasted negative studies. As an (out of practice) molecular biologist and geneticist have a good look at that.

It's just not fair to keep dumping anger on JM alone and ignore the (in my opinion) the more terrible things that have happened.

 

[Bob]

but... I remember being a uni at having people trying to educate me about whatever political/social topic they thought demanded my attention when I just wanted to act a little concerned about that stuff, and then spend most of my time dancing! If you hold people to too high a standard, it can easily feel like baracking, even if that's not how it's intended, especially as all three of us suddenly started chirping on about it in unison. There are plenty of topics more important than PACE which I've not taken the time to educate myself about because of my own indifference and laziness, so one must be understanding when others are the same.

Fair points Esther. But my irritation comes from someone joining the forum to declare that the XMRV research is bad for ME patients, and that nothing Judy Mikovits has ever done can be trusted: "Nothing she has done, it is now clear, can be trusted." This is a rather premature statement to make, based on what we know so far. And it's not just premature - it's speculation based on a snippet of partial information. If people are so concerned about ME patients that they need to join the forum to tell us how angry they are, then I think it's quite OK for me to give them a bit of background information about ME, and to inform them why bashing Judy Mikovits is not at the top of my list of things to do right now. If someone thinks that all of our woes are as a result of Judy Mikovits, then they are entirely mistaken and misinformed, and I think it is really helpful to inform them why we have other bigger historic problems. Then they can do what they want with that information, and hopefully will use it constructively.

 

[FancyMyBlood]

@ ukxmrv:

Silverman? I think he showed definitively that the positive 'XMLV' PCR results were due to plasmid contamination, and confirmed that the early criticisms that the sequences were too similar to the plasmid, and didn't show enough sequence diversity, were correct.

I also think that his reported protections against contamination were stunningly thorough.

I also note that the contaminating plasmids were found in ME/CFS samples and not in healthy controls. This was the result that made me personally sit up and go 'hmmmm.' This is NOT a pattern that one sees with PCR contamination - this is a sample handling issue - at best, patient samples were handled differently from control samples, in a way that caused contamination of patient samples.

I think n evaluating the Silverman retraction, one must also look at JM's claimed ability to reliably find XMRV in patients and only at low levels in controls - and the fact that they were unable to do so when samples were blinded.

Put all this together, and the only conclusion I can find is that - AT BEST - JM's lab were guilty of handling patient samples differently from control samples, in ways that caused contamination of patient samples but not controls.

And given this - I don't believe a thing she has reported. She is - at best - too sloppy to be trusted.

Lee, I don't agree with your logic here. I agree that it is HIGHLY likely that XMRV is a contaminant, but you can't say you don't believe a thing Judy says just because she was 'sloppy'. Because with your logic you can't trust Silverman and the many other researchers either, who 'demonstrated' XMRV in prostate cancer.

 

[asleep]

Actually, given that we now know that they were using 5AZA without reporting it (until the Ottowa conference, in a slide, apparently) we don't know, and cant know, if any of the alleged HGRV results are real.

This is a major stretch based on very selective use of evidence.

Firstly, there are many details we don't know:

Is the "mislabeled" image actually mislabeled? There is only one set of labels for two different WBs in the Science paper. It could very well only apply to the top image while the second image--the one in question--had its labels omitted.

Even if it is mislabeled, is this one gel indicative of their entire WB data-set, or was it merely included for visual demonstration purposes? They certainly couldn't include an image of every WB gel in the paper. Furthermore, in the recent Science article, Judy says they only used 5AZA on two patient samples.

Even if some mislabeling does call into question their WB data, how does that invalidate the remainder of their data, of which WB is only a small part? Unless intentional fraud can be demonstrated conclusively, there is absolutely no logical or scientific reason that invalidation of one piece of data automatically invalidates the entire collection of data. But this is exactly the argument you are implying.

Secondly, even if a very solid case could be made for Lombardi et al being entirely invalid, you seem to conspicuously ignore Lo et al. They found HGRVs in the blood of ME patients. There is no reason to date to doubt the veracity of their findings. Yet you state categorically that "we don't know, and cant know, if any of the alleged HGRV results are real." How can you possibly justify that statement on scientific grounds except by pure omission of major pieces of evidence? I would imagine that a scientifically minded, concerned family member would be at least as interested in seeing the results of Lo et al explored further as he was in burning Mikovits at the stake. But you only care about burning.

You see, this is why people won't give you much credence in this community. You come here with "anger" and "concern" directed at "bad science." Yet a cursory examination reveals that your "concerns" are directed exclusively at the HGRV hypothesis (specifically the work of Judy Mikovits) using cherry picked data and speculative lines of reasoning. You seem to be confusing antagonism with skepticism.

 

[currer]

Lee,

I think your friend is most unusual. Most ME sufferers are grateful for the research done by Judy Mikovits and the WPI.

I, as a sufferer of thirty one years am grateful to them. They have attempted to seriously research this illness for the first time since my illness commenced.

Why should I be angry?

They have not harmed me by trying to investigate this illness. They have done what our governments are determined not to do - they investigated ME from a biomedical perspective because they believe ME to be a medical disease, not a psychological one.

In the UK sufferers can be sectioned for not getting better! Some have deteriorated and died following this barbaric treatment.

So I do not understand why your friend feels so angry because the WPI and Judy Mikovits have investigated this disorder, when our govenments do nothing.

 

[Lee]

"Furthermore, in the recent Science article, Judy says they only used 5AZA on two patient samples."

No, she didn't say that in the Science article. That article is describing the specific WB she showed at Ottowa. The article says that when JM presented that slide, she showed to patient's cells that were treated with 5AZA. She says nothing that I can find about 5AZA and any other experiments.
"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."

She and Ruscetti also say that they think that not mentioning use of 5AZA is irrelevant:
"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. "
But anyone who works in virology or genetic control knows that use of 5AZA changes the experiment in a fundamental way - among other things, it changes the necessary controls. And they not only didn't mention the 5AZA use, they didn't show or describe the necessary controls.

In the just-released Nature commentary, it points out that she described those cells as 'activated.' But 'activated' means something very specific when used to describe immune cells - and what it means is NOT 'treated with a demethylating agent.'

She also admits to intentionally misleading "a patient audience" by saying a control was a patient, so as not to confuse the patients:
"And she chose to relabel a 'normal, untreated' portion of the image with a patient number because the data were the same. "It simplified the slide primarily for a patient audience," she says. "This is not in anyway inappropriate for a presentation as long as the data are correct, and they are.""

All of which is said, so that I can respond to this:

"There is absolutely no logical or scientific reason that invalidation of one piece of data automatically invalidates the entire collection of data."

Which is true, but is not what I'm arguing. What I'm saying is that when Mikovits and Ruscetti have now admitted to mislabeling results in ways that change their interpretation, have admitted to leaving out key experimental details (brushing it off as 'not important'), when Jm admits to intentionally changing misrepresenting an experiment for 'a patient audience' and defends it as appropriate.. if she is willing to do and defend all this, then there is no way we can trust anything she has done.

i'm not saying that invalidating one figure invalidates them all. I'm saying that her admitted willingness to repeatedly misrepresent what she has done, means we can't trust anything she has done. Any of it.

I certainly hope someone goes through her lab books and results to see if there is anything credible in there, and if there is, to follow up on it enough to definitively show or disprove HGRVs. If there are in fact HGRVs in humans, that is huge, and its worth wasting some more time to be sure about it, even if it turns out that everything else she has reported turns out to be as much an artifact as what we know so far. But it better not be JM or Ruscetti doing it - because between them they have admitted to being willing to repeatedly misrepresent what they have done, and defend the misrepresentation as acceptable.

 

[currer]

I find the previous post absurd.

Dr Ruscetti is a researcher of immense stature and integrity.

My fundamental concern through all this has been that this important research should not be prematurely curtailed.

Is this what you would like to see, Lee?
It seems to me that you are working hard here to persuade us against our better judgement to agree with you that it is worthless.

Such being the natural perversity of human nature, I am only the more convinced that this is research you are afraid of.

 

[Lee]

Dr Ruscetti just defended as 'unimportant' not including an experimental detail that any virologist would know is critical - a treatment known to induce expression of endogenous retroviruses, in an experiment trying to detect infecting retroviruses. Personally, I find that stunning.

"Is this what you would like to see, Lee?'
Did you read the part of my post where I said that at this point, someone needs to evaluate and confirm the research to see if there is anything there or not, before it gets dropped - or perhaps to launch it on a sound and valid scientific footing?

 

[Sam Carter]

...

Secondly, even if a very solid case could be made for Lombardi et al being entirely invalid, you seem to conspicuously ignore Lo et al. They found HGRVs in the blood of ME patients. There is no reason to date to doubt the veracity of their findings.

...

If you look at the findings of the BWG, asleep, you'll see that Lo was unable to detect P-MLVs in a single sample, including five he had previously deemed positive.

 

[Bob]

But it better not be JM or Ruscetti doing it - because between them they have admitted to being willing to repeatedly misrepresent what they have done, and defend the misrepresentation as acceptable.

I think you are possibly misrepresenting and sensationalising events Lee, based on partial information that is in the public domain, unless you know more than everybody else.

Dr Ruscetti just defended as 'unimportant' not including an experimental detail that any virologist would know is critical - a treatment known to induce expression of endogenous retroviruses, in an experiment trying to detect infecting retroviruses. Personally, I find that stunning.

If all patient samples were treated with 5-aza, then you would have a point, but if it was only a couple, then that's not so significant.

 

[currer]

Your arguments are over the top, Lee.

I dont find them convincing at all.

I'm sure Dr Ruscetti knows how to find MLVs in his samples.
If you have concerns why dont you e-mail him about it?

 

[Lee]

Bob:

"but if it was only a couple, then that's not so significant."

It was the two they showed. That makes it significant - they omitted a key experimental detail for the actual data they showed. Which, by their own admission, was also mislabeled.

 

[magnetronnie]

I think you are possibly misrepresenting and sensationalising events Lee, based on partial information that is in the public domain, unless you know more than everybody else.



If all patient samples were treated with 5-aza, then you would have a point, but if it was only a couple, then that's not so significant.

Then I wonder, if they thought it wasn't important to mention, then why did they even use it? And why only on some samples?

 

[currer]

My goodness - so many new members on this thread.

 

[leela]

My goodness - so many new members on this thread.

I'm starting to think a good chunk of them are just one person.

 

[ukxmrv]

If you look at the findings of the BWG, asleep, you'll see that Lo was unable to detect P-MLVs in a single sample, including five he had previously deemed positive.

Sam, the BWG was never designed to replicate the work of either Lo or the WPI

 

[ukxmrv]

Then I wonder, if they thought it wasn't important to mention, then why did they even use it? And why only on some samples?

It was just something that they wanted to try. Nothing sinister.

 

[oceanblue]

...
In the just-released Nature commentary, it points out that she described those cells as 'activated.' But 'activated' means something very specific when used to describe immune cells - and what it means is NOT 'treated with a demethylating agent.

Bob says this on another thread, which ties in with my understanding of what activated means in the context of immune cells.:

Perhaps Figure 2C might have the same type of PBMC activation as Figure 2A which says:
"Expression of XMRV proteins in PBMCs from CFS patients. (A) PBMCs were activated with phytohemagglutinin and interleukin-2"

Also, the Figure legend for that gel in the original Science paper says: "Lysates of activated PBMCs from healthy donors (lanes 1, 2, 4, 5, and 7) or from CFS patients (lanes 3 and 6)", which implies all samples were activated, not just the 2 CFS samples.

So maybe I'm missing something, but the explanations of labelling with regard to 5-aza given by Frank Ruscetti in Science and Judy Mikovits in Nature still don't make sense to me.

 

[asleep]

If you look at the findings of the BWG, asleep, you'll see that Lo was unable to detect P-MLVs in a single sample, including five he had previously deemed positive.

You are right about "no reason" being too strongly worded. I don't, however, think that BWG was nearly as damning to Lo et al as some would contend.

For one, it's unclear that they even used the exact same methods. From the BWG supplemental section: "The FDA laboratory of Lo and colleagues performed nested RT-PCR and PCR assays as previously described with some modifications" (my emphasis).

For another, there are claims that the BWG didn't properly preserve patient samples. I can't confirm the veracity of this, but it would certainly help explain Lo's results.

For yet another, the positive samples came from patients on an assortment of drugs. Again, from the SOM: "None of the patients had undergone experimental anti-retroviral treatment at the time of blood collection, and only two of the fifteen were receiving immunosuppressive/anti-inflammatory therapies. Several patients were reported to receive antiviral (such as anti-herpes treatment), antibiotic, and antifungal agents."

Lastly, the macaque study provided strong evidence that detectable viremia in the blood is highly transient. So, having detected viremia in the blood once might not guarantee the ability to detect it at all future time points, all else being perfect.

Edit: My main point was simply that this push to discredit the entire HGRV hypothesis based entirely upon the possible faults of Mikovits while largely ignoring the rest of the data (of which Lo et al are just one piece) is highly unscientific.

 

[kurt]

MOD - please all posters on this thread take a break for awhile to cool off. There is no point in our fighting over these issues, this situation is out in the public square and the institutions in question are sure to take whatever actions they deem appropriate. Please restrict the discussion to the topic and do not talk about other forum members, that type of conversation inevitably leads to rules violations. Also, there is no dogma here, every viewpoint is welcome, so long as it is fairly presented without making accusations of forum members, name calling, etc.