What is the appropriate course of action if a manuscript is submitted without fixing the problems you, as a coauthor, had pointed out?
The goal of an academic scientist is to perform research that advances science, contributes to human knowledge, and gets published. Many scientists, myself included, collaborate with other researchers. Each lab or person has a role or a set of experiments to perform. Each coauthor is supposed to read and approve of the version of any manuscript that is submitted to a journal for publication.
I can imagine that many manuscripts are submitted even with some unresolved issues among the coauthors. For many papers, one senior author serves as the corresponding author. Indeed, for all submitted manuscripts in my field, the journals require a single author for correspondence with the journal, even if there are multiple corresponding authors designated on the final published article. That senior author collects the input from the coauthors, makes the decision about what revisions are necessary, and finally decides when the manuscript is ready for submission.
What should a scientist and coauthor do if he or she brings up concerns about parts of a manuscript and those concerns are not adequately resolved in the version that is submitted to the journal? Is it appropriate to try and block in-depth review or publication?
Imagine this scenario: You have the surprise of receiving an email to confirm authorship on a manuscript that did not realize had been revised and submitted. You had seen earlier versions, but not the final submitted version. When you download a copy of the submitted version, some of the concerns you had raised did not appear to have been addressed. These were not experiments that you had performed or had any role in designing. So, they were not issues that you would have been the one to address through new experiments. Now, you struggle to decide whether to approve authorship or not.
Most journals in my field either contact coauthors to ensure approval of coauthorship or require coauthors to complete an approval process online after the manuscript is submitted. One option would be to not approve coauthorship when contacted by the journal. This is not ideal if the submitted manuscript includes your work along with the data about which you have expressed concerns to the corresponding author. The journal cannot proceed unless all authors agree with submission. By declining to approve coauthorship, procedure of the publication process is blocked. The other scientists cannot even have their work evaluated.
Another option is to stay quiet, approve submission when contacted, and hope that the reviewers or editors have the same concerns that you had and request that the authors address those concerns during the revision. Another is to approve submission when contacted, but then also contact the editor and note the issues that you have to ensure that these issues are evaluated critically at peer review.
Even if the paper passes peer review, many journals now require a statement about author contributions either as part of the published article or as part of authorship information collected with the submitted article. Is it sufficient to know that your role and contributions are clearly provided and those of the other researchers are also provided? At least in theory, any issues that persist in the final version can be attributed to the proper scientists.
I think the answer about what to do depends on the data at issue. If the problem is pervasive throughout the article, I think it would be better to not approve of your authorship when contacted by the journal. If you fear that having the manuscript accepted and published will damage your reputation as a scientist, it would be better not to approve your authorship. Undoubtedly, the corresponding author will be notified and contact you. You will have another chance to reiterate your concerns and ensure that they are addressed before resubmission.
If you do not receive an adequate response, then you can even raise your concerns at the next level by contacting the integrity office at the university or institution or the department head. If you and your coauthors cannot come to an agreement, you can also insist that your contributions be removed from the manuscript. You should be careful though that your work is included and your name simply removed as a coauthor. The COPE guidelines on ethical issues in scholarly publishing cover this situation, so it must happen.
If the data are ancillary or simply one part of the larger body of evidence supporting the main conclusions, and as long as it is clear in the manuscript how and how many times the experiment was done, I think it is ok to let the manuscript go through the peer-review process and even get published. The readers can decide how much confidence to put in those results.
If you decide to approve authorship, be sure to contact the senior author and firmly explain that this should not occur again. Each author, especially one that raised concerns, should have the chance to read the final version before submission.