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Peer Review and the Scientific Process

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Renegade:
Again about trust...

http://www.psmag.com/navigation/politics-and-law/sugar-industry-gums-science-84564/

How the Sugar Industry Gums Up Science
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It goes over a bit how "science" is a bitter joke in the hands of the sugar industry shills.

The article links here:

http://blog.ucsusa.org/added-sugar-subtracted-science-a-new-report-and-a-labeling-debate-at-the-fda-564

Where, thankfully, we can see that there are people that actually care about shilling in science.

Still, I think the most important methodology in modern science is "follow the money", which is an incredibly sad thing.

IainB:
More of this makes a mockery of "science".
(Copied below sans embedded hyperlinks/images.)
Scholarly journal retracts 60 articles, smashes ‘peer review ring’ - The Washington Post
By Fred Barbash July 10
Updated

Every now and then a scholarly journal retracts an article because of errors or outright fraud. In academic circles, and sometimes beyond, each retraction is a big deal.

Now comes word of a journal retracting 60 articles at once.

The reason for the mass retraction is mind-blowing: A “peer review and citation ring” was apparently rigging the review process to get articles published.

You’ve heard of prostitution rings, gambling rings and extortion rings. Now there’s a “peer review ring.”

The publication is the Journal of Vibration and Control (JVC). It publishes papers with names like “Hydraulic engine mounts: a survey” and “Reduction of wheel force variations with magnetorheological devices.”

The field of acoustics covered by the journal is highly technical:

    Analytical, computational and experimental studies of vibration phenomena and their control. The scope encompasses all linear and nonlinear vibration phenomena and covers topics such as: vibration and control of structures and machinery, signal analysis, aeroelasticity, neural networks, structural control and acoustics, noise and noise control, waves in solids and fluids and shock waves.

JVC is part of the SAGE group of academic publications.

Here’s how it describes its peer review process:

[The journal] operates under a conventional single-blind reviewing policy in which the reviewer’s name is always concealed from the submitting author.
All manuscripts are reviewed initially by one of the Editors and only those papers that meet the scientific and editorial standards of the journal, and fit within the aims and scope of the journal, will be sent for peer review.  Generally, reviews from two independent referees are required.

An announcement from SAGE published July 8 explained what happened, albeit somewhat opaquely.

In 2013, the editor of JVC, Ali H. Nayfeh, became aware of people using “fabricated identities” to manipulate an online system called SAGE Track by which scholars review the work of other scholars prior to publication.

Attention focused on a researcher named Peter Chen of the National Pingtung University of Education (NPUE) in Taiwan and “possibly other authors at this institution.”

After a 14-month investigation, JVC determined the ring involved “aliases” and fake e-mail addresses of reviewers — up to 130 of them — in an apparently successful effort to get friendly reviews of submissions and as many articles published as possible by Chen and his friends. “On at least one occasion, the author Peter Chen reviewed his own paper under one of the aliases he created,” according to the SAGE announcement.

The statement does not explain how something like this happens. Did the ring invent names and say they were scholars? Did they use real names and pretend to be other scholars? Doesn’t anyone check on these things by, say, picking up the phone and calling the reviewer?

In any case, SAGE and Nayfeh confronted Chen to give him an “opportunity to address the accusations of misconduct,” the statement said, but were not satisfied with his responses.

In May, “NPUE informed SAGE and JVC that Peter Chen had resigned from his post on 2 February 2014.”

Each of the 60 retracted articles had at least one author and/or one reviewer “who has been implicated in the peer review” ring, said a separate notice issued by JVC.

Efforts by The Washington Post to locate and contact Chen for comment were unsuccessful.

The whole story is described in a publication called “Retraction Watch” under the headline: “SAGE Publications busts ‘peer review and citation ring.’”

“This one,” it said, “deserves a ‘wow.’”

Update: Some additional information from the SAGE statement: “As the SAGE investigation drew to a close, in May 2014 Professor Nayfeh’s retirement was announced and he resigned his position as Editor-in-Chief of JVC….Three senior editors and an additional 27 associate editors with expertise and prestige in the field have been appointed to assist with the day-to-day running of the JVC peer review process. Following Professor Nayfeh’s retirement announcement, the external senior editorial team will be responsible for independent editorial control for JVC.”

Note to readers: Thanks for pointing out my grammatical error. No excuses.

There’s a follow to this story here.

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Renegade:
Yay. The supposed results of the skeptical process need to be skeptically questioned because... just... ::facepalm::

IainB:
Interesting item in Hacker News from peerj.com. It's a link to a .PDF file.
A surge of p-values between 0.040 and 0.049 in recent decades (but negative results are increasing rapidly too).

It is known that statistically significant results are more likely to be published than results that are not statistically significant.  However, it is unclear whether negative results are disappearing from papers, and whether there exists a ‘hierarchy of sciences’ with the social sciences publishing more positive results than the physical sciences.  Using Scopus, we conducted a search in the abstracts of papers published between 1990 and 2014, and calculated the percentage of papers reporting marginally positive results (i.e., p-values between 0.040 and 0.049) versus the percentage of papers reporting marginally negative results (i.e., p-values between 0.051 and 0.060).  The results indicate that negative results are not disappearing, but have actually become 4.3 times more prevalent since 1990.  Positive results, on the other hand, have become 13.9 times more prevalent since 1990.  We found no consistent support for a ‘hierarchy of sciences’.  However, we did find large differences in reporting practices between disciplines, with the reporting of p-values being 60.6 times more frequent in the biological sciences than in the physical sciences.  We argue that the observed longitudinal trends may be caused by negative factors, such as an increase of questionable research practices, but also by positive factors, such as an increasingly quantitative research focus. ...

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Renegade:
If the below turns out to be correct, it's going to be pretty damning against the CDC and "peer review" as we have it now.

http://ireport.cnn.com/docs/DOC-1164794

Fraud at the CDC uncovered, 340% increased risk of autism hidden from public
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More...http://www.naturalnews.com/046535_MMR_vaccines_autism_CDC_whistleblower.html

Vaccine bombshell: CDC whistleblower reveals cover-up linking MMR vaccines to autism in African-Americans
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http://www.naturalnews.com/046566_autism_MMR_vaccine_CDC_whistleblower.html

A medical conspiracy of epic proportions stands to bring down the entire vaccine house of cards following the revelation that the U.S. Centers for Disease Control and Prevention (CDC) censored key data linking the MMR vaccine to autism. A top CDC researcher-turned-whistleblower has come forward with the truth about a study that the CDC has long claimed proves the safety of MMR, when in fact it actually shows the exact opposite.
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http://www.canaryparty.org/index.php?option=com_content&view=article&id=149:rob-schneider-demands-answers-on-cdc-mmr-fraud&catid=1:latest-news&Itemid=50

Rob Schneider Demands Answers on CDC MMR Fraud   

In light of the revelation that Dr. William Thompson, senior scientiest at CDC, has admitted guilt in hiding data that found that black males are 340% more likely to have an autism diagnosis when given the MMR before age 3, Rob Schneider has written to the office of the Governor of California, Jerry Brown, to assure himself that Brown is aware of the fraud, and to demand answers and actions to protect California children.
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http://www.rawstory.com/rs/2014/08/26/actor-and-anti-vaxxer-rob-schneider-i-have-proof-the-cdc-fraudulently-changed-autism-data/

Actor and anti-vaxxer Rob Schneider: I have proof the CDC ‘fraudulently changed’ autism data

Actor and anti-vaccine advocate Rob Schneider contacted California Gov. Jerry Brown’s office (D) claiming to possess documents showing that the Centers for Disease Control has hidden data showing Black children are at a particularly high risk of developing autism from vaccines.

According to the anti-vaccine site The Canary Party, Schneider stated in his letter to deputy legislative secretary Lark Park that he was “compelled” to share his proof of a CDC report the agency suppressed and “fraudulently changed.”

“One disturbing disclosure, AFRICAN AMERICAN CHILDREN were and still are THREE HUNDRED AND FIFTY PERCENT more likely to develop Autism under the current Vaccine MMR schedule,” Schneider wrote. “This according to the original CDC study in 2001.”
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On the flip side, here's the "debunk":

http://www.sciencebasedmedicine.org/did-a-high-ranking-whistleblower-really-reveal-that-the-cdc-covered-up-proof-that-vaccines-cause-autism-in-african-american-boys/

Here we go again.

Regular readers who pay attention to the antivaccine movement almost can’t help but have noticed that last week there was a lot of activity on antivaccine websites, blogs, and Facebook pages, as well as Twitter and Instagram feeds. For all I know, it’s all out there on Pinterest (which I’ve never really understood), Tumblr, and all those other social media sites that I don’t check much, if at all. In particular, it’s been exploding under the Twitter hashtags #CDCwhistleblower, #CDCfraud, and #CDCPantsOnFire. It’s almost impossible to have missed it if you’re plugged in and pay attention to crank websites, as many skeptics do, but here are a selection of the main stories going around over the last few days:
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And:

http://scienceblogs.com/insolence/2014/08/26/the-cdc-whistleblower-manufactroversy-continues-apace/

Here it is, Tuesday already, and the antivaccine underground is still on full mental jacket alert over the biggest story the antivaccine movement has seen in a while. Fortunately, it’s a story that’s been largely ignored by the mainstream media, which tells me that maybe, just maybe, the mainstream media has figured out that it shouldn’t give undue credence to cranks. I’m referring, of course, to the claim that the CDC has for 13 years been covering up smoking gun evidence that the MMR vaccine when administered before 36 months causes autism in African-American males.
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It's a developing story, so I suppose there's not much to do but wait until more analysis comes out.

If it does turn out that there was fraud, then we have some pretty nasty stuff to deal with.

I've not looked too deeply into it, so I have no idea about what is or isn't correct there. It could all just be complete nonsense, but, considering (source):

http://www.ncbi.nlm.nih.gov/pubmed/21623535
http://www.ncbi.nlm.nih.gov/pubmed/24354891
http://www.ncbi.nlm.nih.gov/pubmed/12145534
http://www.ncbi.nlm.nih.gov/pubmed/21058170
http://www.ncbi.nlm.nih.gov/pubmed/15527868

It may not be.

It's not like medical cover-ups haven't happened before.

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