text:
Leaving paper before publication due to personal ethics stance
During my postdoc, I began to question the morality of a part of my group's research project. But I kept working on it, and a year later, we submitted the paper to a journal with me as first author. Shortly after that, I left the lab.
My concerns about the project's morality increased every day and I no longer wish to be an author.
Now the paper has been preliminarily accepted. I contacted my advisor. I told him the situation, emphasizing that I wanted to cause as little inconvenience to the other authors as possible while simultaneously not violating my moral code. I suggested two options:

Remain on the paper after removing the component I found morally objectionable (this is about 20% of the paper), or

Remove myself from the paper, send a brief explanation to the other authors, and allow the paper's contents (including the parts I found objectionable) to remain as is.

Although my advisor tried to be understanding, in the end, they stated that the content I found morally objectionable could not be removed and that I should not remove my name either. They said that redacting my name would be incorrect (as I would then be a ghost author). They also said I was "selfish" for bringing it up. They said I should "sacrifice" my moral stance to keep the situation easy. They finally stated that they are older than me and that they have the wisdom to know that I will be more well-rounded as I age and that my moral objection will lessen over time.
This type of research is not illegal and it easily passes all modern research ethical committees. However, it still is a morally contentious area. I have no concerns about legal liability or anything like that. My concern is about my personal moral objection.
What is a graceful way to move forward with this painful situation? Is the behavior of my advisor or myself or both or neither unethical? Were my proposed two optional solutions suitable?
Some clarifications:

I did not directly participate in the ~20% of the paper I find morally objectionable, nor did I receive money from it.
My advisor did more work, but wanted last authorship, which is why I'm first author. The project evolved over time.
I imagine my coauthors would be even more offended if I made direct/public statements about my moral objection to their work.

As others have said, this was way way way too long. I have made some heavy-handed edits to shorten it. This shortening is a moderation action: please do not roll back the edit or otherwise make it super long again. On the other hand, the edits themselves are a suggestion -- so long as you don't lengthen the post, please feel free to make any corrections / changes you see fit.

Comments have been moved to chat; please do not continue the discussion here. Before posting a comment below this one, please review the purposes of comments. Comments that do not request clarification or suggest improvements usually belong as an answer, on [meta], or in [chat]. Comments continuing discussion may be removed.

Do not let others pressure you into something you consider morally intolerable.
The two options you presented to your advisor are very reasonable. If he is unwilling to choose one he prefers, he must accept the one you choose, whatever the consequences to everyone involved. (And, as far as I can see with my limited knowledge, your two options do no measurable damage to anyone besides maybe yourself — in the form of some burnt bridges.)

Agreed. This does not have to be complicated. If you do not feel right being first author or having your name on the paper at all, you do not have to. It seems that you already know this, and are looking for support. Your reasoning is sound. Stick with your moral compass.

You are right that I'm looking for support (if it's genuine). It's hard not to question myself after being called "selfish" and told to "sacrifice myself" for the "bigger picture". Many responses here on SO seem to state that I should feel obliged to remain on the paper at this point. It gives me something to think about now seeing these comments emerging suggesting that indeed morals should be prioritized here.

You will find that a great many people, including some who like to present themselves as moral and correct, lack integrity. And they do not like it when someone with actual integrity gets anywhere near them. I would personally refuse to have my name associated with research I consider immoral. So yes, thank you for following your own moral compass.

Good to know this viewpoint and thanks for sharing. My roommate went through a similar experience and they regret their papers now and found it difficult to do anything at that point. They also encouraged me to leave beforehand as they wish they had done just that. I think this scenario is not as rare as we might think.

This answer is beautiful - correct, factual and succinct.

What little support I can offer you as an anonymous academic with some decades in the system is genuine. You will likely face these moral dilemmas again in your career, and the only way to live with yourself is to do what you know to be right in yourself. You are not being selfish, you seem to be the only one looking at the bigger picture here, and you should under no circumstances, sacrifice yourself.

While the second option presented to the senior author is a reasonable compromise, there is a reasonable ground for objecting to it. Authorship is an act of taking responsibility for the material. If there is a set of material in the paper that you, and no one else, was responsible for, then someone must take moral and technical responsibility for that material. Taking the name of the person able to take responsibility for a certain set of material off the papers means that the rest are guaranteeing the truth of that material while being in no position to honestly do so.

Then why is the OP's advisor not taking first authorship, even though they did more work on the paper? Isn't that shirking responsibility? It is also quite common for advisors to take first authorship, even when they did very little work on the specific research in the paper. The authorship shell game is the norm, so I don't think your argument holds.

You and you alone decide whether to associate your name with any work. The submission to the journal will ask you explicitly whether you agree to the manuscript. No one can compel you to agree. Once you have refused, it is no longer your affair; you are not responsible for what the other authors decide to do with the manuscript.

Interestingly, if they decide to thank you in the acknowledgments, you have little recourse. Unless they misrepresent your role, but even then I think it would take legal action to reverse, and your would probably have the burden of proof

I'm very sorry you're so anguished over this issue. But it's not clear to me how removing your name from the paper would be a solution to anything. After all, you did participate in the research, so if the research is immoral, then unfortunately it's not possible to erase the fact of your having participated in its creation. If this weighs on your conscience, wouldn't it still weigh on you even if your name were removed from the author list? And wouldn't removing your name be merely a way to mislead other people into thinking that you had nothing to do with the research? (And wouldn't the deception involved in misleading people in that way merely compound the ethically problematic nature of your behavior, rather than diminish it?)
Well, obviously I could be missing something since you have not provided much detail. But if you could clarify (at least to yourself) why removing your name is ethically superior to including it, I think that might help you figure out a way forward.
Now, if your goal with this plan is simply to not be seen to be supporting this type of research which you have come to regard as morally unacceptable, I think this can be achieved without hiding your contribution. Here are a few possible ways to go about it:

you could agree to have your name listed as an author, but insist that the paper must include a statement in which you disavow the research and state your position that it is immoral (without refuting that it is scientifically valid). Obviously the statement will bear only your name and not the names of the other authors, so it seems like something the other authors might agree to include.

you could agree to have your name listed as an author, and not insist that the paper must contain a statement of disavowal as described above, but publish the statement of disavowal separately (for example on your web page, or as a letter to the editor or commentary article that will be published in the same journal where the paper is being published).

you could ask not to be listed as an author of the paper, but to be listed in the acknowledgements section instead, where it will be explained what your contribution to the research was, and where it will be explained (for example with the insertion of a statement of disavowal as above) that you morally object to the research and for that reason asked not to be listed as an author.

Perhaps another goal that you have in wanting to remove your name from the paper is wishing to avoid being rewarded for engaging in the immoral research in the form of an extra publication on your CV. Suggestion 3 above manages to achieve that, while suggestions 1 and 2 are still a bit problematic in that sense. It's understandable that you do not want to profit from immoral behavior.
Good luck, hope you find a way to navigate this tricky situation!

Option 4: you can ask not to appear on the paper, since this is what you seem to really want (afaik there's no obligation not to renounce your authorship! most answers here look like there were, it sounds very odd to me), and also publish a separate statement as proposed by @Dan Romik if, as he suggests, there is also a problem with having participated in this research, beyond authorship.

I'm unfamiliar with scientific publication conventions. Would the conflict of interest statements be an appropriate place to disavow the methods?

I apprecited your feedback, Dan. These are great ideas for me to ponder. I wonder what you think of my newer edits, especially the bolded questions. Isn't it wrong for me to state that I "agree to the contents of the paper" (as is asked for all authors) if I do not agree to its moral content?

I appreciate your feedback @sparusaurata. I am also a bit surprised by many of the responses so far. There seems to be a cultural/traditional viewpoint that one cannot renounce authorship. This does not take into account how large projects evolve out of one's hands, how moral viewpoints evolve, and "dynamic consent" to be an author. I sometimes worry that we as scientists are trained to not develop and act on our own moral codes, and that is secondary to "group collaboration".

@ilctf I read your edits. It sounds like you need someone to tell you it’s okay to completely withdraw from the project, remove your name from the paper and not speak publicly about the topic of the research, either in support or to express your moral opposition to it. Well then: sure, it’s totally okay to do that; it just wasn’t clear to me why that would resolve your sense of guilt, but your explanation makes that a bit clearer, and in any case if that’s how you want to proceed, I don’t think anyone can fault you.

One more piece of advice: when you inform your coauthors of your decision, it might be better to avoid long explanations, examples and analogies of other people removing their names from papers (as in your post), etc. I find these arguments immaterial. Signing your name to a piece of work is entirely at your discretion; you are free to do it or not do it, for any reason or for no reason at all, and you are not required to give a reason even if you have one. Sometimes it’s best to not give reasons because it invites people who disageee you to try to argue. Good luck!

One of the many reasons we, as humans, feel a duty to be moral is that we are seen by others as moral. Wanting to not be associated with a project we find personally immoral is an entirely reasonable request even if it assuages no guilt whatsoever. I'm not saying that this reason applies to OP, but the idea that there's nothing to be gained from withdrawing is frankly naive.

@user121330 sure, I completely agree it is a reasonable request, and has some benefits as you point out. But those benefits did not seem to be what was motivating OP, so I was a bit confused as to why they thought this would solve the main problem that's bothering them.

I agree fully with the answer, you did conduct research which led to the results and removing your name should not really solve anything. However a fourth option not mentioned above might be to include a more precise description of work in the Author Contributions. E.g. ilctf conducted the experiments for A and wrote the paper, author B conducted the experiments for B.

I appreciate the comments @DanRomik. I would feel even more guilt to continue with the project and add my name. The more I support the project, the guiltier I feel. For instance, if I put my name on the paper, then I'm supporting, say, military funding if 20% of the data came from such sources. If I remove my name, then I'm not supporting military funding to improve my career, and I don't feel guilty as I did not collect the data that used military funding, etc.

This is about moral codes, so nobody can tell you what is the right thing to do. We can only come up with suggestions, and hope that one of them feels right to you. Here's one:
Accept authorship, and then write an article/essay/blog post describing your misgivings.
Ultimately, you did author the paper. Removing your name from the paper is always an option, and always your decision and yours alone. However, your co-authors may not feel comfortable publishing without you, if you made substantial contributions, so you'd be inconveniencing them (which you indicate, you don't like doing).
In a way, you can see your authorship on the paper as an acknowledgement of guilt. If you really contributed to research you feel is unethical, the best thing to do is to acknowledge that fact and then to show remorse. This is more honest since you're not hiding your involvement, and it allows you to more precisely refer to what you did that you regret, since your involvement has been clearly documented.
You can use the current threat of pulling your authorship, to get a small ethical statement into the paper highlighting some of the issues you are worried about. That way, you can show that you were already concerned about these issues at publication.
Then, once the publication is done, you can start writing down your misgivings in detail. Point to the original paper, acknowledge that you took authorship and why, and then explain why you regret your contribution to this research. The exact format of this article depends on what you want to say. You may want to go into your personal struggles (as you have done in your question), in which case a blog post or published essay may be a good format. You may want to make a more academic point about these research practices, in which case an opinion paper or even a regular paper may be best. You could even do both.
One upside of this approach is that you are not wasting the energy you poured into obsessing over this issue for the last few years. You can finally use this productively to write about your struggles, while closing the door on a painful chapter in your life. This will be both therapeutic, and help your career.
A downside is that it will definitely sour relations with your current co-authors. As I read it, that ship has pretty much sailed already, and even if it hasn't, you likely can't be on friendly terms with them while being honest about your values. In such a case, it's probably healthier to pick your values , since they clearly weigh heavily for you. If you want to hold your head high, it's probably best to announce up front what you intend to do: say something like, "Yes, I will take authorship, provided that there is an ethical statement, but be advised that in the future I intend to write about these issues more, and that will require me to essentially denounce this paper."

"This is about moral codes, so nobody can tell you what is the right thing to do. We can only come up with suggestions, and hope that one of them feels right to you." Not everyone believes in moral relativism. Even if you do believe in it, there are many moral questions in academia where there is almost universal agreement.

Fair enough, but since the specific issue is not explained, we don't know whether it's one of those cases. The OP clearly doesn't want to give those details, so they should make the decision which course of action fits their moral code.

I can definitely consider some of these options and thank you for providing them. I'm not sure if it is necessarily more honest to stay on the paper though, even if I contributed toward parts of the work. I still need to sign a form stating that "I agree to all content in the final version of the paper", and I quite simply don't. So, if I remain as an author, unless we remove the immoral parts, I would be dishonest when signing that form.

@iclf Yes, I may have phrased that too strongly. Removing your name comes with some ethical questions, but it's certainly not an unethical thing to do. As for the form, that's partly a matter of interpretation. "agree to" could mean that you agree that it's published under your name as a record of what happened, but not necessarily that, in retrospect, it was the right thing to do.
I expect the form is mostly there so the publisher can prove that they published what you wanted them to publish: that is, so that you take responsibility for the published material, not them.

"This is about moral codes, so nobody can tell you what is the right thing to do." <- What a weird thing to say. Morality is not a matter of personal taste.

@einpoklum There are many people the world over whose moral codes don't allow them to do things that I would have no moral problem with. For all I know, the thing the OP finds  morally objectionable is the inclusion of female co-authors. I would find it immoral to find that immoral. So long as they don't tell us the situation, we can only give suggestions and have them decide whether it fits their code.

I know someone who is finalizing their removal as an author right now. I mention this to say that I have some familiarity with the next steps in this process. Regardless of what should happen, what will probably happen is an exchange between the journal and the Committee on Publication Ethics, or COPE, which has worked with academics and journals for the past 25 years on ethical practices in authorship.
COPE has previously handled a case very pertinent to the original question, titled Request for removal from author list for reasons of religious belief:

Case text: We have been contacted by an author of a published article who has requested to be removed from the author list. ... because they no longer want to be associated with the research for reasons of religious belief. They further state that, because they now consider a lot of applications of knowledge in their field to be sinful, they do not want their name to be associated with activities that they no longer agree with, and they do not want to be recognised as someone who is involved in such research.

The COPE Forum came to a consensus in this case that:

Advice: ... accountability for the article is the most important consideration. Since there is nothing wrong with the article itself the author must retain their affiliation with it. While a ‘silent correction’ is possible where an author has requested a name change, that does not apply in the current case since the author is asking for their name to be removed altogether.

(emphasis added). Having said that, the Forum further said:

Advice: ... The journal should, however, consider whether the author is in any personal danger because of their connection with the research. If that were the case then it might be possible to remove their name, but their contribution would still need to be acknowledged in anonymous form. It is not possible to remove an author entirely from their responsibility for the article’s content.

(emphasis added).
So, your case hangs between these two rules. On one hand, safety aside, you must stand as an author of research you originally authored. But your safety is paramount.1 If authorship of this article would convincingly harm your well-being, the norms around scientific authorship accountability would yield to basic ethical principles to "first do no harm".
(The standards are this rigorous because if they were looser, there would be plenty of risk in the opposite direction -- imagine supervisors having the power to instigate removal of their PhD students' first authorships after a dispute!)
COPE would probably then advise the journal to obtain written approval from all authors (including you), and then revise the manuscript to move you from author to the Acknowledgements as an anonymous contributor, following this procedure.
All the best!

1 I am sure you mean no harm or insult to anyone, and I have no doubt that you have withheld more details to protect yourself. But I suspect what you said here:

This is the first time in my life that I have resorted to therapy (and I will likely need it for a while yet).

by itself is not the level of "harm" that rises to such a drastic action. "Therapy" covers a variety of practices and interventions; it may be a life-saving days-long program in a stay-in centre, or monthly chats about old childhood regrets, or anything in between. I myself attend regular therapy to process academic norms and practices that are deeply harmful and abusive; this does not imply that my daily functioning is (or isn't!) impaired enough to risk my safety.
I am sure that what you are going through is more serious than what I am going through -- I say this just to emphasize that we should normalize psychological therapy, and "I need therapy now", by itself, will probably not be treated as safety-threatening impact.

If it helps, you can pass COPE's materials on to your co-authors to assure them that these situations, while infrequent, can be handled in standard ways that will not significantly disadvantage them. (Everyone simply has to come to agreement and then sign a basic PDF form.)

The timing of the authorship-removal-request seems like it might be important - Does the COPE Forum have different rules if the paper is "only" in preliminarily accepted status? The text you've provided makes me think that is for published papers, but I don't know.

The important difference here is that the manuscript has not yet been published

Yes, my situation is before publication. However, I can relay this to my roommate, as they've asked about this exact situation.

The reality is that you have done the work, and took money to do so. In one way or another it was funded, and other people put in significant amounts of time on this. So unfortunately, it exists, and it exists beyond your immediate circle of control.
Pretending it never happened will not change it. Additionally, if somehow the work you did is not allowed to reach the light of day, then who is to say it will not be repeated again either by your former group in order to complete the publication (should your actions compromise it), or by someone else following a similar research trajectory (perhaps in continuation of the partially complete work that may result from your omission).
So, this is unfortunate. But you have made choices and taken actions and these are the consequences you must live with and learn to navigate. I do legitimately feel bad for your personal outcome which has resulted in obviously very unpleasant mental anguish.
I suggest you continue with therapy and look for ways to advocate against the issues you find unethical or immoral. Don't try to erase your contribution but use that as a way to advocate for change, from a point of view of direct personal experience. Without knowing more, there isn't much more I can say.
Good luck!

You response is appreciated. A quick note that I added an edit to my post. I did not do the 20% of the work I find morally objectionable, nor did I receive money for it. I also feel it is untrue/unethical for me to check a box that says that, as an author, I "agree to all contents of the paper". Because I do not agree to all its contents.

Thank you for clarifying. The question about agreeing is not asking you if you holistically agree to all implications of the research. Was the research done following legal guidelines? Has the data been accurately and ethically (within the confines of the legal definition, not your personal opinion) represented/handled to the best of your knowledge? Do you agree to the inclusion of all authors, i.e. is there academic fraud occurring or has everyone made reasonable contributions worthy of authorship, etc...

I would ask your PI to include a footnote at the end of the manuscript where you can politely state your objection to whatever ethical issue you are having. Use professional, not charged language, and provide a statement that this in no way has impacted the integrity of the research (assuming it has not).  As for receiving money, you were part of a research group that used funds to operate which contributed to this work. Therefor you benefited in some way from this work, whether directly or indirectly. Fact of life, you know what to look for in future research work.

Yes, the research is legal and I think most authors contributed enough to warrant authorship. However, your suggestion would mean that, when I receive the final authorship consent form, I should untruly state that "I agree to all contents of the paper". I feel I should answer ethically, and not check that box. Then, I may be asked by the editor to remove my name anyway since I explicitly state that I don't agree to paper's contents. Maybe this could be exempted if I add the statement of disapproval as you suggest -- but my authors may like that even less.

I also don't think someone should put their name on something they morally object to just because they were paid a salary to do projects in some of the labs represented on the paper. This would enslave all of us (since we all need to get paid) to agree to everything that comes out of a lab that financially supported us? Clearly, we each have our moral limits, and mine was passed in this case. This type fo thinking almost feels like a conflict of interest? (i.e. I morally object to the paper but I am financially enslaved to put my name on it since I was paid in this lab).

You have no control of many extrinsic factors, certainly not all of the research directions of a larger group. However, you do take responsibility for what your research project is (whether you are lead or not) and the manuscripts that it leads to. Ultimately, it is not all on you as you are not the lead PI, but those are choices we make when we choose who we get involved with. Certainly one cannot claim that an academic position as a postdoc performing research is ones only means of meeting basic financial/life needs.

Wouldn't this all mean I should be untruthful/dishonest and check the authorship consent form that "I agree to all contents of the paper"? And even sign that false statement too?

That is not what that check box means. It means you think the contents are technically correct. I have never heard of anyone arguing this is an ethical statement.

@Dawn Great comment. You are agreeing to the conclusions, the interpretation of the data, and the accurate representation and reporting of all aspects. It is not a question about your opinion on ethics and morality. It seems the OP is hung up on this tick box, but they are trying to answer the wrong question. In an extreme case, if that's what the question implied, then one author may refuse to sign off on a paper because they found out one of the collaborators was of a race/gender/sexual orientation/politic they do not wish to associate with for whatever personal/religious/cultural reasons.

Many widely-held guidelines for authorship all agree: If you do not approve of the final pre-publication version of the article, and you do not agree to take responsibility / be accountable for the whole paper's content, then you should not be listed as an author.
Here's an example from a book chapter on "Guidelines for the Responsible Conduct of Research" from the National Academies:

On a larger scale, each author has the responsibility to be able to agree with the general conclusions and interpretations of the paper. Any disagreements should be resolved prior to submission of the work for review. Ultimately, any individual author has the right and the responsibility to remove his name from a manuscript if he has substantial concerns with its conclusions.

The Council of Science Editors summarizes several other such guidelines on their page of "Authorship and Authorship Responsibilities". For instance, they cite criteria from the NIH (US National Institutes of Health) including "a willingness to assure responsibility for the study."
They also give another example:

the International Committee of Medical Journal Editors (ICMJE) [...] which defines authorship by the following criteria: [...] 3) final approval of the version to be published, and 4) agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

In many of these guidelines, it doesn't seem to matter why you don't approve of the current state of the article. Even if you had no ethical qualms about the paper, you could simply decline to review & approve the final draft (with no particular reason given), and that should be enough to make you ineligible for authorship under many of these guidelines.

I am very sorry you are experiencing such severe personal distress about an issue that, as you say yourself, "easily passes all modern research ethical committees". This means that the research is not viewed as unethical or immoral by a certified board of experienced scientists. This in itself says something. You yourself seem to see the research as completely unethical and that is your good right and a personal call that of course should not compromise. However, instead of prolonging the situation and your anguish, I think you should make the psychological effort and move on. As other comments state, removing your name from the paper will not change the fact that you performed the research. Start a career in a completely new avenue of science and be careful next time not to proceed with any research you find unethical or immoral and please don't be too hard on yourself.

I have 2 suggestions.  First, consider the position you have put you and your coauthors (specifically your advisor) in.  You have moral misgivings about a small portion (20% by your estimate) of a publication.  You feel so strongly about this that you are willing to have your name removed from this paper...at the worst possible time.  The paper has been through review and has been accepted (if the publisher uses an "open" review then this is worse as this can communicate to the community that you are separating from them (your coauthors) and there was something truly amiss; you cannot avoid perception and speculation).  The time to have a conversation about authorship was when the paper was being drafted.  Further, you are listed as the first author, which, in many academic circles, is a position of prominence.  Maybe your field is different, but in my field this tells me that you made a substantive contribution to the research/analysis that is presented and you wrote the majority of the paper.  Now, you've asked your advisor to remove you from the author list.  At best, this is "bad timing".
Please consider this scenario from your advisor's perspective.  What will he say/think when you begin writing the next publication?  Without a doubt he'll worry about you having another unforeseen moral dilemma as that paper approaches the publishing finish line.  This is not a small change to the paper.
Please also consider how this may be viewed by the editor and the referees.  You, as a postdoc, need to build your career.  Part of this involves collaborations (potentially with your advisor, your current coauthors, the editor, or the people who reviewed your paper).  Another important component of building your career is participating in the review process as a referee.  If you pull out at this point that may raise some eyebrows among the editorial staff at this journal, the referees, as well as your coauthors.
We had a similar situation (years and years ago now, not related to ethics) where an author wanted removed from the author list after the paper was accepted (not yet published, but accepted).  Everyone on the coauthor list viewed this as a personal and professional insult and many bridges were burnt that day.  Whether "burning the bridges" was the right thing to do or not is a separate matter.  You cannot control people's perceptions.
In short, now is the second-to-worst time to request removing your name (the worst time would be after the article is released/published) and there are many potential consequences of this.  You should have raised this issue before the first draft was released but that ship has sailed.  Please understand that I am not saying you should keep your name on the paper.  What I am telling you is there are unavoidable consequences (some more severe, some more likely, than others).  You cannot control people's reactions, perceptions, or speculations.  It is better to accept this now rather than later.  If you still want your name removed and you view the potential fallout as acceptable (i.e., this is a hill to die on) then great.  But if you want your name removed and you want your coauthors to give hearty approval and have no fallout then your attitude will burn even more bridges.  Maybe there will be no fallout (I seriously doubt it) maybe there will; there is little you can do about that.
This brings me to my second (shorter) point, which is a potential solution to this issue.  Many journals allow (some require) an "author contribution" section at the end of the paper.  Here, the first author (you) tells the reader how each coauthor contributed to the manuscript.  This is the perfect place to state "ilctf analyzed data in this section and composed the manuscript and did not participate in the collection or evaluation of this data (whatever it is you find objectionable), rather the objectionable portion of this study was carried out by these authors."  This gets you off the hook of taking responsibility/credit for the objectionable bits, it attributes credit to the folks who did the work, and there will be no burnt bridges.

Is the behavior of my advisor or myself or both or neither unethical?
I think there is questionable behaviour on your side, and I do not think you have adequately considered the ethical questions your advisor is facing.  I sympathise with your dilemma, and do not think you should simply publish with your name on something you believe will cause (or is causing) moral injury. I do think you have to be prepared for this to have lasting (and possibly fatal) impact on your career.  Personally, I would find it hard to ignore that you had tanked the publication of significant work after leaving the team.  I likely would not hire you.
You CAN stop the publication with your name on it by simply withdrawing consent with the journal BEFORE it is made public. I'm not convinced this is a gracious way forward, but it might be your final option.
Were my proposed two optional solutions suitable?
Not entirely.  You are looking at what works for you, but I do not think you are considering the impacts on the rest of the team, impacts that may be significant.
Your advisor cannot ditch part of the team, and their research, without good cause.  Unfortunately, the time to raise your moral concerns was in the past before the work was undertaken - at that point your advisor would have been obligated not to extend the study with you hostage to it.  That is no longer the case as the study was extended with everyone appearing to be on board. There are potentially contractual obligations, ethical considerations of informal collaboration agreements, and just ethical considerations of having impacts on other's careers to consider.
Similarly, removing you as author is not simple.  Your advisor would likely be seen as behaving unethically to publish without you - this impacts their reputation in potentially major ways.  They would also need to sign agreements with the journal that everyone is correctly listed (but you would not be).  Any changes would need to be done with the journal.
What is a graceful way to move forward with this painful situation?
A couple options to explore

Would an author credit statement be something that interests you? That makes clear what your involvement in the project was and highlights it was not with the content you found unethical?  This way you would still be named, but it would be stated what part of the work you were involved with.
Could you be listed under a pseudonym, thereby being properly recognised (lower in the author list, you'd want a genuine name as first author), but without the connection to your professional self that would continue into the future?
Could you be acknowledged rather than an author, with a clear explanation of your contribution to specific parts.  Discussion with the journal would be necessary

If your (previous) university has an ethics officer it might be worth reaching out to them for guidance on how to proceed. They might be able to organise mediation with your advisor to find a way forward.

Thanks. I definitely do not want to cause harm to my advisor. We discussed recently trying to remain positive and support each other, as we did have other produtive papers in high impact journals. I'm a bit sad they called me "selfish" earlier, but I never said anything about it, and I never returned a negative statement about them. We're drafting a letter so all authors know what happened, and make it clear it was my own spiritual decision entirely and that my advisor supported me. So, I'm hoping it will not damage their reputation at all, maybe even show they are supportive in hard times

We've worked on another project together (that I'm not morally opposed to), and we recently submitted it to a conference. My advisor might publish that paper without my name if they don't want to risk me leaving again (even though I wouldn't). But, maybe they would ask me if I want to be an author, and it could demonstrate we are still on good terms in case anyone might view their reputation negatively from me withdrawing from the first paper. I'm just staying silent and letting them decide in the future on that other project and suppor them either way.

I think you are pretty clean in what you want and what you need for your mental health. If you want to distance yourself from the research and remove your name you should do so, instead of have to carry this around with you for the rest of your life, if your advisor and other authors are unwilling to let you remove the morally questionable part.
Life is short and if this has caused you so much anguish already, don't risk it causing you any more by doing something that makes you uncomfortable.
(You mentioned someone did a lot of the work but did not want his name as first author so they put it last, generally the authorship order is in order of most to least work on the paper and research, so I find that strange and would put it in a similar category to removing yourself from the paper.)

Group leaders often go last, even if they don't take corresponding authorship. Basically lets you know what group the work came out of.

I don't think this answer adds anything not already in other answers besides the side comment about authorship contributions that is wrong for many fields

@R1NaNo Agreed that group leaders often go last, but generally in those cases their direct contribution to the research and paper is minimal, they do not typically do more of the work than the other authors/researchers for the paper as the OP has stated

@Dave I'm not sure what you are getting at. In my area, experimental nanoscience/materials science/chemistry, it would honestly be considered pathetic if a PI put themselves first. The rare case is for PIs at PUIs or just starting out where no group members made significant enough contributions to be considered as having led any aspect of the project.

@R1NaNo my area was MEMS and materials, but in other departments/groups and universities I visited, authorship order has typically been in order of contribution to the research and write up for the paper. Basically the person who has done the most work is the lead author. In my experience heads of departments are generally hands off, they will, propose projects, secure funding, review papers, give direction, but their priorities are running their department, while other individuals carry out the work. If my department head had done most of the research, I would expect them to be lead author.


text:
Recommendations for how to discuss in-meeting communication with my PhD advisor?
I am going into the 5th year of my math PhD. In May, I discussed the idea of taking a 6th year with my advisor -- he supported the idea. To financially support my 6th year, I am preparing an application for a fellowship at my university, and I feel good about my prospects.
Unfortunately, my relationship with my advisor is not healthy (I say some about this in my May post about asking for a 6th year), and I offer some more context below. For now, know that I have decided to discuss with my advisor our mentorship dynamics. I am here to ask for advice about how to navigate the conversation.
I am considering statements in the realm of:

"I want to write a dissertation that I am proud of. I don't think I can achieve this without mathematical guidance and support. I come away from our meetings feeling confused, incapable, and anxious. I'd like to discuss ways of creating more positive outcomes."

"I feel that I have no one else I can discuss our research area with, which makes me feel isolated and limits my broader understanding of the area. Could you start inviting people to the weekly research seminar? I see this as additionally benefiting your younger students ____ and _____."

"When I ask a question about something we have previously discussed, I feel incompetent when I hear 'We've already discussed this' without further explanation. I am asking again because I don't yet fully understand. Could we instead briefly re-discuss as to further my understanding?"

"I feel ignored and irrelevant when I notice regular phone use while I am presenting my progress/thoughts. Could we agree to limit phone use during our meetings?"

"I don't like that we schedule our meetings by text, and I feel that email is a more appropriate medium. Can we communicate by email instead?"

My question: What reactions come up for other academics when reading the above list? Do you think other language/emphases might be more effective? I have considered mentioning some personal medical issues, which have mostly resolved as of this summer, to frame a sort of a "new start" perspective. But reading similar situations, like advisor communicates badly, PhD supervisor issues, and communicating personal problems, I feel unsure that this would help.
For what it's worth, here is some context about my relationship with my advisor:

I actively avoid meeting with my advisor, because I dread the way that our meetings make me feel (incompetent, incapable, confused, frustrated, anxious, depressed).

For what it's worth, I have discussed this at length with a personal therapist and with multiple department ombuds. I feel that I am at capacity for how I, personally, can manage my feelings/needs without a healthier relationship with my advisor.
My advisor and I meet around once a month for 1 hour.

I feel dependent on my advisor right now, because I have relatively few mathematical connections. I attribute this to a combination of:

my advisor doesn't invite speakers to department seminars (so I don't meet people in my research area) and hasn't formally connected me with any faculty outside the department;
I have not yet had a project with decent results, only marginal/modest results (which I feel limits my ability to have more engaged math conversations with folks);
Two of the three faculty members on my qualifying/preliminary exam committee are unavailable for meetings due to other academic obligations (e.g. their own students); and
I hold multiple marginalized identities in math which can make networking complex/challenging.

My advisor has repeatedly encouraged me to spend as little time on teaching responsibilities as I can (i.e. my time commitment should be limited to lecture itself). Frankly, I find such an encouragement unprofessional/inappropriate, especially because I am considering a teaching-oriented academic position long-term (which he knows).

Out of curiosity, what does ‘I hold multiple marginalized identities in math’ mean?

I will be blunt. You know there are issues in your interactions. There will be 'issues' in any interpersonal interactions. Does taking the time, energy, and emotional effort to try and re-engineer the interactions now actually benefit you graduating in one year? When you meet, focus on getting what you need out of the meeting to graduate. The rest is fluff at this point. You want out.

To be honest you may not choose a supervisor that matched you in the first place. You may need a more junior advisor that may be more hand-on, but it seems you find a more senior advisor that provided you more resources. e.g. s/he can support your PhD for one more year. Seems s/he is always busy etc.

My question: What reactions come up for other academics when reading the above list? Do you think other language/emphases might be
more effective?

A lot of your phrasing sounds like you're trying to implement some form of couples therapy onto your advisor, without them ever agreeing to participate in this. Moreover, e.g. the example about "can we agree to limit phone use" when you specifically want them to stop using their phone reads as patronising. Similarly with the email- it sounds like you're verbally dressing up the point that you want your advisor to revise their work patterns based on your feelings.
To use similar language to your questions, my reaction is "stop shopping for milk at the hardware store". Your advisor is not responsible for managing your feelings. It's also not their job to network for you. Thirdly, while I understand the moral point about teaching, most supervisors got to this point in their careers because they focused on research- they may be wrong, but they're trying to look out for you.
Some caveats to what I wrote: I'm not saying that your advisor isn't being rude- they are! - or that this working relationship is fine as is. But I think you should focus on dealing with your feelings & health with actual qualified professionals (like your therapist), and on actual steps to graduation/science with your supervisor.
My reactions and advice on the conversation, more specifically:

Plan some coping strategies for the things you can't change

You aren't going to win the screentime or mode of communication battles with your advisor. But you can turn off notifications from your supervisor (and only actively check their texts during working hours), and you can vent to your friends afterwards about phone use during meetings. My former supervisor was also partially fused to his phone- I would usually stop talking if I noticed him getting distracted by it, and if prompted to continue, say something like "No, that's alright- if you need to get that, just take care of it first" and prepare for whatever I wanted to discuss next in the down time. Perhaps they're "just" being disrespectful, but choosing to view their behaviour as a reflection on them - not your worth as a presenter - and giving them some grace to deal with it, worked for me.  It also sets a boundary (I'm not going to split attention with their phone, the meeting resumes once they've put it down) while considering that they genuinely might have something else urgent going on.

Have that meeting with your supervisor, but focus on actionable steps to graduation

Fundamentally, you want support from them, so try to speak their language. What do they still want you to do to graduate? Could they collaboratively express this with you in some form of Gantt chart, or whatever their preferred method of organisation is? Lean of them for the scientific and academic support they have to give, and go other places (therapy, administrators, your phd-mates) for everything else.
Additionally:
*) If you need to re-discuss something, re-phrase it (I know, cheap trick) and try to get an actionable next step out of the discussion. So if they still shut down your topic, stick to asking them what specifically you should do next to resolve the issue. This (in my opinion) is worth a bit of friction- I'm not expecting your advisor to have all the answers, but something like "Well I don't know, I think Bob worked on something like that in the 80s, you know Florida Bob..." gives you a way to move forwards.
*) Find a specific person you want to invite to seminar, and ask your professor to invite them. Just like you want some specific actionable task, it's easier for your professor to send an email to X colleague than to rethink his stance on networking and seminars. Have an argument for why their work relates to yours/the departments. You could also try taking the initiative and contacting them first to try and start a collaboration (without promising an invite)- if you're lucky and things go well, perhaps they will invite you!
*) You didn't ask for this, but try to take the initiative as much as you can and network. Aside from speakers coming to you via seminar, can you go to them via conferences, summer/winter schools, workshops, secondments or seminar talks of your own? Since you're applying for funding anyway, why not see if you can snag a small travel grant too. Are there people you've met at conferences whom you could email? If you feel that "mediocre" results somehow make you less deserving of this, perhaps some resources on imposter syndrome might be helpful.

Some parting thoughts

You mentioned that you recently had a new start related to resolving some medical issues, which- congratulations! Now that you have this energy, it might be worth channeling it into whatever comes next for you - a teaching position somewhere nice? - instead of trying to make over the past. Even with excellent mentorship, the last year of a PhD is insanely stressful. The thing is, your working relationship - if there continues to be one after your PhD - with your supervisor is going to change a lot when they move from "person holding my entire academic future in their hands" to "eccentric former mentor who texts me 1-2 a year about finishing that paper draft one of these days". This change will give you a natural opportunity to reset your interpersonal relationship if you continue to have one. But trying to force these changes in advance is probably doomed.

Thank you for your thoughtful and -- IMO -- rather insightful response! I am finding this quite helpful.

First your comments:

"I want to write a dissertation that I am proud of. I don't think I can achieve this without mathematical guidance and support. I come away from our meetings feeling confused, incapable, and anxious. I'd like to discuss ways of creating more positive outcomes."

Your advisor is not responsible for your feelings. You need to be specific with what you need in order to feel less confused. You feeling incapable or anxious is a you problem, not an advisor problem unless they are actively hostile. Having incompatible personalities is not hostile. If your advisor cannot provide the basic guidance needed in a way you can work with, then frankly they are not the advisor for you, and you should have gotten out long ago. Trying now to re-engineer your relationship, when you are trying to finish is a bit of a lost cause.

"I feel that I have no one else I can discuss our research area with, which makes me feel isolated and limits my broader understanding of the area. Could you start inviting people to the weekly research seminar? I see this as additionally benefiting your younger students ____ and _____."

Why does your advisor have to do your networking for you. Have you brought up people you would like to have invited? Have you provided solutions rather than just complaints? Also the last line of benefiting other students. This is not your call. You do not speak for anyone other than yourself and you are not the advisor.

"When I ask a question about something we have previously discussed, I feel incompetent when I hear 'We've already discussed this' without further explanation. I am asking again because I don't yet fully understand. Could we instead briefly re-discuss as to further my understanding?"

You should ask for an explanation/elaboration when this is happening, not retrospectively as the person may not even be fully aware that is how they handled it.

"I feel ignored and irrelevant when I notice regular phone use while I am presenting my progress/thoughts. Could we agree to limit phone use during our meetings?"

This is an unfortunate fact of modern life. Faculty are busy and get hit with so many emails throughout the day, they may be checking to keep up. They may be looking something up relevant to what you said to get clarification. They may be using it as a coping mechanism for personal issues, anxieties, etc.. They may simply be unaware they are doing it. They are possibly bored with dealing with you. You don't know, and lecturing your advisor on etiquette seems counterproductive to your ultimate goals. Again your feelings of irrelevance are on you to fix, not your advisor. They are not your romantic partner.

"I don't like that we schedule our meetings by text, and I feel that email is a more appropriate medium. Can we communicate by email instead?"

Again what is your outcome here? You are lecturing your advisor on what you feel is appropriate for running a group? Why didn't you just find another advisor?
Honestly, by reading your comments and the context, you are placing too much power on your advisor and making them responsible for your feelings. Similarly, you are making them responsible for your mediocre progress. Take ownership of your networking and career progress. Clearly you have the wrong advisor for your needs.
Not all inter-personal relationships work, so why should all mentor-mentee relationships work? Half of marriages end in divorce after all.... why is academia immune from the human condition? At this point, just focus on wrapping up and leaving, not on lecturing your advisor on etiquette. Advocate for yourself when needed and seek clarification when appropriate.
As for your final statement about teaching. Yeah, your advisor is right. Largely, nobody on a committee cares about your TA'ing if your PhD is mediocre. Focus on wrapping up your research. A PhD is a research degree... the TA'ing is just a bit of training and a means to fund it, not the main focus. The fact that you allude to them as unprofessional for suggesting something that is sensible just proves you have so much resentment towards this person and you should focus on leaving for yourself, and also for them.

This is, IMO, terrible advice. There are many fair grievances that OP raises (using their phone during research discussion is unprofessional, and so is encouraging students not to do their duty as a TA or not ensuring that OP doesn't feel awful after meetings, etc.). OP is not even complaining about this, but they're asking how to best approach the issues: defending the unprofessional behaviour of the supervisor (out of principle, it seems) is not a good answer.

+1 from me. You're maybe a bit harsh toward the student. But overall, my impression is that OP needs to focus more on mathematical outcomes and less on interpersonal annoyances. Normally I would give OP the benefit of the doubt, but here it sounds like this case has already been brought to multiple ombudsmen and that other faculty are starting to avoid the OP. While some complaints seem legitimate (e.g., "we've already discussed this" is a harsh reply to a technical question), others seem very strange (e.g., text messages being offensive).

@Andrea You mistake me defending the supervisor with providing practical advice. I have been the arbitrator for enough graduate student/advisor conflicts to know an untenable situation when I see one. Both advisors and students have rights and responsibilities. It sounds like the OP in many ways wanted an ideal advisor and got a very mediocre one (why they are mediocre is not up for debate, we don't know enough). Faculty however do have academic freedom and can run their groups as they wish, and face the consequences of their choices - such as student attrition, poor reputation, etc... cont..

@Andrea pt 2. Most of the comments the OP is hung up on are immaterial to them finishing their degree and leaving this broken relationship. It appears there are already arbitrators involved so I assume there are no legitimate issues of abuse but rather difference of opinion/unmet expectations. To your comments, there is a difference between doing ones duties as a TA and overcommitting ones time and resources at the detriment of their main focus. We all do it, today I cleaned my office instead of dealing with reviewer comments or getting my course slides ready for the new semester.

@R1NaNo I appreciate that not all interpersonal issues must be resolved, and OP may be better off focusing on finishing rather than solving these issues now, but your response should have said that, while it came off (IMO) as fairly hostile. For instance, "Why does your advisor have to do your networking for you.": OP may benefit from being more proactivve, but it a supervisor's job to help their student grow their network. Or wrt TA'ing: OP said their supervisor wants them to limit their time to the lectures themself, i.e. no preparation. That is unprofessional, it's not simply wasting time

@R1NaNo thank you for the response. I agree that my advisor is not responsible for my feelings. And, for what it's worth, I tried to find other advisors and was unsuccessful as folks with compatible research already had other students.
I have decided to have this conversation to enable me to focus on finishing. I don't see a way for me to produce an adequate dissertation without research support. I have avoided this conversation for over a year in part because I've received a lot of "focus on math, not interpersonal dynamics" advice. Unfortunately, that hasn't worked... (cont)

... I get relatively little out of our research meetings. When I ask questions, they are often dismissed. When I attempt to clarify what is meant by a suggested research direction, I am chastised for not understanding immediately. When I present on my progress, I notice my advisor is often on his phone. These lead to mis-communications on both ends and -- yes -- hurt feelings on my end. All of these reduce my research productivity and generate inefficiency (which affects both of us). I'd like us to work through sources of inefficiency and reduced productivity precisely so that I can finish.

@xion3582 the last case I was involved with where a student was emotionally impacted by their advisor (seemingly in a case like you describe) - i.e. there was very specific incompatibility between the way the advisor did things and what the student needed to feel good about things (the arbitrators found the advisor did not violate any norms) did not particularly end well for either party. Namely upper administration forced the advisor to placate the student, the student kept pushing because nothing the advisor did made them feel better about things (because again we are ultimately responsible

@xion3582 cont... for our own feelings and responses). In the end it blew up for the student as they were forced out of the group and told to write up the minimum necessary to graduate. They did not get what they wanted, certainly no closure or resolution to the relationship, nor the ability to wrap up their thesis how they wanted. I suggest you focus on what you can control to meet your degree goals... i.e. wrap up and get out. An alternative situation where you are placed (forcefully) with another advisor is not likely to lead you to a degree you are proud of, nor a timely graduation.

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How should I discuss the idea of a 6th year with my PhD advisor?
I am a PhD student in mathematics, finishing up my 4th year. I am meeting with my advisor early next week, and we will discuss my plan for next year (my 5th year).
I see my plan as depending on whether or not I am staying for a 6th year. I would like to plan on a 6th year for now. I am wondering: how should I approach the idea of a 6th year with my advisor?
Why do I want to stay for a 6th year?

Reason 1: The results I have do not feel noteworthy to me. I don't feel confident that I will have something sufficient for a dissertation come August, in part based on brief remarks my advisor has made. I would ideally like to come away from my efforts with a PhD, in part because I am interested in the idea of a university-level, all-teaching position.
Reason 2: I'm a hell of a lot happier now. The pandemic plus some medical problems contributed to some depression, which time and improved health have alleviated substantially. My work has undoubtedly benefited.
Reason 3: I feel that my problem-solving ability is improving, as is my understanding of the context of my research. I'm getting better at knowing when not to pursue an idea.
Reason 4: Even if my advisor were to suggest that an essentially inconsequential result would be adequate for a "pre-teaching-job dissertation", I want more time to try for something better. I would ideally like to come away from my PhD with something I'm proud of.
Reason 5: There is certainly a part of me that wants to ensure an uninterrupted source of income. I do indeed view my PhD as a job. (I'll admit I feel unsure if that's a detrimental way to think.)

I worry that my advisor will shut down the conversation, and defer this decision until later. In this case, I see them as expecting me to devote as much time as I can to my research, only to return to this conversation when it's absolutely too late for me to have any chance at dissertation-ready work by the requisite deadline. (Unfortunately, I don't know when that would be.)
Why do I want to have this conversation now?

Reason 1: I want to know if a 6th year will be an option. I see this knowledge as informing my summer and fall plans. If I can't ensure a 6th year now, I want to spend some time this summer, and a lot of time this fall, exploring/applying for jobs. I have uncertainty around the substance of results I could produce in the next couple months. So I would explore both jobs that require a PhD, as well as jobs for which I only need a masters.
Reason 2: I think that there are concrete things we could both improve on going forward. I have wanted to bring them up for a while, and I'm hoping this conversation provides a natural opportunity.
Reason 3: I have to submit an annual department report which includes a plan for my activities next year. I see my plan as depending on whether or not I know my advisor would support a 6th year.
Reason 4: I have an ongoing project I work on, which is adjacent to the research of another professor at my university. If my advisor were to decline the idea of me taking a 6th year, I would like to discuss with the other professor if there is potential for a dissertation-level result in what I'm thinking about. If so, would they support a 6th year?

What do I think I could improve on?

Thing 1: Continue to grow my confidence in my problem-solving ability, and work on letting that confidence motivate me to keep explore ideas.
Thing 2: More consistently text my advisor to meet (we primarily text to schedule meetings, at their request). Right now, I reach out every 3ish weeks (ranges from 2 to 4). I feel I could be a bit more consisent.
Thing 3: I intend to drop a few of my "service" responsibilities (like helping to organize a grad student conference, and co-organizing a graduate student learning seminar in my research group). Other service responsibilites are extremely important to me, especially because I am interested in keeping the option of a university-level, all-teaching position open to me long-term.

TLDR; I am wanting opinions on: how should I approach a conversation with my PhD advisor about the idea of me taking a 6th year?
EDIT: What follows would be best in a separate post as it turns toward a different question. I am keeping it here for record-keeping only.
The other big question I have right now: should I discuss things that I think my advisor could be doing differently? I would of course approach this with "I" language, not "you" language.

For example, my advisor regularly checks/uses/texts with their phone during our meetings. I have considered discussing this with them: "I often feel unimportant in our meetings because I interpret phone use as a sign of disinterest. I tend to dread our meetings because of how they make me feel." I haven't done this yet because I worry about this creating resentment, and coming across as rude/unprofessional/whiney.
As another example, when I email my advisor questions or (short, < 3 page, in LateX) updates, I almost never receive a response. Then, in our meetings, it usually seems to me that they read my emails only in passing, if at all. On one hand, they are extremely busy and I don't want to take up too much of their time. On the other hand, I often feel I have no one to turn to when I need help. Again, I haven't brought this up because I'm not sure if it's an appropriate subject.

How are you funded, and how is funding generally handled in your department or research group? That's a huge variable in such things. If the department and/or adviser operate funding on the expectation that students take 5 years, a 6th year may not be practical for them (or for other current or prospective students they expect to spend the 6th year of funding on).

Welcome to Academia.SE. Too late for this time, since you already have a very comprehensive answer, but in future please remember that posts should (1) contain a single question (your "other big question" should be in a separate post), and (2) be general enough that others could potentially have the same question in future (i.e., try to "boil down" the wall of text into something more modular). Good luck!

Generally speaking, staying for a sixth year is common during a math PhD. I did so myself. Most advisors would be happier to have you stay an extra year vs. a new first-year PhD student, because of all the training that has already gone into your development. At this point, you can add much more to the research group, analogous to what a postdoc brings. It will not take much effort to convince your advisor, if you already have a good relationship. The question has so many parts, I feel an answer must respond one by one. Nevertheless, let's consider your reasons for wanting to stay.

Reason 1: The results I have do not feel noteworthy to me. I don't feel confident that I will have something sufficient for a dissertation come August, in part based on brief remarks my advisor has made. I would ideally like to come away from my efforts with a PhD, in part because I am interested in the idea of a university-level, all-teaching position.

Whenever you ask for funding, don't lead with the negative. Say "I feel like with one more year, I can prove much better results."

Reason 2: I'm a hell of a lot happier now. The pandemic plus some medical problems contributed to some depression, which time and improved health have alleviated substantially. My work has undoubtedly benefited.

That's great, but probably not necessary to say. Anyway, your advisor will be in charge of making the argument to the department about funding for one extra year.

Reason 3: I feel that my problem-solving ability is improving, as is my understanding of the context of my research. I'm getting better at knowing when not to pursue an idea.

Again, not necessary to say. For sure you are better at all grad student skills than the alternative of a brand new first-year PhD student.

Reason 4: Even if my advisor were to suggest that an essentially inconsequential result would be adequate for a "pre-teaching-job dissertation", I want more time to try for something better. I would ideally like to come away from my PhD with something I'm proud of.

Your advisor will probably argue to the department that you need an extra year, due to the pandemic disruption. And that's fine. But I'd give your advisor the impression that, along with finishing your PhD, you could start some new and exciting research, too.

Reason 5: There is certainly a part of me that wants to ensure an uninterrupted source of income. I do indeed view my PhD as a job. (I'll admit I feel unsure if that's a detrimental way to think.)

It's better to embrace an abundance mindset if possible. There are lots of jobs. Surely you'll get one. Most pay better than being a grad student. If you choose to stay for a sixth year, it's because of all the exciting ideas and the chance to work them out with your advisor, who you already know and have a good relationship with.

I worry that my advisor will shut down the conversation, and defer this decision until later. In this case, I see them as expecting me to devote as much time as I can to my research, only to return to this conversation when it's absolutely too late for me to have any chance at dissertation-ready work by the requisite deadline. (Unfortunately, I don't know when that would be.)

Generally speaking, it's best to bring it up early, so your advisor has more time to make the argument to the department, and certainly before it's time to start accepting new students for what will be your sixth year. Try to have more confidence in yourself and what you bring. On to "why do I want to have this conversation now?"

Reason 1: I want to know if a 6th year will be an option. I see this knowledge as informing my summer and fall plans. If I can't ensure a 6th year now, I want to spend some time this summer, and a lot of time this fall, exploring/applying for jobs. I have uncertainty around the substance of results I could produce in the next couple months. So I would explore both jobs that require a PhD, as well as jobs for which I only need a masters.

Yes, clearly you need this info. If a sixth year is not an option you need to gear up for the job market.

Reason 2: I think that there are concrete things we could both improve on going forward. I have wanted to bring them up for a while, and I'm hoping this conversation provides a natural opportunity.

This is vague. I'd just focus on the exciting new research and not interpersonal dynamics.

Reason 3: I have to submit an annual department report which includes a plan for my activities next year. I see my plan as depending on whether or not I know my advisor would support a 6th year.

Again, good you are bringing this up early.

Reason 4: I have an ongoing project I work on, which is adjacent to the research of another professor at my university. If my advisor were to decline the idea of me taking a 6th year, I would like to discuss with the other professor if there is potential for a dissertation-level result in what I'm thinking about. If so, would they support a 6th year?

No, probably not. Once you have enough for a PhD, the expectation is that you will finish and make room for the next cohort. A postdoc might be possible (and might pay more) but it's rather uncommon to get a postdoc at the same place you got your PhD. Best to let your advisor argue to the department that a 6th year is necessary in your case. On to "What do I think I could improve on?"

Thing 1: Continue to grow my confidence in my problem-solving ability, and work on letting that confidence motivate me to keep explore ideas.

Give the impression that you already have strong problem-solving abilities. But yes, do try to increase your confidence, before this conversation and before the job market.

Thing 2: More consistently text my advisor to meet (we primarily text to schedule meetings, at their request). Right now, I reach out every 3ish weeks (ranges from 2 to 4). I feel I could be a bit more consisent.

Yeah, I think meeting more often would be good. I met my advisor once per week, and we made steady progress. You want your advisor to want you to still be around for that sixth year.

Thing 3: I intend to drop a few of my "service" responsibilities (like helping to organize a grad student conference, and co-organizing a graduate student learning seminar in my research group). Other service responsibilites are extremely important to me, especially because I am interested in keeping the option of a university-level, all-teaching position open to me long-term.

Be careful here because you want a teaching job long-term. The service might help. Your advisor can tell you.

The other big question I have right now: should I discuss things that I think my advisor could be doing differently? I would of course approach this with "I" language, not "you" language.

No, I would not do that. By now you know your advisor well. You either want a sixth year or you don't. This is not the time to try to change their behavior. If you don't like it, just graduate at the end of the fifth year.

For example, my advisor regularly checks/uses/texts with their phone during our meetings. I have considered discussing this with them: "I often feel unimportant in our meetings because I interpret phone use as a sign of disinterest. I tend to dread our meetings because of how they make me feel." I haven't done this yet because I worry about this creating resentment, and coming across as rude/unprofessional/whiney.

I think this might come off as whiney in the context of a meeting where you are asking for funding for a sixth year. Instead, maybe try to come to the point faster. The question was insanely long. If meetings are the same, it's kinda natural for one's attention to wander. It is a good skill to be able to get to the point fast.

As another example, when I email my advisor questions or (short, < 3 page, in LateX) updates, I almost never receive a response. Then, in our meetings, it usually seems to me that they read my emails only in passing, if at all. On one hand, they are extremely busy and I don't want to take up too much of his time. On the other hand, I often feel I have no one to turn to when I need help. Again, I haven't brought this up because I'm not sure if it's an appropriate subject.

Three pages is not short, especially if you are dancing around the point or "organizing your thoughts" like in the very long question. Your advisor's time is valuable. I advise you to first organize your thoughts (perhaps in the form of an email you don't send) then write a short, direct, to-the-point message that will be less likely to overwhelm your advisor with a giant wall of text. This is a valuable skill that will help you long term.

Thank you for this extremely thorough and thoughtful response! In particular, the focus on research excitement rather than interpersonal dynamics.

Finish up and leave in your fifth year. No one cares about what happened during the PhD, and if you're not making groundbreaking research, your dissertation will go onto a dusty shelf that will only be read by family and maybe the committee. Pull your boots up, start applying for jobs, get a job, go to your advisor, and say you are defending this semester (or the next if it's past deadlines to submit your dissertation), and get out. It's been four years, and if you are just now getting progress, then what is an additional year or two going to do? Nothing. Just get out. You'll be much happier.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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How badly does failing a core class and retaking it hurt your chances at grad school programs?
I'm sorry if this is in the wrong place.
I'm an undergraduate majoring in biology. I think, this semester, I'll fail a class on Statistics (the class is titled "Statistics for Life Sciences"). While I have the option this semester to use "Satisfactory/Unsatisfactory" and protect my GPA, this is nonetheless a failure that will show up on my transcript.
I know I messed up and I feel really bad... I could have taken an introductory Math class (an option available to those with only an AS Level in Mathematics) before taking this Statistics class and I stupidly chose not to (officially, an AS Level meets the prerequisite for this Statistics class, though most students taking it have a full A Level in Mathematics). But this is no excuse (it's officially allowed, and plenty of AS Math students succeed in this class) and I think in fact reflects worse on my judgement.  :(
I fully intend to retake this course (I can't not take it anyway; it's a core class, plus Statistics is important in Biology) and do much better in it.
How badly does this hurt my chances at a graduate school program in biology? Assuming my other biology-related classes are okay (A grades). I don't know how I'm going to explain it. I was hoping to take a research Master's, then a PhD. Am I screwed?
Thanks for any input and and have a nice day.

Biology students who have trouble with statistics are extremely common.  Retake it and devote a lot of time to it.

These systems are complicated and certainly are not fully meritocratic. Working our way through "meritocratic" systems can take several paths.

At any stage in your career, people who will evaluate whether to give you an opportunity will (or at least should) be looking at multiple aspects of your CV. For each "weak" aspect there should be a "strong" aspect that offsets it. Provided this is true, you should become eligible for consideration. After that, it is often a matter of luck and the competitive nature of the opportunity.
Having said, that, there are places and systems which I personally know of that will automatically reject applications that have a single blemish. These places and systems are making a mistake (in my opinion). In any case, perhaps you would not want to be in a place that does not believe in giving people a second chance.
In summary, I think there are a number of good places which would give you the opportunity if you can counter this particular failure by something---which could even be a good grade in the same course on your second attempt.

It's not about deciding to give people chances; it's about selecting the best applicants from a pool.


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Is it unethical for a supervisor to delay feedback on papers?
We are in a moderate sized group (approx. 10 PhD and 4 postdocs) with a single professor as everyone's supervisor, who is well respected in our field. In our field it is normal that the supervisor is co author on all papers unless it was an external side project / collaboration and so the majority of papers coming out the group require his final say.
The issue we have is the length of time to get feedback and hence publish, as an example there are several group members waiting on feedback of papers for over 1 year. A particular issue is he constantly breaks his self imposed deadlines, he will say he will give feedback by Friday,then Wednesday, then Friday  etc for months at a time. Recently he has taken to playing us off against each other, he says he'll read A's after he's done B's but when A asks B, B has heard nothing. From the group's point of view he is more interested in taking more students / new projects and the delays we experience are his choice.
This is hitting tipping point in our group, there is a lot of discontent and everyone is talking to each other so it's a downward spiral about who has it worse each week, PhD students are missing getting their theses handed in and postdocs are saying the delays are significantly affecting thier career prospects. One recently said if their academic career is over and they have no need for a reference they'll report him for misconduct on their way out.
To clarify this is a top 5 UK institution.
Sorry for the lengthy background, my questions are:
1 Is it considered misconduct / unethical to delay publications through such long delays to feedback?
2 What are the techniques to encourage feedback in a timely manner?

Perhaps speak to him, and suggest a better working model.   I know of a top researcher who has the following model: he/she gets post-docs to first provide feedback, and he only needs to look at almost final draft from PhD students.  He/she mainly deals with post-docs.

My diagnosis is that he is overworked. The solution would be to drop half of you and send you to other advisors. I doubt that he is just lazy if he is "well respected" in the field. I doubt that this is an uncommon situation at high level universities with top advisors and active students.
It isn't unethical if he is being diligent even if he is "late" in giving you feedback. There are only so many hours in the day and he is entitled to a life.
I see two possibilities for moving forward.
The first is to seek feedback among yourselves. You have a dozen people who are at least somewhat familiar with your work. You may not be able to get final approval but if you all put less pressure on the prof he may be able to respond in a more timely manner.
The second is to only ask his advice/permission on vital things and then only by extracting the essential in what you need advice/permission on. If you send one page requests rather than 30 page current versions of a paper it is easier on everyone.
One technique I used with students for review of subsequent versions of work was to have them also send the earlier version as well as highlight changes in the latest. It can be very easy to provide feedback. I used paper, so no paging or technology beyond a pen was needed for feedback.
So, work more among yourselves and reduce the load on the prof.
Complaining isn't going to get you anywhere.

I also suggest you look at student outcomes after graduation. Do his students wind up with a career? The market is harsh now, of course, but if his students get placed as well or better than can be otherwise expected, then it might be worth the short term pain.

I use the same technique, it works wonders for speeding up reviewing.

It would be "unethical" (in the sense of not meeting legitimate expectations) for a supervisor to accept more PhD students than she/he can handle. Not being able to communicate honestly about what students/collaborators can expect when is also unprofessional.

@Wetenschaap hence the subjunctive. Then again, OP says the supervisor "constantly" misses giving promised feedback, which suggests whatever keeps getting in the way at this point can hardly be "unexpected" anymore. I think 10 PhD students is a lot, by the way.

@henning, and others, don't forget the phenomenon of death by a thousand cuts. Ten students may just be too many but lots of small things might have intervened to get to that situation.

Advice 1 is in action (we have a few group members per paper and all contribute and iterate actively). Advice 2 will be our next attempt, we try somewhat (please only comment on section X) but this is often ignored as they prefer to restart from intro each time. I will try the extracting method and send / print only the necessary pages. Their successful students are from early career when they were cosupervisor so them having more students has (potentially) reduced our chance of success in academia.

This sounds like my previous lab. It is an unfortunate situation. Unethical, in my opinion, to take on that many students in the first place, but as others above have said, their behaviour is more of a matter of burnout rather than malice.
When I was a PhD student in this situation, things that helped me get the most out of my PI were:

Giving PI bite-sized chunks to review instead of larger tasks;
Being specific and concise about what you want feedback on. Have a request email read like a Buzzfeed article rather than a novel. Make it easy for them.
Being a bit bold and saying "I think this is the way to address X. If I don't hear from you by next Friday, I'll assume you agree and will do that method going forward...". It is small effort for them to stop you from going off-course, and if you take this pro-active approach, it is less work for them.
Being verbally grateful for the help I did receive. Understandably, many students were very frustrated with their lack of feedback, and were underwhelmed with the level of feedback even when it was received. This attitude can encourage a positive feedback loop where both parties are frustrated.

Hope this helps. Good luck.

Misconduct implies a deliberate action. I don't think that is likely; what would he have to gain? Instead, it sounds like he has too much to do. That is no fun for you, but also no fun for him. So he does not have to be the enemy. Solving this issue would make work more enjoyable for all. This is obviously a very delicate discussion: not many bosses would react well to subordinates telling them how to do their work. This is not necessarily a good thing, but it is the way the world works.


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"Awaiting Reviewer Invitation" after "Acceptance with Minor Revision"
I have submitted an article (media and communication studies) to a ScholarOne journal. The paper was accepted with minor revision (two reviewers both recommended 'minor revision'). I revised the paper accordingly and addressed the feedbacks. After submitting the revised article for a week, a ADM was assigned and the status has changed to "awaiting reviewer invitation." Does it mean that my paper will go through another round of review with new reviewers? I was told that for paper with "minor revision," it is likely like it will not be sent back to the reviewers. Has anyone experienced similar situation?

It is completely normal for papers with minor revisions to go through more than one round of revisions. If the editors deem ir necessary and the reviewers that volunteered for the first round of the review are unavailable, they might need to invite new ones.

Does it mean your paper will go through another round of review? Not necessarily. It depends on whether the editor invites new reviewers. "Awaiting reviewer invitation" should strictly be a very brief status, since the time between the editor deciding to invite reviewers and the editor actually inviting reviewers should be very brief, on the order of a few minutes. The fact that you are apparently seeing this status for more than a brief moment indicates that the journal is using it as a substitute for "Editor assigned".
You can think about the timeline as so:

Your paper is resubmitted. Status shows "Revision submitted to journal".
Either the desk editor (i.e. the employee of the publisher assigned to the journal) or the editor-in-chief assigns an editorial board member to handle the paper. Here the status could show "Editor assigned", or it could show "awaiting reviewer invitation".
The editorial board member could make a decision now, or they could go ahead and invite reviewers. It depends on how substantial the changes requested are, and whether the editor is able to check it himself.

I don't know what "awaiting reviewer invitation" means.
But usually, the paper with minor revision will be sent directly back to the same reviewers for the final decision. They need to check whether you revise according to their reviews.


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"Awaiting Reviewer Scores"after "Minor Revision"
I have submitted an article (media and communication studies) to a ScholarOne journal. The paper was accepted with minor revision (two reviewers both recommended 'minor revision'). I revised the paper accordingly and addressed the feedbacks. After submitting the revised article for a week, a ADM was assigned and the status has changed to "awaiting reviewer invitation." This status has not been changed for a month. Now, the status has changed to "Awaiting Reviewer Scores." Does it really mean that my paper will go through another round of review with new reviewers? I was told that for paper with "minor revision," it is likely like it will not be sent back to the reviewers. Has anyone experienced similar situation?
I have posted before and received answers saying that "Awaiting Reviewer Invitation" can mean "With Editor." But since the status is now "Awaiting Reviewer Scores", does it mean that my paper has been sent for another around of review?
Thank you!

Whether or not a paper has to go through another round of reviews is up to the discretion of the editor. "Minor revision" and "major revision" are gradual, not categorical distinctions and have no guaranteed bearing on how the next round of revision must be treated.


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Where Should I Publish My Artificial Intelligence Paper?
I've been working on an AI project in the past two years. And I found some interesting things that I think might be useful for humanity and can enrich the current status of AI.
So, I wrote a paper, made it open source so that others could benefit from it. And I knew some people that submitted their AI papers on arXiv, so I tried to do the same but my paper got rejected.
I'd like to know where do people usually submit their AI paper. I need a popular platform with good audience; I want my paper to be heard. I obvious can't use arXiv and at this point I don't even like to submit my paper there because they don't understand the value of a paper.
(I've heard about viXra, but I think I can do better than that.)

Unforuntately, if you've gotten rejected from arxiv it means that you will also surely get rejected from any reasonable publication

@Taw so should I just stop?

Welcome to Academia SE. As it stands, there are several issues with your question. Please [edit] it if you can: 1) The only question is in the title and that’s a shopping question. 2) Your academic background/situation is unclear. Are you affiliated with an academic institution? 3) What do you roughly know about academic publishing in general, i.e., where do we need to start explaining?

Would you please provide the reason why your paper was rejected by arXiv?

There are several things that I'd like to add in order to be able to help you in understanding what you're actually asking.
In accordance with your question: I'd like to know where do people usually submit their AI paper.
This is perhaps the authors' preference and needs a background check of the widely available avenues and journals in the area of artificial intelligence. This strongly depends on authors' understanding of the magnitude of their work which is perhaps why it is important to understand where you stand in your research timeline (Independent Researcher, Affiliated to a Research based Company or an academic institution)
Second thing, I'd like to point out what I understood is that you're actually new to research and thereby willing to put your idea out, due to your understanding of it being valuable to the community. It is because, if you had some prior research experience or were slightly aware of several subtleties of research process, you'd know that arXiv is a public repository/ a preprint server where early drafts of research ideas are submitted, so that the ideas are put out for public scrutiny and early access to other researchers in the field, (which in your case was the ideal choice since you want your ideas to be heard).
There may be several reasons why your paper was rejected from arXiv:

Poor writing style with a lot of typos and grammatical mistakes
High percentage of plagiarism, etc

With reference to this: they don't understand the value of a paper:
Try submitting your paper to a journal in your area but with certain considerations prior to submission of your work.

Check whether you've added relevant related literature to help the reviewers understand why your results are valuable
Take any journal specific style and format your paper accordingly.
Make sure to check the plagiarism of the paper from any good plag software like turnitin etc
Proofread your paper and improve it (because arXiv has very minimalistic requirements for a paper to be accepted than any peer-reviewed journal, like @Taw said, if it is rejected from arXiv its highly unlikely that it will be accepted in any journal at all.)
Also make sure you check that your references are not messy.

You can also put it out on Elsevier's SSRN (with possible needed modifications to the paper obviously).


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Re-did my experiment, how to properly mention it?
After doing and evaluating my experiment/model, I decided to redo it (changed some small things based on the results of that experiment), because I believe that this new way would give me even more insight into what I am studying.
How do I properly report this in a thesis? Specifically, where do I mention the description of the second experiment that was done?
The structure of my master thesis is this:
...
4. Experimental procedure
5. Results
6. Discussion
7. Conclusion
Currently I have the original experiment/method in the 'Experiment' section, but I am struggling to find a good place to mention the second/improved experiment/method.
Any suggestions are much appreciated

This is something to discuss with your advisor, but I can make a suggestion.
Some research that is based on constructed models turns out to be questionable if the model lacks stability and resiliency (robustness). There is a branch of science/math called catastrophe theory in which small changes to a system can produce dramatic, non-continuous, results. One way to guarantee that this is not the case is to tweak the model in small ways and determine if the outputs are also similarly small. If not, the model is too sensitive and may not give usable results.
So, what you have done, can be considered a validity check on your model and can be presented as such in a separate section. You have gained some evidence that the model is stable in some dimension. This could come after section 4 and before section 7, depending on how you want to write it up.
But your advisor's advice would be valuable.

Thanks. I have already emailed my advisor, but havent recieved a reply yet, so I thought I would ask here in the meantime. Im still struggling to figure out the best place/section to mention the repeated experiment. Im leaning towards just putting it in the results section, after mentioning the results of the first experiment, and then just mentioning what changes I made, followed by the results of the second experiment.