If a ex-PhD student publishes a paper from his thesis without his ex-supervisor's consent, the paper gets retracted upon his ex-adviser's request to the editor.
My question is: Could there be any exceptions from this rule?
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I can see three main reasons why a PhD student would require permission from the supervisor to publish a paper:
Because the supervisor contributed to the paper enough to deserve authorship.
Because the supervisor is listed as a co-author.
Because university regulation stipulate that students require permission before publishing.
The supervisor is responsible for ensuring that external obligations are met (e.g. ethical handling of medical data; confidentiality agreements with third parties; etc etc.)
Now the third reason does not really affect the journal, but only the internal relationship between student and university. If the student lists the university as affiliation, they may demand to change this, but would not really be in a position to demand a retraction.
If the second case applies but not the first, again a correction of the misleading metainformation needs to be done, but this would probably not be grounds for a retraction.
The first case does merit demanding a retraction, but for this it is irrelevant that the objecting co-author is the former PhD supervisor of the publishing co-author. In particular, it would not really matter how exactly the collaboration of the two broke down.
In the fourth case, the missing permission by the supervisor itself would again be irrelevant for the journal. If the objection however is due to say lacking ethics approval for experiments required those, then the latter circumstance would be cause for retraction. Here, too, the details of the relationship between advisee and advisor are irrelevant, only the potential ethics infractions should impact the journal's decision.