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In my view, the story here is essentially one of censorship. It is important to note that when asking authors to provide a response to criticism of their work, journals typically allow authors wide discretion to respond as they see fit. The response is not subject to the type of rigorous review that an original manuscript would receive because the authors essentially have a "right" to respond to the criticism of their article.
Of course, the journal will screen the response for any material that is inappropriate or out of line, but I have never seen a journal dictate the grounds upon which the authors can respond to the criticism. And I have never seen a journal dictate that the authors cannot use a particular line of argument in responding.
It is entirely appropriate to address conflicts of interest that are present because these conflicts may well have influenced the conduct of the research and the interpretation and reporting of the results. Addressing and considering conflicts of interest is not only a legitimate aspect of responding to a critique, but it is a "scholarly" response. Kulik and Glantz went beyond the call of duty here and provided a detailed accounting of the conflict of interest, noting and documenting the conflicts with 26 references (which is very strong documentation considering that this is merely a response to a letter to the editor).
To argue that addressing conflicts of interest is not relevant to evaluating a manuscript is to undermine the entire purpose of requiring that such conflicts be disclosed. Essentially, what the journal is saying is that while they require authors to disclose conflicts, they do not see those conflicts as having any relevance to the evaluation of the research. Well if that is the case, then why bother publishing the conflict of interest disclosures?
The very purpose of disclosing conflicts of interest is to allow readers to take that conflict into consideration <strong;in evaluating the validity</strong; of the article.
Now I firmly believe that one should never simply dismiss an article because of a conflict of interest; every article must also be evaluated in terms of its scientific content. However, it is not appropriate to go to the opposite extreme and argue that conflicts of interest must be ignored. Both are legitimate and important points to consider in evaluating a paper. And in this case, Kulik and Glantz did also address the scientific aspects of the statistical analysis conducted in the critique.
The rest of the story is that the refusal to allow the authors to address conflicts of interest present in the paper criticizing their work essentially amounts to censorship. The journal is dictating the scholarly points that can and cannot be made and not allowing the authors discretion in how they respond to criticism of their own work. Moreover, the arguments made by the journal in rejecting the authors' response undermine the entire purpose of conflict of interest disclosure.
We do not publish conflict of interest disclosures and then right after that, publish an additional disclosure which reads: "In evaluating this paper, please ignore the above conflicts of interest." But that is exactly what the journal is asking its readers to do.

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