The publications shown to contain scientific misconduct could be withdrawn from PubMed or somehow noted on PubMed that they are questionable.   If authors are relying on printed copies of articles (and printed references at the end of those articles) then they may not know of any retractions or corrections after these have been published.  But further researchers trying to obtain these articles by using Pubmed would find the retractions or notes of misconduct on PubMed, if this system were in place.  

I don't know if PubMed actually does this or not; but it is one possible solution to "contamination" of the literature.  On the other hand, complete withdrawal of an article from electronic databases may not be appropriate because it may still contain useful information.   Another related solution would be for PubMed or journal publishers to have a category noting whether the research has been confirmed, refuted, or neither.   But since study designs and study populations can be different from study to study even with the same research question, non-confirmations may legitimately occur.  In any case you're talking about true misconduct and fraud, not legitimate differences in findings.   The bottom line is that once something is printed, there is no way to know from the printed copy if the findings have been retracted or changed later.  But with electronic databases, this kind of updating is possible.  Journal editors should have a way of checking to see if a reference in a manuscript refers to a paper that has been withdrawn or embroiled in misconduct.  Some responsibility also lies on authors to not reference retracted work, but the journals should have better access to this information---perhaps an automated journal publishers' clearing house for retracted or adjudicated work would be useful.  

In my experience the peer-review process is over-rated.  A large percentage of manuscripts submitted for review are not fully understood by reviewers, especially the statistical procedures; and much published research is never replicated or confirmed simply because no one even tries to do so.   And some research manuscripts are shot down for publication for purely political, non-fact-based reasons by reviewers and editors who are trying to preserve their piece of scientific turf, so to speak.   That's another form of misconduct which hides from scrutiny.  The answer to poor peer review may be more peer review.    But on the whole, big, important and well-researched subject matter does get honed to accuracy and advanced by the peer-review process---at least to the extent possible within our present scientific world-views and paradigms; but paradigms can shift.    

Jerry

An excellent appraisal of peer review!

"A large percentage of manuscripts submitted for review are not fully understood by reviewers, especially the statistical procedures; and much published research is never replicated or confirmed simply because no one even tries to do so." well said Jerry.

yes,  the peer-review process is often over-rated. 

I agree completely with Jerry Miller. One additional remark. I have observed that the number of empty articles in mathematics has increased notably. Saying empty article I mean articles which don’t contain new information. It cannot be clarified as plagiarism. Some authors without appropriate citation publish results which were known say many years ago. Maybe that those authors don’t know these results but the reviewers and editors should know.

The study by Seife raises an important issue which is: the courage, that some academics have, to submit seriously flawed studies for publication without worrying about the evidence of their misconduct found by a government organization such as the FDA. Is it the lack of follow up by their institutions or the lack of serious repercussions of academic misconduct on their careers?

I have been protested against many false medical Court messages - when there are most of forensic technician exact nonsenses. I was injured by concateantion of many technician medical mistakes by implantation THA in my private orthopaedic case. I am a State investigator as an international expert for Health and Safety. I have been used exact criminology traceing only by heavy occupational injuring or in case mortality in the dangerous working technologies. I never need a usage of medical knowledges, because I am able detect the all regulations and Laws, biomechanical traceing, product instrukction by "CE" Conformity Assessment, technician requirements of Directive 93/42/EEC Medical Devices, Pythagorian theorem, Geometry 3 D, crimi analyses of mandatory Health documentation with detection preliminary Health status, patient acceptance of surgery THA, being Preliminary processing Plan of surgery, taking firm instruments for implantation, usage of radiological mask of planned choice of stem to controlling useable set THA, timing of radiology testing, functional testing set THA on surgeon hall, etc. etc. I was a patient - so as a State investigator including. My conclusions were: There were never fullfilment of technician condition to begin the suergery - when there were no Preliminary Plan, there was absency preliminary diagnoses Postdysplastic declination of femural neck...there were no individual adaptation of processing Plan to implantation on the hall, etc., etc. Summ I detect about 10 fatal mistakes contrary Technician requirements of Law....the oficial Knowing Institut - Central Army Hospital Prague with a team of  forensic Physicians detect NO ONE! They are absolut out of Crimi traceing praxis in their broadminden tolerancy to medical fatal mistakes of Orthopaeds, Radiologists, etc. I am a pensioneer State investigator - thatsfor I have beem just asked the Crimi Policy Czech Republic to control all my evidences in the frame of penalty Claim of  State prosecutor to repeate all origin Civic Court, because there were a conspiracy between the culprits - Doctors from the Hospital so as with the author team of forensic Physicians from Central Army hospital Prague to cover medical fatal mistakes! It is a world premiere judicial case....individual patient has been taking mass technician evidences about consicous false medical testimony and medical Court message in civic Court about responsibility of heavy injuring and with biostatistical  shorten life of State inspector Health and Safety - about minimal 5 year! Conclusions for you:...In medical praxis are mass daily usage Medical Devices for many dangerous medical treatments - but the doctors are ignoring systematically product instructions, Laws and exact technician conditions to safety usage Medical Devices...the Policy of States OECD never used the independent random Criminal monitoring of frequency medical mistakes and adequated prevency! Thatsfor many patients are nedless heavy injured or dying yearly - under legal being duties! I suggest to analyse about 2% of patients Health documentation from each hospital with Crimi Anthropology Labour fluently yeraly! Rescue legal medical working active ways! Utility model 21532 Czech Republic. It will be held the interest world legal scandal with the private  premium - SHORTEN MY LIFE CONSEQUENTLY OF ILLEGAL MEDICAL WORKING! Help me.

Besides some way to let others know when an article or paper has been deemed based on scientific misconduct or research error, there should be some way to let other researchers know about so-called academic publishers that are actually pay to play type publications.  Some academics may pay them so they can claim to be published, but these publishers should be exposed as publishing some or most of their books as a vanity press.  Maybe there might be some way to privately share these names.

For peer reviewed research to regain its glory, a trusted process must be in place. The definition of this kind of infallible process can be ambiguous and difficult to achieve though. This is because in the past, many authors complained that several good works were refused the opportunity to get published because of reasons ranging from political to lack of knowledge of reviewers in the subject matter. Hence the emerging of new found love for open access journals and its proliferation.

I am not an advocate of shutting down new journals but very much in support of the development of a quality process that would help researchers showcase new knowledge. A good help will be for publishers to fastidiously ensure that manuscripts are reviewed only by the experts of a subject matter. It may mean raising the bar of minimum qualification expected of any reviewer to be invited.

Also, new and properly designed standards for publishing academic works must be in place to guide all existing journals. Any defaulting organization to this kind of accreditation system should then be blacklisted.

Aderogba, it is certainly true that good works are sometimes denied publication because of lack of knowledge by reviewers or for political reasons.   But raising the bar for reviewers, so that only expert reviewers are chosen, will be difficult as long as reviewing manuscripts is done for free.   Experts (or any reviewers) often do not have enough time to thoroughly review and understand a manuscript by re-reading, researching material themselves, checking statistical methods, checking what cited works really say and so on.   It is therefore important to place emphasis on academic integrity (which most institutions do) but also to train scientists to write better (which most institutions don't).   One method I've found that helps me write a manuscript is to do a poster first.  A poster has to be concise and usually has to explain the research to a broader audience and capture their attention for a relatively short time.    Going through this process helps frame the resulting manuscript itself.   Sometimes manuscripts are unnecessarily complicated and the statistics are unnecessarily obtuse for no good reason.  Simplicity is often better; but for some reason academics have gotten away from that, sometimes I think because it makes their subject matter sound more intellectually meaningful than it really is.  

We must also keep in mind that research papers are investigations in progress.  No one paper is the final word on a subject.  Ideas are put out there for the purpose of debate and criticism---and confirmation.  There is always a research front where new advances are investigated, as well as backward-looking to say 'this was wrong' if that is justified.   So errors are an accepted part of the process.  One might say researchers have a 'right to be wrong', as long as their wrongness is well-intended.    

Sir,

I agree with your views fully on these points:

.....We must also keep in mind that research papers are investigations in progress. No one paper is the final word on a subject. Ideas are put out there for the purpose of debate and criticism---and confirmation. There is always a research front where new advances are investigated, as well as backward-looking to say 'this was wrong' if that is justified. So errors are an accepted part of the process. One might say researchers have a 'right to be wrong', as long as their wrongness is well-intended.

I agree with Jerry Miller and he has given a very good explanation.

One of the issues I didn't see mentioned here is the fact that the FDA must begin to publish details they obtain about such misconduct.  Otherwise, there is no way for reviewers, publishers, or anyone else to know such misconduct occurred.  There was a prior issue of misconduct in trials that the FDA became aware of well over a year ago which related to nearly 100 generic medications being approved for use and the FDA continues to refuse to publish the list of medications that were involved.  If the FDA doesn't make that information public, how can we possibly do anything about it? 

In my opinion, the FDA has been consistently dropping the ball when it comes to oversight.  I recently published an article highlighting the deficiencies in one of FDA draft Guidance documents on Suicidality (Sheehan DV, Giddens JM, Sheehan KH. Current assessment and classification of suicidal phenomena using the FDA 2012 Draft Guidance document on suicide assessment: a critical review. Innov Clin Neurosci. 2014;11(9–10):54–65. [see link]) .  The article has been out for months and there is still no indication that the FDA is even attempting to correct the issues we highlighted. 

Until the FDA starts to publish the details of these issues in some format that is easy to search and review (possibly have it listed based upon some centralized clinical trial number so it is easy for reviewers to search through and require every paper submitted to contain this clinical trial number to see if there were any issues), we can try to rely on the other regulatory agencies around the world, but that doesn't mean those agencies will have all the details that the FDA has about such issues.

http://innovationscns.epubxp.com/i/425963/54

I also agree with Jerry Miller, he has given a good explanation

Jerry Miller has given a excelent explanation

I may have some answers to Jerry Miller's pertinent comments. See this blog post / self-published paper and references therein for some clues. I hope this is useful.

http://blogs.lse.ac.uk/impactofsocialsciences/2016/12/06/citing-retracted-papers-has-a-negative-domino-effect-on-science-education-and-society/

https://www.researchgate.net/publication/311443367

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