Thanks RRM, that is the only evidence I am aware of. I don't think it's accurate to say that this means the patient and control samples were "handled differently".
They were collected from different sources, at different times, but in the same states (therefore in geographically diverse locations), and the control samples were drawn in 2004-2007 so they too must have been frozen. Whether the control samples were also stored in the WPI's repository is not stated. Whether the collection procedures were identical is not stated. But they may well have been, one would presume that efforts were made to ensure that they were, and so the evidence of these statements in itself is therefore not evidence establishing as "fact" that the samples were "handled differently"
When they say in the supporting material that "Samples were prepared within 6 hours of blood draw and frozen immediately in ‐800C or liquid nitrogen depending upon the sample type" that is the part of the [collection] process that might be said to constitute "handling differently", but it is not stated here that the controls and patient samples were handled any differently in this respect prior to freezing. So again, while it's possible that the samples may have been collected in a different way, before freezing, that is not stated here.
As I pointed out when I reviewed Singh's paper after Barb commented on it, Singh emphasises that the type of difference in source of samples that we are discussing here applied to all the XMRV research, including the subsequent negative studies (prior to her own), and was considered standard practice. Most of the studies I have seen (McClure's included) took the patient samples from some bank of ME/CFS patient samples (in McClure's case, interestingly, a bank of samples previously used for some previously-unknown research which tested ME/CFS samples for another retrovirus some years ago, which raises interesting questions) and compared them with banked (frozen) samples from controls. This was not considered to be an important or confounding issue; it was normal practice - so it's misleading to present it as if it were not.
I am surprised to learn that this unscientific approach and the assumptions it entails is not and was not unusual practice in this kind of research, at least according to what I have read. I think it would be a good lesson to learn to say that, in future, when patient samples are drawn, matched control samples should always be drawn in parallel, and banked together (if they are being banked). There should be no such thing as a bank of samples that is not matched with control samples in the bank - that is potentially a worthless bank. So that ought to be standard practice: that is one of the lessons that everyone could learn from this. In future, all samples should be matched with controls right from the point of collection, and handled identically. And this is what I have been pointing out in my post above and elsewhere: learn the lessons from this: it is not good enough to use it as an excuse to discredit someone you don't like because you see them as a bit of a maverick, and not good enough to assume that this was a sloppy error rather than something systematic that everyone does routinely (including Robin Weiss when the same thing happened to him) - if there was an experimental flaw, you should figure out exactly how things went wrong, so that everyone can avoid any potential mistakes in the future.
So I do think it is extremely important to point out that what you are describing in shorthand as samples being "handled differently" is in fact a difference that is standard in nearly all research of this kind. The raw statement of "handled differently" suggests or implies bad practice, and that could be an unfortunate spin, because it is not the handling in the experiment that your quotes refer to, but the collection of samples, and indeed there's no evidence here that the way those samples were handled during collection was different, other than taking place at different times.
Finally, and crucially, on careful analysis there is still no real answer in the differences you've highlighted which would give a known explanation for the kind of systematic contamination required to explain the Lombardi et al results. The WPI repository itself contained frozen samples, and these samples were frozen prior to arriving at the lab (within 6 hours of blood draw) and the samples were drawn from geographically diverse locations. Provided that the controls and patient samples were thawed at the same time and in the same place, this seems to give no opportunity, under known processes, for systematic contamination. Can those frozen samples be contaminated while frozen? Would this not require that XMRV can survive at -800C? Are you suggesting that may be the case? But I may well be missing something: could you perhaps explain where the window for systematic contamination lies, based on the evidence you've quoted, and how the evidence you've presented proves it as a "fact" that the patient and control samples were "handled differently"?
They were collected from different sources, at different times, but in the same states (therefore in geographically diverse locations), and the control samples were drawn in 2004-2007 so they too must have been frozen. Whether the control samples were also stored in the WPI's repository is not stated. Whether the collection procedures were identical is not stated. But they may well have been, one would presume that efforts were made to ensure that they were, and so the evidence of these statements in itself is therefore not evidence establishing as "fact" that the samples were "handled differently"
When they say in the supporting material that "Samples were prepared within 6 hours of blood draw and frozen immediately in ‐800C or liquid nitrogen depending upon the sample type" that is the part of the [collection] process that might be said to constitute "handling differently", but it is not stated here that the controls and patient samples were handled any differently in this respect prior to freezing. So again, while it's possible that the samples may have been collected in a different way, before freezing, that is not stated here.
As I pointed out when I reviewed Singh's paper after Barb commented on it, Singh emphasises that the type of difference in source of samples that we are discussing here applied to all the XMRV research, including the subsequent negative studies (prior to her own), and was considered standard practice. Most of the studies I have seen (McClure's included) took the patient samples from some bank of ME/CFS patient samples (in McClure's case, interestingly, a bank of samples previously used for some previously-unknown research which tested ME/CFS samples for another retrovirus some years ago, which raises interesting questions) and compared them with banked (frozen) samples from controls. This was not considered to be an important or confounding issue; it was normal practice - so it's misleading to present it as if it were not.
I am surprised to learn that this unscientific approach and the assumptions it entails is not and was not unusual practice in this kind of research, at least according to what I have read. I think it would be a good lesson to learn to say that, in future, when patient samples are drawn, matched control samples should always be drawn in parallel, and banked together (if they are being banked). There should be no such thing as a bank of samples that is not matched with control samples in the bank - that is potentially a worthless bank. So that ought to be standard practice: that is one of the lessons that everyone could learn from this. In future, all samples should be matched with controls right from the point of collection, and handled identically. And this is what I have been pointing out in my post above and elsewhere: learn the lessons from this: it is not good enough to use it as an excuse to discredit someone you don't like because you see them as a bit of a maverick, and not good enough to assume that this was a sloppy error rather than something systematic that everyone does routinely (including Robin Weiss when the same thing happened to him) - if there was an experimental flaw, you should figure out exactly how things went wrong, so that everyone can avoid any potential mistakes in the future.
So I do think it is extremely important to point out that what you are describing in shorthand as samples being "handled differently" is in fact a difference that is standard in nearly all research of this kind. The raw statement of "handled differently" suggests or implies bad practice, and that could be an unfortunate spin, because it is not the handling in the experiment that your quotes refer to, but the collection of samples, and indeed there's no evidence here that the way those samples were handled during collection was different, other than taking place at different times.
Finally, and crucially, on careful analysis there is still no real answer in the differences you've highlighted which would give a known explanation for the kind of systematic contamination required to explain the Lombardi et al results. The WPI repository itself contained frozen samples, and these samples were frozen prior to arriving at the lab (within 6 hours of blood draw) and the samples were drawn from geographically diverse locations. Provided that the controls and patient samples were thawed at the same time and in the same place, this seems to give no opportunity, under known processes, for systematic contamination. Can those frozen samples be contaminated while frozen? Would this not require that XMRV can survive at -800C? Are you suggesting that may be the case? But I may well be missing something: could you perhaps explain where the window for systematic contamination lies, based on the evidence you've quoted, and how the evidence you've presented proves it as a "fact" that the patient and control samples were "handled differently"?
