xmrv
sa smith | August 22, 2011DNA Extraction Columns Contaminated with Murine Sequences
This paper makes me very thankful for two things:1-- Bossman is extremely neurotic about controls (this apparently, is inheritable, because I am too).
2-- I dont work on a mouse virus.
If the list of potential sources of contamination in the XMRV-->prostate cancer, XMRV-->CFS stories werent long enough, here is yet another source of contamination to add to the list:In assessing the prevalence of XMRV in prostate cancer tissue samples we discovered that eluates from naïve DNA purification columns, when subjected to PCR with…
sa smith | July 20, 2011The simplest, simplest definition of evilution: Change over time.
Your children are different from you. You are different from your parents. Your parents are different from their parents. And so on and so on and so on.
But if Person A is older than you and has different DNA, that doesnt automatically mean Person A is one of your parents. If Person B is younger than you and has different DNA, that doesnt automatically mean Person B is your child.
You might think the above statement is obvious, but that is precisely the faulty reasoning used in a previous publication on XMTV/MLV-like/…
sa smith | June 22, 2011Today I spent the day driving home-- one of my best friends since the seventh grade is getting married this weekend. Look forward to pics of me in a 'beautiful' hot-pink bridesmades dress soon...
Anyway, since I was on the road all day, I of course wasnt connected to the internet. So I just got a minute to check my email and found:
yo pig. post my shit. or are you scared?
Posted by: ron lassof | June 22, 2011 1:11 PM
So I wandered over to the trashbin, expecting to find a signature XMRV nut 'comment': an OCD collection of links and copypastes from those links, thus trapped in the spam trap…
sa smith | June 3, 2011Judy Mikovits is playing whack-a-mole in her responses to the legion of anti-XMRV papers published to date:
She bitches about one thing, or another thing, as the papers are published, but she misses the big picture. Its not that there are moles randomly popping up. The problem is youre entire 3 acre lot is full of fucking moles. Its not one thing or another that is 'the problem'. A negative paper here or there wouldnt be a problem. The problem is the implications of all the negative papers taken together in their entirety.
I really want to take a post to sum up everything that has…
sa smith | June 1, 2011ERV readers will absolutely love this paper.
Recombinant Origin of the Retrovirus XMRV
Okay, we all know ERVs are awesome evidence for evolution and common descent. But, imagine we could do classical ERV research one better. Imagine that we had DNA from one of THE common ancestors of humans and chimpanzees-- an ancestor who is the proud owner of a new ERV. Imagine we have its DNA, and the DNA of its parents, and the DNA of their parents. Then imagine we had the DNA of its children, and their children.
Imagine the fun evolutionary research we could do, what we could see, with those kinds…
sa smith | May 31, 2011Sometimes papers make me laugh because they are so bad.
Sometimes papers make me laugh when they do or report something particularly clever.
This paper is the latter:
No Evidence of Murine-Like Gammaretroviruses in CFS Patients Previously Identified as XMRV-Infected
I literally laughed-out-loud several times while reading it.
Quick summary-- Other people looked for XMRV in patients that had previously or were concurrently determined 'XMRV positive' by the WPI and their commercial branch, VIPDx. None of these 'XMRV positive' individuals were actually XMRV positive in a lab that controlled for…
sa smith | May 17, 2011I finally understand, Whittemore Peterson Institute. I get it. You exist to torment me. (video NSFW if you will get in trouble for throwing up at your desk)
There are a couple things people have been asking me to write about re: WPI & XMRV.
1-- The new paper
The lead PI on the "XMRV-->CFS" paper is a woman named Judy Mikovits. She is a nutbar. Everyone is out to get her, everyone is part of conspiracies to discredit her research, she consorts with anti-vaxers and snake-oil peddlers-- aka, nutbar. One of her many claims of persecution was that she has allllllllll these papers…
sa smith | May 11, 2011I want to bake our favorite ninja/journalist, Trine Tsouderos, some cupcakes.
Awesomesauce:In an email, retrovirologist Jonathan Stoye suggested that if the methods described in the original paper don't hold up, it should be retracted.
"Sooner or later they are going to have to face up to the fact that [their] paper is almost certainly flawed beyond repair," wrote Stoye, head of the Division of Virology at the UK Medical Research Council's National Institute for Medical Research. "What is more, WPI cannot simply blame others for failing to reproduce their protocols."
"Rather they must ask…
sa smith | May 10, 2011I want you all to see an article I just found via Relative Risk Blog. Its about 'Chronic Lyme Disease'. About a young woman who was aggressively treated by a 'questionable' practitioner who had 'cured herself' of 'Chronic Lyme'. No one believes in 'Chronic Lyme'. 'Everyone' was 'against' this practitioner, while she insisted she 'KNEW' what she was talking about. Questionable tests. Off-label prescriptions. And this practitioner almost killed this young woman.Janet Love and Dana Rosdahl come across as sincere in their belief that doctors routinely misdiagnose the disease, leading to…
sa smith | May 5, 2011From a basic, logical perspective, XMRV as the causative agent for any disease has been dead in my eyes, for quite some time. One would literally need to bend the rules of basic epidemiology, basic cancer biology, basic immunology, basic virology, time/space for 'XMRV' to be 'real'.
But of course, in the real world, especially with virology, things dont always work logically.
So for me, XMRV was officially dead when logical, putative explanations for contamination were put forth last December. It went beyond "this doesnt pass the smell test", to "this is an explanation for why you would get…
sa smith | March 22, 2011Because I am having so much fun at mah conference, I missed my chance to plug a Q&A ninja/journalist Trine Tsouderos hosted with Paul Offit, vaccine inventor.
Im sorry you all missed the chance to participate (Im hoping most ERV readers are Respectful Insolence readers, so you all got the info that way). I mean, Im having so much fun interacting with people working with HIV-1 vaccines right now, and I get all giddy nuts about that, and you all could have gotten a taste of it by having the chance to interact with Dr. Offit.
I sorry :(
BUT!
On the bright side, the Q&A was recorded and…
sa smith | March 3, 2011Scientific conferences are so cool :-D
It s bunch of really smart people getting together to pow-wow about a common interest, sharing their newest data, brainstorming new ideas, trouble-shooting, arguing, finding new collaborators-- its just so friggen cool :-D
Unfortunately, us smaller labs can only budget for one/a couple of these a year, so I am missing out on the 2011 Conference on Retroviruses and Opportunistic Infections :( Its also kind of a downer that Average Joes/Janes arent really allowed to come, not that most people could take a week off work to attend anyway.
Lucky for us…
sa smith | February 25, 2011
Breast Cancer Show EverTags: SOUTHPARKmore...
After all the XMRV on ERV, as Wendy would say, "Im finished!"
Its over.
At this point, there are innumerable lines of evidence suggesting that XMRV is not a real human pathogen-- from its magical ability to be spread despite no virus in any body fluid, including blood, including in HIV-1 patients, to its inability to infect its 'target cell' while it infects other cells, to its refusal to mutate more than two nucleotides on its own or in response to human mutagens in vivo, except that it does in vitro, its inability to give rhesus macaques even…
sa smith | February 21, 2011Though I am definitely (and I hope clearly) a supporter of animal research in science (plug for Speaking of Research), it is also definitely something I do not like to do. Contrary to how animal lib freaks frame us, while I fully and absolutely support and appreciate my fellow scientists who are animal researchers, I personally have psychological issues with performing animal research myself*.
I feel it is a big part of my responsibility as a lab-bench researcher to do the best damn in vitro work I can do, to make animal researchers jobs as painless as possible.
Everything I do in the lab is…
sa smith | January 12, 2011I was reading the next segment of Brian Deers expose on Andrew Wakefield this morning, and I couldnt help but notice some similarities between Andrew Wakefield and Judy Mikovits.
Mikovits was plucked from obscurity by people with an agenda. The only thing the people with the agenda didnt have was science to support their agenda. Mikovits provided them with that 'scientific support'-- one paper. High profile journal. High PR/news coverage. That one paper has lead to a gold-mine of 'diagnostic' tests (owned by the people with an agenda + Mikovits), drugs (Ampligen, an antiretroviral that…
sa smith | January 3, 2011Long time readers of ERV know that I do not believe a 'new' retrovirus, XMRV, is the causative agent of any human disease. It does not make sense as a real human pathogen, unless you disregard field basics (or make up new 'rules').
New cell transformation/cancer rules.
New transmission/epidemiology rules.
New immunology rules.
New virology rules.
New genetics/population biology/evolution rules.
Over and over and over with XMRV, Ive typed in frustration "THIS DOES NOT MAKE SENSE!!!!!"
Occams Razor, though not always useful in science, does provide us with a basic logical guide: Either XMRV is…
sa smith | December 20, 2010Hey, you all know earlier this year, this summer, shit kinda hit the fan here at SciBlogs?
I didnt care about the idiots leaving. I was more annoyed at the lack of communication from The Overlords.
They will be watching my blog while Im gone.
This is my revenge for that.
XMRV and the MLV-Related Viruses? The sequences that have been submitted to GenBank indicate that these 'Magic Eye Viruses' are almost certainly ERVs.
Not a real human pathogen.
Contamination.
Disease-associated XMRV sequences are consistent with laboratory contamination
Pop-Sci article from Welcome Trust.
This paper…
sa smith | November 22, 2010Knock knock.
Whos there?
Not XMRV in African blood donors or HIV/AIDS patients.
Absence of detectable xenotropic murine leukemia virus-related virus in plasma or peripheral blood mononuclear cells of human immunodeficiency virus Type 1-infected blood donors or individuals in Africa.
This is the third study not to find XMRV in HIV/AIDS patients. HIV/AIDS patients have every other pathogen under the sun at higher rates than healthy people. Except XMRV? Uh huh. Right. There is simply not enough evidence to believe XMRV is a real human pathogen, much less that it is the causative agent in a…
sa smith | October 15, 2010Im totally done with XMRV-->CFS. It appears that scientists have gotten their heads back, and this last slew of testing was officially the death-blow for this hypothesis for me: Theres no XMRV in HIV-1 patients. Three studies now, not to find an association between the two. HIV/AIDS patients get everything and anything, and when they get it, it is pathogenic (even if its no big deal in fully healthy humans). Unless of course, XMRV is, once again the 'exception' to basic biology/immunology/retrovirology.
Can XMRV infect humans? Almost certainly. Does it, and does it cause disease? I…
sa smith | October 1, 2010Thanks once again to Trine Tsouderos:Chronic fatigue and XMRV -- what one researcher (who's been there) has to say
Weiss' main point is that the history of retrovirology is littered with the debris of papers finding a link between a virus and a disease that later turned out to be false results caused by contamination. "There has been a long succession of 'rumor' viruses posing as tumor viruses and promulgated as the cause of chronic human diseases," Weiss wrote.
Researchers at the Whittemore Peterson Institute for Neuro-Immune Disease, which led the team that published the original paper,…