Abbie Smith is a graduate student studying the molecular and biochemical evolution of HIV within patients and within populations. She also studies epigenetic control of ERVs.
Laboratory #3--
Huh.
This letter was written by the lead author of the Netherlands study on XMRV in CFS on April 22.
Here it is (looks at calendar), May 5th, and I have yet to see this 'response' published online anywhere but here.
Its so weird that the Whittemore Peterson Institute didnt post it online yet, considering how 'Web 2.0' they are.
Huh.
I mean, I dont even know how I got it, and I got it and published it online. What is holding up the WPI? I dont understand...
Dear dr. Whittemore,lol @ 'Dr. Whittemore'
Apparently you wrote a letter to dr. McClure in which you make serious allegations about us (letter of 12 April published on your website www.wpinstitute.org). We would have appreciated if you would have been so professional as to inform us first hand. Furthermore, we feel some aggression in your letter that is unscientific.
To rebut the points you make:
1. At the cytokine meeting in Lisbon, dr. Judy Mikovits has told the audience that the Lake Tahoe cohort was investigated. One of us, prof. Mihai Netea, has asked critical questions about this at the discussion session, and the use of this cohort was defended as being representative for CFS by dr. Mikovits. In addition, dr. Mikovits admitted not using any sporadic cases of CFS in her studies. At the end of this public discussion at the session, she also admitted that "epidemic" and "sporadic" cases of CFS may represent different diseases.
2. At the moment you reported your findings on the Nijmegen samples, our paper was under consideration of the BMJ (after being rejected after a 5-week review process by the Lancet). Since our findings were based on solid, sensitive PCRs (described in detail in our paper) that efficiently detected XMRV in a cell line, as well as in positive samples that were provided to us by Dr. Judy Mikovits, we suspected contamination of our samples in your laboratory, the more so as XMRV was detected at a similar frequency in CFS patients (2 out of 7) and healthy controls (1 out of 3). Of note, the samples that you found positive were repeatedly negative upon retesting in our lab. Given the robustness of our paper, we considered it scientifically premature to report this finding before having settled the reason for the discrepancy. To solve the discrepancy, we proposed to exchange cohorts on February 9. Unfortunately, to date we have not received any response.
Again, we regret that you write letters like these, in which you do not hesitate to question our integrity, and distribute these via your website without giving us a fair chance for rebuttal.
Yours sincerely,
Frank van Kuppeveld, PhD.
lol @ 30% positive controls, 28.6% positive CFS patients
This is example #19472371612 of "Other People Are Nicer Than Abbie". If someone had done to me what that crazy ass housewife 'Annette Whittemore, Founder and CEO of WPI' did to van Kuppeveld et al, and McClure et al, it would have been physically impossible for me to be as composed as Dr. van Kuppeveld just was.
So, *tip of the hat* to you, good sir.
Medicine & Health
Comments
I love the Dutch. They raise casual indifference to the level of high art.
Posted by: Prometheus | May 5, 2010 10:08 AM
I'm curious how you got the letter. I would assume that their professional response would be a private communication.
Posted by: Crowhed | May 5, 2010 10:52 AM
What's that part about "we suspected contamination of our samples in your [Whittemore's] laboratory"?! It sounds like the Dutch group sent some samples for WPI to test, and that WPI found 2 positives in 7 CFS samples vs. 1 positive in 3 control samples. Yet the Dutch could not confirm any of those positives in their own lab, using the sample samples!
Is this new info? I haven't seen any previous reference to it. However, there is this bit from Whittemore's letter to Dr. McClure:
If I'm understanding this correctly, this is as close as anyone's yet come to showing that WPI's results are due to lab contamination.
Posted by: qetzal | May 5, 2010 11:53 AM
I think the WPI came very close to it themselves when they reported their sequences to NCBI NucCore. How very bizarre that the sequences of retroviruses hanging out in outbreak patients since 1984 are virtually identical to the positive control from Silverman.
Posted by: Sandy Slim | May 6, 2010 12:30 PM
Strange that both sides are claiming that they wanted to swap samples, and the others are not replying.
More letters.
McClure to WPI:
https://www.wpinstitute.org/news/docs/mclure-wpi_ltr_apr10.pdf
Reply from WPI:
https://www.wpinstitute.org/news/docs/wpi-mclure_ltr_apr10.pdf
Funny article/ press release that portrays Francis Ruscetti and John Coffin as rather supportive of the WPI:
http://esme-eu.com/news/dutch-press-release-positive-xmrv-study-a-matter-of-time-article340-7.html
I'm always a bit suspicious of this sort of quoting and paraphrasing though.
There are rumors of a couple more negative studies coming soon, and of positive (?) studies being expanded. I think that this is going to go on for a fair bit longer.
Posted by: gf1 | May 6, 2010 12:39 PM
Here is WPI's exact methodology. http://www.iacfsme.org/BULLETINSPRING2010/Spring2010MikovitsLetter/tabid/427/Default.aspx
Either way giving this level of detail is going to bring this to a head one way or the other.
Also read this quote... Are Coffin and Ruscetti consider quacks as well?
Dr. Ruscetti, one of the co-authors of the original study, evinced considerable frustration as he let loose with a blast probably rarely seen in the staid retroviral world calling the Dutch researchers burial of contrary results unethical and poor Science to boot ""I do not know how they think they get away with this ethically," said Ruscetti. "I do not think this is good science." Dr. Mikovits said she'd never seen anything like it and Dr. Ruscetti apparently never has either. He noted, as Dr. Mikovits repeatedly has, that the WPI, NCI and Cleveland clinic tested XMRV in four different ways and all checked out. The negative studies only looked for XMRV in one way (PCR) using a methodology that both researchers felt was problematic. Dr. Ruscetti also expressed his dismay about what he called a 'whisper campaign' about contamination.
Dr. Coffin, a top retrovirologists, strongly defended the XMRV finding. In a translation of a Dutch report Dr. Coffin reportedly said "People have raised the issue of contamination but nothing is known about at the moment. There is no proof. Much of the research is done at the NCI, in the laboratory of Francis and Sandra Ruscetti. They have a long experience with these viruses and are very cautious." Indeed, both of the Dr's Ruscetti are long-time employees of the National Cancer Institute - one of the most highly thought of institutions in the world. Dr. Coffin also noted a key difference between the original Science paper and the 3 validation studies; the fact that only the WPI study has 'grown' the virus:"None of the negative studies have been published so far, the virus is grown," said Coffin. "Only in the Science study has been done, and that is a very strong point."
Posted by: Impish | May 6, 2010 9:50 PM
qetzal-- :D
gf1-- McClure is a kick ass lady.
Impish-- I think Coffin and Ruscetti were lied to by Judy and Annette, either purposefully or because those two women are fantastically stupid. In any case, I do expect Dr. Ruscetti to send an apology to Dr. van Kuppeveld, now that he knows the real deal with the Dutch samples.
Coffins completely credulous take on XMRV-->CFS has been a point of discussion among some of us. Its odd.
Posted by: ERV | May 6, 2010 10:50 PM
@ ERV: Did you have a look at the 'How to find XMRV the WPI way' piece Impish posted?
Does its virology make any sense? Could it help explain the differing results? It could be complete nonsense, and I don't think I'd be able to tell. Thanks.
Posted by: gf1 | May 7, 2010 8:23 AM
Isn't Ruscetti Judy's former boss? She was a technician, grad student, and post-doc at NCI, was she with him the whole time or just part of it?
Posted by: Sandy Slim | May 7, 2010 12:12 PM
http://imedia.unr.edu/cmm/cmm.html
Hunh. No steeple. No stained glass. No pews. How is anyone supposed to know that you go there to tithe and worship?
Posted by: lvlhded1 | May 7, 2010 1:02 PM
gf1-- The protocol looks completely dull and uninteresting.
I have invented several things in the lab which have required specific tips/tricks that people might not think to do, to make the system work ie, you have to have the annealing time extended up to two minutes, not 15-30 seconds, need 5 times as much forward primer in the second round of PCR to get the size product you want, need to clone using a double digest as sequential will not work, you have to let the fluorescent protein mature for 5 days, not 2).
There are any number of 'weird' things that you sometimes have to do to make stuff work in the lab. When you have to do weird stuff, you make a point of putting that in your published protocol, or else no one can duplicate your results.
There is nothing weird in that PCR protocol.
I wouldnt have used a random oligo in the RT, since you know what you are looking for, and I think they added too much DNA into their PCR (Ive found theres not much of a point to adding more than 100 ng with Real-Time, otherwise your just increasing your background), theyre also adding about twice as much primer as I do, but, meh.
Not enough detail for their second round of PCR for me to judge it. Second round PCR can be tricky.
But again, there is nothing weird (ie, 'We had to anneal at 54 C and do a 0.2 touch-down' or 'We had to do a 2 minute extension, even though its only a 500 bp fragment' or 'We had to do 50 cycles, not 35'). She also doesnt mention that extra-special 'culturing' Ive heard mentioned before.
There is no reason why this very standard PCR should be so 'difficult' for other labs. There is no reason why this protocol should be considered super/special/magic.
Sandy-- heh. Good for her. Bossman would kick my ass if I was pulling her shit (technically, Bossman is a stickler for controls and always being 100% sure-- a perfectionist. I am too. we wouldnt have gotten into this mess in the first place).
Posted by: ERV | May 8, 2010 12:59 PM
Thanks for that ERV. I was surprised that it didn't seem to mention the culturing that others had said was important (I thought the WPI had said this too).
I'm also a bit surprised they said "despite the current assumption that PCR answers all questions, there are serious flaws in this assumption" - surely that misses the point. If their PCR tests are picking up an XMRV/CFS correlation, and no-one elses are, that's a problem regardless of their other testing.
If their immune response tests are less specific, maybe they've found something other than XMRV? But then, they're meant to have sequenced whatever they found and confirmed it was. (Pardon the surely garbled terminology here).
Posted by: gf1 | May 8, 2010 4:57 PM
Science has published 3 comments from other scientists and a response by Mikovits and Ruscetti. The links can be found in this note:
http://www.facebook.com/notes/the-cfids-association-of-america/more-on-xmrv-and-cfs-in-may-14-issue-of-science/429943395538
We await your commentary. :)
Posted by: Smurfette | May 13, 2010 8:28 PM
Wow to the Science letters, Ruscetti's going all the way for Mikovits. Silverman, Peterson and the rest didn't sign the response, they stayed out of it. Good choice. Changing stories, inaccurate language, and we still don't know where damn samples came from. Or which local medical practice provided the controls. You know, "You stupid Dutch people didn't understand my presentation" isn't an effective response to criticism of holy-shit jaw dropping sloppiness. Or classy, but we didn't expect that from Judy.
Posted by: Edo Parnassus | May 13, 2010 11:29 PM
I am not a scientist so ERV would be much better qualified to respond to the details of this but I am annoyed by several pieces of information in these letters. I am busy today so I will do these one at a time. The first one is this…
In the letter from Wessely they state “CFS is likely to arise from complex genes-x-environment risk factors, making a simple causative link between XMRV and CFS unlikely.”
Seriously… You have the balls to write in a scientific journal in a response outlining how you think someone’s science is bad a statement like that with absolutely nothing backing it up.
I think that x is true even though I have no proof so that obviously means that your assertion that y is true is false. Wow…
Posted by: Impish | May 14, 2010 11:36 AM
On the other hand, WPI is full of crap whtn they say that they don't want to raise false hopes. They are all over the place basically saying XMRV = CFS. Many of the people who suffer from this now have a great deal of hope put into the link between XMRV and CFS largely due to the publicity efforts of this lab. If this turns out to be false they should be tarred and feathered.
On the other hand a bunch of the scientists on the other side have been advocating Cognative Behavioural Therapy and gradual increasing exercise as a treatment for what is clearly a physical disease. This continues even though a recent (too lazy to cite at the moment) study showed absolutely no positive effect on patients this treatment is given to. Literally millions of dollars have gone into this form of non-treatment as well as a good deal of the CFS research dollars in Europe.
If it turns out not to be XMRV hopefully this whole thing will cause someone to figure out what it actually is as it certainly is not a mental illness.
Maybe ERV will find it :-)
Posted by: Impish | May 14, 2010 11:58 AM
Regardless of your opinion of the WPI, it looks like the WPI, Cleveland Clinic and and the NCI are not alone any longer. The CDC expedited this for the June issue:
Xenotropic Murine Leukemia Virus–related Gammaretrovirus in Respiratory Tract
http://www.cdc.gov/eid/content/16/6/pdfs/10-0066.pdf
3% XMRV+ in respiratory secretions for the controls.
10% XMRV+ in immuno-supressed transplant patients.
http://www.cdc.gov/ncidod/EID/index.htm
Perhaps XMRV can swim.
Posted by: sc | May 18, 2010 12:50 PM
Why do you think that paper has anything to do with WPI, or their claims on the association between XMRV & CFS?
Posted by: ERV | May 18, 2010 1:10 PM