Author Topic: The real story about XMRV coming out today?  (Read 3751 times)

since

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Re: The real story about XMRV coming out today?
« Reply #15 on: September 23, 2011, 02:22:35 PM »
Things are making more sense now, not less.

So I wonder how similar that "JHK" retrovirus that was discovered circa 1991 is to the virus WPI and Lo/Alter found if full sequences were to be done?
Quality over quantity.

Tango

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Re: The real story about XMRV coming out today?
« Reply #16 on: September 23, 2011, 02:47:49 PM »
The section of JHK in the GenBank it very different.  Something like 13% if I remember correctly.  But you get this with other gamma retroviruses.  1 to 2% diversity amongst a variant strains and then big jumps between some variants, but again 1 to 2% diversity
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subtr4ct

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Re: The real story about XMRV coming out today?
« Reply #17 on: September 23, 2011, 03:47:22 PM »
So I wonder how similar that "JHK" retrovirus that was discovered circa 1991 is to the virus WPI and Lo/Alter found if full sequences were to be done?

Does anyone remember the threads where we were discussing JHK a couple of months ago?  I can't seem to find them using the search feature.   Thanks
Disclaimer: I am not a medical doctor.  This post is not medical advice.  Consult your physician before taking any action.

flex

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Re: The real story about XMRV coming out today?
« Reply #18 on: September 23, 2011, 04:36:03 PM »
The methods and the assays where laid out clearly in the Lombardi paper for everyone to follow and the WPI where willing to work with anyone who wanted to work with them.

They made it specifically clear that they did not use VP62 to set their assays to and so did a large number of patients on this forum when countless "world renowned scientists" came here with the help of Cort Johnson and others from  form Phoenix Rising to sing the virtues of using a synthetic clone to search for a new Human gamma retrovirus.

Time and time again we explained this was a set up and could never possibly find the Lombardi HGRV finding and that exact replication was absolutely necessary.

No one listened.

No scientists listened.

Any new discovery is a new discovery so replication is utterly crucial.

Imagine discovering a new island somewhere in the middle of an ocean and giving exact instructions how to find it an even photographing it.

What is more important, a fight over the subjective name or following the instructions to the letter of the law. Its no good just saying, "oh ye I have seen islands before, if its there ill find it!"

Now Coffin has claimed he knew the source of the lombardi discovery all along and it was a recombination event that happened in the nineties. He even got published in science on a bunch of theories claiming "pre XMRV1 and pre XMRV"". He claimed it was the source of the "lab contaminate" in Lombardi.

How can Science excuse that publication being accepted as an explanation for "contamination" when half of the so called recombination event was pure fiction?

Its abundantly clear that Coffins immaculate recombination happened in 2006 when Silverman combined strains from three different prostate patients.

Retract Coffin now!!!!

All along the WPI have been shouting from the rooftops this is a new HGRV here are the instructions how to find it.

They even told everyone this was a family of new RVs and the only one who listened was Alter and he validated the Lombardi findings. They even photographed the P budding virus. 

Yet scientific publication after scientific publication preferred to publish half arsed attempts at finding a synthetic clone of a non HGRV in cohorts of non ME patients.

Now they have declared the blood safe!

One basic lesson they should all know from science 101 is ......
REPLICATION REPLICATION REPLICATION!!!
« Last Edit: September 24, 2011, 12:11:11 AM by flex »
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anciendaze

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Re: The real story about XMRV coming out today?
« Reply #19 on: September 23, 2011, 04:43:28 PM »
Does anyone remember the threads where we were discussing JHK a couple of months ago?  I can't seem to find them using the search feature.   Thanks
Is this or this the one you want?  The search feature on this forum is seriously broken.  I've been using google search with mecfsforums as a prefix. 

Tango

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Re: The real story about XMRV coming out today?
« Reply #20 on: September 23, 2011, 04:44:04 PM »
Especially when the only way 22rv1 could contain vp62 is by contamination in the last few years, because vp62 was created in 2006.  :D :D ;)
"I suspect there have been a number of conspiracies that never were described or leaked out. But I suspect none of the magnitude and sweep of Watergate." Woodward

"I would favor any name that does not impose (or give the appearance of imposing) taxonomic preconceptions on the nomenclature." Coffin

subtr4ct

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Re: The real story about XMRV coming out today?
« Reply #21 on: September 23, 2011, 05:01:43 PM »
Is this or this the one you want?  The search feature on this forum is seriously broken.  I've been using google search with mecfsforums as a prefix.
Yes -- thanks very much, Ancientdaze
Disclaimer: I am not a medical doctor.  This post is not medical advice.  Consult your physician before taking any action.

bullybeef

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Re: The real story about XMRV coming out today?
« Reply #22 on: September 23, 2011, 05:30:31 PM »
Just the fact these denialists rarely mentioned, or declared an interest to validate or even replciate the Alter/Lo paper screams how much they are afraid of it. At the moment it is our golden egg, and full federal validation of the Lombardi paper. And it's now official!!!
BB

asleep

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Re: The real story about XMRV coming out today?
« Reply #23 on: September 23, 2011, 06:29:16 PM »
This is all starting to make more sense. I do have on major lingering question:

What are people's thoughts on why there was relatively little concordance between positive samples from (and even within) the Ruscetti and WPI labs?

If we consider a sample positive if Ruscetti and/or WPI marked it as (definitively) positive for any aliquot, then there were only 6 negative samples in the study. But the positive samples received positive hits inconsistently across these labs and even across aliquots within the same lab. Could this merely the result of unreliability of blood testing? Would this indicate other shenanigans being in play (and if so what)?

B8b_E

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Re: The real story about XMRV coming out today?
« Reply #24 on: September 23, 2011, 06:38:08 PM »
''The big news that is lost in all the press about the BWG is that Silverman admitted that his lab had likely contaminated his part of the Lombardi study - which were the full sequences that he identified as XMRV and prompted the authors to use the term XMRV in the first place.''

Round of applause for Silverman.

If WPI had never used the title 'Detection of XMRV', we'd not all be in this shit now.
Thiking back to the SOTK meeting at the NIH, I'm sure Judy said SCIENCE forced her to use the word XMRV too?
Which if I'm correct would be very interesting indeed as Coffin peer reviewed the paper.

 :(

« Last Edit: September 23, 2011, 06:44:59 PM by pMRV_d0minAtriX »

asleep

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Re: The real story about XMRV coming out today?
« Reply #25 on: September 23, 2011, 06:51:30 PM »
Just the fact these denialists rarely mentioned, or declared an interest to validate or even replciate the Alter/Lo paper screams how much they are afraid of it. At the moment it is our golden egg, and full federal validation of the Lombardi paper. And it's now official!!!

When not outright ignoring Alter/Lo, the storyline has been to casually brush it off because "what matters is validating the original findings in Lombardi et al." It is of course nonsense to claim that one study doesn't merit further investigation because it came in response to another (now partially problematic, though problematic in an ironically enlightening manner) study. I would expect an intensification of such memes as a means to avoid consideration of Alter/Lo.

ETA: This same flawed notion that the entire outlook of a general line of scientific investigation (HGRV in ME) rests on the limited shoulders of the very initial investigation (Lombardi et al) has been and is being applied more generally. It is being used right now on PR to short-circuit any discussion of testing other tissues besides blood: e.g. "if the results of the Lombardi paper don't hold, there's no reason to look in other tissues." Fallacious to the bone.
« Last Edit: September 23, 2011, 06:56:34 PM by asleep »

Gerwyn

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Re: The real story about XMRV coming out today?
« Reply #26 on: September 23, 2011, 07:52:26 PM »
One point I want to make, if I can get anyone to notice in this scrum, is that the common integration sites are evidence of contamination by cells, not simply virus, in Silverman's lab.  WPI went to great lengths to exclude mouse cells from its laboratory, using a new room which had never been used before.  While this was aimed at eliminating contamination by mouse cells, it should also limit opportunities for other contamination by cells. 

The common source for problems in replication studies has been identified, Silverman's laboratory and the VP62 plasmids used to validate assays.  Which laboratory did not stop with VP62 when it came to validation?  WPI.  Some of you may remember I was never thrilled with the lack of variation in XMRV. 

Finally, a few words of caution from a distinguished source: 

"N'attribuez jamais à la malveillance ce qui s'explique très bien par l'incompétence."
--N. Bonaparte.

"Never ascribe to malice what can be explained very well by incompetence."

When a field is new, no one is competent.

agreed with most but a great number of retroviruses show little or no sequence variation because they dont propagate using RT they can but mostly they dont

Gerwyn

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Re: The real story about XMRV coming out today?
« Reply #27 on: September 23, 2011, 07:57:12 PM »
They were 3 full length (1 almost) clones done by Silverman.

The WPI and NCI found the gag region, that is what the data is the 67% is based on. 

68 positives, but only 3 fully sequenced by Silverman.

The gag region of Lo and Lombardi when compared are 99% identical and only 3 neuclotides different.  Same virus!

yes if you take silvermans errors out of the equation the virus in the Lombardi study the lo study and the hansen  study are the same or all polytropic variants

modified polytropic by the way is a metaphor coined by stoyle and coffin to describe ervs

mclaughlinjill

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Re: The real story about XMRV coming out today?
« Reply #28 on: September 23, 2011, 08:33:06 PM »
The CFIDS Assoc get behind it? They are spreading doubt and disbelief as fast as they can.
But see - now we can move on with a clear conscience. There are SO many other solid leads
in the last 2 years that are as noteworthy as XMRV. Is it any wonder that we get
nowhere with such incompetent representation.

Virus Theory for Chronic Fatigue Syndrome Discredited
XMRV Virus Probably Not a Cause of CFS; Original Study Partially Retracted
By Brenda Goodman

"Time to Move On?

Patient advocates say it's time to refocus research efforts on credible science.

“We share the deep disappointment of many CFS patients and scientists that the initial data did not hold up. Whether you have been diagnosed recently or have been ill for decades, this news comes as a blow to hope for rapid advances in the care available to CFS patients,” says Kim McCleary, president & CEO of the CFIDS Association of America, in a prepared statement.

“There are many other solid leads that merit the same rigorous follow-up as XMRV has received over the past two years,” McCleary says."

-

I have no idea but now all the ME/CFS community no, we have to get behind this and so does the CFIDS association and the ME Association in the UK.

Basically the blood supply is still at risk.

There are many retroviruses we're told. This is serious and needs looking into. This is a public health disaster. I think Dr Judy will give us more information later - we need to find out as much as we can about her presentation today, we need to act now.


anciendaze

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Re: The real story about XMRV coming out today?
« Reply #29 on: September 23, 2011, 09:03:58 PM »
Officials don't like the idea of looking for a new retrovirus?  How about this alternative:  HTLV-1. 

It is real, it is in humans, it can be found all over the globe and in every ethnic group from Aborigines to Eskimos.  In the U.S. (at least) it is found in high percentages of urban IV drug users.  Drug users form such a large subpopulation that deaths from drug overdoses now outnumber deaths from automobile crashes, (though most drug abusers are not known to be IV drug users.) 

IV drug users tend to avoid doctors, who might recognize their condition, but they do turn up at surprising rates in prisons.  Do you think prisons test for HTLV-1?  Screening tests of donated blood rely on serology.  This is more sensitive than PCR when infection is active, but we now know there are many asymptomatic carriers with latent provirus -- who may not have a strong antibody response. 

This is the kind of disregarded subpopulation with high infection rates which kick-started the AIDS pandemic.