New research suggests more problems with the Paprotka et al XMRV recombinant paper

[RRM]

And yet one of our esteemed posters suggests the Paprotka study was a very good one, unlike the Lombardi study.

And luckily, most if not all scientistst actually agree with said poster.

And for good reason, because there is (again) nothing in this letter that should convince anyone to the contrary. In fact, I think it is pretty obvious that no one has actually read and understood much of it, as it is riddled with errors and unsubstantiated and unreferenced assertions.

For instance, this letter begins the actual critique with:

The term "XMRV specific" is misleading.

Yet, the relevant quote from the Paprotka et al. paper says (emphasis mine) "we developed a real-time PCR primer-probe set that specifically detected XMRV env and excluded murine endogenous proviruses present in BALB/c and NIH3T3 genomic DNA (Fig. 1C)"

How can the writer (or anyone else reading and understanding the critique) miss this essential difference? It is right there in the quote.

The primer probe set (primer 3f-8r) was complimentary to sequences in the env region of XMRV/VP62 and EndoERV-2.

Wrong again, and this is only the second sentence of the actual critique. This primer set was designed to detect the env region of "EndoERV-1" (also known as PreXMRV-1), as well as the env region of XMRV itself.

And, on a side note, the label EndoERV is really pretty ridiculous in itself, as the "E" in ERV already stands for "Endogonous".

The real-time PCR actually established a figure of 68 copies per 100 cells for EndoERV-2 and 3 copies of EndoERV-2 per 100 cells in the CWR22 cell line

Again really an strange and seemingly easy to spot error. There are 68 copies of "EndoERV-2" in CWR22 and 3 copies of "EndoERV-2" in CWR22 at the same time? It's like saying "there are 7 billion people and 10 billion people on planet earth".

This is incorrect from the initial paragraph. The provirus detected was EndoERV-1 and not XMRV.

It almost seems to be getting like a bad joke at this point. First (and again), the writers did not assert that they detected XMRV but XMRV env. This is again very clearly stated in the actual quote. And second, if anyone would read just one sentence beyond the quoted section, this person would note how the authors simply explain that the XMRV env sequences detected were not from XMRV but from "EndoERV-1" (emphasis mine):

The absence of XMRV in the CWR22 tumor and early passage xenografts. Using qPCR assays, we estimated that the early xenografts contain ~1?3 XMRV env copies/100 cells (Fig. 1C), which correlated with the amount of mouse DNA in the early xenografts (0.3 ?1%; Fig. 1D), and the estimated 1 XMRV env copy/cell in the NU/NU and Hsd nude mice (Fig. 1C). Since no XMRV was detected in any of the early xenografts, the XMRV env sequences detected are from the endogenous Prexmrv1 provirus in the nude mouse DNA.

It really goes on and on but for now, I won't.

 

[jace]

You are right about endoERV being tautologous, RRM, but sometimes one has to drive home a point. At least it is more accurate than the preXMRV label. However, bowing to your sensitivities, I have removed the tautologous emphasis from the original post, but not from the quotes you used, with one exception.

the writers did not assert that they detected XMRV butXMRV env.

They detected what they assume to be a part of XMRV-VP62 env and they call it preXMRV (emphasis mine).

The absence of XMRV in the CWR22 tumor and early passage xenografts. Using qPCR assays, we estimated that the early xenografts contain ~1?3 XMRV env copies/100 cells (Fig. 1C), which correlated with the amount of mouse DNA in the early xenografts (0.3 ?1%; Fig. 1D), and the estimated 1 XMRV env copy/cell in the NU/NU and Hsd nude mice (Fig. 1C). Since no XMRV was detected in any of the early xenografts, the XMRV env sequences (they left out the word assumed here lol) detected are from the endogenous Prexmrv1 provirus in the nude mouse DNA.

Estimated, assumed. They did not detect any XMRV/VP62 env sequences in any NuNu or Hsd mice. They detected ERV sequences, at 68 copies per 100 cells. Inaccurate and misleading, as is the whole paper.

In the following I made an error using ERV2. It should read ERV1.

The real-time PCR actually established a figure of 68 copies per 100 cells for EndoERV-2 and 3 copies of EndoERV-2 per 100 cells in the CWR22 cell line

Again really an strange and seemingly easy to spot error. There are 68 copies of "EndoERV-2" in CWR22 and 3 copies of "EndoERV-2" in CWR22 at the same time? It's like saying "there are 7 billion people and 10 billion people on planet earth".

In the OP I have inserted the qualifier (in the NuNu and Hsd mice) after "68 copies per 100 cells for EndoERV-2" and corrected ERV-2 to read ERV-1. The man that never made a mistake never made anything, hey? The paragraph should have read (and now does in the OP)

The real-time PCR actually established a figure of 68 copies per 100 cells for ERV-1 (in the NuNu and Hsd mice)* and 3 copies of ERV-1 per 100 cells in the CWR22 cell line. There is no history of this primer being able to detect XMRV/VP62 env sequences at a concentration of less than 2000 copies per 100 cells. The serial dilution method used here has come in for a great deal of criticism, and the copy number estimates in mice and the early CWR22 xenografts are highly likely to be unreliable.

You do know that cognitive issues are part of the illness, don't you? What's Paprotka's excuse? And if you split hairs about 58 and 68 copies, well it will look like clutching at straws.

Paprotka et al say different things in the supplementary materials (which few study) to what was said in the main paper...

This quote is from the main paper

to estimate 20 proviruses/cell and used the 22Rv1 DNA to generate a standard curve. The CWR22 xenografts had significantly fewer copies of XMRV env (<13 copies/100 cells) compared to the 22Rv1 cells (2000 copies/100 cells). The CWR-R1 cell line had ? 0003??copies/100 cells, and the NU/NU and Hsd nude mice, thought to have been used to passage the CWR22 xenograft, had 58 and 68 copies/100 cells, respectively.

(emphasis mine)

In the above quote, they give the impression that their quantitative PCR could detect XMRV env sequences at a copy number of less than three per 100 cells to convince their readers that their single round PCR could detect XMRV env if present. This is totally misleading. They know they did not detect XMRV env and it was misfeasence to state that they could in the main paper.

In the supporting materials they said

The absence of XMRV in the CWR22 tumor and early passage xenografts. Using qPCR assays, we estimated that the early xenografts contain ~1?3 XMRV env copies/100 cells (Fig. 1C), which correlated with the amount of mouse DNA in the early xenografts (0.3 ?1%; Fig. 1D), and the estimated 1 XMRV env copy/cell in the NU/NU and Hsd nude mice (Fig. 1C). Since no XMRV was detected in any of the early xenografts, the XMRV env sequences detected are from the endogenous Prexmrv1 provirus in the nude mouse DNA.

In the main paper they gave the false impression that their PCR could detect XMRV env at a very low copy number, so people were then drawn in to believe that the second PCR which was single round could too.

the writers did not assert that they detected XMRV but XMRV env.

Exactly. That's what they did in the main paper. In the supplementary materials, however, they qualify that, as quoted above. They called the section of an endogenous retro virus a portion of a specific clone, VP62, of an exogenous retrovirus. Wishful thinking, IMHO. They said that they detected XMRV ENV when in fact they detected ERV1 env. That is a totally false statement made in the main paper.

I leave you with this thought:

"Its just not sufficient to show that something can detect something in a plasmid template. Its hard to know if its going to detect something in a matrix thats as complicated as blood or cellular DNA. So I think thats probably one of the biggest reasons for why people find different results.."
Ila Sigh, 'TWiV 94: XMRV with Dr. Ila Singh' (TWiVl, 8 August 2010)

 

[RRM]

The man that never made a mistake never made anything, hey?

And he certainly didn't write this letter.

But you drive home a good point: the persons that wrote this critique, never really produced anything that would even remotely resemble an original experiment in the field either. They've just wrote some nonsensical and factually incorrect "rebuttals" every time a paper that they didn't like was released.

Everybody can do this, really. Any person with the elementary google skills can produce a "rebuttal" of any accepted scientific theory that goes beyond the knowledge of the avarage reader on a forum like this (and thus may seem slightly believable to this reader, especially if this reader is a sick and vulnerable patient). However, that does not prove anything about the validity of the theory in question.

I was merely poiting out, through some examples that any reader can easily verify, that there were some very obvious errors in this letter (there still are, by the way) that should really stop any critical reader from reading even beyond the opening paragraphs. This way, even the least informed reader can check that the writers of this letter are not as knowledgable as they would like you to believe.

On a side note, any critical reader should also want to have at least some source for many of the assertions made in the letter. For instance (and I am again merely supplying a couple of examples from the beginning of the letter), the following assertions cannot be "just" made like they are here:

The serial dilution method used here has come in for a great deal of criticism

A bold assertion like this cannot even be covered by a single, primary reference but should really be backed by a multitude of primary sources (i.e. original research) or, of course, a reliable secondary source (a review paper on the subject).

Primer 3f-8r using a single round PCR was unable to detect XMRV/VP62 in the later xenograft

This is an assertion that is apperently derived from the Paprotka et al. paper, but it is totally unclear where exactly this information has been derived from (which part of the text, which figure?). Any reader can also note that it is really strange to not even name which of the late xenografts is under debate here.


To give yet another line of evidence that any informed or uninformed reader can easily verify, I make the following observation regarding the "XMRV specific" of "XMRV env specific" argument that is the main point of your reply:

The exact quote from the paper that this part of the critique (and the response to my post) refers to, has already been used earlier by the same people that wrote this critique, but then to "prove" something that totally contradicts what they now think it shows: that the early xenografts (and thus the original patient tumor) were infected with XMRV.

It appears to have been a "major" finding - note the number of exclamation marks.

Rest assured, this is based on a misinterpretation of this part of the paper too. It is actually very easy to point out why these people are wrong on both occasions, but would anybody be really interested? At this point I think it suffices to just note that these people are being totally inconsistent. It should show anyone that it is only about throwing as much dirt at these "negative studies" as possible and hope that some if it "sticks".

I leave you with this thought:

I don't really see how this relates to the research in question. Anyway, it just goes to show you that scientists don't have to follow "the party line".

Dr. Singh was at that point still convinced that XMRV was involved in ME/CFS or at least in some human disease, and she gave an explanation that she thought made sense at that time. However, this quote was made when "only" four negative studies had been published, and before many more labs would fail to reproduce Mikovits's results, before research would show many reagents to be contaminated, before phylogenetic research showed the reported sequences to be highly suspect, before Ila Singh herself published a negative paper on the possible association between XMRV/PMLV's and ME/CFS, before Paprotka et al. was published, and before Mikovits and Ruscetti and Lo were totally unable to reproduce their earlier findings on the very same patients. And that is just a sample of the mounted negative evidence that was produced since that quote.

In fact, in May of 2011, the very same person was quoted as saying:

"I'd urge people to move on rather than to keep their hopes hanging on the link between XMRV and CFS".

 

[jace]

Again, RRM, you do not engage with the central points, but only attempt to slur with rumour and allegation. The fact remains, as has been clearly shown, that Paprotka is based on a series of unsafe assumptions.

* XMRV is only the sequences uploaded to Genbank by Silverman (the VP62 clone) whereas we know that there are many clones

* A partial sequence of the env of and endogenous murine virus is labeled XMRV env in the main paper, and preXMRV in the supplementary materials

Nothing you have said so far refutes well founded concerns with Paprotka et al., which has been lauded in certain circles as explaining the one-and-only origin of XMRV in 1991 or thereabouts in some lab or other. Gamma retroviruses associated with ME have a history going back at least to the early 1970s.

The Singh quote stands, whatever she has now been persuaded to believe. May I remind you:

"Its just not sufficient to show that something can detect something in a plasmid template. Its hard to know if its going to detect something in a matrix thats as complicated as blood or cellular DNA. So I think thats probably one of the biggest reasons for why people find different results.."
Ila Sigh, 'TWiV 94: XMRV with Dr. Ila Singh' (TWiVl, 8 August 2010)

Nothing to do with beliefs at all, merely a warning that there are pitfalls. And her statement "I'd urge people to move on rather than to keep their hopes hanging on the link between XMRV and CFS" is correct, if rather belittling of its intended audience. We all know now that the clone VP62, because it was the only clone to have sequences published from the Lombardi 2009 paper, became "XMRV". Because of that, everyone went looking for just those sequences, setting their experiments to a too tight specificity, looking for the wrong thing. However, XMRV as a label encompasses more than just one clone, and no-one is "hung up" on that clone, and we are also aware that we may be dealing with more than one virus, perhaps a polytropic, perhaps not. The science is still a skein of confusion to be untangled, which is being worked on now.

We do science no favours by basing our beliefs on a paper that is so full of assumptions and conjectures and beliefs without hard evidence. We need to keep our minds open, for reality is complex, and our understanding now must be allowed to take all the evidence (hard evidence) into account. Why some members feel it necessary to try and shut down debate in any area of research is beyond me.

 

[RRM]

but only attempt to slur with rumour and allegation

A classic example of the pot calling the kettle black.

you do not engage with the central points

The problem is really that there are no "central points".

You need to first substantiate your assertions, and then try to follow this up with a logical and understandable argument without obvious errors. Then, perhaps, there are even "central points" to engage with.

XMRV is only the sequences uploaded to Genbank by Silverman (the VP62 clone) whereas we know that there are many clones

Where do you get the notion that VP62 was the only sequence the authors looked at and/or calibrated their assays to? I can assure you this is again incorrect and it is clearly verifiable by just reading the paper. The authors mostly used 22Rv1 as a positive control. They did not use VP62 plasmid, did not "calibrate" their assays to "just" VP62 (as their 22Rv1 positive control was reliably positive) and only used the VP62 sequence for their phylogenetic analysis (along with other XMRV sequences, I might add).

Like I explained, with such obvious errors (that you refer to as your main points), you can't really expect people to seriously consider this letter.

A partial sequence of the env of and endogenous murine virus is labeled XMRV env in the main paper, and preXMRV in the supplementary materials

Again this is completely wrong.

It should be perfectly obvious to anyone (except apparently the writer of this critique) that has read the paper that the authors never detected (and never meant to say that they detected) the actual XMRV (partial) env sequence of XMRV in these mice strains, but the (identical) XMRV env sequence of PreXMRV1.

After all, their entire Paprotka et al. paper hinges on the assertion that XMRV is not found in mice!

But now, someone thinks that they did say that they detected actual XMRV env in mice strains to "mislead" people into thinking that their assays are more sensitve than they actually are?

But hey, don't let my logic convince you. In the main body of the paper, or no, at the end of the very same paragraph, the authors actually clearly conclude that the XMRV env sequences detected in those mice were not from XMRV itself but from PreXMRV-1:

Overall, these results indicate that PreXMRV-1 is an endogenous murine provirus that is present in the NU/NU and Hsd strains, but neither of these strains contains XMRV

It baffles me how someone can present these ideas as fact when they are both illogical as well as directly contradicted by the text of the paper.

Nothing to do with beliefs at all, merely a warning that there are pitfalls.

And as everybody will surely remember, the search did not stop this, or after one, two, three or even ten more negative studies. Everyone was (and is) aware of the potential pitfalls, though I might add this does not only apply to negative findings.

Singh believed this was still a reasonable explanation for the discrepant results at the time she made the statement. Since then, a lot of research has been performed, that overwhelmingly supports the notion that the Lombardi et al. results are incorrect and indicates that the explanation expressed in this quote is not a reasonable explanation anymore.

everyone went looking for just those [VP62] sequences, setting their experiments to a too tight specificity, looking for the wrong thing

Again, "citation needed".

Can you privode us with even a single study that was performed/published after the Lo et al. findings (that showed more diversity), that "just" looked for XMRV/VP62 sequences? In any case, for every study that you will provide, I will provide you with two studies that (also) looked at the wider variety of viruses reported by Lo et al.

It is just yet again a totally wrong assertion to make. The only problem is that most people trust these people to be truthful about these things and do not question assertions like these, hopeful as they are that these persons might be "on" to something.

We need to keep our minds open

Yes. But as a wise man once said, don't keep it too open, or your brains may fall out.


For instance, if Mikovits and Ruscetti yet again fail to reproduce their original results using their self-chosen methods, this time on an independent cohort, are you open minded enough yourself to accept the fact that perhaps, somehow, the original results were wrong?

 

[jace]

A classic example of the pot calling the kettle black.

The problem is really that there are no "central points".

Here they are again:

If term XMRV env is used in one paragraph then the term should mean the same throughout that paragraph unless it is specifically stated otherwise

The argument in the previous post, as I understand it, is that it is obvious to the reader that the authors meant the term to have different meanings. The gentleman's argument is that the authors referred to XMRV env as env sequences of the virus in the 22rv1 cell line and then in the same paragraph used the term XMRV env to describe the env sequence of ERV1 quite deliberately. In his opinion the authors did not attempt to mislead anyone or that this usage of the same term having two different meanings would have mislead anyone into believing that the term XMRV env meant the same thing throughout the same paragraph

This next section is reproduced from the main paper (The only one that almost everyone will read )

"To quantify the amount of XMRV DNA in the CWR22 xenografts, we developed a real-time PCR primer-probe set that specifically detected XMRV env and excluded murine endogenous proviruses present in BALB/c and NIH3T3 genomic DNA (Fig. 1C). We used quantitative PCR of 22Rv1 DNA to estimate 20 proviruses/cell and used the 22Rv1 DNA to generate a standard curve. The CWR22 xenografts had significantly fewer copies of XMRV env (<13 copies/100 cells) compared to the 22Rv1 cells (2000 copies/100 cells). The CWR-R1 cell line had

 

[jace]

continued in a new post - mods, please combine if you want to.

The CWR-R1 cell line had 3000 copies/100 cells, and the NU/NU and Hsd nude mice, thought to have been used to passage the CWR22 xenograft, had 58 and 68 copies/100 cells, respectively. Since xenograft tumors are expected to contain a mixture of human and mouse cells, we quantified the amount of mouse DNA by analyzing mouse intracisternal A-type particle (IAP) DNA as previously described (18, 19). Approximately 0.31% of the total DNA from all 6 xenografts consisted of mouse DNA (Fig. 1D); this result is consistent with the <13 XMRV env sequences/100 cells detected in the same samples (Fig. 1C)."

These are the same facts but worded differently

To quantify the amount of XMRV or ERV-1 DNA we developed a real-time primer probe sequences, which could theoretically amplify a sequence which was common to "VP-62" env and ERV-1 env, and excluded endogenous proviruses present in the DNA of mice which were not used in the creation of the 22rv1 cell line. The 22Rv1 cell line contained 2000 copies per 100 cells of "VP-62" XMRV env. We used the DNA from the 22Rv1 cell line to generate a standard curve and assumed the amplification efficiency of all PCR reactions were the same. The CWR-R1 cell line, produced by a different laboratory, contained 3000 copies per 100 cells. And the NU/NU and mice supplied by the Hsd (Harlan Sprague-Dawley) laboratory, which we think might have been used to passage the CWR22 xenograft, had 58 and 68 copies of ERV-1 env respectively. The CWR22 xenograft was found to contain 1-3 copies of ERV-1 env. We have no copy data on "VP-62" env sequences below 2000 copies per 100 cells. We did not test wild mice, but did test wild derived mice using a different primer and thus dont know whether this assay could detect "VP-62" env sequences or ERV-1 env sequences in wild derived or wild mice.

22Rv1 - 2000 copies/100 cells of VP62 XRMV env
CWR-R1 - 3000 copies/100 cells of "VP-62" XMRV env (created in a different lab, different mice from different suppliers)
NU/NU - 68 copies/100 cells of ERV-1 env
Hsd - 58 copies/100 cells of ERV-1 env
CWR22 - 1-3 copies/100 cells of ERV-1 env

They cannot say they detected XMRV env sequences in the cell lines and then say that they detected XMRV env sequences in the early xenografts and mice, and now claim that XMRV env sequences had a different meaning when they used the term to describe sequences detected in the cell lines than when they used the term to describe the sequences detected in mice and early xenografts. Any reasonable person would conclude that XMRV env would have the same meaning through out the same paragraph unless they were specifically told otherwise.

Next we should have determined the amplification efficiency of our real-time PCR assay when applied to target PCR from the different xenografts but we chose not to. Instead we used a different PCR entirely. The least sensitive PCR of all. A single round which had never detected XMRV in prostate cancer tissue.

You need to first substantiate your assertions, and then try to follow this up with a logical and understandable argument without obvious errors. Then, perhaps, there are even "central points" to engage with.

Are we there yet?

Interestingly, the main Paprotka paper is no longer available on the Science website. This is a very recent development.

 

[Sam Carter]

...

Interestingly, the main Paprotka paper is no longer available on the Science website. This is a very recent development.

The full paper and supporting online material are still available on the Science website, Jace.

Linkies:

Science. 2011 Jul 1;333(6038):97-101. Epub 2011 May 31.

Recombinant origin of the retrovirus XMRV.

Paprotka T, Delviks-Frankenberry KA, Cingz O, Martinez A, Kung HJ, Tepper CG, Hu WS, Fivash MJ Jr, Coffin JM, Pathak VK.

http://www.sciencemag.org/content/333/6038/97.full

Supporting Online Material for Recombinant Origin of the Retrovirus XMRV

Tobias Paprotka, Krista A. Delviks-Frankenberry, Oya Cingz, Anthony Martinez, Hsing-Jien Kung, Clifford G. Tepper, Wei-Shau Hu, Matthew J. Fivash Jr., John M. Coffin, Vinay K. Pathak

http://www.sciencemag.org/content/suppl/2011/05/31/science.1205292.DC1/1205292s.pdf

 

[RRM]

If term XMRV env is used in one paragraph then the term should mean the same throughout that paragraph unless it is specifically stated otherwise

The argument is still that the authors mislead you by implying that they detected XMRV in mice, while their enitire paper relies on the fact that they couldn't find XMRV in mice?

The argument in the previous post, as I understand it, is that it is obvious to the reader that the authors meant the term to have different meanings.

Then I have apparently failed to properly convey my argument.

In the paper, the term "XMRV env" refers to the partial sequence that can be found in XMRV, but that is not *necessarily* from XMRV itself. In other words, it could have come from another virus that contains this exact same sequence of "XMRV env".

This is not just implied, but blatantly obvious from the very same quote that is used to supposedly refute this notion. After all, the authors state the following (emphasis mine):

To quantify the amount of XMRV DNA in the CWR22 xenografts, we developed a real-time PCR primer-probe set that specifically detected XMRV env and excluded murine endogenous proviruses present in BALB/c and NIH3T3 genomic DNA

If the authors truly meant to say that their assay was specific for the env of actual XMRV, the authors would never have had to state that it also excluded endogenous proviruses. From this context, it is perfectly clear that the authors mean to say that this "XMRV env" specific assay can detect the actual env of XMRV as well as an identical "XMRV env" region in another virus.

Therefore, the meaning of "XMRV env" is consistent and apparent throughout the whole paper and your notion that the authors ever said that this assay was "XMRV specific" is clearly incorrect.

And this quote was also from the main paper:

Overall, these results indicate that PreXMRV-1 is an endogenous murine provirus that is present in the NU/NU and Hsd strains, but neither of these strains contains XMRV

So, even if you assumption that this main paper is "the only one that almost everyone will read", it should still be perfectly obvious to everyone that the authors meant to say that those strains of mice did not contain XMRV (and that, therefore, the detected XMRV env sequences were not from "actual XMRV).

Interestingly, the main Paprotka paper is no longer available on the Science website. This is a very recent development.

Surely you jest now? The paper is perfectly available, and this would also not be the way to correct this if there was anything wrong with the paper.

 

[jace]

Hi Sam, not when I tried using the link in my previous post (the long one on page two). Perhaps the address has changed, or maybe my link got scrambled. Certainly my last post messed me around big time. I'm glad to see it's still available (though many of us have saved a copy, I bet).

RRM, you do not comment on the fact that Paprotka is full of assumptions, conjectures, and possibilities, and not facts. That, together with the misleading use of language, the failure to follow through, and the selective use of different tests at different stages (remember the cake recipe?) are the nub of my objection to the way the paper has been lauded as the be all and end all of the origin of XMRV. If you cannot understand why I and others find that problematic, after the many many times it has been explained, then thats OK. You can take away from this discussion whatever you wish. Others will draw their own conclusions too.

 

[RRM]

Perhaps the address has changed, or maybe my link got scrambled

It's your link. Somehow you apparently copied and pasted a shortened link.

For instance, the (working) link to the SOM is also shortened in the post in question. Only when you hoover over the link, you will note that the full link address will become visible (in the lower left corner if you are runnig Chrome).

However, when you would just copy and past the (shortened) text of that link instead of the link itself, the resulting "pasted" link would also be dead.

RRM, you do not comment on the fact that Paprotka is full of assumptions, conjectures, and possibilities, and not facts.

I do not comment on that because I have not seen anyone make a valid attempt at serious criticism. We have only discussed the beginning of that letter because it is already riddled with so many inaccuracies that it is impossible to get past those.

But to give another example, because you insist, now regarding those assumptions made in the paper: you completely fail to take into account in your critique that some assumptions are made that work against the argument.

For instance, suppose I want to convince you that participating in the lottery isn't smart, then I could say:

"Even if we assume that you would buy 100 tickets, then the chances of you winning would still be as low as 1 in a million."

Now, it's not hard to see that I have made the assumption against my position and in order to make it possible to still conclude that I am right under a "worst case" scenario.

Furthermore, some assumptions are realistic to make and/or are not expected to have much influence on the outcome. For instance, in the lottery example, we would have to assume that the organisor of the lottery draw is honest. Also, even when the organisor is honest, the lottery balls could be slightly off in size and weight and influence the draw. Therefore we would have to assume that the balls are of equal size and weight (and they are of course never precisely)

However, despite me naming just three "assumptions" that I have made in order to estimate the lottery winning chances, nobody in their right minds would argue that my calculation would be worthless.

The same apllies to these assumptions in the Paprotka et al. study. If you want anybody that has any influence on these things to seriously consider an argument like this, you cannot just say "they made five assumptions and that is so wrong, na-na-nana-na". You would need to show why an assumption was unfairly made, that this could have made a significant difference to the experiment, etcetera

As it is, the assumptions made by Paprotka are perfectly reasonable and some of them are actually working against their own argument. Therefore it is also hard to take this part of the critique seriously.

(remember the cake recipe?)

Which is why they run controls, to ensure that the "recipe" is working properly.

 

[Mark]

To give yet another line of evidence that any informed or uninformed reader can easily verify, I make the following observation regarding the "XMRV specific" of "XMRV env specific" argument that is the main point of your reply...

Since you promise something easy for me to verify, I thought I would do so in this case...

The exact quote from the paper that this part of the critique (and the response to my post) refers to, has already been used earlier by the same people that wrote this critique, but then to "prove" something that totally contradicts what they now think it shows: that the early xenografts (and thus the original patient tumor) were infected with XMRV.

It appears to have been a "major" finding - note the number of exclamation marks.

The thread in question is over 6 months old, and Gerwyn's only comment on it is:

"nothing to do with me credit goes to you and cath"

Jace does not seem to have posted on that thread.

So I am wondering who are "the same people" you are referring to? Presumably, the entire membership of that forum? Some members of that forum once posted an argument that is contrary to Gerwyn's letter above - and this is your complaint?!

Really, all I am left with after checking that easily-verified example you promised is puzzlement over your definition of "the same people". I can only interpret you are treating the whole membership of those forums as a single entity ("that lot" perhaps?) and requiring that everything any of them ever says should be consistent with anything else a member of that forum may say, now or in the future. And if that condition is not satisfied, you assert that they should all be ignored.

Rest assured, this is based on a misinterpretation of this part of the paper too. It is actually very easy to point out why these people are wrong on both occasions, but would anybody be really interested? At this point I think it suffices to just note that these people are being totally inconsistent.

I'm afraid I don't feel at all reassured by this. You've highlighted that two different mecfsforum members have made apparently contradictory interpretations of a detail of Paprotka et al, with a 6 month gap between the two interpretations. You assert that it would be easy to explain why both interpretations are wrong, but your main point is that "these people" should just all be ignored because they contradict each other, and you suggest that nobody is interested in anything they may say. I would rather see calm refutations of the claims, interpretations and assertions instead of blanket comments that they should just be ignored because they contradict each other.

It should show anyone that it is only about throwing as much dirt at these "negative studies" as possible and hope that some if it "sticks".

I doubt many people have delved into the detail of your earlier posts, and I really haven't time to do so very often myself, but I picked one that you said was easy to verify, and what I found was that your argument was unfair and unreasonable, and amounted to 'throwing dirt' itself. Perhaps I was unlucky in the example I chose to investigate, but my tentative conclusion is that, in this case at least, it is you who are guilty of "throwing as much dirt as possible and hoping that some if it sticks".

 

[RRM]

Since you promise something easy for me to verify, I thought I would do so in this case...


The thread in question is over 6 months old, and Gerwyn's only comment on it is:



Jace does not seem to have posted on that thread.

So I am wondering who are "the same people" you are referring to? Presumably, the entire membership of that forum? Some members of that forum once posted an argument that is contrary to Gerwyn's letter above - and this is your complaint?!

I meant to say Gerwyn and V99(/Tango).

If you check again, you may notice that V99 thanks Gerwyn for his contribution in her opening post. Therefore, Gerwyn was involved in the finding before the "publication" of this finding in the original post. He does give "credit" to the persons that "spotted" the apparently great finding, but it is clear that he contributed to this, most likely by "reviewing" it and giving it the thumbs up.

Also, although Jace does not specify it, V99(/Tango) actually provided the graphic that is included in this most recent critique.

Really, all I am left with after checking that easily-verified example you promised is puzzlement over your definition of "the same people". I can only interpret you are treating the whole membership of those forums as a single entity ("that lot" perhaps?) and requiring that everything any of them ever says should be consistent with anything else a member of that forum may say, now or in the future. And if that condition is not satisfied, you assert that they should all be ignored.

For me, not all members of the mecfsforums are the same, but Gerwyn and V99/Tango certainly seem to be part of the "same team" that breaks all scientific papers they don't like apart. I cannot really see how you would extend your conclusion to the idea that I then must mean the "entire" other forum.

As it is, I agree that it would have been better if I had specified this a little bit better. It's pretty easy to see that the two posts are not in line with each other, but it was not that easy to verify that both V99 and Gerwyn were involved in both of these.

I'm afraid I don't feel at all reassured by this. You've highlighted that two different mecfsforum members have made apparently contradictory interpretations of a detail of Paprotka et al, with a 6 month gap between the two interpretations.

I seriously cannot see how you can see the "6 month gap" (which is actually 8 months) as something that is not reassuring to my position. After all, it goes to show that Gerwyn (and V99) first thought this was apparently a great finding 8 months ago and now, without any of them questioning this apparent important deduction from that quote (then or later), suddenly this interpretation is being put forward by Gerwyn and is not criticized by either.

It goes to show everybody that these two people lack the necessary intellectual consistency, by abondoning an earlier "clear" interpretation of a quote and replacing it with another "clear" interpretation of the very same quote. Does Gerwyn at least now agree that the original explanation was wrong?

I doubt many people have delved into the detail of your earlier posts, and I really haven't time to do so very often myself, but I picked one that you said was easy to verify, and what I found was that your argument was unfair and unreasonable, and amounted to 'throwing dirt' itself. Perhaps I was unlucky in the example I chose to investigate, but my tentative conclusion is that, in this case at least, it is you who are guilty of "throwing as much dirt as possible and hoping that some if it sticks".

And now I find your argument unfair and unreasonable, and amounts to "throwing dirt" yourself.

But seriously, you can never conclude this on a sample size of 1. It would be too easy - just see the sentence above. It's perfectly acceptable for you to miss that part from the post, and it as at the very least not sufficent for me to conclude that you are then throwing dirt at me or something similar.

You would really need a pattern, which is why I concluded what I concluded about this letter after I had given multiple examples earlier. Also, even when you decide to base this on a single example, you would really need to investigate this single example more rigorously than you would multiple examples. Apparently you did not, as (I assume) you missed essential information from the linked thread.

But please feel free to check my other "easy to verify" issues with this letter/post. I heartily welcome any criticism.

 

[lansbergen]

I seriously cannot see how you can see the "6 month gap" (which is actually 8 months) as something that is not reassuring to my position. After all, it goes to show that Gerwyn (and V99) first thought this was apparently a great finding 8 months ago

You presume.

 

[Mark]

I meant to say Gerwyn and V99(/Tango).

If you check again, you may notice that V99 thanks Gerwyn for his contribution in her opening post.

I saw that, of course.

Therefore, Gerwyn was involved in the finding before the "publication" of this finding in the original post.

Hold it right there with this 'therefore': it does not follow that Gerwyn was involved and we don't know from this comment precisely what Gerwyn was being thanked for.

And "publication" and "finding" should both be in quotes: this was merely a short-lived forum thread that lasted less than 24 hours and was then forgotten about. I think it's wrong to expect that all these forum conversations should always be complete, accurate and rigorous: they are conversations aimed at developing an argument, and many of them die away forgotten and uncompleted when other threads come up to take their place; that's just the way it is. If this thread was an early reaction to the paper, and they have re-interpreted things since, I don't see a problem with that. All that matters is whether the current argument has merit or not; what people may have said somewhere in the past, and their perceived credibility, should not mean that any given individual might not spot something significant or hit on a good point.

He does give "credit" to the persons that "spotted" the apparently great finding, but it is clear that he contributed to this, most likely by "reviewing" it and giving it the thumbs up.

Again, I just don't see how you can conclude this with any confidence from that thread. Tango says "thanks to Cath and Gerwyn", and Gerwyn responds "nothing to do with me credit goes to you and cath". To conclude, only from these words, that it is "clear" that Gerwyn contributed, and "most likely" reviewed it and gave it the thumbs up...well, I just don't see how you can draw that conclusion from his words "nothing to do with me" in response to a simple "thanks" for something unspecified.

Also, although Jace does not specify it, V99(/Tango) actually provided the graphic that is included in this most recent critique.

And if V99 (who you say is Tango, I have no reason to doubt that but also no evidence to assume it's correct) provided the graphic for Gerwyn's latest critique (the letter?) then so what? They work together, they provide bits and pieces to each other, but surely that doesn't mean that if one of them says something once and another says something different later then that's a contradiction? I don't see how this assumption of collective responsibility for all the words of other members of this team is justified.

For me, not all members of the mecfsforums are the same, but Gerwyn and V99/Tango certainly seem to be part of the "same team" that breaks all scientific papers they don't like apart. I cannot really see how you would extend your conclusion to the idea that I then must mean the "entire" other forum.

OK, fair enough, you were referring to these few individuals only and I was overstating it when I mentioned the whole of the forum. Point taken, but it wasn't clear who you were talking about when you referred to 'the same people' and 'these people'.

As it is, I agree that it would have been better if I had specified this a little bit better. It's pretty easy to see that the two posts are not in line with each other, but it was not that easy to verify that both V99 and Gerwyn were involved in both of these.

And as I've said, it still isn't clear to me how it's verified precisely what the involvement of these two was in the brief forum post and in the letter. I've had a go, but actually I can't easily see why the two posts aren't in line with each other, but in any case, it doesn't trouble me even if they were both the sole responsibility of the same person and are contradictory, because I don't see anything wrong with changing one's mind about something on closer analysis.

I seriously cannot see how you can see the "6 month gap" (which is actually 8 months) as something that is not reassuring to my position. After all, it goes to show that Gerwyn (and V99) first thought this was apparently a great finding 8 months ago and now, without any of them questioning this apparent important deduction from that quote (then or later), suddenly this interpretation is being put forward by Gerwyn and is not criticized by either.

As I say, I don't understand what is so problematic with changing one's mind, if indeed that is what has happened here.

It goes to show everybody that these two people lack the necessary intellectual consistency, by abondoning an earlier "clear" interpretation of a quote and replacing it with another "clear" interpretation of the very same quote. Does Gerwyn at least now agree that the original explanation was wrong?

Fair question, and I would accept that it's a fair point that somebody saying one thing dogmatically and with confidence one day and something contradictory later on, again with the same degree of certainty, undermines one's confidence in the author. But even so, still it's the case that all that really matters is the current argument or claim, and whether it holds water or not. I certainly don't mean to imply that I think everything Gerwyn and V99 say is accurate and consistent - I just don't think it needs to be and I don't think that's relevant to the truth or otherwise of a specific claim being made by them at this point in time.

And now I find your argument unfair and unreasonable, and amounts to "throwing dirt" yourself.

OK, well I can see how you might read it that way. I suppose by responding and highlighting what looked like an ad hominem attack by you, perhaps I was in some sense making an ad hominem attack myself. But I still think my argument above is fair and reasonable, and I think you're being harsh in your criticism, which seems to be aimed at undermining the credibility of your opponent by highlighting something they and their associates said 8 months ago, rather than sticking with the argument they're trying to make right now.

But seriously, you can never conclude this on a sample size of 1. It would be too easy - just see the sentence above. It's perfectly acceptable for you to miss that part from the post, and it as at the very least not sufficent for me to conclude that you are then throwing dirt at me or something similar.

Good: we're in some agreement here. I didn't conclude anything about you in general from this example I looked into, I just concluded that you're being unfair in the one example that I did examine. And you're right to not conclude that I'm throwing dirt at you from this one example either. But I didn't miss that part from Tango's post, I interpret the exchange the same way as before. "Nothing to do with me" is pretty clear.

You would really need a pattern, which is why I concluded what I concluded about this letter after I had given multiple examples earlier. Also, even when you decide to base this on a single example, you would really need to investigate this single example more rigorously than you would multiple examples. Apparently you did not, as (I assume) you missed essential information from the linked thread.

As I say, I didn't miss the point you highlighted, and I've looked over the issue I highlighted again just now, and I still see it the same way. So I feel OK on the depth in this case. As for the breadth, well, I've read quite a few of your posts but I haven't had time to look at any other issue in detail...I'm not drawing any sweeping conclusions from this yet anyway.

But please feel free to check my other "easy to verify" issues with this letter/post. I heartily welcome any criticism.

As do I, so long as it's constructive. I doubt I'll have time to verify any other such issues any time soon, I'm too busy to post much these days I'm afraid.

But in conclusion I'd just say that I still don't think your criticism of the 'inconsistencies' in the 'team' was a strong or relevant argument, and I don't see any value in arguments that focus on the credibility, reliability or history of the people making the arguments that are presented - I'd much rather see a focus on the actual claims being made. If those claims are poorly expressed or contain inaccuracies, then it's fair to point out that this won't play well with scientists, but on this forum, for patients who have a lot of very difficult challenges in their lives and are doing their best to express themselves under those circumstances, I think it's preferable to work with the poster to try to determine precisely what claim is being made, and then examine with an open mind whether there might be any merit in it. Hopefully I'll see that spelled out later in this thread...

 

[Firestormm]

Well. That's that then. Phew...

 

[RRM]

I haven't had the opporunity to read the forums lately and now it may be a little late to still reply, but there are some things that I think lie at the heart of the "problem" so I think it's worthwhile to still address:

all that really matters is the current argument or claim, and whether it holds water or not.

This sounds enirely reasonable, yet I still disagree to a large extent.

I have said earlier in this topic that almost any person (with the necessary time and motivation) could post a "refutaton" of any scientific theory there is. But if someone tomorrow posts a supposed refutation of the theory of special relativity and no one at this forum could/would refute that critique, what exactly would that prove? I would say that it wouldn't prove anything with regard to this theory. We could really only conclude that the critique went over everybody's heads.

And what's more: even if (for instance) you would take the time and effort to post your reply to the critique and your reply would totally destroy the original critique, how would the forum ever be able to recognize that the original critique was wrong and your reply was correct? In my view, it's not realistically possible, and this is also mostly why people tend to send their detailed critiques of studies to journals (in order for the original authors as well as other experts in the field to consider your points) and not to forums or journalists.

To pre-emptively evade a possible strawman: of course it is still extremely worthwhile to discuss science at a forum like this. However, I would argue that it is primarely in the sense of understanding basic scientific principles. For instance, anybody should understand the value of finding something in 67% of patients and only 4% of controls and the fact that they used several methods to verify these results. But when you start going into every little detail of a certain study or even at the underlying accepted methodology (for instance, questioning the use of Bayesian probability theory in phylogenetics), you cannot expect the "audience" in question to understand both the original study at the required level, as well as the critique in question, to really make a "judgement call" on the critique.

The above really applies in this case too. While it may seem that I use some sort of authority argument, it is really critiques like this one by Gerwyn that almost solely rely on an "authority argument". After all, Gerwyn mostly targets a layman audience and does not really try to persuade this audience with arguments that they will fully understand, let alone put in the context of the original finding. He basically relies on his audience to trust him as having enough knowledge on the matter.

And like I said above in a general sense, it really does not matter much when some of Gerwyn's arguments are destroyed. After all, who is going to be the judge on this? Therefore, although I feel many of Gerwyn's current and past arguments have been properly and totally refuted, it sometimes makes as much or even more sense to point out flaws and inconsistencies in earlier arguments that are possible for everyone to understand. It goes to show that Gerwyn is lacking the authority that many are relying on him to possess for the analyses that (some/most/all) people on these forums do not fully understand.

And if V99 (who you say is Tango, I have no reason to doubt that but also no evidence to assume it's correct) [...]

It's good of you to question this. I assumed people know this because I have read the other forums and just didn't give it any more thought. However, although I could say something like "investigate yourself", when somebody like this is not obvious to the reader, it is really up to the person making the assertion (in this case me) to back it up if it is being (explicitly or implicitly) questioned.

Anyway, although you didn't really ask, it's pretty easy to show. Just click this link for instance. You will note that a post by Tango is being quoted two postst later and the later post "says" the original quote was made by V99. This will work with any old post that you look up from Tango that got quoted by somebody else. After a name change on a forum, the forum software will also change your name on all posts before the change, but it will not change the names in quotes from earlier posts.

Now, even when people rely on the authority of Gerwyn's arguments, I would suggest that people should question some of his assertions too - even if just as a check of the authority some assume he possesses. For instance, I mentioned earlier that I have not seen any source for the statements that "primer 3f-8r using a single round PCR was unable to detect XMRV/VP62 in the later xenograft" and "the serial dilution method used here has come in for a great deal of criticism" in this particluar letter, even though assertions like these must really be substantiated, even without them being questioned.

For people that have seriously questioned some of Gerwyn's (and V99's) assertions, it should be pretty evident that they have been clearly wrong on many occasions and also on a very basic level. It goes to show that one cannot just rely on the more detailed and complicated writings to be correct either.

 

[Esther12]

It goes to show that Gerwyn is lacking the authority that many are relying on him to possess for the analyses that (some/most/all) people on these forums do not fully understand.

I agree with some of this, and had a post in this thread deleted (wrongly imo) because it focused upon the reasons that we should not assume Gerwyn has any particular authority on this matters given some of his past claims, which the moderators felt was a form of personal attack. However, when the the personal authority with which Gerwyn makes his pronouncements seems such a key reason as to why his posts interest a dwindling group of supporters, attacking that authority by pointing to the absurdity of his past errors seems entirely legitimate to me.

More generally though, I disagree with what seems to be RRM's argument about the merits of on-line discussions of research, which requires more faith in the processes of science than I think is reasonable. Such an approach may work well in the areas of the hard sciences where there is considerable attention and interest from a wide range of researchers (eg: the recent claim that particles had been shown to be travelling faster than the speed of light was always going t be thoroughly investigated), but much CFS research takes place in a quasi-scientific backwater, where objective data is hard to come by, and the claims of researchers receive little interest or critical analysis from within the systems of science.

(eg Esther Crawley recently claimed, in a paper aimed at NHS commissioners, that the PACE trial showed that the treatments she is paid to provide offer a 30-40% recovery rate for CFS. Tate Mitchell explains some of the manipulation of results which explains that claim here: http://forums.phoenixrising.me/show...Trial-Protocol&p=224448&viewfull=1#post224448 These sorts of distortions of reality have a really important impact upon the way patients are treated, and funding is allocated, yet receive no real examination from those other than patients, because CFS is seen as such a joke diagnosis.)

I think that some patients have taken this legitimate scepticism to much of the work that surrounds CFS, and misapplied it to the recent XMRV controversy. Virology does allow for the collection of clear and objective data, and for the sort of blinding we saw with the BWG results, and will see again (hopefully) with Lipkin's study. This leaves far less room for the prejudices of researchers, or for the manipulation of statistics and presentation of results.

 

[Marco]

I agree with some of this, and had a post in this thread deleted (wrongly imo) because it focused upon the reasons that we should not assume Gerwyn has any particular authority on this matters given some of his past claims, which the moderators felt was a form of personal attack. However, when the the personal authority with which Gerwyn makes his pronouncements seems such a key reason as to why his posts interest a dwindling group of supporters, attacking that authority by pointing to the absurdity of his past errors seems entirely legitimate to me.

More generally though, I disagree with what seems to be RRM's argument about the merits of on-line discussions of research, which requires more faith in the processes of science than I think is reasonable. Such an approach may work well in the areas of the hard sciences where there is considerable attention and interest from a wide range of researchers (eg: the recent claim that particles had been shown to be travelling faster than the speed of light was always going t be thoroughly investigated), but much CFS research takes place in a quasi-scientific backwater, where objective data is hard to come by, and the claims of researchers receive little interest or critical analysis from within the systems of science.

(eg Esther Crawley recently claimed, in a paper aimed at NHS commissioners, that the treatments she is paid to provide offer a 30-40% recovery rate for CFS. Tate Mitchell explains some of the manipulation of results which explains that claim here: http://forums.phoenixrising.me/show...Trial-Protocol&p=224448&viewfull=1#post224448 These sorts of distortions of reality have a really important impact upon the way patients are treated, and funding is allocated, yet receive no real examination from those other than patients, because CFS is seen as such a joke diagnosis.)

I think that some patients have taken this legitimate scepticism to much of the work that surrounds CFS, and misapplied it to the recent XMRV controversy. Virology does allow for the collection of clear and objective data, and for the sort of blinding we saw with the BWG results, and will see again (hopefully) with Lipkin's study. This leaves far less room for the prejudices of researchers, or for the manipulation of statistics and presentation of results.

Good post (if you don't mind me saying).

 

[Esther12]

(if you don't mind me saying).

How DARE YOU!!!!

edit: Oops. Just had one person be unsure as to whether I was outraged with marco, so thought I'd better make clear that I was just playing. Thanks Marco.