text:
Is talking about quitting to your supervisor a point of no return?
I have been feeling miserable about my PhD degree situation for a bit of time, and I just started therapy. So far I've tried not to take drastic decisions such as quitting, because I know I am strongly influenced by my condition, but lately I can't think about anything else.
I wonder if it is possible to convert my contract in a research assistance, or what is a graceful way out so to continue deserving recommendation, or what is an adequate resign notice period, etc., but I know it would much better to finish the PhD degree, and so continue trying.
Is talking about quitting possibilities with your supervisor a point of no return?

"I have been feeling miserable about my PhD situation" You have already passed the point of no return.

Isn't feeling miserable like a part of been a PhD candidate? :D

I talked to my PhD supervisor about quitting and then didn't quit. It certainly wasn't a point of no return.

@itcouldevenbeaboat: I couldn't disagree more.

@N0ir (1) Drudging on despite feeling miserable shouldn't be necessary to make a good researcher. (2) I know the statement was made in jest, but someone suffering from depression or similar would also describe themselves as 'feeling miserable'. Part of the problem is recognising that it's more than just that and the OP seems to have done that by starting therapy, so kudos to them. Telling them it's just par for the course can be incredibly insensitive and counterproductive, as it implies they should just 'toughen up and get on with it', which is the worst you can tell someone in that situation

Point of no return from whose perspective? Yours? (Agree with other comments here, chance to change something.) The supervisors? (Depends on the supervisor and how s/he handles these situations.) BTW, your question reminded me of this presentation https://www.youtube.com/watch?v=4MkRMp3roKQ by Hayton who reached a low point and used it. No two people experience a crisis exactly the same (and doing a PhD can have a lot of them), but perhaps its useful.

Talking with your advisor can be a point of no return. Even if it's unlikely, be prepared for the worst.

Talking about quitting with your supervisor (or someone else in your supervisory committee or department) is not a point of no return. In fact, it can be a turning point.
PhD students all go through ups and downs and part of the job of the supervisor, and others in the department and university (head of department, counsellors, etc) is to help you get through the rough patches.
If you do not talk about it and things get so bad that you actually quit, then it may be a point of no return.
Full disclosure: I quit my PhD. The first my supervisor heard of it was the day I quit. Luckily, someone else gave me another chance a few years later.

Signed in just to upvote this. Couldn't agree more.

+1 and even the process of thinking about what issues you would raise and how can be beneficial.

This is not an attack, I am genuinely curios to know: Isn't your answer a bit absolute? I mean, should one also consider the relationship between the supervisor and phd candidate? Aren't there some supervisor whom such conversation might affect all their future considerations of the student? What if the supervisor him/herself is one of the reasons that OP is finding the job exhausting? Again, I am not attacking and I myself upvoted your answer. I couldn't however, be sure if it is a general rule to consider supervisor so supportive in the times of despair.

@Pouya: Good points. Other people in the network should be consulted in that case. In any case, quitting should be the last resort.

@Pouya if the supervisor is one of the reasons, that is an even stronger case to talk about it.  That is the best hope of finding a solution for it.

I talked to my supervisor about quitting my Master's thesis option not once but twice (turbulent times, I had) but I finished my Masters. I have known colleagues who had the same issue during their PhDs but they all finished with the same supervisor.

This question resonated with me, so I signed up just to answer. The short answer is that one would hope that it shouldn't be a point of no return. But, of course, it depends heavily on your supervisor’s temperament.
I was in a similar situation where I was deeply unhappy with the direction and content of my PhD research and despite my best efforts at raising these concerns I struggled to alter things. This was partly due to having two supervisors with not entirely overlapping areas of expertise. However, my main (on paper) supervisor and I met for a coffee in a neutral location, i.e. off campus and not his office, to discuss things. He was non-judgmental and supportive and, having done a PhD himself (naturally), he understood the situation. I did end up leaving the PhD programme but it was not because I couldn’t discuss things with my supervisor (I’ve since completed my PhD at a different University).
So my suggestion would be definitely do not simply quit, you should feel able to discuss issues with your supervisor. After all (at least in the UK) supervisors are expected to provide some level of pastoral care, as well as directing research. If you'd feel more comforatble suggest a neutral location.  Further, I’d reiterate what Dave Clarke said in that I don’t know a single PhD student who, at one time or another, wasn’t fed up with some aspect of their PhD.

Re. your last paragraph, if you are not feeling frustrated, it is not called research. (Tongue in cheek).

Absolutely not.  Even quitting may not be a point of no return, if you have a good relationship with your advisor.  I know of a student, for example, who actually withdrew entirely for reasons of mental health, but was explicitly told that their return would be welcomed if their circumstances changed.  What is most important is to find a way that you can be honest about your struggles and planning.  If you don't feel you know how to talk safely to your advisor about this, you should start by talking with your therapist, who can help you plan an approach and figure out how to talk about it without revealing information that you wish to keep private.

I quit and returned and succeeded and look at me know. A regular on [Academia.SE].

I would assume the answer to this question depends on the area. In mathematics (where I work) or humanities your supervisor will most probably try to help you not to quit, and if you do quit welcome you back after two years. In other disciplines, where Ph.D. students consume significant resources, things are different. The supervisor might well think "If I let someone play with my 12 million dollar gadget, and he quits, then I wasted a lot of money. Better invest this into a student who actually finishes."

There are few points of no return, else we'd all be lying at the bottom of cliffs.
Are you going to GET the PhD?  If so, finishing it and putting up with being miserable for a bit longer is an option you should consider.  If you're convinced you're going to flunk it, talk to your supervisor, it's what he's there for.  Maybe you'll be reassured that in fact you're doing OK.  Maybe he'll agree you should try to succeed at something less ambitious.
If you have the choice, not too long in the future, of having a PhD or not having a PhD, which would you prefer?


text:
How serious should I regard the "compliments" in an email denying my application?
A school, whose PhD program I applied to, denied my application with words such as "Your record is strong, but...". I am kind of confused. Is such a reply simply a "polite" way to decline a person? Should I believe that the sentence "your record is strong" is a compliment, or it is simply a decoration?
To me, such a compliment does not seem to help because obviously, for the school, my record was not strong enough to be admitted, so speaking of "your record is strong" is almost meaningless?

Doesn't matter, you should ignore compliments as you would ignore insults.

It may be a genuine compliment. Normally, when a letter is just trying to be polite, it will say things like "We get a long of strong applications and can't accept them all." This was specifically targeted at you, so it may be that the letter writer actually thought this.

If it says something personal then it's likely to be a genuine compliment, otherwise not.

I would take it as simply a polite way to decline your application.  They no doubt really do get a lot of strong applications (every decent program does), and in many cultures such as the US there is a tendency to "sugar-coat" bad news with compliments (I don't know if your application was in the US, but I believe this practice turns up elsewhere as well).  You would actually probably get less praise if you got in---after all, the acceptance is compliment enough.

Many thanks! Exactly what I would like to know. Just want to check if my intuition is correct to a certain degree.

+1 for "you would probably get less praise if your application was accepted"

It is funny to note that higher-up in the academic food chain, rejects tend to get less and less sugar-coated. I have received rejections for faculty positions that more or less verbatimely read "We think your track record is not good enough for our insitution." Of course every reject implicitly says this, but it was awkward to see it spelled out like this.

@xLeitix Perhaps because the higher up you are in the academic structure, the more professional you can assume your peers are?

@Nit This is a very optimistic assumption.

Those kinds of general compliments are typical platitudes included in rejection letters, whether for an academic application or a job search.
In general, if the letter feels impersonal or looks like it might be a standard boilerplate or form letter then there is no point in trying to interpret any deeper meaning behind the contents. There is simply no way to tell from such a letter alone whether they really considered you a strong candidate or are just sugar-coating their rejection.
Only if you can tell that the letter was written for you personally or when it references some particular quality you have should you accept it for the compliment it really is.

if the letter feels impersonal or looks like it might be a standard boilerplate or form letter then there is no point in trying to interpret any deeper meaning behind the contents - exactly. +1.

What would you do about it anyway? Whether the compliment is genuine or part of a boiler plate rejection letter, so what? Aside from softening the blow of rejection, what difference does it make?
I suppose if a compliment was very specific, like, I don't know, "you are very articulate and your grammar is impeccable", that might tell you that this is NOT the area that you need to work on but rather you should concentrate on other things to improve your chances the next time around. But something like "your record is strong" is so general as to mean almost nothing.

Thanks. To me, a question is raised in its own right; no reason is needed to "justify" why a question is raised. I asked the question because of pure curiosity. So, sorry, I think it is more suitable for the present "answer" to be a comment.

@chou I'm not challenging the validity of the question. The poster asked, "how should I regard these statements?" My answer is, "ignore them because they're irrelevant." Seems to me that's a direct answer to the question. If you don't agree, that's fine. Post your own answer.

Jay, @Chou IS the original poster. You might not have noticed the subtle highlighting of her user name in this thread.

@VaibhavGarg Oops, no, didn't notice. I think the content of my comment stands, just worded incorrectly given that.

I agree @jay. It's only a minor quibble in an otherwise excellent point.

The only times I would recommend to entertain the idea of a compliment in a rejection email is if 1) The compliment is something specific to your resume or work, such as 'Your paper on X was very impressive...' (im not sure this ever happens with a rejection) and 2) You are asked to apply or automatically accepted into a different program.  Of course in this situation you were rejected from the one you wanted, but the compliment is not empty-handed.  I have seen this in both art/design and music. For example, applying to a specialized program for '3d animation', and being rejected to that program, but automatically considered and accepted for the 'new media design' program.

'im not sure this ever happens with a rejection' - I have done this in rejections. I don't write insincere compliments, but sometimes I do feel that certain aspects of a paper or an application are strong; expressing that strength is then sincere, and I believe that it makes the rejection more human. However, I'd be interested in hearing other people's opinion on this.

@MarkPeletier  well im glad you do that, I was just assuming it can be a liability of someone being rejected and complaining

@user1938107 To what your "it" refers?

@Chou I was referring to being told a specific thing was good, but still being rejected.  As I mentioned, im not sure if it happens or not, i dont have personal experience with it.  That being said, I was pondering the impacts of rejection letters and how someone can follow up, either saying denied entry because of affirmative action (harvard law suits, michigan law) or apparently some schools allow appeals, http://www.wsj.com/articles/SB124096471555766239 .  A school might not be happy if specifics are mentioned that help too many people appeal, but i dont know how it works

When I got in the MS program I received a note from the coordinator prior the decision was posted to my account. In that note I was merely congratulated and informed that they let me know sooner in case it would be helpful to me.
On the other hand however, wherever decided to reject me sugar-coated the decision letter and it usually came when I myself was almost sure that they did not want me there.
I got the acceptance email a month before the deadline! While I thought I would not be hearing from them for at least two weeks after the deadline. Bottom line is, if they want you they let you know quickly; otherwise, it is just a formality to help people get less disappointed.

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text:
When do I use a footnote in a thesis and when do I use parenthesis for extra information?
I have one question for my masters thesis. If I have A, which is also known as B or C, can I write:

A (also known as B or C)

(or similar) or can I use a foonote like this:

A¹

¹ Also known as B or C

Or more in general: When do I add extra information (like synonyms) between parenthesis, and when do I add them as footnote?

A thesis is no different from any other document in this respect.

This is mostly about the reader's flow. Something that is parenthesized is something you expect the reader to actively read, but you're signalling that it's secondary information. The main drawback to parentheses is that if the text in them becomes too long, the reader has to work very hard to remember the main point you're making. You're essentially talking about a lot of unimportant stuff while you have an unfinished, important sentence going. So make sure you put only short, simple things in parentheses.
If you put something in a footnote, you're signalling that the reader should skip it on first reading and they should only investigate if something is unclear, or if it's a second reading and they need all the details. The drawback to footnotes is that they are often more tantalising than they should be. While the reader should ignore them, they are too curious, and break their concentration to look up the footnote. This pulls them out of the text for something they were supposed to ignore.
On the whole, try to avoid both as much as you can. In your example, ie. this method is also known as X, parentheses should be fine and a footnote is probably overkill. However, you could also consider finishing your main point first, and moving the parenthesized statement to the end of the paragraph as a full sentence. That way the reader can finish absorbing the primary information unencumbered by details, and gloss over the aka's once the hard work is finished.

Good point about interrupting the reader's flow. Unless the parenthesized text is about 5 words or fewer I try to re-work the paragraph so that the parenthetical text is either not necessary, or comes at the end of a sentence.

One way to "force" the reader to avoid footnotes would be to put them all at the end of the thesis/chapter instead of at the bottom of each page. In my experience you get tired easily of going always at the end to read the notes and you end up ignoring them on first reading. When they are needed you are willing to go at the back and look.

@Bakuriu No, end notes are a scourge!

@curiousdannii That claim could be a new question on this site.

To a large degree, it all depends on your chosen writing style guide and, perhaps, your institution's and/or advisor's recommendations. Having said that, I would suggest using the following heuristic (rule of thumb) to determine potential use of footnotes versus text in parentheses: if information in question is short, such as "also known as B or C", it is preferred to use that text in parentheses, otherwise (for a longer text) consider one of the two alternative options, as follows.
The first alternative option is to use a footnote; however, using footnotes is discouraged by major writing style guides (i.e., by APA Style Guide) or advised to be limited, especially for explanatory, non-bibliographic notes (i.e., by MLA Style Guide). That aspect is likely to be very field-dependent, therefore, you can consider the second alternative option: simply adding explanatory sentence(s) after the text that requires such explanations or clarifications.

An expansion to the heuristic: a footnote can¹ run to more than one sentence which gives you more options for phrasing it clearly.     ¹ I said can. I didn't say should. That's a debate for another time.

@ChrisH: Thank you for your comment (+1). Generally, I agree with your point. However, the same effect could be achieved by what I called in my answer "explanatory sentence(s)". The advantage of this approach (vs. footnotes) is not breaking the text's flow logically and visually. Of course, that applies only, when those sentences are closely tied to the main thoughts, in other words, "belong" there (which is quite subjective). Otherwise, your approach indeed might be a better option.

I seem to have given a lot of upvotes here (including to you), but also I've answered the question myself, hopefully giving another viewpoint which you allude to with "belong".

@ChrisH: Thank you for your upvote. I have noticed your answer and upvoted it 9 hours ago.

Looking at my PhD thesis (a little over 200 pages) I have 11 footnotes. 7 of these could be in parentheses with no rewording, the other 4 need at least a full sentence.  Picking a few pages at random I often have 2-3 pieces of extra information in parentheses per page.  Parenthetical commas aren't so easy to count, but I'd assume there are at least as many as parentheses.  Explanatory sentences are also hard to count and too numerous, but can be a good way to inset this information.  In fact you may find in proofreading (by you or someone else) that your parentheses get edited into new sentences to avoid run-on sentences.
I think there's a hierarchy:

parenthetical commas
parentheses
footnotes

in order of decreasing relevance to the main flow of the text (not decreasing importance).
It could easily be argued that I've used all these options too much but it suggests that (in my writing style at least) footnotes are a last resort.  Where I have used them it's generally because I have a line of reasoning in which a point needs to be mentioned for avoidance of doubt, but to mention it inline would break the thread of the argument.  That's the aim at least.
Incidentally, because I used a numeric-superscript citation style (a common one in my field, and I had the choice), counting was easier.  I chose to use lower case alphabetical footnote keys reset per page (easy in LaTeX) in case I had a lot, and to avoid confusion with numbered footnotes or other uses of (e.g.) asterisks.

Good point: parenthetical commas are often a better alternative. You could even extend your hierarchy with parenthetical dashes at the top; for the situation where the parenthetical information is more important than the surrounding text.

In mathematics, footnotes aren't very common nowadays (and used to be used for providing references).  The differentiation is of course a choice of personal style, but one approach is: treat footnotes like annotations (as if they are written in another voice by another person--say author's comments to the reader).  Another is: never use footnotes.1
1(Personally I like footnotes2, but I use them sparingly in academic papers but semi-often in less formal things like online notes.)
2(and parentheses)

Given that people may be searching for B or C, I think using the parenthesis is better.    That way a search takes them to the text, also when Google shows the context of the search result, it is more likely to be useful.
Foot notes are also hard to read where you a using a device with a small screen that has issues displaying pages.   Text with parenthesis is a lot easier to reformat for different display sizes etc (reading mode on IPhone for example).

A good point, but at least a footnote will take them to the right page, and I've never found google's context to be of much use inside theses/papers.

@ChrisH, google also uses the context to help in ordering of search results.

Perhaps in such a case B and C should be in your index.

This argument also holds for scanning the text on paper: you're more likely to see the thing you're looking for if it's in the body.

I'm not sure however if readability on an iPhone should be a major design goal for a PhD thesis ...

@HagenvonEitzen, the same factors effect a blind person using a text to speech system - however agreee it should not be a major design goal, but I think footnotes should only be used where a clear case can be made that they are the BEST option.

I just browsed through my dissertation. I use quite a lot of footnotes: I count 45 in 200 pages.
Looking through them, I now find that many contain the words "strictly speaking".  These are aimed at pedants such as myself who think they've spotted a mistake or inaccuracy: they explain how to deal with technicalities, why an abuse of notation is justified, etc. As explained in other answers, having these remarks in the main text would distract from the normal flow of reading, and the reader can often do quite well without them.
In your example, I'd use parentheses. I found one similar instance in my dissertation where I actually use both:

... chordal (also ambiguously* called triangulated)...

Here, I used a footnote to describe the other meaning of "triangulated", because it's not really in scope for the text, whereas it is a relevant fact that the term "triangulated" is sometimes also used.

Now if that footnote also contained parenthetical dashes, that would show mastership of all means of parenthesis :)

@HagenvonEitzen You can have footnotes inside footnotes :)

Looking through my thesis, I was able to find another use case for footnotes, which has not been mentioned so far. Sometimes I define a concept or a symbol in a way which is slightly different from some other sources. I then include a footnote which describes how the symbol is used elsewhere. This could be important if the reader is trying to compare my result with other results or to follow a chain of citations which use different terminologies.
I think that in this case, including the alternate definition in the main text would be dangerous.  For example, saying "we define $X = a + b$ (other sources define $X = a + b + 1$.)"
The reader would get confused between which is my definition and which is the alternate definition. By keeping the alternate in a footnote there is a much stricter separation between these two.

That depends mainly on the citation style required by your publisher, or requested by your supervisor. Some of them are parenthetic (Smith, 2015) some are footnotes (1: Smith, 2015)
On a more particular note, generally Citations refer to the source from which you take your assertion [i.e.: "This is cool" (Smith, 2015)] whereas footnotes just expand a concept without referring to a source [i.e.: "This is cool"1 1: "The term cool varies, but we use it here in its more common meaning"]
Your example is quite vague though, so my answer aims to be general but might not fit to your case.

The question seems to me to be independent of citation.  As phrased it's equally valid for footnote, parenthetical, numeric superscript, etc. citation styles.

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text:
Rejection from a legitimate journal, with reviewers recommending me to try a Beall's list journal
Recently I received a rejection by the editor of SCI Expanded journal (which I consider to be a legitimate journal):
The reviewer's comments (just a few days after I submitted the manuscript):

Sorry, this paper lacks novelty, is not well written, and will not be considered due to overwhelming submissions to X journal (SCI Expanded journal).
  Suggest to try: (gives me a URL to a journal listed in Beall's List of predatory journals).

(I have removed the names of the journals above. I have personally checked https://beallslist.net/ and confirmed that the suggested journal falls inside the Original Beall's List. The suggested journal comes with a publication fee of 1500 euros for each article.)
I am quite new to academia. Is the above considered normal practice for a reputable journal listed in the Science Citation Index (Expanded)?
Any advice of what I can do?

Update:
I found that a member of the editorial board of the SCI Expanded journal, is also in the editorial board of the Beall's list journal.

The reviewer may have a conflict of interest. Use caution. There are other legitimate journals you can try.

What @Buffy said, but also: There are some borderline cases on at least some versions of Beall's list (like MDPI and Hindawi) that engage in some bad practices but are not widely known to do so (e.g., if you only interact with them as a reader, you'll just think of them as glorified preprint services, unaware of APCs). The referee might be meaning well.

Hmmm. I wonder how influential that person was in the rejection. Perhaps it was really improper.

If the person (reviewer or editor) knew that the journal being suggested was predatory, then I consider the suggestion to be unethical behavior.

If the reviewer thinks the paper is "not well written", what reason could there be for recommending submission anywhere without first improving it?

I'm not a scholar, but would it not be reasonable to request that this journal be added to the list of predatory ones?

From your comments tot he accepted answer, it sounds like you dodged a bullet. It would be good form at this point to name the journal involved so that others can consider avoiding it too; or at the very least, report to Beall's List so that they can consider listing as a feeder journal to the predatory one.

Re "...by the editor of SCI Expanded journal (which I consider to be a legitimate journal)": Is "SCI Expanded" really the name of the journal? It is very close to the two lists Science Citation Index (SCI) and Science Citation Index Expanded (SCIE). Do you mean "by the editor of an SCI Expanded journal..."?

What is an APC?

I am quite new to academia, is the above considered normal practice

No. This is abnormal and unacceptable for a reviewer or editor to suggest this.

Any advice of what I can do?

If the journal you submitted to really is legitimate, contact the editor and escalate this. Simply point out that the review you received pointed you to a predatory journal, and ask if the editor can reach out to the reviewer to see if this was a mistake.

Update: I found that a member of the editorial board of the SCIE journal, is also in the editorial board of the Beall's list journal.

This is a red flag, and the review you received is another red flag. These red flags suggest that the journal you submitted to is not reputable. I would check with online journal ratings, impact factor, etc. to make sure you are not already submitting to a very low-quality journal (even if it is not predatory).

I'm not sure about the final paragraph here, but the other advice is sound. The editor needs to know. If this reviewer was especially influential in the rejection, perhaps the result can be overturned, though another review might be needed. I'd give the editor a bit more benefit of the doubt without knowing more, though.

Unluckily, I just researched that the founding editor of the SCI journal is precisely the same guy also in the editorial board of the Beall’s list journal... I think there should be no hope for me for appealing. (I suspect the “reviewer” in my case was just the above-mentioned editor himself.) I will just try another journal. Thanks!

That seems to seal the fate of that journal. Yes, find a better alternative. Look here for updates to Beall's original list. https://academia.stackexchange.com/questions/83764/with-bealls-list-gone-how-can-i-tell-if-a-journal-is-spam?rq=1 Maybe you were lucky to be rejected.

@Buffy "Maybe you were lucky to be rejected." - this made my day. Great quote.

-1 because this answer assumes that the journal listed on Beall's list is indeed predatory.

"I found that a member of the editorial board of the SCIE journal, is also in the editorial board of the Beall's list journal."  This means nothing.  Plenty of people have no idea they are on the board of a predatory journal, because nobody has told them.

@yoyostein "...and will not be considered due to overwhelming submissions to X journal". Of course, it is the editor who rejected your paper. How does the reviewer know about the number of submissions in journal X.

@KratosMath Good point, and I agree with you. In the rejection email though, it was explicitly listed as “reviewers’ comments”.

@AnonymousPhysicist that seems unlikely in this particular case when they are recommending that journal.

@Kat The person making the recommendation is anonymous, as far as we know.

@yoyostein in some sense, the editor is also a reviewer. But more realistically, in the editorial management systems I'm familiar with, when the editor desk rejects the system auto-generates an email which says "unfortunately we're not considering your paper" ... etc and then at the end appends the "reviewer comments", if any. Odds are the editor simply wrote their comments at the end of the email.

"Unluckily, I just researched that the founding editor of the SCI journal is precisely the same guy also in the editorial board of the Beall’s list journal" Sounds like the SCI journal you submitted to might need to be on that list as well. I'd suggest they review that "legit" journal for addition.

First: it's likely you mistook the decision - it's not a reviewer's comment, it's the editor's comments, and they are desk rejecting your manuscript. In this case it is decently common for the editor to suggest another journal (especially if it's published by the same publisher). I would not find it a red flag if they did - it is after all only a suggestion which you are under no obligation to follow.
You write that the editor recommended a journal on Beall's list, but remember that Beall's list is not gospel, especially since it is now defunct and not being updated. There is a real chance that the editor does not consider the journal predatory, or even that the journal isn't predatory in the first place. The editor is very unlikely to have anything to gain if you submit to a predatory journal either - the other journal might not even know your paper has been referred.
If you do not want to submit to that journal (especially since it is open access with an APC), simply ignore the editor's suggestion and submit your paper elsewhere.

I found that a member of the editorial board of the SCIE journal, is also in the editorial board of the Beall's list journal.

This doesn't mean anything. It is conceivable that a reputable academic will elect to serve on the editorial board of a "predatory" journal (inverted commas because what is predatory isn't well-defined). Or it could be that the predatory journal is simply listing the editor's name without their consent. Either way, this doesn't say anything about the SCIE journal.
Even if this editorial board member is the editor who rejected your paper, it's still possible they are be acting with completely benign intentions (if your colleague told you their paper's been rejected from X journal and you knew of journal Y which would consider it, would you suggest it?). Bear in mind that if they are editorial board members of both journal they would have a pretty good idea of the standards of the other journal, and that your paper meets those standards.
I would take the fact that the journal is indexed by the SCIE as a very strong sign that the journal is reputable (anyone who's ever tried to get a new journal into the SCIE will be able to vouch for how difficult this can be).

@MishaLavrov if you believe that, almost all open access journals are predatory.

Thanks for your detailed answer and valid points. I totally agree that the SCIE journal is reputable, that’s why I was quite shocked at the reviewer/editor recommending a Beall’s list journal with 1500 Euro APC.

@yoyostein 1500 EUR is not that high - compare e.g. Springer's average APC (https://www.springernature.com/gp/open-research/journals-books/journals), which is around 1700 EUR.

Yes, perfectly reputable journals can ask quite high fees; for more examples than @Allure's, ACM asks 1700$, Cambridge University Press often asks >$3000 (for instance for JFP). And all open access publishers are somewhat in a conflict of interests. But not all act on it.

This answer is on point. I will only add that it is common in some fields for editors to make such a suggestion; in such cases they offer to transfer the manuscript to another journal by the same publisher.
This practice is followed by a very reputable journal in my field of materials science/engineering. The second journal is new, doesn't even have an impact factor yet, but researchers appear to welcome this option, because it is affiliated to the primary, reputed journal.
The reason for adding this is that such practices are not always unethical; use your caution and check the referred journal. However, ensure that it is an actual transfer that is being proposed, not just a suggestion to resubmit (without the mechanism of carrying the submission/review history).
In the present case, I concur that you should report this reviewer to the editor.

Thanks. It is a suggestion to resubmit rather than an actual transfer. Also, after googling I realize the editor himself (likely to be also the reviewer) is also the person in the editorial board of the Beall’s list journal. Is there any higher authority that I can report to (since the person in question is suspected to be the editor)?

@yoyostein You can tell the editor-in-chief or publisher of the SCIE journal.  But phrase it along the lines of "I'm concerned about ..." rather than being outright accusatory unless you are sure that other journal is a predatory one (cf Allure's answer).

I don't think it's unusual for a reviewer to suggest another journal if they are recommending rejection for the reason of "not strong enough for this journal". I try to do this myself; sometimes I receive an article to review that strongly suggests the author is not very familiar with the relative strengths of journals in the field, so this comment may be helpful.
There are other worrying signs in this case, though. It is very unusual for a review to come back so quickly (in fact it would be surprising that the submission has even reached a reviewer by this point), and the editor doesn't seem concerned about the perfunctory nature of the review. One might even start to wonder whether there really was a "reviewer". Of course the fact that the journal is on Beale's list may be a legitimate mistake or an historical artefact, but with these other factors I would be suspicious about both journals.
I wouldn't want to publish in the original journal any longer. Just resubmit to another journal of your own selection, and count yourself fortunate not to have lost more than a few days.

This wasn't an unexpectedly quick accept decision - it was an unexpectedly quick reject decision. Most likely, it was a desk rejection.

@Allure OP said these were the reviewer's comments, not the editor's., meaning that the journal is claiming that it's not a desk rejection. Of course, as I suggested above, one might be sceptical about this claim.

It actually reads like a desk rejection. No reviewer could know that the journal's receiving an overwhelming number of submissions.

@Allure that's exactly the point I'm making in my answer. If it sounds like a desk rejection but the journal is pretending it's something else, avoid them!

First, given the wording, this is the editor desk-rejecting your paper, and you are confused because you are new to all that. If the editor somehow implied the reviewer wrote that, ignore his recommendation and run away, submitting elsewhere. Otherwise, consider that if the paper is in fact as weak as the editor claims it is, you are likely to be unable to publish in any much better journal. This is hard for you to judge - we all have blind spots for our own work.
You can submit to that journal and check the review process there by yourself. If it seems suspiciously short with few or no relevant comments regarding contents of your manuscript, this journal is indeed predatory and will publish whatever crap anyone sends. Then, you can either opt to publish to get it over with, or let them know you changed your mind and that you will publish elsewhere because you were unsatisfied with their review process. Sure, you will waste some time to get the response, but you can simply keep working on other stuff while you wait for that response.

"editor desk-rejecting your paper" That is not my interpretation of the question.  It is possible the editor assigned the paper to themselves to review.  Or to a friend.

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text:
How can I appeal an apparently unethical decision to take down a job posting early?
I've found a call for PhD students or data scientists at a certain university. The instructions were very clear that applications would be accepted until Oct 12th 2023, and only then they would be reviewed.
However, around Oct 8th 2023, when I was going to send my application, I've noticed that the page for the call had been removed. I've managed to search the university's website and found that there was a listing of all open positions at the university, so I got the e-mail address I needed and sent it anyway.
Needless to say, I didn't even get a reply saying that that application was received nor if I was rejected, leaving the impression that the position was already occupied even before the deadline for applicants ended.
I've been spending endless hours gathering all the documentation, writing motivational letters, convincing former supervisors to give their names as reference and I feel it's extremely unfair to do so. I'd like to do something about it. However, I also understand that someone's probably already working on the project, and even if I am a better fit, little will be actually done about it.
What would be the mature decision here? I'm unsure whether the position have been cancelled or filled. Either way, I'd like to get in touch with them and see this through without damaging any possibility of applying for another new position in the future.
Also, as a follow-up question: is it common to have things like this happen, completely out of the original time table?

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Where in the world is this?

The instructions were very clear that applications would be accepted until Oct 12th, and only then they would be reviewed. However, around Oct 8th, when I was going to send my application, I've noticed that the page for the call had been removed.

Unlike other people, I do think it is somewhat unethical to do this. Dozens of people might have been spending long hours crafting their applications.
If something changed so that the position was no longer available, the university should have posted an apology. For example, perhaps they could edit the page to put a message at the top, and disable the Apply button. If the system does not allow this, perhaps they could post messages to the relevant mailing lists, or think of some other way of doing it.
But as the person who was writing an application, there is not much you can do. It would be OK to ask why it was taken down. But make your message very concise and clear, and don't sound like you are complaining.

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You have no basis for appeal, and no basis for saying anything is unethical here. Sorry.
You haven't been treated unfairly. The position is no longer open at the moment for reasons you don't know. Yes, it might have been filled. It might have been put up in error. The money might have disappeared. Someone who was expected to leave is now staying. Lots of possibilities.
But they were wise to take down the notice if the job isn't still open. Much better than to string people along thinking that they have a chance that they really don't.
You can enquire why it was taken down, but you have no basis for making a change to the situation, so an "appeal" is not possible.
Your timeline also suggests that the notice had disappeared already when you sent your mail, giving you even less basis for any appeal.
Sorry that you are disappointed, but you need to take constructive action for your career and this isn't it. Move on.

Let me also add, just for completeness, is that the withdrawal of the announcement might be a temporary thing while they reevaluate their needs and resources. If it appears again, you can apply again. But it would be worse if you complain to them and claim they are unethical.
Moreover, if you really think they are unethical, you should surely search elsewhere. I've worked at places that are, indeed, unethical in their process and it isn't fun.

Good answer. I think the most important thing to emphasise is that the asker does not know why the posting was taken down and jumping to conclusions is a bad idea.

@Buffy, would you say it is ethically OK for the university to post no apology or explanation, and make no effort to tell people who might be in the middle of writing applications?

@toby544, what I would say is that they need to be honest with people who ask. But I'd also expect anyone with an interest who saw the ad disappear to ask. And for the others, they wouldn't likely see the apology anyway if they haven't looked again. Don't make it different or more complicated than it is. The OP saw that the ad had disappeared and there was no notice otherwise on the university's site and then, only then, made application. The OP can enquire, as I noted.

@Buffy You are not really answering my question, but I suppose it is clear that you think the answer is yes, it is ethically OK for the university to post no apology etc. I was not making things different or more complicated - you said there is "no basis for saying anything is unethical here," and I was disagreeing with that.

This is a good answer.  The only thing that is missing is OP apparently put in a lot of effort to make an outstanding application.  Considering that this is going to nothing, maybe it is better for OP to put in some effort to make a decent application.  If it gets tossed as apparently this one was then it does not matter how much effort was put in.  If OPs application is reviewed it only has to be good enough to make the first cut - any effort above that is wasted.

IANAL but you seem very confident that this is true in all jurisdictions without knowing where the university in question is located.

@emory I did put a lot of effort into it, but because they did require a lot of information from us. A personal motivation letter and letters of recommendation, which creates a bit of an uncomfortable situation, because I had to ask a couple contacts to write letters, informed them of their deadline and they did as requested. But the university decided to change the deadline without further infos...

@EricLino I will agree with you that they are jerks for even if they did not make you do this work - they strongly encouraged you to put all this effort in and it was for nothing.  But there is nothing to be done.  That is why I always put in a minimal application.  For the most part, my applications are canned but I feel that was going to happen anyway.  If they read my application and like it they can ask for more.

Your frustration is justified and reasonable.
A job advert is an invitation to apply. This is an implied social contract, where both parties assume responsibilities and have expectations.
A University expects applicants to read job specification and send well-prepared  applications tailored to the specific role, formatted under certain guidelines and often including material written specifically for this role. Applicants expect that their applications will be carefully evaluated and that the process is genuine and that applicants who meet selection criteria and have appropriate skills will be invited for the interview.
If University closes the job search earlier without warning, the effort of candidates is wasted and frustration is justified.
Compare it to invitation to a wedding. You bought a suit, you wrote a speech, and suddenly you are uninvited and the festivities go ahead without you. Is it unfair?

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I understand the frustration, but these things can happen for a variety of reasons.
Anyway, be proactive, it was surely not meant against you, so you should still keep a positive attitude and you should contact them telling that you saw the opening and you were planning to apply, unfortunately you did not complete the application in time but you are interested in similar positions coming up.
Maybe you will discover that they are still consdiering applications, but they prefer to keep a low profile for the opening. Or they will tell you when to apply for the next similar position.
There is only part that you can blame yourself: applying "late". Maybe the position was open since 3 months ago, and they were tired of receiving application from all over the world, so they pulled down the opening earlier.

If the consideration of applications is done on a rolling basis and the position can be closed before the deadline, the job advert should have explicitly say so. Otherwise, it is fair to assume all applications made by deadline will be considered.

@DmitrySavostyanov I agree. But we still do not know why the opening was pulled down. Some zealant clerk in the administration? some academic overwhelmed by applications? all is possible, but nothing is helpful to OP situation.

We also do not know the actual wording of the posting (the whole posting). Just some snippets that may not be the actual words.

What would be the mature decision here?

Well, some might say it would be to assume you have no chance of being accepted + don't feel like trying to rectify the conduct of the university.
I would say you should at least ask what happened. But - obviously, the application email was insufficient to get a reply, so you should figure out where you could make a voice call; could be one of:

The intended PI.
The research group administrator.
The departmental secretariat.
The staff member in charge of Ph.D. admission/recruitment.
The department chair ??

Find the right person to call. Through this first person, find who was responsible for this recruitment process and contact that person. Then (or even on the first call) you can ask whether the posting was filled or whether the ad was removed for another reason.
Assuming it was just filled with an applicat through the ad - explain to them why this is a problem for applicants who had assumed they could submit at any time until the 12th, so that the process becomes unfair. If you were to make this call until the 12th or a little later, you could even request that additional applicants, including yourself, be considered (though it would be a bit of a long shot). at this point it's probably hopeless though, but at least you got to politely admonish them. Maybe they'll give it a bit more thought next time.
Important: In all such conversations:

Avoid raising your voice, and keep a slow and calm speaking tempo;
Avoid making strong accusations, and perhaps any accusations; prefer making suggestions or pointing out diffuse problems;
Avoid using harsh language (e.g. "I was robbed of my chance", "it is immoral to", "it cannot be tolerated" etc. - don't say that)

... not because that's what you should believe, but because you have no leverage over anybody and they might just cut off the conversation with an unknown person who's annoying them.

The only then clause is odd. I have never added that myself to any job ads I put out, never seen anybody else do it, and it makes no sense that I can see to do it.
One can evaluate applications as they come in, collect them all and do them in batches, or any suitable combination thereof, but all of that is internal admin business. Saying "We promise we will sit on them and not look at any of them until after the closing date," really serves no purpose other than giving a late applicant a reason to feel hard done by when we decide to renege on that promise.
So if they really said that and actually filled the position (rather than, say, were unable to appoint anybody because an audit suddenly revealed internal fraud and froze all hirings - and yes, I have seen that happen more than once, in different institutions!), yes, then they have been unethical as well as pretty erratic, which probably means you dodged a bullet.
(Some further details: filling up a PhD programme is not the same as appointing for tenure track. For PhD students, it makes sense to make offers as good candidates come along, whereas for a permanent position you would want to wait past the closing date before you shortlist for interview, let alone appoint. If an institution deviates from these common sense guidelines, there may be more going on, and the ten-foot pole principle applies.)

Perhaps they wanted to signal that an early application or a late application was an irrelevant signal. It is a signal in some places (early applications, send at the earliest humanly possible time, are looked at more favorably).

I agree on your verdict of "erratic", but "unethical"?!? I recommend you replace that vage bullshit term by a meaningful one, "immoral", and think again. Is it immoral to remove a job application?

For PhD students, it makes sense to make offers as good candidates come along it's very common in some parts of the world for PhD programmes to have defined annual intakes. And in this case applications are reviewed all at once, after a set deadline.

Question not clear from your post (sorry, comments not active for me yet). I don't disagree with sone of above, but there seems to be some information not provided and a perspective not discussed
You say the "ad" is taken down but you found the posting (and application link) still on the University website, correct?
IME (US, R1s mostly, including applying and hiring) - to me this sounds very common. Often there are only funds to post external ads for part of the job opening window (i.e. PhD applications we start advertising in August (informal), applications close Dec1, and the ad in Science magazine (and therefore scraped by Indeed, LinkedIn, etc) only up for October 1-31). The job ad then is now gone, but the posting is not closed (we just can't afford to pay the ad longer)  perhaps this is the same for your application. If so, then if your application is in before the deadline it should still be considered as normal with no input from you. There are other scenarios, of course, depending on the exact wording but if you saw a paid ad somewhere this would be my most likely explanation.

In some jurisdictions, universities are required to post positions online for at least 24 hours, regardless if it’s filled or not. That way, they’re not facing lawsuits about internal filling without public knowledge. Sorry it has to be like this but that’s life.

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text:
Technical editor changed author order of the paper
Recently, I attended a conference as a corresponding author of a paper with five authors. After the paper was published in the conference proceedings, I realized that the technical editor changed the authors order by grouping them according to their affiliations. Is this acceptable?
I feel a bit responsible to my coauthors (being the corresponding author) even though this publication style also affected other papers in the proceedings. But what should I do?

I think some journals (in some fields) require that authors be listed in alphabetical order.

This was not the case here. The authors were grouped according to their institutions.

Is this a field where author order is assumed to matter (e.g., applied CS)? If yes, this is completely unacceptable. If no, it is still very strange, but maybe not a big deal in the end. I can only imagine that your paper was handled by a very inexperienced technical editor who is simply not aware that the order of authors is not just a stylistic question, but actually has CV implications (in some cases, at least).
One way or another, you should get in touch with the organizers of the conference (e.g., the publication chair if they have one, the general chair if not) and let them know. Maybe it is still possible to fix this, but at least the responsible people should be aware of this issue.

Even in fields where author order is not normally used to indicate different levels of contribution or seniority (for example, theoretical CS), this is completely unacceptable!

In some sense it matters more in fields where author order doesn't matter, because in these fields all papers will be in alphabetical order unless there is some strong reason otherwise. If the authors of a math paper are listed as "Bethe, Alpher, and Gamow", readers will assume that Bethe made an extraordinary contribution to the paper so overwhelming as to override the usual conventions of the field.

Had the same issue on a highly respected publisher. They ended up publishing the paper again with the correct order.

(Copy Editor speaking.)
This is completely unacceptable and even for more than one reason:

They obviously did not ask you to proof-read the final version. If they did, you would have spotted this change I suppose. Not making final proofs is acceptable only in small local workshops and seminars where minor mistakes don't matter since the publications are not quite real publications, and also where things are usually easy to correct.
They deliberately changed the order of the authors. In fields where each position is something different, this is completely unacceptable. In fields where this is not the case and the authors are listed alphabetically, it's still pretty bad, because it raises a question why you chose this order (people won't assume it was the technical editor who changed the order).

What should you do?

Inform your co-authors. Let them know what has happened, that it wasn't your action and that you're looking into it more. The sooner you do this the better, to avoid confusion whether you're cheating them.
Raise it up. Ask both the publisher and the Program Committee chair for explanation of this action. Ask them to change it instantly -- they will probably tell you that it's impossible and they'll likely be right, but it doesn't matter. It's their mistake, not yours.
If you want, you can also speak about copyrights. The order of authors is, in my opinion, an integral part of the paper, and it means that they published something for which you did not transfer the copyrights.

I don't think you can change anything for your paper (it's probably too late), but you can certainly change something for other people publishing with the same publisher in the future. In my opinion, this is worth it.

Even if the editors cannot change the paper in the sense of replacing the faulty version with a correct version, if they want to they can certainly publish a correction somewhere.  That would still be useful to the OP: he can place a link to that corrigendum on his CV / webpage and then people who care will believe him when he says he didn't do this.


text:
How can I tackle self-doubt while writing my first paper?
I finished my Bachelor's degree this year. I worked on some research with my advisor and after a few months, we decided that there's enough interesting research to be able to write a paper. This will be my first paper. He told me that I'll be the first author and asked me to start working on it. After the initial excitement wore off and I sat down to actually start writing the paper, I was, and continue to be, plagued with self-doubt and confusion. Following are a few aspects I find daunting about the process of paper writing:

I am suddenly unsure if my results are even correct or sophisticated enough. I feel worried that I have either made a mistake somewhere or that my results are incomplete and there's more to be done.
I am intimidated by the prospect of writing the introduction, which is usually a high-level literature overview. Although I have read multiple papers for my work, and based my project on a seminal few, I am worried I won't be able to describe the state-of-the-art in the field well enough or forget to cite an important paper that I don't know about.
My writing's not academic enough.

I did tell my advisor about this, and he assured me that he understands and asked me to share the manuscript with him. But I cannot bring myself to do it because a) it's very incomplete and b) I feel worried that he'll go through it and be disappointed in me. I know it's probably irrational but I cannot help feeling this way.
These feelings have severely hindered the progress of my paper and research. Is it normal to feel this way and how do I tackle them and get on with writing my paper?

Congrats for the opportunity!
It is normal to feel that way. Research is both challenging and rewarding.  There will be always a lot of ups and downs. Don't be discouraged.

He said "Start working on it" ... so it is natural that you will have a partial manuscript to share with him, then he will reply with comments, or even re-written sections.  And you continue, back-and-forth like this, the paper getting better as you go.  It is OK if your first draft does not even have an intriduction.

Regarding the two reasons you don't allow yourself to give your manuscript to your advisor: a) is precisely one of the main reasons people give their manuscript to their advisors; usually there's a constant come-and-go between both to polish (and sometimes rewrite!) the manuscript until it's ready to be send to revision to other people which will also return your paper to be more polished; THIS IS PERFECTLY NORMAL; b) no advisor ever expects to receive a (almost) perfect first draft; there's hardly a chance for dissapointment specially when you've been told that your research is worth a paper-

Slightly off-topic and probably a somewhat tangential advice, but what I'm detecting here is a (quite heavy) fear of failure on yourself; this could cause serious problems for you from here on, so I suggest that (independently on what you do to push and allow yourself to write this paper) seek help for that issue on a personal level. Congratulations on your chance and best of luck with your publication.

Don't worry about your writing begin "not academic enough". Trying to copy a writing style blindly will just lead to everyone copying the same bad habits (in addition to the good ones). Write for clarity and precision (and probably conciseness, depending on the page limits used in your field). The good parts of the common academic writing styles are generally in service of one of those goals.

Terence Tao has some advice on his blog post https://terrytao.wordpress.com/advice-on-writing-papers/

Thanks everyone for the comments, they were very helpful :-) @JoshPart I think you might be right about the fear of failure. Sigh.

@Tom thanks for the link! Really useful stuff.

Let me start by pointing out that the usual way to learn how to write an academic paper is to write a really bad draft, get it critiqued by a supervisor, to rewrite it to make it slightly less bad, get it critiqued again (or even directly rewritten, if there is an imminent deadline); and to then repeat the process a couple of times. You have done Step 1 ("Write a really bad draft"), and proceeding to Step 2 ("Give your supervisor the chance to tell you what is wrong is it") is the natural next step.
To your specific points:

Worry that the results are not sophiscated/interesting/impressive enough.

You aren't really qualified to judge this. It is common to feel that since you understand your own work, whereas what other people have done is harder to comprehend, your own work must be too simple. Ignore this feeling. If your supervisor thinks the results are enough to try and publish, wait and see what the referees say.

Worry that your results are wrong.

This one is a good worry, as long as it is productive. Double-check, triple-check. Include the steps you have taken to be absolutely sure in the draft.

Worry that your results are incomplete.

It is very rare to have the ultimate answer in any one paper. If you have concrete ideas, discuss with your supervisor whether it is worthwhile pursuing them before publication. If you just have the generic feeling that there is more to be done, ignore it. It's probably right, but it doesn't matter.

Writing the introduction

There are two ways to handle writing the introduction: A. Write a sloppy one at the start, then write the paper, then completely rewrite the introduction. B. Write the introduction last.
Definitely don't try to write a good introduction early on in the process, that just causes writer's block. Moreover, the introduction is where you put your stuff into the broader context. Naturally, the introduction will be the section where it makes the most sense to have your supervisor write it (if it is a co-authored paper). So don't worry about this, and don't let the remaining worries derail or delay writing the rest of the paper.

Writing style

The one experienced that helped me develop my own writing style the most was writing a draft, and then reading the complete rewrite a coauthor of mine did to it. I could still see the thoughts I had brought to paper, but they were expressed much clearer, much more elegantly. By studying the changes I learnt a lot. So, going back to what I wrote first: Yes, your style may be bad. Your supervisor is going to expect a bad draft. You'll get better by getting feedback and learning from it, which means you have to let your supervisor read the bad stuff you have written.

Thanks so much @Arno! Lots of useful advice here.

Do not worry!! This is 100% normal. Trust your supervisor - they are an expert and they think your work is good.
Don't worry about being sophisticated. No one really wants to read sophisticated stuff anyway - given a chance to read a simple, interesting paper and a complex "sophisticated" one I know which I would prefer.
And also, don't forget that whatever you write and submit to a journal will then be looked at by the editor and a couple of peer reviewers whose job it is to a) check it's good and b) suggest ways you can make it even better.
"Academic writing" is often dull, uninspired and unreadable. Just write as clearly as you can. Your readers will thank you for it. Don't try to be "academic" with it.
You got this - don't stress - trust the process!

Thanks a lot @Flaming Ducks! This is reassuring.

Congrats for the opportunity of writing your first paper!

I did tell my advisor about this, and he assured me that he understands and asked me to share the manuscript with him.

If your supervisor gives you this opportunity, and wants to sit down with you on the manuscript, definitely take advantage of it and do it. That's what supervisors are for - they serve as mentors. As long as you don't get any input from outside, it's hard to improve. If you take the opportunity to learn from them, you will automatically improve your academic writing style - which is difficult to get into in the first place.
The fear that the state of your manuscript will reflect badly on you is therefore, in my opinion, somewhat unfounded. If your supervisor trusts you enough to write a paper, they already have a good opinion of you and will certainly not lose faith in your abilities because of an incomplete paper.

Thanks a lot @pbaer! :-)


text:
How do you comment on rapid improvement in a student's performance?
Sometimes, it can happen that a graduate student who is struggling on a project finally sees everything "click," and becomes far more productive. It might be due to a change in attitude, an improved work ethic, serendipitous success, or some combination of all of the above.
In writing recommendations, how do you comment on the student's rapid turnaround, without making the previous state of the work (in which the student was working, and clearly understood what needed to be done, but didn't have the results to show for it) seem like it was a weakness or liability on the part of the student. Given how real signs of weakness can cause problems for people reviewing the letters, how do you call attention to the fact that the student underwent such a startling transformation, while acknowledging the previous struggles and not harming the student's chances?

without making the previous state of the work...seem like it was a weakness or liability. — Sorry?  It was a weakness and a liability!  Recognizing and overcoming one's own weaknesses is a strong indicator of success. Why would you want to hide that?

I want to convey that the issue was not the fault of the student's. But I want to avoid leaving the impression that the student wasn't working hard enough, which isn't the case.

I agree with JeffE's comment -- this is an opportunity to show fantastic improvement, which looks great in a letter.  If the improvement really was because of "serendipitous success," it seems that it would be difficult to sustain, unless it happens that the groundbreaking work was so monumental that it is prize-worthy (and even then, chance favors only the prepared mind).
If I'm writing a positive letter (which is almost always the case--I'll try to convince a student that I'm not the correct person if I feel I won't be able to justify a strong letter), my goal is to convince the letter-reader that I'd hire/accept the person now, and why.  Something like the following might fit this case:

I have been particularly impressed by X's recent work on her project, Nuclear Powered Time Travel via a Modified Consumer Vehicle.  Despite a frustrating set of circumstances that returned limited results in the early stages of the project, her hard work and persistence led to a breakthrough that she is currently preparing for submission to The Twin Paradox Journal, and will undoubtedly lead to further successful results.  Specifically, she was finally able to properly shield the flux-capacitor plutonium containment compartment in her design, reducing temporal errors by 99% and leading to far greater box office returns.

If the student's previous attitude, or struggles don't put her in a particularly good light, don't include them explicitly.  Again, it goes back to would I hire or accept the student now?  If you believe that by not including the specifics you're not being honest, then maybe you wouldn't feel comfortable with such a positive letter anyway.