Version 1
: Received: 7 August 2017 / Approved: 8 August 2017 / Online: 8 August 2017 (08:27:48 CEST)
Version 2
: Received: 24 February 2020 / Approved: 25 February 2020 / Online: 25 February 2020 (11:45:37 CET)
How to cite:
Teixeira Da Silva, J. Evolving the Correction of the Literature: Manuscript Versioning, Error Amendment, and Retract and Replace. Preprints2017, 2017080029. https://doi.org/10.20944/preprints201708.0029.v1
Teixeira Da Silva, J. Evolving the Correction of the Literature: Manuscript Versioning, Error Amendment, and Retract and Replace. Preprints 2017, 2017080029. https://doi.org/10.20944/preprints201708.0029.v1
Teixeira Da Silva, J. Evolving the Correction of the Literature: Manuscript Versioning, Error Amendment, and Retract and Replace. Preprints2017, 2017080029. https://doi.org/10.20944/preprints201708.0029.v1
APA Style
Teixeira Da Silva, J. (2017). Evolving the Correction of the Literature: Manuscript Versioning, Error Amendment, and Retract and Replace. Preprints. https://doi.org/10.20944/preprints201708.0029.v1
Chicago/Turabian Style
Teixeira Da Silva, J. 2017 "Evolving the Correction of the Literature: Manuscript Versioning, Error Amendment, and Retract and Replace" Preprints. https://doi.org/10.20944/preprints201708.0029.v1
Abstract
Academic publishing is undergoing a highly transformative process, and many rules and value systems that were in place for years are being challenged in unprecedented forms leading to the evolution of novel ways of dealing with new pressures. One of the most important aspects of an integrated and valid academic literature is the ability to screen publications for errors during peer review to weed out mistakes, fraud and inconsistencies, such that the final published product represents a product that has value, intellectually, and otherwise. It is difficult to claim the existence of perfect manuscripts. The level of errors that exist in a manuscript will depend on the rigor of the research group, as well as the peer review that screened that paper. When errors slip through into a final published paper, either through honest error or misconduct, and are not detected during peer review and editorial screening, but are spotted during post-publication peer review, an opportunity is created to set the record straight, and correct it. To date, the most common forms of correcting the literature have been errata, corrigenda, expressions of concern, and retractions. Despite this range of corrective measures, which represent artificially created corrals around pockets of imperfect literature, certain cases do not quite fit this mold, and new suggested measures for correcting the literature have been proposed, including manuscript versioning, amendments, partial retractions and retract and replace. A discussion of the evolving correction of the literature is provided, as are perspectives of the risks and benefits of such new measures to improve the literature.
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Received:
8 August 2017
Commenter:
Aceil Al-Khatib
Commenter's Conflict of Interests:
I have collaborated and co-authored more than 10 articles with Dr. Jaime A. Teixeira da Silva on publishing related issues.
Comment:
I read the article with great interest, the author raises important issues that are timely, important and of interest to all academics.
Before I add my two comments, below, I would like to disclose that I have collaborated and co-authored more than 10 articles with Dr. Jaime A. Teixeira da Silva on publishing related issues. Next are my two points:
1. Line 172: the author states: "Although, in general, preprints should not be cited as they represent incompletely scrutinized documents".
I assume, and I might be mistaken, that preprints undergo screening before posting. So, unless there include material errors, I believe preprints can be cited. For more than one reason, most importantly because some authors may lose interest and not publish a final version. In this context, what is the difference between a preprint and a published flawed article awaiting PPPR?
2. Any correction, amendment, errata, retraction, etc.... should be open access, even if the original article is behind paywall. IMHO.
Commenter's Conflict of Interests:
Tough to tell. I have possible intellectual conflicts with several of the parties critiqued in this preprint. I can expand if necessary, should any reader or member of the public raise any issue.
Comment:
Aceil, thank you for your encouraging feedback and pertinent comments. I should note, as somewhat of a disclaimer, that this preprint had been submitted to bioRxiv 24 hours before it was submitted to MDPI's preprint.org, and was personally screened, and rejected, by Dr. John R. Inglis, the co-founder of bioRxiv. I have vocally protested that rejection as being unfair and based on non-academic principles.
Regarding your questions and comments. As I see it, preprints are a hot topic right now, and a platform for possible abuse. Please do not mix up peer review with superficial screening. In general, from my crude understanding, is that preprints are "crudely" screened within 24-48 hours for "appropriateness", and then released as quickly as possible to the public. This is very different from peer review (when properly done) which involves in-depth critique and analysis. Also, as I see it, preprints offer an opportunity for open public discussion, critique and amendment, as we are doing right now, so this is excellent, and something that traditional peer review does not offer. It allows for us to improve the paper based on a wider pool of voices (of critique or of support).
That is precisely why the unfair and biased rejection of this paper by Dr. Inglis at biorXiv is serious. Because he has deliberately prevented the open and public discussion of this extremely important topic. And in that sense, MDPI has excelled in recognizing this point and allowed the publication of the paper as a preprint.
Note that I don not state that preprints must not be cited. I state that "generally, they should not be cited" because they are a crude form of ideas. Note that in more recent papers and even in this preprint, I have cited at least three preprints, when they deserve to be discussed. So, I do not propose a hard and fast rule, just a cautionary suggestion.
Regarding point 2, I absolutely agree with you and (I stand corrected) this should be the case according to COPE policies (at least for retractions).
This is my first preprint, and I am excited about the feedback, criticism, and working towards improving the paper. I am hoping that the authors of the preprints critiqued in my preprint will also come forward to participate in this public debate (e.g., Barbour, Fanelli, etc.). Especially given that such individuals are among the leading class of the "open science" movement.
Received:
10 August 2017
Commenter:
Klaas van Dijk
Commenter's Conflict of Interests:
Legal representatives from four stakeholders have contacted me in relation to the efforts to retract a fatally flawed study on the breeding biology of the Basra Reed Warbler which is published in a Taylor & Francis journal, backgrounds at https://www.academia.edu/33827046 and at https://www.researchgate.net/project/Retracting-fraudulent-articles-on-the-breeding-biology-of-the-Basra-Reed-Warbler-Acrocephalus-griseldis .
COPE is one of these stakeholders.
Comment:
This is a very readable preprint about an important topic within the field of publication ethics. Preprints publishes a wide range of articles, including essays and reviews, and this preprint fits thus within the type of preprints which are published at Preprints. It is therefore towards my opinion also no problem that this preprint contains many views of the author and that the author refers to many of his own publications to support these views. This preprint can towards my opinion be regarded as a response / comment on a recent preprint about this topic by Barbour et al. at http://www.biorxiv.org/content/early/2017/03/24/118356
My name is listed in line 237 (page 13) . It is correct that I had for a while the opinion that the Barbour et al. (2017) preprint had to be retracted, mainly because BioRxiv had at that time the policy that they did not publish preprints which are essays / white papers / policy papers (etc.). BioRxiv quickly adapted their categories when I was communicating with BioRxiv about this issue. The Barbour et al. (2017) preprint thus fits now within the categories of preprints which are acceptable for BioRxiv. There is thus now also no need anymore that it will be retracted.
A summary of my comments on the Barbour et al. (2017) preprint can be read at https://forbetterscience.com/2017/03/29/cope-the-publishers-trojan-horse-calls-to-abolish-retractions/#comment-4922 It is disappointing that there is until now no response from any of the authors of Barbour et al. (2017) on my comments. The Barbour et al. (2017) preprint does not list a corresponding author. It is thus unclear who is responsible for the tasks of a corresponding author. Preprints has at https://www.preprints.org/instructions_for_authors#requirements clear instructions for the roles and the responsibilities of corresponding authors ("Take full responsibility for answering questions/comments regarding the announced preprint, as well as providing data or materials requested.").
Commenter's Conflict of Interests:
I have expressed my concerns with biorxiv about it changing publishing policies to suit the needs of the Barbour et al. preprint. Neither Barbour, nor biorxiv's Inglis or Sever, bothered to respond.
Comment:
Dear Klaas, Thank you for your feedback and for indicating the evolution of your stance towards the Barbour et al. preprint, i.e., from requesting its retraction to requesting its correction/amendment. I will most certainly adjust my statement to reflect your request. What was extremely important in your statement, and a serious issue that must not be overlooked by preprint proponents, was the that publication policies were adjusted by biorxiv AFTER the Barbour et al. preprint was published to accommodate the Barbour et al. preprint. If one would consider such a situation in a regular journal, i.e., a publisher adjusting the rules of publishing to meet the needs of one of its submitting authors, perhaps because they represented powerful lobbying groups, what would academia say about those groups, and, more importantly, about that publisher? So, your revelation, which I had also noted in fact, should be the focus of an ethical investigation at biorxiv, in my opinion.
Comment 4
Received:
11 August 2017
Commenter:
Judit Dobránszki
Commenter's Conflict of Interests:
I have co-authored several papers with the author of this pre-print.
Comment:
I think this is a good review and evaluation of the recent state of literature correction including its advancements, recent shortcomings, challenges and emerging models, together with their insufficiencies, as well. It is not a problem but rather discussion-triggering that the author presents his own viewpoints via his own publications.
Considering the problem I think the most important part of the paper is the evaluation of the new endeavors or models for correcting the literature and their present insufficiencies. Therefore I think it would be worthy to highlight and so to repeat and list briefly the issues (as an alert) which should be solved in the near future, like correcting the citation of retracted papers, treating preprints, responsibility of different parties in the handling of corrections, etc. in the conclusion section.
Received:
15 August 2017
Commenter:
Klaas van Dijk
Commenter's Conflict of Interests:
Legal representatives from four stakeholders have contacted me in relation to the efforts to retract a fatally flawed study on the breeding biology of the Basra Reed Warbler published in a Taylor & Francis journal, backgrounds at https://www.academia.edu/33827046 and at https://www.researchgate.net/project/Retracting-fraudulent-articles-on-the-breeding-biology-of-the-Basra-Reed-Warbler-Acrocephalus-griseldis . COPE is one of these stakeholders.
It seems therefore reasonable to conclude that the claims ‘editors [journals] do not conduct investigations themselves’ and ‘conduct[ing] investigations (..) is the responsibility of the institutions’ are unsubstantiated. I propose that the author of this preprint will address this issue in a new version of his preprint, together with solid references to support his view about this issue.
Commenter: Aceil Al-Khatib
Commenter's Conflict of Interests: I have collaborated and co-authored more than 10 articles with Dr. Jaime A. Teixeira da Silva on publishing related issues.
Before I add my two comments, below, I would like to disclose that I have collaborated and co-authored more than 10 articles with Dr. Jaime A. Teixeira da Silva on publishing related issues. Next are my two points:
1. Line 172: the author states: "Although, in general, preprints should not be cited as they represent incompletely scrutinized documents".
I assume, and I might be mistaken, that preprints undergo screening before posting. So, unless there include material errors, I believe preprints can be cited. For more than one reason, most importantly because some authors may lose interest and not publish a final version. In this context, what is the difference between a preprint and a published flawed article awaiting PPPR?
2. Any correction, amendment, errata, retraction, etc.... should be open access, even if the original article is behind paywall. IMHO.
Commenter:
Commenter's Conflict of Interests: Tough to tell. I have possible intellectual conflicts with several of the parties critiqued in this preprint. I can expand if necessary, should any reader or member of the public raise any issue.
Regarding your questions and comments. As I see it, preprints are a hot topic right now, and a platform for possible abuse. Please do not mix up peer review with superficial screening. In general, from my crude understanding, is that preprints are "crudely" screened within 24-48 hours for "appropriateness", and then released as quickly as possible to the public. This is very different from peer review (when properly done) which involves in-depth critique and analysis. Also, as I see it, preprints offer an opportunity for open public discussion, critique and amendment, as we are doing right now, so this is excellent, and something that traditional peer review does not offer. It allows for us to improve the paper based on a wider pool of voices (of critique or of support).
That is precisely why the unfair and biased rejection of this paper by Dr. Inglis at biorXiv is serious. Because he has deliberately prevented the open and public discussion of this extremely important topic. And in that sense, MDPI has excelled in recognizing this point and allowed the publication of the paper as a preprint.
Note that I don not state that preprints must not be cited. I state that "generally, they should not be cited" because they are a crude form of ideas. Note that in more recent papers and even in this preprint, I have cited at least three preprints, when they deserve to be discussed. So, I do not propose a hard and fast rule, just a cautionary suggestion.
Regarding point 2, I absolutely agree with you and (I stand corrected) this should be the case according to COPE policies (at least for retractions).
This is my first preprint, and I am excited about the feedback, criticism, and working towards improving the paper. I am hoping that the authors of the preprints critiqued in my preprint will also come forward to participate in this public debate (e.g., Barbour, Fanelli, etc.). Especially given that such individuals are among the leading class of the "open science" movement.
Commenter: Klaas van Dijk
Commenter's Conflict of Interests: Legal representatives from four stakeholders have contacted me in relation to the efforts to retract a fatally flawed study on the breeding biology of the Basra Reed Warbler which is published in a Taylor & Francis journal, backgrounds at https://www.academia.edu/33827046 and at https://www.researchgate.net/project/Retracting-fraudulent-articles-on-the-breeding-biology-of-the-Basra-Reed-Warbler-Acrocephalus-griseldis . COPE is one of these stakeholders.
Preprints publishes a wide range of articles, including essays and reviews, and this preprint fits thus within the type of preprints which are published at Preprints. It is therefore towards my opinion also no problem that this preprint contains many views of the author and that the author refers to many of his own publications to support these views. This preprint can towards my opinion be regarded as a response / comment on a recent preprint about this topic by Barbour et al. at http://www.biorxiv.org/content/early/2017/03/24/118356
My name is listed in line 237 (page 13) . It is correct that I had for a while the opinion that the Barbour et al. (2017) preprint had to be retracted, mainly because BioRxiv had at that time the policy that they did not publish preprints which are essays / white papers / policy papers (etc.). BioRxiv quickly adapted their categories when I was communicating with BioRxiv about this issue. The Barbour et al. (2017) preprint thus fits now within the categories of preprints which are acceptable for BioRxiv. There is thus now also no need anymore that it will be retracted.
A summary of my comments on the Barbour et al. (2017) preprint can be read at https://forbetterscience.com/2017/03/29/cope-the-publishers-trojan-horse-calls-to-abolish-retractions/#comment-4922 It is disappointing that there is until now no response from any of the authors of Barbour et al. (2017) on my comments. The Barbour et al. (2017) preprint does not list a corresponding author. It is thus unclear who is responsible for the tasks of a corresponding author. Preprints has at https://www.preprints.org/instructions_for_authors#requirements clear instructions for the roles and the responsibilities of corresponding authors ("Take full responsibility for answering questions/comments regarding the announced preprint, as well as providing data or materials requested.").
Commenter:
Commenter's Conflict of Interests: I have expressed my concerns with biorxiv about it changing publishing policies to suit the needs of the Barbour et al. preprint. Neither Barbour, nor biorxiv's Inglis or Sever, bothered to respond.
Commenter: Judit Dobránszki
Commenter's Conflict of Interests: I have co-authored several papers with the author of this pre-print.
Considering the problem I think the most important part of the paper is the evaluation of the new endeavors or models for correcting the literature and their present insufficiencies. Therefore I think it would be worthy to highlight and so to repeat and list briefly the issues (as an alert) which should be solved in the near future, like correcting the citation of retracted papers, treating preprints, responsibility of different parties in the handling of corrections, etc. in the conclusion section.
Commenter: Klaas van Dijk
Commenter's Conflict of Interests: Legal representatives from four stakeholders have contacted me in relation to the efforts to retract a fatally flawed study on the breeding biology of the Basra Reed Warbler published in a Taylor & Francis journal, backgrounds at https://www.academia.edu/33827046 and at https://www.researchgate.net/project/Retracting-fraudulent-articles-on-the-breeding-biology-of-the-Basra-Reed-Warbler-Acrocephalus-griseldis . COPE is one of these stakeholders.
It seems therefore reasonable to conclude that the claims ‘editors [journals] do not conduct investigations themselves’ and ‘conduct[ing] investigations (..) is the responsibility of the institutions’ are unsubstantiated. I propose that the author of this preprint will address this issue in a new version of his preprint, together with solid references to support his view about this issue.