New Science article: Ruscetti standing by Mikovits & saying he did western blots

[RustyJ]

I do agree Angela... If only the PACE Trial had a fraction of the attention that this has.

Isn't it strange... When patients complain about the inaccuracies, data manipulation, flawed methodology in the PACE Trial, we get accused of being extremists, and told by so many establishment figures that it is a gold standard paper...

But when there is a tiny flaw in a biomedical paper, then we are told by so many establishment figures that it is disgraceful and fraudulent, and that patients are again being extremists...

Nailed it Bob.

 

[Esther12]

I'm exactly the same... I'm going to have to take some time off soon!
I see you're still posting though Esther! So, more semi-conscious rambling for you today Esther?!? lol

It's addictive, and I'm foolish. I have no better excuse.

lol - this was a week when I was going to be able to have some spare energy to do something productive, after having finished off some chores/forms. I should probably be firmer with myself. I am doing other things on the PC right now, but still click back here every 10 mins. I'll work on my will power.

 

[Undisclosed]

Bob. You seem knowledgeable about these things. Could you please explain what the difference between anti-RT and anti-gag is. The Science paper image is labeled as anti-gag, the original gel seems to be labeled as anti-RT. This seems significant.

 

[Bob]

It's addictive, and I'm foolish. I have no better excuse.

lol - this was a week when I was going to be able to have some spare energy to do something productive, after having finished off some chores/forms. I should probably be firmer with myself. I am doing other things on the PC right now, but still click back here every 10 mins. I'll work on my will power.

Don't worry Esther... You're not alone!

 

[Bob]

Bob. You seem knowledgeable about these things. Could you please explain what the difference between anti-RT and anti-gag is. The Science paper image is labeled as anti-gag, the original gel seems to be labeled as anti-RT. This seems significant.

Well, I'll do my best, but I'm not an expert.

I believe that the two sets of Western Blots labelling say the same thing apart from the following two discrepancies:

1. Some of the negative lanes have been relabelled from patients (without 5-aza) to normal controls. But this could be just for convenience of presentation. As long as you do have the data, then a negative lane is exactly that, and it's not misleading to relabel a negative lane, as another negative lane. It's just a short cut for presentation.

2. The 5-aza was not mentioned in the original paper. However, someone has found some text on this from another source which says that only two patient samples were treated with 5-aza, and that the rest of the samples were not treated. So these samples might not affect the outcome of the study. We need to know the full information before we can make any conclusions.


As for the details of your questions, I can't be sure exactly, but this is what I've been able to work out...

The Western Blot image shows the expression of XMRV proteins in PBMCs from CFS patients and controls.

The Science paper says "Lysates of activated PBMCs from healthy donors were analyzed by Western blots using ... goat antiserum to MLV p30 Gag"

The slide says "goat anti-RLV" and "p30".

"p30" is a protein related to MLV Gag, so both sets of labelling are consistent there.

And I believe that "anti-RLV" and specifically "anti-RLV-p30" is the name of an antiserum to MLV (murine leukaemia virus.)

So both labels say they use goat anti-serum, and are looking at p30 Gag protein, and entirely agree with each other.


I might have some minor details wrong, but it all seems to fit into place correctly.


You specifically asked about "anti-gag", and this is just short-hand for an 'antiserum to MLV Gag'.
And you asked about "anti-RT". I haven't seen this anywhere on the images. If you could point out to me where this is, then I'll have a look.
"anti-RT" would probably be "anti-reverse transcriptase", but I haven't seen that anywhere associated with these images. Could you be mistaken on this point?

 

[oceanblue]

Also - we still don't really know what was happening. Were all of their positives treated with 5-AZA? Were all healthy controls? I thought that these important questions could have been easily answered.

1. Some of the negative lanes have been relabelled from patients (without 5-aza) to normal controls. But this could be just for convenience of presentation. As long as you do have the data, then a negative lane is exactly that, and it's not misleading to relabel a negative lane, as another negative lane. It's just a short cut for presentation.

2. The 5-aza was not mentioned in the original paper. However, someone has found some text on this from another source which says that only two patient samples were treated with 5-aza, and that the rest of the samples were not treated. So these samples might not affect the outcome of the study. We need to know the full information before we can make any conclusions.

I do think the mislabelling is very important because it changes the meaning of the slide. My interpretation is:
1. As presented in Science: "positive patients and negative controls". Clear and simple
2. According to the new slide: "ha! patients are positive but if you don't use 5-aza to unmask the MLV you'll miss it (as others have done)". Unfortunately, since they don't show 5-aza being used to unmask any MLV in controls, the slide doesn't prove that point at all.

Of course we don't know about the treatment +/- 5-aza of other controls and patients in the Science paper, but the point is the authors CHOSE this gel to illustrate their point, presumably the best example they have (or at least representative of the other samples). If the chosen figure doesn't hold up, that matters. It would have been nice to hear Frank Ruscetti explain the situation for all the samples but, as far as I can tell, he hasn't even managed to adequately explain the situation with his chosen example.

I do agree that individually mislabelling a negative lane might not be that crucial, but taken as a whole, the original Science and newly labelled slide appear to have very different meanings. I'll be delighted if someone can show that I've got this wrong.

 

[oceanblue]

I totally agree Angela... If only the PACE Trial had a fraction of the attention that this has.

Isn't it strange... When patients complain about the inaccuracies, data manipulation and flawed methodology in the PACE Trial, we get accused of being extremists, and told by so many establishment figures that it is a 'gold standard' study...

But when there is a small omission in a biomedical paper, then we are told by so many establishment figures that it is disgraceful and fraudulent, and that patients are again being extremists...

Yes, if only. What I've liked most about the whole XMRV episode is the amount of scrutiny and attempts at replication - not to mention people trying to pull the original research apart. In my book, that's proper science - it can be bloody, but it gets to the truth (eventually, even if we are not there yet). By contrast, PACE received almost no critical attention from scientists; I don't recall any Lancet letters from any scientists whio were not personally affected by the illness. Mainly it was left to patients to point out PACE's many flaws. It's no wonder that the science is going nowhere if there's no real scrutiny by the research community.

However, I'm not sure all the 'extremist' accusations were directed at those that wrote in to point out errors in the science (though I think Lancet editor Richard Horton came close) - the examples given often focused on the level of vitriol directed at researchers, much as has been the case with XMRV. And I do think that such an aggressive stance does harm our cause.

Also, I'm not sure if 'Gelgate' is a small omission, irrelevant to the meaning of the paper, or if it will turn out to be more important than that. I suspect it will be some time before we know for sure.

 

[Bob]

However, I'm not sure all the 'extremist' accusations were directed at those that wrote in to point out errors in the science (though I think Lancet editor Richard Horton came close) - the examples given often focused on the level of vitriol directed at researchers, much as has been the case with XMRV. And I do think that such an aggressive stance does harm our cause.

Before the Wessely accusations were broadcast, even Prof Hooper had been labelled as 'malicious', along with 'malicious patients' (and other negative descriptions of patients), by Horton and his colleagues.
Horton & co might not have used the word 'extremist' - I can't quite remember - but it was very similar to Wessely's stuff - but without the mention of personal threats.
So they still painted a picture of patients being unbalance, and possibly extremists.

Wessely did a good job of getting the BBC to conflate 'legitimate complaints against the research' with 'illegal threats against researchers'.

Also, I'm not sure if 'Gelgate' is a small omission, irrelevant to the meaning of the paper, or if it will turn out to be more important than that. I suspect it will be some time before we know for sure.

Agreed. It's too early to understand the implications.

 

[oceanblue]

Before the Wessely accusations were broadcast, even Prof Hooper had been labelled as 'malicious', along with 'malicious patients' (and other negative descriptions of patients), by Horton and his colleagues.
Horton & co might not have used the word 'extremist' - I can't quite remember - but it was very similar to Wessely's stuff - but without the mention of personal threats.
So they still painted a picture of patients being unbalance, and possibly extremists.

But was the 'malicious' label referring to extremist attitudes towards researchers or simply the criticism of the science? And while Malcolm Hooper made some great points, he made some quite strong attacks on the researchers themselves. I'm not sure that helped.

Wessely did a good job of getting the BBC to conflate 'legitimate complaints against the research' with 'illegal threats against researchers'.

Indeed he did, the man is a very skilfull persuader. Shame his science isn't of the same standard (whoops, is that an ad hominem attack?)

 

[MDL]

The comment 'snarky blog' has to be one of the biggest understatements in journalistic history. Jon Cohen - in the interests of balance, really should have addressed the inflammatory comments Abbie Smith has repeatedly made against Judy Mikovits for a long time now. Smith has repeatedly attempted to smear Mikovits good name and assault her integrity, though anonymous followers have also taken part in this. It has been shocking to watch. Comments from Abbie Smith (ERV) alone (without the other chiming in) include:

"It could TOTALLY be what Judy says it is NOW, she just 'forgot to label it' and 'forgot to talk about 5-AZA' in the Science paper! That is an excuse I had not expected. Judy should keep it in the bag for the next time one of these 'accidents' pops up. LOL!!...But Im sure Judy (or that damn post doc) just accidentally scanned the wrong image that just happened to have the pattern they 'saw' with their epigenetics assays"

"ATTENTION JUDY MIKOVITS AND WHITTEMORE PETERSON INSTITUTE: Game over. DONT F*** WITH SCIENTISTS. DONT F***K WITH SCIENTISTS." (please note the asterisks NOT used on the blog).

"I will not let Average Joes/Janes think this woman is scientifically trustworthy." (referring to Mikovits)

"Why do I get the feeling that this evidence does not exist, and Mikovits is just a gigantic fucking c**t?" (please note asterisks NOT used on the blog)

"So, now she is a deceitful, conniving, gigantic fucking c***" (please note asterisks NOT used on the blog)

"So once again, Mikovits is being manipulative, suggesting another groups scientific statements are actually personal attacks, 'attacking us', while providing no scientific response. Like a Creationist"

"Aaaaand now weve graduated from 'deceitful, conniving, gigantic fucking c***' to just good old fashioned dangerous. We are now well into Kook Kountry here"

"Judy Mikovits? You suck. Grow the f*** up and learn to be a scientist." (please note asterisks NOT used on the blog)

These are just a few examples. There are plenty more. I do not personally care about the rude words (I've only asterisked them in order to prevent ME being prevented from posting here, ironically!) - but it's the fact they are directly used to attack a scientist, Judy Mikovits, already accused of having fire shooting out of her eyes and being a Joan of Arc (i.e religious fanatic and heretic) in Science itself last week! These attacks on a scientist by a 'snarky blog' writer are part of this story, as are many other things conveniently ignored in the press about this whole issue. Looking at this level of attack - one sees how there has been a concerted smear campaign going on. Now THIS should be investigated.

This is sickening. Anyone who writes this sort of thing clearly needs professional help.

 

[Bob]

But was the 'malicious' label referring to extremist attitudes towards researchers or simply the criticism of the science?

As far as I remember, it was both, but I'd have to get out the transcript of the ABC radio interview to be certain.

 

[oceanblue]

As far as I remember, it was both, but I'd have to get out the transcript of the ABC radio interview to be certain.

If it's Horton you're talking about I seem to remember it's ambiguous (my original post said:"I'm not sure all the 'extremist' accusations were directed at those that wrote in to point out errors in the science (though I think Lancet editor Richard Horton came close)").