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Discussion Starter · #1 ·
This was the Tomljenovi and Shaw paper that I mentioned being retracted in another thread a week or so ago. Now that the study has been officially retracted as of a couple days ago, I thought I'd start a new thread instead of derail the other one.

From the Journal

This article has been withdrawn at the request of the Editor-in-Chief due to serious concerns regarding the scientific soundness of the article. Review by the Editor-in-Chief and evaluation by outside experts, confirmed that the methodology is seriously flawed, and the claims that the article makes are unjustified. As an international peer-reviewed journal we believe it is our duty to withdraw the article from further circulation, and to notify the community of this issue.
http://retractionwatch.com/2016/02/...-vaccine-to-behavioral-issues-gets-retracted/

https://www.washingtonpost.com/news...oral-problems-to-gardasil-has-been-retracted/

Along with co-author Lucija Tomljenovi, Shaw has previously been blasted for two studies suggesting that the aluminum content in vaccines could be linked to autism. Those studies were also deemed "seriously flawed" and condemned by the World Health Organization.

This is the author members here said they found credible by the way.

Orac (Dr. David Gorski) went over the many issues of the study before it was officially retracted. Here is the link if anyone is interested in reading an in depth analysis (http://scienceblogs.com/insolence/2016/02/17/no-gardasil-does-not-cause-behavioral-problems/)

The shortish version from the link is this:

So, basically, the investigators injected mice with either saline (negative control), adjuvant only, Gardasil, or Gardasil and pertussis toxin (presumably the positive control), and there were 19(!) animals per experimental group, which is a huge number for most animal studies. The various injections were scaled down from an estimated 40 kg teenaged girl to a 20 g mouse (a 2000-fold difference). The mice received three injections, spaced one day apart. The behavior of the mice, as measured by the parameters above, was then examined at three and six months.
He noted some huge issues with the study. First, the experiment was not blinded to the observers. This is a HUGE problem in this kind of study. The observers must not know which mice received the vaccine and which didn't in order to remain objective. Next issue is that they only looked at the brains of 5 mice from each group, which is a really small sample.

Biggest problem is that they didn't use the correct statistical analysis for the study. As Gorski explains:

Take a look at the statistics section:

Results are expressed as the mean ± SEM. The differences inmean for average immobility time in the FST, the staircase testparameters (number of rearing and stair-climbing events), novelobject recognition and Y maze tests were evaluated by t-test. Significant results were determined as p < 0.05.

Those of you unfamiliar with basic statistics (and, believe me, the problem with this passage is very, very basic) won’t recognize the problem, but those of you who’ve taken a basic statistics course will recognize immediately what the problem is here. What is the t-test? No doubt the authors are referring to Student’s t-test, which is a test designed to look for differences between two groups. Now, how many groups are being tested? Yes, indeed! It’s four. In other words, it’s a number of experimental groups for which Student’s t-test was never intended. What is the significance of this? Basically, it means that the authors must have compared, pairwise, all the groups. So what? you might ask. Here’s the problem. The more comparisons you make, the greater the chance of finding a “statistically significant result” by random chance alone. That’s why other statistical tests were developed, specifically the ANOVA test, which would have been the correct test to use to analyze these data. That’s another thing I would have insisted on the authors redoing, if I had been a reviewer.
He concluded:

Basically, this study is worthless, as it’s unblinded and doesn’t use the correct statistical analysis. Had I been a reviewer, I would have pointed these issues out and recommended rejecting the paper. I can see why Dr. Poland was probably horrified to discover that this paper was published in his journal. Perhaps he should ask himself how such a travesty could have been published in his journal.
 

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It's disturbing how pro-vaxxers tend to do such a 'happy dance' when concerns regarding vaccines are suppressed, e.g. retracted.

Apparently linking to whale.to is not allowed or discouraged. The same should apply to orac as he typically makes ad hominem attacks and his diatribes are often so obnoxous.

http://news.nationalpost.com/health/medical-journal-yanks-study-that-questions-safety-of-hpv-vaccine
Shaw stood by the research, saying it is not “unfriendly” to the vaccine but points out behavioural effects already seen in humans. He decried what he said is a trend toward journals retracting some controversial papers, especially those critical of vaccines.

“I don’t think the literature should be culled for something you don’t like,” he said. “Bad science is corrected by better science, not by subtracting it from the literature as if it never existed.”
Suppressing research that is negative regarding drugs or vaccines causes big problems:
 

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It's disturbing how pro-vaxxers tend to do such a 'happy dance' when concerns regarding vaccines are suppressed, e.g. retracted.

Apparently linking to whale.to is not allowed or discouraged. The same should apply to orac as he typically makes ad hominem attacks and his diatribes are often so obnoxous.

http://news.nationalpost.com/health/medical-journal-yanks-study-that-questions-safety-of-hpv-vaccine


Suppressing research that is negative regarding drugs or vaccines causes big problems:
https://www.youtube.com/watch?v=RKmxL8VYy0M
I'm quite happy when a vaccine supporter links to Orac or Skeptical Rapture. If they are willing to undermine their own credibility, who am I to object?

Just as I cringe when a vaccine critic links to a weak or unreliable or offensive source. Overall, though, I think that the vaccine critics are less careless, probably due to being attacked so much.
 

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Discussion Starter · #5 · (Edited)
So no one is going to actually address the problems in the study that were brought up?

It is not at all surprising that an author who has had several of their studies deemed "seriously flawed" by even the WHO and had studies retracted thinks retracting studies is wrong and a suppression of freedom of speech.

Shoddy research should not be published in peer reviewed journals...that's kind of the point of peer review. I'm glad the study got retracted. Keeping it in that journal only gives it legitimacy that it doesn't deserve.
 

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The WHO deems forced prepuce removal from male babies only (they're against forced female genital cutting) to be a good thing. They even have a manual on it - BARF! One must think critically about what they endorse (like the AAP).

Sus
 

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Let's start with a few obvious caveats:

1. The HPV problems, according to vaccine critics, largely come down to a) unknown length of efficacy and b) safety concerns due to a high level of parental reports of problems coupled with really lousy safety studies (we went through this last week in depth)

2. The retracted study of Tomlijenovic and Shaw was never a cornerstone study wrt HPV vaccine rejection. It had a fairly small group of mice in it - the most anyone could have credibly said is "need more data".

3. Finding the study might be hard (I have not tried). Thus, we only have Orac's word on it, and while vaccine zealots might find him credible, many don't.

So, we do not have much from the Journal on why it was retracted. We have nothing specific. We have speculation from Orac, and he does not like the non-blinding aspect nor the type of statistical analysis they used. Big deal. I could see one arguing the study was not very good, or was quite limited, due to this. I might even agree (see caveat #2 ). But retraction worthy? I doubt it. I have read a few articles on retraction in the last 2 days, and "I think your study is weak" or even "poor methodology" is not typically grounds for retraction. Genuine mistakes and malfeasance are. My 2 cents.
 

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From Orac:

"The journal published an uncorrected proof of “Behavioral abnormalities in young female mice following administration of aluminum adjuvants and the human papillomavirus (HPV) vaccine Gardasil” online on January 9th, 2016. In its place now is a note that says:"

And yet, numerous other places say retraction is a complicated process and takes a fair bit of work. This article says the average time to retract an article is 2 years, yet the Vaccine article was retracted in 6 weeks or so.

"Retractions are a huge amount of work for journal editors and publishers. Typically, the decision to retract an article is taken after extensive consultation among the journal editor(s), publisher and the author(s). Because the issues are so sensitive and involve potential damage to author reputation, employment and income, investigations tend to take place in secret. The average time to retract a published article is estimated as two years, longer when a senior scholar is involved (Chen, Hu, Mllbank and Schultz, 2013: 239). Normally, but not always, the journal publishes a formal retraction statement explaining the reason or reasons for withdrawal, and the article appears with a large “retracted” watermark across the front page or entire article (see the example on this page)."

http://ethicist.aom.org/2013/10/retraction-mistake-or-misconduct/

Here is good (albeit slightly old) read on the process of retraction and why it takes so long. Nature wanted to retract an article and it took 3.5 years.

http://www.nature.com/nm/journal/v9/n9/full/nm0903-1093.html

i think it is fair to ask if the retraction of this article was fast-tracked.
 

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Discussion Starter · #9 ·

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Meanwhile, the big Scandinavian study that dismissed problems following vaccination with Gardasil missed over 1,000 possible reactions. Didn't analyze them and explain why they don't count. Just straight out missed that there were reports from all over Denmark from girls who became quite ill following the vaccine. No calls for retraction, no reconsideration...all that there has been so far is an attack on one of the doctors who has been looking at the girls who are ill.

Yikes!
 

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Shoddy research should not be published in peer reviewed journals...that's kind of the point of peer review. I'm glad the study got retracted. Keeping it in that journal only gives it legitimacy that it doesn't deserve.
It's curious that orac et al aren't demanding that the shoddy 'research'/studies by vaccine manufacturers, to get their vaccines approved, be retracted. Such as the placebo is often not a true placebo, but is often another vaccine or contains everything except the antigen, i.e. includes toxins such as aluminium.

BTW, the retracted study was peer-reviewed. Interesting that a study showing problems with a fast-tracked vaccine, is fast track retracted. Probably the real reason it was retracted was that it was negative regarding a vaccine. Orac et al diatribes are just smoke and mirrors.
 

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Actually, there are mountains of shoddy, ghost-written studies supporting the use of various drugs and these articles are almost never retracted. Consider, for example, the tragic history of GlaxoSmithKline and Paxil. Dead and suicidal teenagers.

But not a concern apparently for the passionate defenders of "good" science.
 

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I found this comment (on the second article) very apt:
Promiscuous retraction suggests an assumption that once a paper is published, it is sanctioned as correct by ‘science.’ This is a naive understanding of the scientific publishing process. Publication is the BEGINNING of criticism, not the end. Peer review is a minimum standard, a gatekeeper that simply lets the critical process begin. Peer review – and publication – should not be seen as a stamp of approval, requiring retraction when faults are later found.
....
Let’s keep the big gun of retraction for extreme cases – the literature self-corrects, with no need of official retraction.
The HPV vaccine study is not an 'extreme case' that could justify retraction.
 

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I found this comment (on the second article) very apt:

The HPV vaccine study is not an 'extreme case' that could justify retraction.
Vaccine science is a special case. If it makes a vaccine look bad, then it has to be bad science and a pre-emptive strike is needed. Otherwise people will die from infectious diseases. Preventable infectious diseases.

Just simple logic. :frown:
 
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Tweety...yeah the second link is very interesting.

I have done some reading on retractions in the last day or two, and it does seem the most common reason for retraction is fraud of some sort (falsifying data, plagiarism, etc) followed by honest errors. The guideline for retraction are here:

http://publicationethics.org/files/retraction guidelines.pdf
Journal editors should consider retracting a publication if:
• they have clear evidence that the findings are unreliable, either as a result of misconduct (e.g. data fabri- cation) or honest error (e.g. miscalculation or experimental error)
• the findings have previously been published elsewhere without proper crossreferencing, permission or justification (i.e. cases of redundant publication)
• it constitutes plagiarism
• it reports unethical research

Note: "we don't like the conclusions you came to or how you got there" is not listed.

That being said, there does seem to be an emerging trend of retracting work to "correct" science. The second link in post 11 speaks to that.

"One of the issues that comes up again and again on Retraction Watch is when it’s appropriate to retract a paper. There are varying opinions. Some commenters have suggested, given the stigma attached, retraction should be reserved for fraud, while many more say error — even unintentional — is enough to merit withdrawal. Some others, however, say retraction is appropriate when a paper is later proven wrong, even in the absence of misconduct or mistakes."


The comments underneath are great. Almost all oppose using retractions to "correct" science.

Here are a few:

"What happens when a new paradigm replaces an old one? Newton retracted by Einstein?
Retractions have a useful, if partially fuzzy function. Let’s not blow them out of proportion." Bob

"I think you are in danger of making a fundamental mistake here. The guidelines call for retraction in the case of fraud/misconduct or honest error that has lead to an unreliable result ....

But there is a huge leap to stating that papers should be retracted “if a paper’s major conclusions are shown to be wrong”. Should the first estimates of the mass of the electron be retracted because later estimates converged on a different number? Should papers that showed potentially significant relationships in small samples that didn’t hold up in larger trials be retracted – even if potentially that data was used as part of the meta-study? This cannot be justified.

The literature is a record of the progress of science – and that progress is not linear. By erasing by-ways and diversions that end up not contributing directly to the ‘final’ answer (whatever that is), you are imposing a view of science that is not true to itself and is perhaps sanitised beyond the point of usefulness.

If you erase from scientific history the merely mistaken (as opposed to the fraudulent or compromised) you are doing a disservice to the notion of science itself."

I suspect this is what is going on with the HPV paper. There is no evidence of misconduct (which even Orac admits) or errors (such as calculation errors) - the retraction seems to fall under the murky, controversial area of using retraction as a tool to "correct" science.
 

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The literature is a record of the progress of science – and that progress is not linear. By erasing by-ways and diversions that end up not contributing directly to the ‘final’ answer (whatever that is), you are imposing a view of science that is not true to itself and is perhaps sanitised beyond the point of usefulness.
When I was in library school studying how to do research, I did a project on the history of science, practicing following up references and citations. One of the commentaries I came across discussed how the history of science is usually taught as a reasonable process of new discoveries and progress, not the way it usually occurred--which is many dead ends, delusions, fixations, old guys preventing young guys from trying something new and so forth. The real history of science consists of a lot of meandering, misunderstandings, and even some disasters. There are occasional breakthroughs.

Preventing people from coloring outside the lines or making mistakes doesn't improve the process of science.
 

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Discussion Starter · #18 ·
I find it pretty ironic that members here are arguing against retracting papers that use poor methodology. Aren't you guys always arguing that we need to improve what is accepted as peer review? This is part of that. These authors used the wrong statistical analysis for the number of groups they had. I am not buying for a minute that if a pro-vaccine study objectively used the wrong statistical test for a study you would be against a journal retracting that study for poor methodology. Not for a minute.

Your quote even said more are for removing studies that have unintentional errors than are against it.

And a general time frame for retraction is not applicable to this scenario. Those time frames are often for fraud and misconduct, and those claims can take a long time to substantiate. Wakefield had to go to trial, for example. That is not something that typically happens in a matter of a few weeks. Comparing the process of retraction for those reasons to a retraction for poor methodology is comparing apples to oranges.
 

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I find it pretty ironic that members here are arguing against retracting papers that use poor methodology. Aren't you guys always arguing that we need to improve what is accepted as peer review? This is part of that. These authors used the wrong statistical analysis for the number of groups they had. I am not buying for a minute that if a pro-vaccine study objectively used the wrong statistical test for a study you would be against a journal retracting that study for poor methodology. Not for a minute.

Your quote even said more are for removing studies that have unintentional errors than are against it.

And a general time frame for retraction is not applicable to this scenario. Those time frames are often for fraud and misconduct, and those claims can take a long time to substantiate. Wakefield had to go to trial, for example. That is not something that typically happens in a matter of a few weeks. Comparing the process of retraction for those reasons to a retraction for poor methodology is comparing apples to oranges.



I do not think I have ever called for retraction because I thought the study was weak or limited. There is a difference between saying a study has limits and branding it with a Scarlet R. I don't recall anyone else doing so, either. What I do know is that studies with actual fraud or likely fraud in them that support vaccines have not been retracted. Thompson said significant data in an MMR study was omitted and that study protocol was not followed. No retraction. Thorson stole money and is wanted for fraud. Have the studies he worked on even been re-looked at ? No retraction. Researchers on the mumps portion of MMR said data was fudged - no retraction. It is scary how much power pro-vax forces have - that they can get a study retracted basically because they do not like it. The power is scary because unchecked power is scary. Absolute power corrupts absolutely.

I think you are misunderstanding the quote:


"Some commenters have suggested, given the stigma attached, retraction should be reserved for fraud, while many more say error — even unintentional — is enough to merit withdrawal. Some others, however, say retraction is appropriate when a paper is later proven wrong, even in the absence of misconduct or mistakes."


Bolding mine. Assuming Orac got it right (and let's face it - he would have a field day if they committed fraud or made an error) the paper is being withdrawn because the powers that be feel it is wrong (last bolded section).


As per your last paragraph, meh, I think that is weak. I strongly suspect you know little more about retractions than I. All we both know is that this retraction happened much, much faster than usual. One of the articles I read (Nature) said journals often try to work with authors around retractions, see if they can come up with wording that everyone find acceptable.....there is no way anyone of this happened in the shockingly short retraction time.
 

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Discussion Starter · #20 ·
A limited study does not warrant retraction. All studies have limitations. That is very different from poor methodology, like using the wrong statistical analysis in a study for example.

Second, you seem to be confusing "a person says X" and actual evidence that there is something wrong with a study. Two totally different things. If Thompson has direct evidence of fraud, he has yet to produce it and it has been well over a year.

Lastly, Thorson stole money but that had absolutely nothing to do with the study or how information was gathered and analyzed. I count at least 12 or 13 authors combined in the two studies he participated in. There is absolutely nothing to suggest there is anything fraudulent about those other authors or the paper. This is a logical fallacy known as Guilt By Association. If a single author of a study goes and steals a Corvette, we don't just throw the whole thing in the trash without even a hint of evidence that anything is actually wrong with the study itself. Thorson wasn't even a lead author in any of those studies.
 
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