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OK, so I'm a bit of a PLOS groupie, but this seems like a huge mistake by PLOS ONE and Pathogens. It's going to tell people to not publish negative data. (via +Elizabeth Iorns )

+Jennifer Lin Do you know the story here?
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This really concerns me - we want researchers to publish their updated findings without fear of retraction
yep, seems like the antithesis of what science is all about
Yeah I feel like it would be better to not remove information from the record even if it is shown to be totally incorrect. I feel like having the retraction (and the full information in it) tied to the original paper would be much better than just retracting the paper. That way people could see all the information in the original (incorrect) paper and then compare it to the follow on studies and it comes closer to showing 'true' scientific research. Research is a process that is messy and this just further presses scientists to publish the perfect story (not the whole truth). 

I think it really does send a very bad message to the scientific community - who are already disincentivized from publishing negative results. Now that they may have their original paper retracted if they publish a follow on correction - researchers will have absolutely no incentive to call their own previous findings into question and the wasted time and effort that others will spend on trying to follow up the incorrect result will continue unnecessarily.
All this discussion could be left as comments on the Pathogens paper if it wasn't retracted.

I think the issue here is that some people in publishing still think they're curating the literature so it only contains true statements, but we know now that that's futile, so why retract anything done in good faith? Especially if it's a error like a spurious result due to contamination. Mistakes happen in the lab, so why do we try to scrub any evidence of imperfection from the scientific record? This really sends the wrong message. I get that they were trying to avoid retraction and I understand why PLOS would want to avoid being put in the position of enabling someone to avoid retraction, but I also think there shouldn't have been a retraction, so the argument works both ways and it only makes sense to retract if you think you're curating the literature for truth.

And now all this commentary (which isn't all so meta) is entirely hidden and unlinked from the papers themselves.

It almost feels like PLOS just chickened out instead of actually setting an example here when they had a perfect opportunity.
Ok, that actually addresses my main concern. Thanks, Cameron. Now if we could only do something about the stigma associated with what's a normal part of the scientific process. Partial retraction would indeed be useful.
Thanks Cameron! That explanation really helps me to understand why PLOS did that (except I still think they should have discussed it with the authors first). You are absolutely right that what we need to do is change the stigma around corrections and retractions - science evolves and the original story will never be perfectly correct. Maybe we should change the name from 'retraction'?
Thanks, +Jennifer Lin I'm glad there's an official statement out on this, but it remains frustrating that all this discussion we're having about the reasons for the retraction isn't happening in the comments section for the paper and is thus inaccessible to everyone who might come across the paper in the future.

The major difference between my point of view and that of PLOS (and other publishers, too, I reckon) is where the decision to retract is extended to honest mistakes as well as deliberate deception. As a scientist and as a student of altmetrics, I know that the majority of the literature consists of honest, well-meaning but mistaken conclusions. The literature is not a solid foundation upon which to build, and by it's very nature cannot be. There is no scientist I know which assumes that any result in the published literature is necessarily replicable, so in the absence of partial retraction, I probably would have gone with an erratum, despite it being one of the major claims of the paper, or used some other mechanism which doesn't penalize self-reporting of mistakes so strongly.

So the main issue is how the extension of retraction to cover honest mistakes disincentivizes self-reporting of mistakes, and it's unfair given that so much of the literature is mistakes that just haven't been uncovered yet. The high-profile nature of the case is just why it got uncovered in this case.

I really did think PLOS had begun to move beyond thinking of themselves as the gatekeepers of truth.
This is such a bad retraction policy in general.

In this particular case, there should be a correction, that there was contamination, which changes the conclusion from "XMRV is associated with prostate cancer", to "contaminated reagents produce spurious results". 

Maybe PLoS doesn't like to have papers with such trivial conclusions, but why is that a problem for anyone but the editors of PLoS? 
The editorial suggests that it's more about the medical editors thinking it's their job to curate the literature for "truth". Apparently the editor in this case was at the Lancet for the vaccine-autism nonsense and they wanted to try to squash any conspiracy theories.
Heavy handed forced retraction is not the way to squelch conspiracies. 

It was the authors of the first paper that did the work that conclusively showed that the earlier work was due to contamination.

That is nothing like the Wakefield-Lancet paper.  The Wakefield paper was fraudulent (in multiple ways) which Wakefield continued to deny but presented no evidence it wasn't fraud.  All the authors (except for Wakefield) retracted the Lancet paper. 

If editors are going to be the gatekeepers and curators of the scientific literature, they need to get it right, and this forced retraction in this instance is not getting it right.

Finding errors like this is a unique event.  It is not something that a "one-size-fits-all" policy is going to address.   
Let me be clear, I don't have any insider knowledge about what anyone was thinking, and I don't know anyone involved personally, so I'm only speculating here.
I certainly didn't mean to suggest that the editor had any role in the Wakefield affair. My read of the situation was that the reason they're making a big deal of this retraction is partly an attempt to start a conversation about the role of retractions, which they certainly did, but also to try to correct the scientific record in the mind of the public. It is an issue that corrections and retractions don't get as much attention from the media as the original claims. By comparing this incident, where a novel virus was erroneously linked to cancer, with the Wakefield affair, where vaccines were erroneously linked to cancer, I meant to suggest that the editor's decision to unilaterally retract was informed by the discussions of what went wrong with the Wakefield decision. I was a bit sloppy in that Virginia wasn't actually at the Lancet when that decision was made, so please don't read my above comment as suggesting she had anything to do with it.

I'd rather attention be focused on whether or not retraction should be used for things other than outright fraud.
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