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Why can't we just use platforms such as arXiv for proper peer-reviewed publishing?
Many of you will know that, whether per subscription fees or via open access models, there is a ridiculously absurd amount of money flowing to many big (or medium-size) publishers for getting our research outputs (i.e. papers, etc.) published in high-quality venues in the field.
The problem: Content and peer reviews (I think, the most important artifacts from a scientific point of view) are delivered largely for free and voluntarily.  In some fields, such as math, physics, CS, EE, and related, even proper camera-ready type setting (e.g. via LaTeX) is also very often done by the researchers themselves.  Moreover, in fact, the downstream (i.e. after-acceptance) editorial process in traditional publishing companies is nowadays (for a number of reasons I don't want to elaborate on here) more likely to introduce faults through the various conversions and process stages that are involved. I'm speaking not only of my own experience but have even seen publications that have been corrected using post-prints, personal copies of authors, etc.
So, my question again: Can't we just extend well-known and widely-used archival platforms such as arXiv, biorXiv, zenodo.org, etc. with a light-weight infrastructure to perform peer review (e.g. via an integration with EasyChair or the like and building up editorial teams) and transfer the whole peer review life-cycle from established publishers (with over the years questionably evolved business models) to such platforms?  A tiny fraction of the (mostly tax payers') money currently flowing to such publishers would be invested in running the mentioned infrastructure.  My naive assumption is that no relevant quality loss (if not even a gain in quality) is to be expected in certain fields of science after an appropriate ramp-up phase.
The only relevant issue, I can see for now, is the issue of a lacking reputation or trustworthiness of such a platform as a publishing venue where, I suppose, it will be a matter of time for this issue to be overcome.
One of the reasons why I am asking is because I think that the mentioned amounts of money can be better invested in science for the public than it is now. A question (totally obvious to me) that I've pondered over for a long time but was afraid to ask.  Thanks for your thoughts on these, I apologise, probably too progressive and naive ideas. Fortunately, similar concerns are shared elsewhere.
In response to some of the comments: Archival has very little to do with publishing. This question is about modern peer-reviewed publishing. Please, also note that with this question I very much value professional editorial work and am looking for solutions in support of EiCs, editorial committees, and reviewers. By no means is this question to be understood in any way as a critique of any of the work done by EiCs, editorial committees, and peer reviewers, not at all. If so then it was definitely not my intention.

That doesn't seem so different from OA journals. A related question might then be why we haven't all moved to OA journals and/or whether OA journals have indeed contributed to resolving the problems you mention.

Right. So, if you mean by OA journals the journals of big publishers with e.g. gold OA option or OA journals (e.g. registered on DOAJ), both strategies often charging significant APCs, then I'd say, problems have not really been solved well. I suppose, arXiv + peer-review should still be much cheaper after a quick ballpark figure.

There is a lot of administrative work associated with peer review for a large journal.  It's one thing to be program chair for a large conference once (or once every several years).  It's another thing to handle 10 times that volume every year on an ongoing basis.  It really is a situation requiring a paid staff person.

@Alexander: Absolutely, there needs to be staff to handle some administrative tasks and possibly an EiC will need to be paid. But, I suppose, a full-time paid post or two per journal are well within the range of costs we are talking about here.

"Can't we just ... ?" Yes, and people do it.

@cheersmate: Awesome! That's exactly what I was looking for. Brilliant.

"even proper camera-ready type setting (e.g. via LaTeX) is also very often done by the researchers themselves." This is common in math, physics (?) CS and related fields. Over all of "science" it's not "very often." The vast majority of academics do not know how to use LaTeX.

The entire editorial process might not be as cheap as you think. As an example, see the financial overview of PLOS, a non-profit running several reputable journals. Their APCs are easily €/$/£2000, yet they don't seem to be drowning in money.

@TooTea I suspect they spend a lot on stuff that an arXiv overlay journal just wouldn't need. The ballpark of actual costs I've heard is more in the £200 range.

@Azor Ahai -him-: I don't think we are discussing "all academics" here, just those in STEM fields.  If there are a few who don't understand LaTeX, they can learn.  It's probably far easier (IMHO) that whatever they're using now.  And if they don't want to bother, they can hire an undergraduate RA to transcribe their quill pen originals :-)

@jamesqf There's a trend on this site that people assume everyone knows LaTeX because this site's demography is fed by SO, Math.SE, etc. I can assure you, even if you take "in STEM fields" (and not the humanities, who have the same problem, so idk why we're excluding them) the vast majority do not know LaTeX and haven't heard of it. I love LaTeX, but I come from a programming-ish background. It is not easier than using Word ... If the field doesn't use LaTeX, where are they going to get URAs who know it?

People suggest LaTeX all the time, but frankly, even though I like it, I don't want to spend all my time formatting my articles instead of analyzing and doing research. The answer to "Why don't we have scientists typeset their own articles?" is "Most scientists don't know any typesetting software."

This is all distinct from the main thrust of the question, which my comments aren't addressing, to be clear.

@Azor Ahai -him-: You need to consider what I said in context.  While I know very little of humanities publishing, open access seems much less of a thing there.  And if people writing papers don't know typesetting software, then just what the heck are they using to write?  Quill pens, as I jokingly suggested?  Typewriters?  Even fer gawdsakes Microsoft Word?

I was voting to close but my vote closed the question entirely, so I retracted the close vote. I think this question is a duplicate, or at least closely related to, Why are journals used in modern scientific academic research?

-1 because this question keeps getting asked by people who think papers are really interesting and they should be paid more to write, edit, and review them even though the average paper is read by no more than 10 people. If anyone thinks they can do it better, try setting up an arXiv overlay journal and maintain it till it becomes self-sustaining. Don't point at the arXiv overlay journals that already exist; that's like pointing at Messi and saying it's easy to earn £500,000/week playing soccer. Set up your own journal.

@Allure: I do not think the question you pointed to is a duplicate. Moreover, archival of preprints or other artifacts should definitely not be mistaken with peer-reviewed publishing. Just using arXiv is by far not enough. I'm suggesting something different, please, reread the question. Also, I do indeed think papers are really interesting, but we need to create an environment where this principle is supported and not violated. If, as you refer to, they are only read by 10 people on avg., why do tax payers then accept such APCs/costs for getting them published?

@Mario Who are these "tax payers" to which you keep referring? I would hazard that the total number of "tax payers" who are not academics who know about this is as close to zero as to be equivalent.

@CGCampbell: E.g., in the German system, universities (and most libraries even outside unis) are to a very large extent funded by tax payers' money, which I think is a very good thing in general. Hence, I'm referring to those people, most of them, as you correctly point out, will have no clue whatsoever about how much of their money is wasted in APCs and subscription fees due to obsoleted publishing business models. I'm also such a tax payer myself.

@jamesqf Ah, tone is hard to read over text. I didn't realize the whole comment was a joke, I just thought the last sentence was.

@Azor Ahai -him-: No, the whole comment was not a joke.  It was quite serious: even if people wanting to publish papers don't know LaTeX, it is simple to learn enough to do most formatting.  At the most basic, you just include your on-line journal's format package.

@jamesqf In that case, I have nothing further to add to the points I already made

@Mario If, as you refer to, they are only read by 10 people on avg., why do tax payers then accept such APCs/costs for getting them published? I feel like you already know the answer to your question. Let's word it differently. If a funding agency were to ask you "why should we fund your work when it's read by only 10 people", what do you say?

@Allure: Right, there are a number of justified questions to be asked, no doubt. I am happy to avoid wasting my funding/time for voluntary reviews and pay from this very funding to publish my own work. But coming back to my question here, whether a paper is read, cited, published, etc. does in a specific field often say little about it's relevance or irrelevance. Overall, I have the feeling that many of us agree on the need and usefulness of the proposed change, and even better, that such a change will be easier to implement than expected.

Your comment illustrates exactly why I downvoted - it is what on the Politics.SE would be considered a "push question" that isn't actually meant to ask a question but rather to advance a particular viewpoint. Also, if you really believe that "many of us agree on the need and usefulness of the proposed change", and that it "will be easier to implement than expected", as I wrote above - set up your own journal.

@Allure: I have led/organised several events and PCs in my field, currently I don't see myself in a position to create a journal from nothing, as a nobody. Unlike programming SEs following the Q&Solution pattern, I've misunderstood Academia.SE as a platform to share thoughts and opinions. I do definitely not intend to advance a particular view but pinpoint an arguably severe problem of our academic systems, mea culpa, from the narrow CS perspective. Suggestions to move this discussion to elsewhere are appreciated. If you think, my question is worth being deleted from SE, please, go ahead.

@Allure: My conjecture is that the reasons for a reputable EiC/journal committee to stick with a traditional publisher (under nowadays conditions and contexts) are IMHO rather artificial. That conjecture can be well interpreted as my (maybe unjustified) view or it can turn out that this observation of a few people here is actually a quite general one. And that the discussed change/solution might be against others' interests is totally clear.

@Mario read your comments again - you've said you're a nobody, but you also know better than reputable EiC/journal committees, and the reason your model hasn't been widely adopted is because it goes against unnamed others' interests. Your two comments come across as so rude that I will not comment further. I'll only repeat what I wrote above: if you think you can do it better, try setting up an arXiv overlay journal and maintain it till it becomes self-sustaining.

@Allure: I've neither meant to be rude, and I think I wasn't, nor did I mean to say that I know anything better than EiCs/journal committees. But I do have an informed opinion from soon two decades of experience that I feel should be expressed in form of a question. I'm sincerely sorry if that opinion differs from yours. But I felt it worthwhile asking my question and hoping for a solution to a real problem that, I know for damn sure, many academics in my field seem to experience in very much the same way I am experiencing it. Thank you for your suggestion of starting a journal.

I work at a non-profit that publishes research performed on behalf of utilities, foundations, municipalities, etc. We are one of many, such as the Rocky Mountain Institute, Natural Resources Defense Council, etc. We don't use a formal peer-review process, and being outside of academia would not be considered by typical journals unless we're partnering with academics. I wonder if there could be an avenue through arXiv to get our work reviewed and published? Adding this whole body of research could create demand that would attract others who are interested in this work.

@LShaver The arXiv itself is only for storing/disseminating the preprints, in a limited range of subjects (https://arxiv.org/category_taxonomy). But I think the question of what steps you'd need to take to turn what you have into an academic journal might be a very interesting one. Please post it!

There are Diamond open access journals (which are free to both author and reader) run as arXiv overlay journals. An example in my area is Logical Methods in Computer Science, which is generally well-regarded in the field (and indexed whereever it needs to be).
Besides the already existing journals, there also seem to be plans for additional journals of this type to better cover the various disciplines. However, founding a new journal takes a lot of effort from a team of respected (and thus very busy) academics. Early on, it will not be on all indices and thus less attractive to the unfortunate amongst us whose administrations force these issues. Taking an established journal away from a publisher to move to this framework is, even where possible, a radical act and usually pure inertia will stand in its way.
Nevertheless, my sentiment is that Diamond open access (with arXiv providing the long-term storage) is the way to go; and I believe that this is a rather popular perspective.
Despite being lightweight, an arXiv overlay journal still has some monetary costs. They seem to be enough to be an issue, but also to pale in comparison to journal subscriptions or open access charges by commercial publishers. My best guess why institutions/governments aren't more eager to support them is that traditional publishers have a lot of lobbying power, while arguing pro-Diamond open access is more of a hobby.

Thanks, Arno. Very good points, I haven't been aware of Diamond OA. So, there is also EPTCS (http://info.eptcs.org/), which is well integrated with arXiv for peer-reviewed workshops and conferences run e.g. using EasyChair. EPTCS would indeed also follow that model while not being a journal, though. But your example and mine seem to be among the currently still very few exceptions. There are costs, indeed, but the question is how many orders of magnitude less ;)

Another example: https://scipost.org/

Another example: The Open Journal of Astrophysics.

How do these "journals" effectively reject poor submissions? Would this not create a conflict of interest in some cases if the decision is done by the same people who submit their own stuff to the journal?

@And You seem to be under some kind of misapprehension. There is no reason for scare quotes here. The refereeing process works in exactly the same way as any other journal. Whether or not a journal accepts submissions by editors has nothing to do with whether it is Diamond OA/arXiv overlay/published by a society/published by a commercial publisher/printed/online only/etc.

There are overlay journals, there could also be overlay platforms. Example of a defunct experiment: the Selected Papers Network: https://gowers.wordpress.com/2013/06/16/the-selected-papers-network/

It is not at all clear that prepublication peer review adds value to the process. Perhaps it mainly serves as an entry barrier without which journal publishing would not be profitable. This is what the open access model suggests.

If you restrict attention to areas like pure math, where papers are  mainly text with equations, then Arvix overlay journals can work really well.  However, different areas of science have needs that are not so compatible with the Arxiv.  Of course, other preprint servers might work.
One problem is with supplemental files.  Consider the supplemental videos and how they appear one this webpage of the Proceedings of the National Academy of Science.  Nice descriptions, links to forms for copyright permission.  Now consider the supplemental videos in this preprint of the arxiv.  All you get is a title.
Images on the arxiv are another issue.  A few of my papers I did not post on the arxiv as the images do not compress well and I did not want to fiddle with creating low-resolution images just to get the figures small enough for the arxiv.  (The size limits used to be smaller.)
Recently the Arxiv has added the "papers with code" feature, but this mostly assumes hosting the code elsewhere.
I think the needs of journals are too diverse to count on overlay journals to cover too much of math and science.

Recently (actually, apparently it was a little over a year ago) arXiv increased the default size limit to 50 MB, so having too large images (or too many) should be much rarer than it used to be.

@Anyon  Good to know about the increase.  Thanks.

@TerryLoring Absolutely, arXiv would need a bunch of further features, such as support for supplemental material (videos, code, data) and further meta-data. I like https://zenodo.org in this regard. And the possibility to add comments/post-pub peer reviews. I like https://pubpeer.org in that regard. Overall, I don't think that the required implementation of such features in arXiv would be a showstopper for the suggested change/solutions. arXiv seems to be on its way to widen its applicability for Diamond OA journals and the like.

In a software as a service world, one could organise peer reviews via EasyChair, forward papers to arXiv (like eptcs.org), upload supplemental materials to zenodo.org, code to bitbucket, and allow post-publication discussions on pubpeer. And arXiv or someone else could provide an interface that collects and distributes the data. Funding for such a project should be acquirable.


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Start a research project with a student in my class
I am a postdoc. One of the students in the class I am teaching has reached out about getting involved in research. I would be happy to work with them on a project. Are any ethical issues with this given that they are currently in my class?
Obviously, PhD students frequently take classes with their advisor, but I wonder if this is entirely analogous given that a PhD is fundamentally different from undergrad.
Edit: It seems some answers/comments bring up the distinction between me being a postdoc/professor. I'd be interested in expanding the discussion to include both, including potential differences between the situations.

I don't see a conflict here, though others may differ. The student isn't offering you something of value in return for special consideration in the course.
Undergraduate students wanting to do any sort of research with a faculty member will likely find themselves in such a position. Likewise any faculty wishing to guide student research. The concerns are separable.
But, to be extra safe, discuss this with someone who supervises you, perhaps the department head. You don't have a lot of independent authority as a postdoc so ask someone who does. You might even want to have someone with a permanent position to "look over your shoulder" in grading decisions. I doubt it is necessary, but might be useful.

There are likely ways to formalize a relationship. I suggest asking if such a student can sign up for an independent study or research assistant position under you. It's generally best to make sure a student's time provides them (formally) the CV elements they are likely looking for in graduate school & job applications.

Taking on students must provide some benefit to their mentor, otherwise nobody would advise students. For instance, students provide labor towards the research projects they are working on, and these projects benefit the mentor.

First, thumbs up for worrying about ethics.
One thing I can think is, does your position as instructor mean that the student doing research with you might be perceived as unfair? That is, could anybody (the student, other students, profs, etc.) believe that doing research with this student might influence the mark you gave the student? Up or down. Not sure if that is even a reasonable concern.
Another thing I can think is, since you are a post-doc, can you arrange that any research the student does with you gets credit with the university? That is, this would be something unofficial. So the student is not going to get course credit or credit for "extra work" or anything like that. If the student believes they will get some kind of extra credit, they could be misled into expending more time than is reasonable.
First make sure you understand the context in this regard. And then make sure the student understands it.
Also, make sure the student understands that you are a post-doc, not a prof. So, for example, a letter of reference from you carries the corresponding (probably smaller relative to a prof) weight.
Agree in advance if you will try to publish, assuming something interesting results. Agree in advance who will get their name on any journal article that gets published. And if it's a case where it isn't alphabetical, what order the names.
As another answer has suggested, chat with somebody who is already doing supervisory tasks.

I have seen lots of UG students doing research work with a professor they're taking a  class with.
There's nothing inherently wrong with it.

The question is about a student working with a postdoc, not with a professor.

Is this a distinction which matters? I had assume most of the potential ethical issues would be regarding power-imbalances which are present regardless of whether I am a postdoc or professor.

That "lots of people do it" is not a very convincing justification for something being ethical. I can think of plenty of examples of widespread practices in academia which I would call unethical.

I was in both situations (as a student doing work for/with a PhD candidate (an older guy who was working in the dept for eons and who wanted to finally get his PhD) and then I had a student volunteer to do similar work for/with me.
In both cases, the exam was waived with a top mark (thus no ethical issues over marking unfairly) with the rationale that this work requires way more preparation and knowledge than the course brings. It was OK'eyed by the Dean (but it was a formality)

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Choice of I vs we in job applications and grants
In mathematics, it is standard to use "we" instead of "I", even in single author papers.
Is this the case for job and grant applications as well?
For instance, suppose I wish to say something to the effect of:

To study (problem), I will extend (technique) from my past work [citation].

Here are several considerations, although I'm sure there are many more:

I want to emphasize that I am the one driving the proposed work forward. Using "we" in place of "I" emphasizes this less. On the other hand, I do intend to collaborate with others on this work.
The past work is not mine alone, even if I was the "main" contributor (whatever that means). I could omit "my" entirely, but the fact that (technique) is something I've worked on before is important in justifying why I am suited to study (problem), and I don't think people will necessarily take the time to read the reference entry. I could also be more explicit and say something like "past collaborations", but this comes at the cost of wordiness.

TLDR: Is there a convention for pronoun use in job applications and grants? Are there any resources which discuss best practices for writing choices like this in job and grant applications?

I don't know how universal this is, but I have generally observed people using "I" in job applications, and "the PI" in grant applications, in place of the "we" that is used in papers.

In math usually there is no PI.

@quarague NSF, the primary funding source for math in the US, does refer to the lead person on a grant as the PI.

In general using "I"  in job and grant applications is perfectly fine.
For grant applications one possible alternative is to introduce an acronym or short name for your project (this often mandatory for EU grant proposals). Many instances of "I will do this/I will do that", can then be replaced by "PROJECT will do this/ PROJECT will do that". Besides getting around the sometimes awkward use of "I", this also helps emphasize that funding the project is essential to get these things done.
(The use of "I" on the other hand can help emphasize that you are a crucial ingredient in bring the proposed work to a success.)

This is just my personal taste, but I think using the acronyms will look somewhat ridiculous in a non-European context, especially if you really mean things you will do yourself and not as part of a team.  The only context I've every seen these used is ERC grants.

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Ethics of asking student vaccination status
I work at a large public university in Washington state. Until recently, many buildings on campus have been closed, masks have been required, etc. Campus is now opening up, and vaccination is required for students and employees unless they have medical, religions, or philosophical reasons for not getting vaccinated. Anyone who does not vaccinate is supposed to wear masks, but vaccination status is self reported by checking some boxes (no actual proof).
We have just received the following guidance:

Vaccination attestation information is private and confidential.

Instructors may not ask their students about their vaccination status, nor will they have access to students’ records or be expected to verify students’ vaccination status. Instructors may broadly inform students that individuals who are not fully vaccinated need to wear face coverings in the classroom.

It seems unreasonable to rely on the higher powers to somehow enforce what seems to be an essentially unenforceable mask mandate for unvaccinated people. I understand that asking questions about why someone has not been vaccinated, etc. may constitute harassment as it may force people to disclose information such as medical issues, etc. However, that does not preclude asking vaccination status as a yes/no question.
What are the ethical considerations surrounding this mandate? In the absence of such a mandate, is asking student vaccination status unethical? In the presence of such a mandate, what are potential consequences for doing so?

Are instructors permitted to require masks, possibly with exemptions if  the student provides proof of vax status? What if the instructor is immunocompromised or otherwise high-risk?

This has nothing to do with Academia.  The same question would apply in any nonacademic organization.

@AnonymousPhysicist Strongly disagree. Students are different than other members of the general public and may be protected by laws that don't apply anywhere else. Additionally, public universities in particular are branches of government and what they can do may differ from what private companies can do.

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It is usually, but not always, unethical for an employee to unilaterally decide that a policy of their institution — by any account, a policy reached after considerable debate and consideration — doesn’t apply to them and go against that policy; and it is particularly so when going against the policy means forcing or pressuring students who are subject to your authority to disclose private medical information.
Instructors have a right to a safe workplace, yes. Students have a right to privacy, and to bodily autonomy. And yet, people tend to get overly dogmatic about their rights and forget that rights are not absolute. “I have a right to X” almost never means “I have a right to X under any possible circumstances, even when my right to X will violate someone else’s right to Y”. So, both students and instructors have to give up something: in the case you are describing, the students will have to get vaccinated unless they qualify for an exemption, and disclose their vaccination status to the institution. The instructors will have to trust that the vaccination policy the institution put in place will be enough to ensure their workplace safety, and resist the urge to use their authority to compel students to disclose information they might feel entitled to. There is nothing unusual or ethically problematic about such compromises, it is exactly how ethics works in other contexts, and conceptually similar to lots of other situations we encounter in other areas of our lives in which the rights of two groups of people are in conflict and compromises need to be made.
In the end, any policy an institution chooses is going to offend some group of people. As long as the decisions were reached in a thoughtful and reasonable way and following applicable laws, the offended people don’t have much of a leg to stand on, legally or ethically.

Thanks for the response, I think it does a good job of explaining this situation. I do disagree with the generality of your first sentence though- there are plenty of situations where the morally correct choice is in direct conflict  with an employer's policy.

@overfullhbox good point, edited to clarify.

The conflict isn't remotely symmetric. Voluntarily unvaccinated people put everyone else at risk, even beyond the university. Moreover, the risk to others by refusing to get vaccinated is many orders of magnitude worse than the risk to the individual by requiring them to give up some "bodily autonomy."

@ElizabethHenning I never said it’s symmetric. But it’s a fact that there are two groups of people and both are being asked to give up something they might care about strongly (yes, “bodily autonomy” is actually a thing despite you putting it in quotes). Maybe one of them is more reasonable in caring about it than the other, but the vaccination mandate itself is not really what this question is about, so I don’t see a need to discuss it here. OP was asking simply about the issue of reporting vaccination status and instructors being assured that all unvaccinated students are wearing masks.

Despite its popularity in some circles, the "bodily autonomy" framing is misleading because it doesn't apply in matters of public health. It's deceptive rhetoric that gets used to both-sides this issue, not unlike "skeptic."

@ElizabethHenning: I'm not so sure about the orders of magnitude and the asymmetry: As first approximation, AFAIK, an average unvaccinated 60yo  instructor infected with SARS-CoV2 has roughly the same risk of dying of Covid as they'd have without this infection of dying within 1 year. Said instructor can reduce their Covid risk by an order of magnitude by getting vaccinated themselves, and gain at least another order of magnitude by reducing the probabiliy of being infected by properly wearing an FFP mask and enforcing fresh air policies and distance rules to be followed. It is thus in...

the power of the instuctor to lower their own additional risk due to Covid to single digit percentage of their general life risk - without even a single student vaccinated or wearing a mask. As for the unvaccinated student, I don't see how we can attribute to them more than R_0 (which is AFAIK around 5 for the currently prevailing variant where I am) * percentage of vaccinated and/or recovered new infections, even without any NPIs being involved...

@ElizabethHenning sure, I see where you’re coming from. If I understand correctly you’re basically saying the phrase has some legitimate uses but has been politicized/appropriated by crazies and therefore one should avoid using it. Yeah, seems reasonable…

Over here the standing committee on vaccination says the scientific evidence is not yet sufficiently in favor of the vaccination for < 16 yo without risk factors to recommend vaccination. It is reccommended for the student age group, but IMHO (here my opinion/judgment starts) they are sufficiently close to where their personal risk : benefit ratio isn't that clear that it would be unethical to pressure them towards vaccination. In survey data I've seen for the US 3/4 of those with college education were inclined towards vaccination. Taking all this together, I don't see sufficient reason for

... asking students to reveal health data to all their instructors: the established processes to deal with senitive data such as health data are IMHO clearly sufficient. I.e., I'd be fine with asking them to provide a medical attestation saying "no mask" without giving reasons - just like we deal with any other medical issue.

It is exactly because it is deemed unethical to inquire about a persons vaccination status (or any other health related issue), my institution did not make a difference between vaccinated and unvaccinated persons and is still requiring everyone to wear a wask (at least for now until the general vaccination numbers are higher).
I don't know if this an option in your case, but maybe you could just ask everyone to wear a mask BECAUSE you cannot and should not ask people if they are vaccinated or not.

I wouldn’t assume that an instructor has authority to compel a student to wear a mask when that student is already in compliance with the school’s mask policy. If the instructor is not authorized to make such a request, I’m pretty sure this advice will lead to all kinds of unnecessary conflict and ultimately won’t do anyone any good, least of all the instructor.

I was a graduate student and am now an employee in a medical school/clinical department at a public university in the US. Even though I have no contact with patients, it is required for me to be up-to-date on certain vaccines, in particular the annual flu vaccine. There is currently no such mandate for the COVID-19 vaccines, but this may change once those vaccines get full approval rather than approval emergency use. Employment status, including as a graduate student, is a bit different than student status legally, I believe, but that's not the important thing I wanted to mention:
Enforcement of this requirement has never been up to individual professors or supervisors. Some people may qualify for waivers to not get the annual flu vaccine, but there is a system and process for managing those waivers that goes through HR and the university's health service. That health service is bound by all sorts of additional laws like HIPAA (which may or may not apply to others like professors). None of this is an instructor's job, shouldn't be, and doesn't need to be.
I'm not sure what the best ways are to manage this information. So far my institution has used a hybrid approach, treating student housing residents a bit more strictly than the general student population (the argument being that you don't need to live in a dorm if those requirements are too onerous on you), asking for voluntary disclosure, and asking for compliance with the rules. They had a phone app for building access during the Spring semester that gave a "green light" for people allowed to enter buildings, but no one seeing that information knew the reason for the green light (or red, for that matter): it could be due to vaccination status, a recent test, or some other decision to exempt an individual. I think all these steps are reasonable compromises between personal health privacy and public health safety, but none of them rely on the discretion of instructors.
If you have concerns about how your university is handling these sorts of things, take it up with the health officials at your university. Don't try to implement any special policy in your own classrooms. Going against these policies could result in severe sanctions against you including loss of your position, especially in the case that anything you do brings legal risks or costs to your department or institution.

I'm not disputing your advice about compliance with policy, but the choice of policy is very heavily influenced by state-level politics rather than concern about community safety. So the covid vaccine is a little special.

@ElizabethHenning I'm sure the specific pressures vary by locale, and yes of course there is a political aspect here. However, that doesn't change whether individual professors should make their own policies. Surely they can do what they feel necessary on an individual level to protect themselves, and they can lobby their university and local government, it's just not advisable to put themselves in the middle of a political fight, especially if it's going to put them on shaky legal grounds.

There is no need here for the instructor to violate their students' privacy.

It seems unreasonable to rely on the higher powers to somehow enforce what seems to be an essentially unenforceable mask mandate for unvaccinated people.

Why do you think the situation should be different than from any other health-data related situation?
Where I am, if a student claims they're sick/disabled/..., it's not the instructor who judges the student's health status and what the appropriate measures are. This judgment is done by a medical professional (or possibly the disability office) who then writes an attestation saying what accomodation is appropriate, but never why.
Exemptions from mask requirements can be handled in the same way without unduly compromising privacy. Whether such an exemption is because they are vaccinated, because they already had the infection or even because some medical condition that means they should be exempted even if they are not immune is none of the instructor's business.
In addition, if your school doesn't offer any privacy rights compliant way for you to check, ask the respective office to send someone who is qualified to see that health data to check whether your students comply. This is their proper business.
But do not yourself violate your students' right to have their health data treated appropriately.

Would you hesitate to give first aid to a student because you don't know their hepatitis vaccination status?

Vaccination against coronavirus is spreading in many countries, and in the United States, a "train" with vaccines literally flies across all states, because the head of the White House, Joe Biden, promised to vaccinate 70% of the population by July 4. Nevertheless, some voluntarily continue to refuse doses of the vaccine. Some wondered why the issue of vaccination could be a problem, while others felt that it should remain a personal matter for everyone, and should not put pressure on their friends.
I think it's okay to ask this. You have the right to ask if your colleagues are vaccinated for example. They have the right not to answer, but then it is reasonable to assume that they are not vaccinated. The guys at my job who are vaccinated are happy to announce this. I believe that silent people are unvaccinated. Time will tell since vaccinations have to be confirmed in order to work.

I'm sorry, but the first paragraph is irrelevant, and the second is opinion without argument.

(-1)  I see a whole lot of a difference between asking a colleague (with whom you are on the same level of power) all kinds of questions and asking someone who is under your power questions whose answer belongs into a specially protected kind of data, such as health data.

Wouldn't a train that flies be a plane?


text:
What can I do if a grant proposal was rejected by a reviewer making false claims and using straw men?
Being an experienced reviewer, I know that rejection can be frustrating, but also fruitful and a good learning experience. There are many kinds of reviews (good, bad, constructive, opinionated, short, missing the points, etc.) and as many kinds of responses (revision, rebuttal, abandonment, etc.). My question focuses on a specific case, a bit different from those considered here previously.
I received a notification about a grant proposal (I'd prefer not to say which agency I submitted to), already being evaluated as a fundable or excellent one, and quite critical to my career (really a lot of stuff depends on it, and one can see this from my CV). One review was plain positive (no criticism at all), and one was grossly negative. The two reviews had almost diametrically opposed conclusions. (There were only two!)
My problem: The negative review made several false claims (the evidence was easy to pinpoint) and put up a range of straw men (rather generic rejection arguments pinpointing irrelevant or inappropriate details). For example, they criticized the oldest of my papers I had cited and used this as evidence that I was insufficiently experienced in this field, but they overlooked the next seven papers I had also published in the same field (some in prestigious journals).
At this point, I suspect the reviewer was not knowledgeable of the topic or even had a certain conflicts of interest. In either case, they IMHO should have declined the review request.
However, the evaluation committee explained that they had to particularly take into account the negative review to inform their decision (without giving a reason), and interestingly, added further negative criticism.
What can I do about this notification? Should I contact the funding agency, write a rebuttal with the details, and request a third review and a revision? Should I think about legal action because there might be gross negligence or reputational damage at play? I don’t have any idea, because talking to funding agencies is like trying to fly to Mars. Re-submission, even if possible, will take another year because it will be treated like a new application. It is, at least, unclear whether there are other options.

Can you resubmit?

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.

Contacting the program manager
You can, and probably should, contact the program manager at the funding agency to point out the flaws in the negative review. This is an easy action to take, with little downside that I can see, other than the effort you would spend and the possible disappointment if it doesn't produce the outcome you want.
If you do contact the program manager, I recommend:

Focusing on factually false statements the reviewer made. Matters of fact are objectively verifiable, and a conscientious program manager would likely regard errors of fact as one of the only reasonable grounds for overruling a reviewer and soliciting a new review.

Do not waste your time disputing subjective matters. If the reviewer makes a subjective objection not based on a factual error that you perceive as a straw man attack or as misguided for some reason, I don't think you stand a chance of getting the proposal's rejection reconsidered based on such a flaw, however frustrating it might be for you. Subjective disagreements are too common, everyone who gets rejected thinks the subjective criticism against them is misguided, and at the end of the day, the standard response to someone objecting to such criticism is that, well, if the reviewer didn't understand what you were proposing then that means you just didn't explain it well enough — try harder next time.

If you can get your proposal and the review looked at by some colleagues with a good reputation, who agree with your views that the review contains falsehoods, and those colleagues are willing to write a letter supporting your objections (about factual matters!) and have you attach it to your letter of rebuttal, I think that might be helpful. It isn't guaranteed to help, but it won't hurt. If you do this, be sure to state clearly any conflicts of interest that those colleagues have which might influence their opinion (for example, that they are your collaborators or work in the same department as you).

The idea of filing a lawsuit
I can't say if this idea makes sense or not. Neither can anyone else here who isn't a lawyer (let alone a lawyer in your particular jurisdiction, which you haven't specified). Please don't listen to some of the nonsense I see in the comments, written by people with no legal expertise, about what constitutes defamation, gross negligence etc. If you want to know whether a lawsuit stands a chance of success, consult a lawyer.
On the academia side of things, I think it's true that a lawsuit will likely have effects on your reputation and affect the way you are looked at by some of your colleagues. On the other hand, the funding agency may also have reasons to fear for its own reputation from a lawsuit (or the threat of one, or even the threat of you going public with the incompetence being shown in the evaluation you got), so this argument cuts both ways. So, I don't think you've given us enough information to completely rule out the idea of a lawsuit.
That being said, I think you should consider whether your position that the reviewer and other people who played a role in your proposal's rejection are sabotaging your career (and should be held accountable for that, including using the legal system if needed) is really that reasonable. The funding agency has no responsibility to help you with your career. It is offering grants and has a process for evaluating proposals asking for funding, which you have voluntarily agreed to take part of. If your career is so dependent on a single grant that it will be irreparably harmed by this rejection, I think there's a strong argument to be made that this is the fault of your employer and the flawed system they have for evaluating academics. Or possibly — I hope this is not the case, but can't rule it out — it's your own fault for reaching a vulnerable stage of your career with a track record that is still kind of marginal and that necessitates a 100% success rate to keep your career going. (To be clear, I'm not saying this to be mean or to criticize you, but simply showing you what possible objections can be raised to the logic of your arguments. If I don't raise these arguments now, it's quite likely someone else will raise them later, so it's better for you to be prepared.)
Anyway, I'm sorry about your grant rejection. Good luck trying to get this situation fixed!

Thanks, Dan. This is a great answer! I totally support your comments and point of view. I am self-reflective enough to agree with the fallibility of my own argument. It was very helpful to raise this question here at SX to balance my view with the result that I still have the feeling that I'm on the right way with not accepting everything happening here in the academic world. Cheers.

Shouldn't one address straw men? Regardless of whether they're acting in bad faith or whether you just phrased it poorly, clarifying your intended meaning should eliminate the criticism in any case, and make for a stronger proposal. If it were me, I'd want to know about clear misunderstandings that influenced the decision (especially if given other reasons to distrust the reviewer). Although it may make sense to address these separately as an addendum, since a reviewer making objectively false statements is much more severe than them interpreting what you say differently from how you meant it.

I think this is implied in this answer but was discussed in the comments. If you decide to go with a lawsuit it should be against the funding agency, not against the anonymous reviewer. Even if the reviewer had a major conflict of interest, showed bad faith or similar it is still the responsibility of the funding agency, they screwed up by using an unsuitable reviewer. The funding agency separately may have an argument with the reviewer but that is none of your concern.

When contacting, remember that the PM is not against you necessarily, so you are not against him. You are actually not trying to get the rejection reversed as such. You are trying to get a decision (even if it is rejection) for the right reasons. You are doing this in order to preserve the integrity of the review process. If the PM understands that you are being constructive, the response is likely to be more constructive as well. Even if the end result is “no change”, there will have been something positive about the whole exercise.

"get your proposal and the review looked at by some colleagues with a good reputation" Do this first, maybe you are wrong or the case is not so clear.

Thanks. I have had 5 established senior academics (all professors) look at the proposal and included their feedback. Also, 6 other anonymous reviewers stated that this is a very good to excellent proposal. The last one stated that this is a definitely fundable proposal. It underwent at least four revisions with lots of literature review and technical improvements. How much more could I possibly do?

@Mario no need to explain, it's completely possible you have been doing more than anyone can reasonably ask for. Unfortunately it's also possible that that would not be enough to get the decision reversed. The world is full of injustices both small and large. I sympathize with your situation, but I think in terms of useful advice that we can offer, there isn't much more that can be said. Good luck!

You can of course contact the program manager, but in all of my experience, not very much will come out of it.
I don't know whether you have been part of funding panels in the part and so have experienced the dynamics of people debating proposals. What often happens in cases such as yours is that the two reviewers of the proposal present their cases for whether they think the proposal should or should not be funded. If there are opposing opinions, the panel has to come to some kind of conclusion of what to recommend, and others often jump in to read all or parts of the proposal with an eye towards the specific points of criticism. They may not have the time or inclination to write a full review of the proposal, but they will be able to participate in the discussion and, in your case, they appear to have thought that the negative review needed to be given some weight, and the discussion found other points to critique as well that then ended up in the panel summary.
Program managers are typically reluctant to substitute their own opinion for that of the panel (for good reasons). As a consequence, it may be useful to the program manager to know if a reviewer was completely off topic, if only to know that they shouldn't invite that person again as a reviewer. But I would suspect that your chances of getting another shot with this proposal are rather slim.
Because this is so, my perspective on these things is to not dwell too much on the reviewer's failings -- because that is something I cannot change, and dwelling on things I cannot change do not help me move through life. Rather, I try to assume that it was my own fault that the reviewer did not get what I was trying to say, and use that as an opportunity to question how I presented what I wrote, and how I can improve in the future. In other words, I use these occasions as learning opportunities.

Thanks, Wolfgang, for this immediate, very helpful response. I agree with your assessment, except for where false claims come into play. A false claim is not an opinion, reviewers can be sued for making false claims. My case is perhaps a little more intricate, I suppose. But you are right, I don't expect changes. The thing is, that reject will have  likely destroyed my career for IMHO no good reason. 6 other reviewers had evaluated that proposal already for being very good to excellent. There was nothing to improve. So, I do have quite a portion of motivation to do something about that.

Wolfgang, also, I'm unsure whether a scheme relying on only two reviews and too much panel discussion for proposals is a good process. For example, big EU and UKRI schemes do rely on 4-6 reviewers. Good journals are usually using 4-5 reviews to eradicate opinion from the game. Lately, I was a reviewer for a paper that got 6 reviews.

You can of course also complain about the reviewing system, but that too is unlikely going to change the program manager's decision.

As for false claims: What you're saying is that the reviewer made claims in bad faith, (rather than based on an inattentive reading of the proposal, or ignorance) and that the whole panel and the program manager went along with it. That's a strong claim, as is the claim that you believe the proposal could not possibly have been improved. Having seen more than a hundred proposals in my life, and hundreds of reviews, I will say that I have a hard time believing either.

Indeed, that's what I meant by "trying to get to Mars" :) I'm, however, by far not the first to recognize that proposal decision making is much closer to a lottery than what we would expect. The VW Foundation, e.g., has changed their main scheme to replace part of the panel discussion by a raffle.

Wolfgang, both claims are strong, absolutely. Evidence for the false claims are straightforward. No worries, I can provide that easily. But, yes, every proposal can be improved, so can mine, of course. But, I would go as far as saying that that proposal was good enough for getting funded there, just from taking together what (actually 7) other reviewers said. I'm not as experienced as you are, no doubt. Hence, I'm taking your opinion quite serious.

@Mario IANAL, but what grounds would you sue someone on? Breach of contract? I see no contract. Libel/defamation? You'd have to prove they did it deliberately to harm you, and that the panel members were all in on it - almost impossible to do. You can't sue people just because their actions harmed you, they must have broken some legally enforceable duty to you. The real unfairness here is that your career rides on this single proposal, because, as you said, whether a proposal is funded or not is pretty much a lottery.

Ian, I don't really know. Perhaps I wouldn't at all or, naively thought from my 1 1/2 decades as a reviewer, try to go for gross negligence. It is more like a single funding scheme that is most valued in job applications in my country and, importantly, accessible for senior postdocs. You can't just apply for anything as a senior postdoc or non-prof. Sometimes, you can't avoid single points of failure, it seems.

@Mario The thing is, gross negligence with regards what? Being negligent isn't an offence in and of itself. It's gross negligence leading to another offence. This reviewer isn't employed by the funding body (unless other fields are way better funded than my own), so no gross negligence can lead to them being fired. Defamation is a non-starter. Reviews by their nature are opinions, not stated as fact. You cannot be sued for giving your opinion on someone's work. Lastly, suppose you won. What happens to peer review then?

Just to continue the defamation vs opinions thread: If I write that "A's work is garbage and should never be funded, and this proposal is a waste of electrons," that is not defamatory. I am clearly giving my opinion. If I add, "also, I know that A does a tonne of hardcore drugs and also steals from his work", then it's defamatory. The former has to be an opinion, as someone's work cannot be terrible as a matter of immutable fact. The latter is a factual claim, is refutable, and is actionable.

Thx, David. The point is, the review report also contains the latter ...

I'm sorry this is happening to you. Unfortunately, you have no realistic recourse. If this is truly destructive of your career, the best use of your time is to figure out what you are going to do next in a different career. The race doesn't always go to the swift, the battle to the strong, nor the academic career to the most qualified.
I'm not saying you should accept the bad reviewer's behavior. But my experience is that your acceptance doesn't matter. Academia doesn't correct its mistakes for individuals. Even if it comes out next year that this reviewer has an email chain saying "I don't like Mario and I'm super dumb, so I'm going to shoot his proposal down," the best you will get is an opportunity to apply again. At that point the money will have been already distributed to the other applicants. In my experience, the best use of you time is to move on, unfortunately. Whatever that means for you.
I hope that you overestimate the negative effects this will have for your career.

As others have said, there is not much you can do against a dishonest reviewer, if they already have support of the grant panel. Consider resubmitting your idea to another funding agency if you can.
One thing though -- time may be of essence. Your reviewers may have left those unjustified comments because they misunderstood your work or did not make a proper effort to understand it. But it could also be that they actually understood the ideas, and purposefully decided to shoot it down, to delay your progress and to exploit the ideas themselves. Keep an eye for similar ideas to appear in preprints, grant applications, etc. Try to protect your ideas by publishing them at least as preprints, but under your name, before your reviewers publish them under theirs.

Thx. I'm very much hoping that what you describe (and what I've actually heard many times through the grapevine and could never really believe) won't come true.

I don't see the following relevant point being raised in either the question or the answers: the program probably has its rules and regulations regarding appeals (of course without details it's impossible to say).
These may be vague, and not very helpful to you. Harsh reality is that the peer-review process does not encourage second-guessing the peers reviewing a rejected proposal, as it's assuming their expertise. This is only mildly annoying with publications (just submit elsewhere) but less so when, say, applying for a grant from a national institution is virtually the only career route you can take, and a time-limited one at that (e.g., several European countries have such institutions and competitions for young scientists - and without a particular grant at this early stage, it can be challenging to pursue an academic career later on). In my particular country (details omitted as well), the appeal may only be raised against a formal failure in the due process, not against a disagreement with reviewers. The reviewers are bound to academic honesty by the grant authority, but it can be tricky to show that they were negligent, and that their rejection is not their honest expert opinion. And, frankly, I admit that when being a rejected party myself in the past, my judgement might have been sometimes clouded. But for what is worth, I sympathize with the dread of missing something you see as crucial for your career.
However, I do know people who successfully appealed such decisions. This is more about a yearly grant proposal cycles, not a one-off call for grants. The agencies I am aware of, all publish information about awarded grants, including success rate of appeals. This is not something on the top of their web pages, but this information is often available. If your particular grant proposal is a recurring one, this info can give you the overall feeling, whether an appeal is worth your time. You may also want to try to contact people that were successful with their appeals, but that depends on your networks (see below).
I personally appealed a rejection once, having a strong feeling that a reviewer was biased and not honest (personal favorite - the main objection was that the research I planned in that grant was not published yet). The appeal was overturned, as the reviews were deemed within bounds of an expert opinion (the publication thing - should I publish this research earlier, I would score more points for my academic achievements, therefore the reviewer was right to hold that against me). On the other hand, a colleague of mine was able to conclusively show that their reviewer did not read the whole proposal (raising points that were explicitly addressed beyond abstract and such), and their appeal was upheld.
I emphasize that I was able to acquaint myself with my colleague's case by sheer coincidence, as I would not contact a total stranger that went through with an appeal to ask them about that. So I'd advise to talk to your colleagues, who will know more about the context of your grant proposal - and perhaps know someone that can be more helpful in your specific case.
Finally, I strongly second @Dan Romik in that if you contemplate legal action, talk to a lawyer, better yet, one that has specific experience with academia in your country.

Thx, lemon314, for your insightful answer. I'm aware that I am not the only one having this problem. Yet, there are variants that may need more drastic action, perhaps not necessarily legal ones, but definitely an informed and well-argued appeal to the PM.

Aside from contacting the appropriate portfolio manager, as described in a previous (excellent!) answer, another action you can take is to examine the roster of reviewers, and if you're aware of any real conflicts in the reviewer pool, let the program officer know.
Note that being very expert in the area is not a conflict.
If a conflict is identified, then that would probably mean that particular reviewer would be disqualified from reviewing a resubmission.  If the program manager knows for a fact that a person you deem to be in conflict trashed your application, there may be fixes available to them -- maybe even a re-review.
Keep in mind that you will likely not find out who reviewed your grant.  Also, it may be the case that a person you think is in conflict may even have been your biggest proponent during the review process.  My impression from being on Study Section is that reviewers tend to get very provincial about their subfields, and like to see money ending up in the area, even if that money doesn't go to them. (Note that this is clearly not a desirable approach for a reviewer to have!  I'm just letting you know that I've seen people I think may have been behaving in that way)
Of course, the go-to option is a resubmission addressing the reviewer's points.  Be diplomatic, but if you don't believe the points are valid, and believe you can convince a study section that you're right, then give it a go.
Lastly, while the situation comes up over and over again, having important parts of your career success hanging on the outcome of one grant is a very stressful situation (though, to some extent, this is simply the unpleasant nature of the beast).  Many departments have informal or formal faculty mentorship arrangements that can really help investigators fine-tune their approaches to grantsmanship.  If such a program exists for you, by all means, ping this situation off of a mentor.


text:
Do associate editors or editors in chief get any monetary compensation, and to what extent?
I'm aware that academic editorial work is to a good extent a voluntary service to the community. Peer reviewing, to my knowledge, is always a voluntary service, for a whole number of good reasons, e.g. to remain independent and impartial, or to avoid scientific misconduct. Anyway, because of the different task profile and responsibilities of editors in chief (EiCs), associate editors, guest editors, and other academic editorial staffs, I wonder about types of journals, which pay these roles for their services? I'm aware that some less known/traditional/established publishers pay parts of their academic editorial staffs. (I am not referring to paid full-time employees of publishers, such as management staffs and members of production teams.) I also wonder how much in terms of a full-time equivalent salary that would typically be? Ranges or percentages by country, discipline, or even publisher would already shed light on this.

It's important to distinguish between full-time employees of the publisher that handle the details of typesetting and publishing manuscripts and the academics who manage the peer-review process.  For the academics who manage the peer-review process and make publication decisions, some are paid but many are not.

I've never been editor-in-chief but have/had a number of Associate Editor roles. I am not and have never been paid, however occasionally the publishers send me vouchers that allow me to buy books at discounted price - this isn't worth much as I'd still have to pay something and chances are all kinds of people get such vouchers - and I think I got some two books for free. We're talking about several journals over many years (statistics).

@BrianBorchers Thx, I've modified my answer to better accommodate that distinction.

I'll focus on the editor-in-chief because the role of the associate editor is journal-dependent.
Not every journal pays the editor-in-chief, but many do. It's generalizing, but if the journal is making solid profits then there's a good chance the editor-in-chief is paid. An order of magnitude estimate is about $10k/year.
That also explains why editorial board members are typically not paid - splitting the budget of $10k/year among all members of a typical editorial board would mean each member gets a pittance.

If only as a means of retention, many journals will pay editors-in-chiefs a small sum for the trouble.

To the best of my knowledge, only the very largest and prestigious journals (say, Science, Nature, JMA, NEJM, etc.) have editors-in-chief that are salaried. For sure, in mathematics and computational science (my fields), none are paid -- although we are paid by our universities and the work we do for the job of associate editor or editor-in-chief is simply part of our work responsibilities, which do include after all that we do service to our community. In other words, one could argue that our universities pay us for the job of editor.
In most departments, being an editor or editor-in-chief is highly regarded and counts quite positively towards annual evaluations. That is, it is considered part of the usual workload, not an additional task one takes on outside the departmental expectations.

Following your final paragraph, I conclude that editors are, in fact, paid, but by their home institutions, not by the journal. A quarter time release from other duties for a senior academic is something more than chump-change.

Unfortunately, there are many universities that simply do not have the financial ability to give release time for faculty taking on editorial duties.  At many other universities, this reassignment of duties is purely nominal - faculty are expected to teach as many classes, do as much research, and serve on just as many committees as before they became editor, even if now 15% of their time is now technically devoted to being editor.  It may count positively in evaluations, but since there are no raises and one is already a full professor, that means nothing.

This answer by the way (correctly) implies that (public) universities subsidise private publishers big time.

@AlexanderWoo In many places it is not so much release from standard duties. Rather there is time for "research and other stuff" and this is part of it, meaning that with an editor role you can score some points that otherwise would have to come from publications, grants, conference organisation, public engagement, whatnot.

@AlexanderWoo I think that criticism can be applied to pretty much every activity under the "service" banner, save perhaps some of the most intensive university administrative service that are full positions themselves. You don't get breaks in your expected teaching or research because you've done outreach at a local high school or community festival, or because you've served on an additional committee.

@AlexanderWoo is right. I have been an associate editor for ~15 years and an EiC for 3+ years now. At both universities where I worked during that time, I got no release from other duties, but my department heads during that time also never gave me additional/unnecessary committee assignments as is often done for colleagues whose service is otherwise "thin". They did understand and appreciate the job I was doing.

At least where I have been working, there were pay raises (most years), and I am certain that taking on service roles that exceeded the expectation of whatever position I was in in any given year played a role in me now having a very comfortable salary.

I'm downvoting because I'm aware of several (much) smaller journals that also pay their editor-in-chiefs.

@Allure I hear you.  Not that much, but still non-zero pay.


text:
Bad experiences with the production of an accepted manuscript
The long and erroneous publishing process after a recently accepted  (Open Access) paper has led me to ask this question. I'll explain its context briefly.
We submitted a journal paper (a LaTeX manuscript including supplemental material) which after, in my domain (Computer Science) somewhat reasonable, 7 to 8 months time got accepted subject to minor revision. The journal has a very good reputation, the reviewers unanimously liked the manuscript and gave very helpful and detailed feedback. I handed in the revision not quite a month later. About 4 months from then I got the final acceptance notification. Although I felt already that took quite long, what followed seems like an Odyssey to me: after more than two months I got the first online proof which had numerous (100s of) typos, type setting and conversion errors introduced, tables wrongly formatted, cross-references lost, etc. I had to invest considerable time to point out all the errors, and after several more weeks (about two months in the meanwhile) and two proof revisions, I'm still stuck with waiting for another iteration of the proof. The editorial office has politely and helpfully handled the corrections with the production team, however, my requests/concerns also got a bit lost in translation. Overall, we are about to reach 9 months after acceptance with minor corrections and, after a couple of emails with the editorial office, I have no idea how long it will still take to at least see something like an official online-first version, not talking of the journal issue the article will possibly be included.
I believe that journal's procedure seems inappropriate inasmuch as I opted for full Open Access according to the funding policies and my Uni accepted (by a default waiver for that publisher) to pay a decent amount of article processing charges (I believe from their library budget). This inappropriateness stems from the long production time and that the conversion of the LaTeX manuscript caused so many further issues and required several proof iterations. Maybe strange, but again, I would have expected a more accurate production process than for a non-OA publication. But OA might not play a role here.
Just for comparison: a year earlier, we had a non-OA article accepted with minor for another (even higher ranked) journal where it took them about six weeks from this acceptance to complete publication, no typos introduced, and those six weeks even included our time to submit the minor revisions.
That whole thing made me wonder what expectations one ought to have on the paid portion of work done in the production process, other than reviewing and editing which in the majority of cases is purely voluntary in my field? How could one improve this situation? E.g. would a notification of my Uni (maybe our library) be exaggerated, so they can consider blocking future APC waivers for that journal/publisher?
I believe my concerns go beyond this interesting question about long review processes.

Please ask only one question.  Also, what do you want to achieve?

Thanks, reduced the number of questions. I just want to know whether I expect too much, and if not, what can I and others do?

It doesn't matter whether you paid an APC or whether the publisher is getting money from subscribers for seeing your article.
There are journals that have very significant production backlogs, so that accepted papers are not produced for months or even years.  A long production backlog is not really cause for serious complaint, though undoubtedly both you and the editors of the journal are not happy about it.  Note that frequently the only way to fix a production backlog is to stop accepting papers (or accept very few papers) for some period of time.  (In particular, back when people mostly read papers by going to their physical library, there was no reason for the production backlog to be any better than the publication backlog, and some publishers still think this way.)
However, the number of errors in the production process and the amount of time and number of iterations it has so far required to fix them is completely unheard of in my experience.  I have had some production issues twice in 20+ papers (both times with the same publisher but different journals), but they were nowhere near what you are describing.
At this point, you should let the editors know what has happened and ask them to complain strongly on your behalf.  (Of course, you should be nice and understanding about it, since it's not their fault in any way.  But they have leverage that you don't.)  They are on your side.  They can see you have been treated badly, and they know that incidents like this are very bad for their journal.  This should be a serious issue, to the extent that, if these kinds of production issues are a common occurrence, the editorial board might try to switch publishers (if they own the name of the journal) or resign.  (You don't know if your case is a one-off or common, so you can't very well ask them to do this, but they should want to know and should take this seriously.)
Finally, I think you are well within your rights to not submit to a journal run by this publisher until you have some indication they have improved their processes, and you should quietly let anyone who asks you for journal advice know about what you have gone through.  (If someone reads this question, figures out who you are, and e-mails you, you should let them know who this publisher is.)

Thanks. Well, about half of the errors stemmed from changing the LaTeX package configuration, although, I have only used fairly standard packages, packages that I've also used elsewhere without issues. However, they could have double checked the impact or gotten back to me before altering the code such that LaTeX compiles with lots of artefacts.

Note that frequently the only way to fix a production backlog is to stop accepting papers (or accept very few papers) for some period of time the way to fix a production backlog is to hire more production people! (Or move them from other parts of the publisher)

@Allure: Springer or Elsevier can hire more production people.  Mathematical Sciences Publishers might be able to.  The University of Michigan Math Department (which publishes a reasonably well regarded journal) cannot.

@AlexanderWoo they should outsource to freelancers then ...

@Allure: and pay them with what money?  We're talking about a journal with something like a US$25K/yr annual budget, most of which goes to the department staff member who spends 15 hours a week working on the journal.

When I worked in production, we had a timetable of roughly 30 working days to get a manuscript published. The 30 days would include all the steps in the process: copyediting, 1st typesetting, proofreading, author checking, 2nd typesetting, author sign-off, and uploading online. Lots of people were involved, up to 5+.
Sometimes the timetable would not work. Why not? Usually it's because one of the 5+ people dropped the ball. Do remember that in general the staff are not the "journal's" staff, they are the publisher's staff, and the publisher probably has more than one journal. This means things like these can happen:

A paper for journal A arrives, but six papers for journal B arrive at the same time, and the staff choose to work on those six papers first (because those six papers are urgent, because the editors request it, etc).
One of the 5+ people goes on leave for a few days. That's not long enough to really have someone else cover for them, but more than long enough to upend the schedule for everyone else.
One of the 5+ people is focusing on something else, e.g. if you are in charge of uploading the paper online, perhaps you are also in charge of maintaining the journal's website or editorial management system, and there's something about the website that needs to be fixed.

Taken together this means there is room to expedite a paper - certainly a very important/urgent paper can be completed in a few days, for example - but the speedup happens at a cost to every other paper, and there's no guarantee that papers take the same amount of time.
You might have experienced something similar. Say you are reviewing papers by Alice and Bob. Alice's paper is smooth and easy and you finish it in one week, well before the deadline. You then put Bob's paper aside for a while to grade your students' assignments, then you have to deal with unhappy students, and then it turns out that you need a paper Bob referenced to finish the review so you contact your librarian, and it ends up taking a long time. From your perspective you've done the best you can do under the circumstances. From Alice's and Bob's perspective, they both submitted to the same journal and yet one review was very fast and another took an unpleasantly long time.
One more thing: my experience with Open Access is that it literally does not affect the publication process, except at the end when we instruct the sales department to charge the author. It is possible some publishers expedite OA papers, however.
In your specific case: it's hard to tell what happened from the outside. If you submitted a manuscript in a difficult-to-parse format (e.g. if you used Word when the staff are trained with TeX), then they might have encountered problems converting it. You write that "The editing office has politely and helpfully handled the corrections with the production team". Assuming the editing office is the editorial office of the publisher, then they've done all they can, and it's the production team that's at fault. Still, one can't tell from the outside what's going on - for example, you could simply have gotten a bad (or new/overworked/depressed) typesetter. What certainly shouldn't happen is for the bad manuscript to make it to you in the first place, simply because one of the 5+ people in the production process should have caught the issues before it got that far.
I'm almost certain getting your library to impose an open access "sanction" on the publisher is kind of missing the point, since it almost certainly doesn't address the problem(s). It's not clear how to address the problem either - from the publisher's point of view, what needs to be done is for the 5+ people involved to be more careful and/or willing to ask for help, which isn't something that management can just implement.

Thanks for this insight. I don't know the exact circumstances for what I believe to be a dramatic delay and quality breach. Too many manuscripts for too few staffs is certainly an explanation. The reason I mentioned OA-based APCs is that it creates (at least to me as an author) the impression that I'm now paying for the processing more directly than through the traditional subscription-based funding and, therefore, I could expect better results. I might err. However, I don't want to follow up on the seemingly difficult OA vs. non-OA discussion having taken place elsewhere.

I agree with what Alexander Woo said, to the effect that "numerous typos" should not be taken lightly, and that you should consider contacting the editorial board.
When something similar happened to me once, I sent a long and angry email to the publisher, and demanded the process be started over from scratch. This produced the desired results.
Also, again agreeing with Alexander Woo, the scheduling concerns are more ambiguous. In my experience, asking you to wait forever is a bit annoying, but par for the course.
I have an additional suggestion: as you suggested, contact your librarian. They might be familiar with this publisher; ask them how typical your experience is.
I don't think that they would block APC waivers based on a single complaint, but if they received many such complaints then they might consider it. In any case, they might be willing to suggest a course of action, or to contact the publisher on your behalf.
Good luck!


text:
How to cite a working paper, preprint, or manuscript?
How I can cite a submitted manuscript which I am not supposed to publicly archive (e.g. on arXiv) because the review process is double-blind (i.e. the manuscript is anonymized and should not be archived in a way that reveals authors' identities) and/or the journal has a restrictive archival policy?
This manuscript may therefore not be assigned a permanent link (like it would have been with biorXiv, arXiv, OSF, some institutional repos, etc.). I am aware of platforms such as Zenodo allowing anonymous archival but these do not necessarily imply a citation format to be used. However, I'd like to share the manuscript among colleagues who might want to refer to it. So, I want to suggest to them a citation format while it's under review.
I found this, suggesting me to do that:

Doe, J., & Smith, A. (2012). A study on the difficulty of getting manuscripts published. Unpublished manuscript, Department of Sociology, The Top University, New York.

where manuscript can be substituted by something like working paper or preprint. See also that SE comment. However, I am not sure whether this is the best way to do it. Any better suggestions?
Thank you.

Could you first explain what "a preprint (likewise a working paper, or a manuscript) which I am not supposed to officially archive because of a longer double-blind review process with an anonymized version of that preprint" means in plain English?

Thanks for the hint. I hope that reads better.

Check the style guide that you are writing against, these often have guidelines on how to cite unpublished works. For example, the CA Style Guide (from Chicago Manual of Style) states:

Unpublished Work

Forthcoming works (works that have been accepted for publication and are in the publication process) are listed in the References Cited and are cited as references, with "forthcoming."

Manuscripts that are not in the formal publication process (e.g., that have been submitted but not yet accepted for publication) and other unpublished work are cited parenthetically in the text or explained in a footnote.

Unpublished work should be identified as a manuscript, a letter, an e-mail, a personal conversation, or "unpublished data." The citation must include the full name of the person and a date or a year, if possible, as well as the brief description.
(George Hamilton, personal conversation, May 2009)
(William Lewis, Donald Steadman, and Peter Larsen, unpublished data)
(Mary Pat Stearns, unpublished manuscript, 2008)
(Dan Peterson, e-mail, January 13, 2008)

Thank you, @Mike. This answer includes the other one and represents a nice summary.

I'm not sure this is a better solution, but you can be cited by name (and possibly place), with the paper described as "private communication.". Include a date (29 Aug. 2018) but not the name of the manuscript.

Doe, J., & Smith, A.. Private communication, (29 Aug. 2018). Department of Sociology, The Top University, New York.

Once the publication becomes official contact your circle with the information and an updated reference. They may be able to update their own work in some cases, depending on timing, etc.
I'll note that it isn't impossible that the title of your work will change after review, making a more specific title obsolete.

Thanks @Buffy. I think that pretty much addresses my problem, sounds like a good way to go.

It is reasonably common, actually, @Mario. Now we have to argue about which university is "top" in NY. ;-)