Phylogenetic analysis of MLV sequences from longitudinally sampled Chronic Fatigue Sy

[RedRuth]

This is a very good point which is why it's important that they have an expert on viral genomics as an author. http://www.sanger.ac.uk/research/faculty/pkellam/ and it's sure to have been peer reviewed by experts on phylogenetics. They also say

We propose that the detection of murine virus in human
samples be more rigorously controlled using IAP PCR (26) to rule out murine DNA
contamination and robust phylogenetic analysis to rule out random amplification of
endogenous proviruses (12), which can exist at high copy number in the genomes of
mice or in cell lines that become infected with mouse viruses during routine
experimentation.

 

[RedRuth]

As far as i know they tested for mouse DNA at the Lo lab and found no contamination of that sort (or any other sort).

They only tested for mitochondrial Mouse DNA and not the more sensitive IAP based PCR test. There's also the problem of contaminated cell lines.

Also, i find it hard to believe that Lo and Alter, who looked at these samples, the new ones and the 15 years old ones, would not have seen that the sequences in the older ones can't be ancestral to the newer ones. I just don't believe they would not be competent enough to do that analysis.

Why? Phylogenetics is an extremely complex field, are either of them experts in this field, like one of the authors of this paper? These authors imply that their analysis wasn't 'robust' enough and a criticism of the original Lombardi paper is inadequate phylogenetics analysis.

 

[RRM]

They only tested for mitochondrial Mouse DNA and not the more sensitive IAP based PCR test.

I believe knowledge about the IAP test being (way) more sensitive became known only after publication of both the Lombardi and Lo papers.

While Mikovits will not (re-)test their positives for contamination using the IAP test because she fears the IAP test can return false positives for contamination (based on this paper by the way), Lo/Alter have reported on one or several occasions that they have restested (at least some of) their samples with the IAP test and they still turned up negative. However, Lo/Alter also reported that their IAP test was actually less sensitive than the test for mitochondrial DNA. Please check this transcript for that; it's in the Lo presentation at page 174 or press CTRL+F and search for "IAP" and see the second result. This would indicate that they might have been doing something wrong, as several research groups have indepedently reported that the IAP assay is way more sensitive than the mitochondrial DNA assays).

 

[currer]

Hi RRM, just come from Jamie Deckoff-Jones Blog?

http://treatingxmrv.blogspot.com/2011/08/keeping-it-simple.html#comments

Remember we are suffering here from this disease. It is not a game to us.
People are dying from this illness. I have two friends, both young men, who have died.
They got no medical help.

What is your reaction to that?
Are you here to help us?
Why do you want the research to stop?

 

[eric_s]

They only tested for mitochondrial Mouse DNA and not the more sensitive IAP based PCR test. There's also the problem of contaminated cell lines.



Why? Phylogenetics is an extremely complex field, are either of them experts in this field, like one of the authors of this paper? These authors imply that their analysis wasn't 'robust' enough and a criticism of the original Lombardi paper is inadequate phylogenetics analysis.

Like it was said, at least one lab also used the IAP test. And there are serious doubts about this test. I believe people like Lo, Alter, Ruscetti or Silverman would either be able to do that analysis by themselves or then realize the need for somebody else to do it and know who to ask.

 

[eric_s]

Hi RRM, just come from Jamie Deckoff-Jones Blog?

http://treatingxmrv.blogspot.com/2011/08/keeping-it-simple.html#comments

Remember we are suffering here from this disease. It is not a game to us.
People are dying from this illness. I have two friends, both young men, who have died.
They got no medical help.

What is your reaction to that?
Are you here to help us?
Why do you want the research to stop?

I agree with this. I appreciate the input of scientists on a forum like this one, the more professionals that get interested and that can help explain things and answer questions, the better. But at this point we don't know for sure yet, what the truth about XMRV/MRV is, and also i don't really see the sense of criticizing or trying to disprove one topic after the other, without replacing it with another direction research and our community could follow. I don't know about IVI, but as far as i know, neither RRM nor RedRuth have ME/CFS. That's good and i'm happy for you, but then i would like to ask you, what can you do for your relative who has the illness, as you say, and for the remaining couple of millions of us? What do you think in which direction research should go, if it's not XMRV? What can you do to make this happen? RedRuth, could you try to raise awareness of ME/CFS among your colleagues and their colleagues? Could you try to get them to conduct more research into the etiology of it, so effective treatments and one day a cure can be found? Could you get them to take a position against the Wessely camp? Your family member depends on this to happen, unless he or she will recover spontaneously, which is quite rare, or one of the existing treatments will work. And as far as i know, usually those treatments don't lead to a full remission, even if they work, and the effects don't always last. Also people says it hard to impossible to even get them in the UK.

 

[free at last]

The 'reference' is to another online forum where the prevailing attitudes are pretty well summarised by the quoted phrase Science can be defined as the belief in the ignorance of experts. It's difficult not to see this proposition as a call to embrace the Dunning-Kruger Effect as the descriptor of M.E/CFS activism. The attitude even has its own self defining logic - expert X has published material which is 'wrong' and with which 'we' disagree: therefore all experts with whom we disagree are wrong. There is also a supporting logic sequence which runs - expert X has been unkind/unhelpful to 'us': therefore we disagree with expert X (who is therefore wrong): therefore disagreement = untrustworthiness: therefore: expert Y who agrees with expert X is untrustworthy (repeat in infinte branching links as required).

Saying 'science doesn't work like this' doesn't unfortunately break this line of thinking because "thats what experts say" and ....... Science can be defined as the belief in the ignorance of experts cue vapid commentaries about "appeals to authority' et etc etc. 'Sigh'.

IVI

No i just think its mistrust when we see, ( KNOW ) the way Patients like Sophia Mirza and her mother were treated by the so caring authority' etc etc ect
lynn gilderdale the list goes on.

Its not hard to see why that mistrust spills over into the scientific process. because many scientists and doctors, can hold that blinkered view that leads to the kind of deaths im speaking of here.

so when you dont know who to trust. it gets a little fuzzy Not our fault, that many have been treated like this to the point of not being able to trust much of the scientific process.

Untill the scientific process comes and saves us. for the most part it has failed us, and it has been failing us for many many years. of course im wrong about that NOT

I wont even talk about politics.

I find people who try to find fault with those who are finding fault with the very people, process, scientists and doctors, who are failing us so badly. Are often part of that flawed process that leads to neglect, and death. in patientsto to begin with.

That harsh blinkered view on and on. ( we know it when see it, because we dont just see it, we feel it ) speaks volumes of a real lack of understanding why so many are mistrusting

If they had been treated as badly as many have on this forum, and the world over. they would not be so trusting of the authority' and the scientific process that has failed us all for so many years. its just so obviouse, sorry it is. No amount of superiour intellect can hide that from us. Infact all that does is make it more obviouse. And i really dont care who dissagrees, i only have to go to sophia Mirzas web page to know im right about everything ive just said. i might be wrong about certain individuals granted. But not all, as mentioned earlier its hard to tell sometimes isnt it. I dont mind finding fault with authority or the flawed scientific process. ( not all science is flawed, im not completely stupid ) but its Fuzzy fuzzy fuzzy

 

[RedRuth]

@ Eric. This is a fair point and I have to keep reminding myself that this isn't just an academic game (like the creation/evolution debate), it's about real people with a real debilitating disease. I didn't ever intend posting here but I was really saddened to see that people really believe there's some kind of conspiracy among scientists about XMRV and ME, I don't doubt that ME sufferes have been treated badly but this is ridiculous. There is no conspiracy theory, sometimes mistakes just happen but science is self correcting there will be a consensus. Sadly it really looks like the Lombardi and Lo studies were the result of contamination of cell lines and/or reagents, this isn't really anyones fault though it was probably premature for Science to publish. But, this has got some big names in virology interested in ME so hopefully the impetus will continue.

I really think I should consider my motives in posting here and I probably won't post again, but please stop accusing scientists of being dishonest or part of a conspiracy, conflicting results happen all the time, it doesn't mean someone is lying or 'toeing the party line' it means methodological and contamination issues have to be sorted out. Anyway, I sincerely hope the future holds at the very least answers if not a cure to your disease.

 

[eric_s]

Thanks, RedRuth. It's of course up to you, if you like to post here or not. While i often don't agree with what you say, i would prefer if you stay, but i would really hope you could find a way to help accelerating the progress of research in ME/CFS. I don't know what is going on, it's impossible for me as an outsider to know, so i try to not guess too much. But i do believe there might be reluctance among policy makers and businesses to accept ME/CFS, because it would mean expenses. Of course, for other businesses it would mean income. Also i'm sure that among scientists there can be rivalry and a fight over who gets the fame and the money connected to a discovery. But i also believe that in the end science gets to the truth.

 

[liquid sky]

We do not have to keep reminding ourselves that this isn't just an academic game. We feel the pain and suffering every day. We have no motives but to find a cause and treatment. Whether you believe it or not, scientists can have other motives, fame, money, prizes, etc.

You keep saying that Lombardi and Lo were contamination, but it has not been proven. You need to understand who has their lives on the line. Remember your humanity.

 

[Firestormm]

Is this thread about the Aris Katzourakis paper? Just wondered if anyone has read it is all.

 

[eric_s]

When i checked it was not accessible for free.

 

[WillowJ]

@ Eric. This is a fair point and I have to keep reminding myself that this isn't just an academic game (like the creation/evolution debate), it's about real people with a real debilitating disease. I didn't ever intend posting here but I was really saddened to see that people really believe there's some kind of conspiracy among scientists about XMRV and ME, I don't doubt that ME sufferes have been treated badly but this is ridiculous. There is no conspiracy theory, sometimes mistakes just happen but science is self correcting there will be a consensus. Sadly it really looks like the Lombardi and Lo studies were the result of contamination of cell lines and/or reagents, this isn't really anyones fault though it was probably premature for Science to publish. But, this has got some big names in virology interested in ME so hopefully the impetus will continue.

I really think I should consider my motives in posting here and I probably won't post again, but please stop accusing scientists of being dishonest or part of a conspiracy, conflicting results happen all the time, it doesn't mean someone is lying or 'toeing the party line' it means methodological and contamination issues have to be sorted out. Anyway, I sincerely hope the future holds at the very least answers if not a cure to your disease.

Hi, RedRuth. I agree with eric's posts.

I was wondering, do you have some alternate explanation for why Towers would be telling the media things that went so far beyond the appropriate conclusions of the studies?

I would rather not believe in conspiracy theories. On the other hand, experience has taught me that there are indeed a few scientists (the (bio)psychosocial school which discounts any and all biomedical evidence) who cannot be trusted in any case. This is the minority of scientists, but unfortunately it tends to be a very powerful minority. (it's not exactly a secret society, though, so it doesn't formally qualify as a conspiracy)

Importantly, this group of untrustworthy scientists does not automatically include any scientist with a negative XMRV finding; I still trust Singh, for example.

 

[RustyJ]

@ Eric. This is a fair point and I have to keep reminding myself that this isn't just an academic game (like the creation/evolution debate), it's about real people with a real debilitating disease. I didn't ever intend posting here but I was really saddened to see that people really believe there's some kind of conspiracy among scientists about XMRV and ME, I don't doubt that ME sufferes have been treated badly but this is ridiculous. There is no conspiracy theory, sometimes mistakes just happen but science is self correcting there will be a consensus. Sadly it really looks like the Lombardi and Lo studies were the result of contamination of cell lines and/or reagents, this isn't really anyones fault though it was probably premature for Science to publish. But, this has got some big names in virology interested in ME so hopefully the impetus will continue.

I really think I should consider my motives in posting here and I probably won't post again, but please stop accusing scientists of being dishonest or part of a conspiracy, conflicting results happen all the time, it doesn't mean someone is lying or 'toeing the party line' it means methodological and contamination issues have to be sorted out. Anyway, I sincerely hope the future holds at the very least answers if not a cure to your disease.

Though hopefully optimistic that your belated introspection is a sign of honesty, without elaboration I cannot be sure. What I am sure about is that your contribution to this forum has not been positive, despite your stated intentions.

I am disappointed you did not apply your skills towards more constructive discussion of XMRV. I also am puzzled by your defensiveness regarding our accusations against scientists. For decades the scientific consensus has been that ME is a psychological disorder, and that is the continuing consensus. For twenty years I have been treated as if I have a psychological illness, while physical symptoms are ignored and go untreated. Until this situation changes, I will regard the scientific consensus view as dishonest. I will also view any scientist who supports this view as dishonest. That includes scientists who sit by and allow that situation to continue. Why is this unreasonable? If I am being defensive in my claims, I have good reason.

 

[currer]

If Redruth keeps forgetting that this debate is about real people, doesn't it put into question her assertion that she is here because her sister has/was thought to have ME?

I support PRs policy of openness. I do not think posters should be excluded just because they disagree with most of us, as this would damage and limit our discussions here.

But I think if people come here thay should be honest with us about why they are here and not invent (if that is what has happened) an excuse to post on a patient forum.
And Redruth if she stays should try to use her scientific knowledge to our benefit and stop arguinjg purely from a negative standpoint. It makes for very boring posts and damages the discussions that can take place on these threads

What disturbs me most about the virologists opposing the WPI is their lack of concern for the patients. They are not clinicians, their professional life never introduces them to a patient, they have no empathy for us. They frighten me frankly. I think they have lost awareness of the consequences of their science for people. Maybe they become scientists so they do not have to meet people and feel safer looking into test tubes.
These people have created a lot of artificial viruses. How safe is that?

And Rusty you are right. The scientific consensus view is dishonest. I am astounded that the professional bodies that represent both psychiatrists and medical clinicians in Britain have never protested against this and attempted to defend their patients. It is a scandal and a shame on them, and ordinary GPs who have to try to help their patients with no support from their own profession are realising this.

 

[Firestormm]

When i checked it was not accessible for free.

It is around. Very complex to try and understand though - as Redruth commented earlier. Be good to try and understand it though don't you think?

I do not understand why these scientific papers and the discussion that follows can't remain objective and try to help others understand the science without it degenerating into emotive and conspiratorial finger-pointing.

Perhaps this paper though is too complex? Still it would be useful to talk science in these threads and not question the authors' let alone other contributors' motives for once.

 

[free at last]

Here we go again. Sorry it works both ways, and certain comments by a couple of posters often leads to emotive discussion, distracting from the original subject. if posters want to stay on topic, and debate this particular paper im all for it.

But untill they do, ill give my viewpoint, pull it as far away from topic as i see fit. Just to respond to those WHO ARE ALREADY GOING OFF TOPIC in a ( for me personally ) uncaring and blinkered fashion ( whats new ) It only takes a couple of those posts to induce a wave of disgust and despair. in many patients on here.

I notice when such said patients defend themselves like this and there conspiratorial viewpoints ( which they are entitled to, be it right or wrong ) from certain individual people on here. we often get a backlash from the ( there is no mis treatment at patients, there is no conspiracy ANYWHERE your all to emotional brigade ) If its just the paper you really want to debate theres nothing stopping you.

But thats too easy isnt it. which leads me to my other conclusion. that such said emotive and conspiratorial finger pointing. really rubs you up the wrong way. The way possibly a psychatrist of the wessley school might get rubbed up the wrong way, when presented with distaste from disgruntled patients not happy about the way they are being treated. why is that ?

Just ignore such said posts you see are distracting you. ( like this one. mmmm what to do reply or not. im not sure now ??? ) that tactic works quite well i think, and often gets the topic back on track.

if everybody stays on the science and doesnt keep giving there veiwpoints on conspiracys and other stuff being mentioned. like this constant tug of war. then im all for it. but i notice words like emotive being used. which leads me to suspect which side of the conspiratorial fence you sit on. call it suble signs. or is it just me

 

[eric_s]

It is around. Very complex to try and understand though - as Redruth commented earlier. Be good to try and understand it though don't you think?

I do not understand why these scientific papers and the discussion that follows can't remain objective and try to help others understand the science without it degenerating into emotive and conspiratorial finger-pointing.

Perhaps this paper though is too complex? Still it would be useful to talk science in these threads and not question the authors' let alone other contributors' motives for once.

Yes, it would be good to understand it. This one and other ones. But as a non-scientist, i usually don't read the papers. I know others read them, but as far as i'm concerned, i don't think it makes too much sense for me. I think i would probably not understand enough and get to wrong conclusions. What i really want to see is more funding and more real scientists work in the field of ME/CFS and with the right intentions and looking at it in an ubiased and open way, not in the way we sometimes see it happen in the UK and other parts of Europe.

I think you do understand why this happens, Firestormm. In my opinion these discussions have not been objective and about the science from the start. It begins with the choice of what papers to post for discussion. Most have been anti-XMRV. So people who are looking for a balanced discussion have to criticize this, in order to achieve a balanced discussion. Only if you discuss both viewpoints can you get an objective discussion if you only talk about the papers.

These authors, Towers, Hue and others have already published a similar paper about 8 months ago, coupled with a press release that was circulated acorss UK media in the manner of a PR campaign. They did not use "scientific language" like "the data suggests", etc., they made statements like that XMRV is not associated with ME/CFS, period. Which seems unscientific to me and made me wonder what their motivation was. Why this desire to call it over so quickly, when other groups of experienced and respectable scientists don't think it's over at all? Why are the UK media so biased and serve as a PR tool? Since this happened i honestly don't trust the UK scientific establishment and media too much anymore. And it's sad and also frightening to see that this includes even the BBC. Not saying there are not good people there too, i'm sure there are many good scientists and journalists in the UK, in fact probably the best ME/CFS research in Europe also comes out of the UK. But there are also things happening there that i can't understand. I'm not calling it a conspiracy, but i believe that we must not let what some people in the UK are doing distract us and that we should not believe them too quickly. Luckily, there are also other scientists in other countries. So that's why i didn't care about this paper too much right from the start. I know what these authors believe and i have concluded for myself, that until i see other researchers i trust and respect change their position, i will take this as one point of view, but not as something proven.

 

[RRM]

Currer, I feel genuinely sorry for your loss.

However, I don't think it is fair to questions one's motives when one person doesn't happen to agree with the other person. I realize this is about real people, in fact it is the reason I am posting comments.

I don't really post on this patient forum (or any other) because I feel it is exactly that: a forum for patients. I became a member here because in my view Cort had made an innocent but potentially damaging mistake in some post of his and I felt it should be corrected as soon as possible. After that, I have really only tried to post some factual statements here. Reading back, perhaps my post in this topic was too much of an actual argument and shouldn't have been made at this place.

However, outside of patient forums, I feel that views should be rightfully challenged, especially on topics like science. In my view, you cannot expect others to hold back their views on a subject when you choose to participate in public debates or at public blogs, no matter what your state of health is. If one enters public debate, one should expect exactly that: debate from both sides.

To give you an example outside of the field: I certainly feel for cancer patients and I would certainly never argue about any (unrelated) individual's choice of treatment on the internet, even if I would consider it to be very harmful to that person. However, I would certainly try to (respectfully) debate with even the most terminal cancer patient that would try to advance his views that I believe to be harmful to others in (virtual or non-virtual) public places. Of course, you are free to call me insensitive because of that, but I would feel insensitive if I didn't do that.

Finally, I'd like to point out that, notwithstanding the above, I consider a blog to be the "property" of the blogger and myself as the "guest". I would certainly stop posting comments on the blog you linked to or any other blog if the blogger would indicate that I was not a welcome guest.

Sorry for this long post and derailing post but I felt I needed to explain myself. The best to all of you, and I will refrain myself from posting here.

 

[markmc20001]

I'm elated at the consensus on this thread.

Thanks everybody for tactfully pointing out the problems going on here.