text:
Could I use colors to distinguish variables in a paper?
Often when distinguishing one variable from another we use different characters or if using the same character different subscripts.  For instance we might use x for one variable, and y for another, or we might use x_1 for one variable and x_2 for another.  I was wondering if in a paper I could get away with using the same character but with different colors when referring to different variables.  So for instance if I was referring to two different objects, then I might refer to variables related to one object using the color red and variables related to the other object using the color blue, and variables related to both objects using the color magenta.  So for example the schrodinger equation for a system of particles only interacting with each other would be written in the form

Would writing equations with variables denoted with color make a paper less likely to get published assuming that I explained what the colors meant?

Related: https://academia.stackexchange.com/q/13616/68109

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For accessibility purposes (USA) one must use some other mechanism of distinguishing such as font, style, etc.  See answers also.

So to clarify, you mean to use \red{x} instead of x_1, \green{x} instead of x_2 and so on, were x_i, y_i, z_i is for particle i, right?

So you mean the red $1/m$ is different from the green $1/m$? If I saw this in print, I doubt it would occur to me that the sum of second partial derivatives with respect to the $x,y,z$ of one color is a different thing from the sum of second partial derivatives with respect to the $x,y,z$ of another color.

@PabloH That's right!

Why not use $\green{x_1}$ and $\red{x_2}$?  Meaning use both subscripts and color in agreement with each other?  Then the color adds to the paper and makes it easier to read, but those with the problems below can still read it.

I personally like it, but it is plainly obvious that publisher will not.  If you are writing the article to persuade, inform, etc. me then smooth move - but I have no tenure granting power so WHY?  The people that will matter in your career will not like it and it will not help you advance.

BTW I did something similar when I was a graduate student.  I found that using colored pencils could help me understand some difficult equations better.  But I never attempted to publish my lecture notes.

It is a good question, because it may seem a good idea when your (working)life is fully focused on a certain topic.
The answers will provide plenty of reasons why it is not a good idea.

By the way, as in @emory's comment, according to HCI and InfoViz, colour (as in hue, i.e. chrominance) is best used to convey categorical (a.k.a. nominal) attributes. So perhaps it'd be more helpful to colour per kind of element. E.g. constants versus variables versus symbols, or plain versus derived, and so on. Similiar to syntax highlighting in code editors.

Do not do this.  Those of us who prefer to read on paper and have black and white printers will be extremely confused.

Also reduces accessibility, e.g. for the colour blind.

It would also be a pain for a reader with a colour printer or working on screen, who wanted to make notes

Also I've seen people reading papers on e-ink screens (admittedly back when there was a large-screen kindle)

Or if you are taking notes/working on this, and you don't have a multi-colored pen on hand with the same colors the paper uses.

"printers"? What is this ancient technology you speak of?

@Evorlor They magically turn what is on you screen into a physical object. Like a replicator.

@GoodDeeds a very hip thing to say and yes it's true.  But the color approach can help those with dyslexia.

@Evorlor a 'printer' is like a 3d printer, but it only 3d prints a single layer. It sounds ridiculous, I know.

Even if it isn't printed, there's still a good shot that someone else might need to write down the equation to manipulate it, and it's annoying to get colored writing utensils.

FWIW, there is some historical precedence for using color (though in a different context). See Bryant's take on "Elements of Euclid". It was reworked in ConTeX recently and you can buy a physical copy, if you like

Potential Citations will also be an issue, as it makes it either hard to cite the paper in question, or straight-up requires follow-up papers to do the same thing. In general, referring to the paper (as in a conversation) will be more difficult, how would even the oral communication work? "If we take a look at x blue..."?

(Personal opinions, so a fully anecdotal answer, but too long for a comment.)
My immediate thought when seeing that screenshot was "wait, aren't those red and green ones the same variable?" (Obviously, I don't know the Schrödinger equations.)
I automatically expected that of course you meant to use color only for emphasis, while still keeping the "traditional" subscripts or whatever to actually distinguish them. I could see some uses in using color as a helper, while keeping the same equation readable if, no, when it gets turned black-and-white. But color as the only distinguishing feature seems unconventional enough to be surprising.
Even if colors are used only for emphasis, the choice of them can be somewhat problematic. My immediate second thought was about the blue-on-black being almost completely unreadable. Someone with bad eyesight, or color blindness, or such might have different problems. Switching the background from black to white might also require reconsidering the colors.

exactly. problem isn't for just non-colourblind or black and white prints. even for the regular reading with colour it is confusing like w/c variable is what.

And of course if you prefer a black background, as I do, the dark blue variables which I assume are in the third parenthesized group are effectively invisible.

I did this in a StackExchange answer, once. But I also made sure to include an explanation of the issue in the surrounding text, and to phrase that explanation in such a way that the variables could be identified without needing to see the colors. I also called out the fact that the variable clash was confusing, and renamed the (bound) variable on the next line. IMHO this is OK, but even so I was a little concerned that the color might not be fully accessible to everyone.

FWIW I do know the Schrödinger equation fairly well and I had the same thought as you did, ilkkachu: the same variable in different colors still looks like the same variable.

FWIW, as I understand the law where I am, it's fine to use colour as an aid, as long as it's not the only way to distinguish things; there must always be some other way that colour-blind folks can use. Now, I doubt any law applies in this case, but I think it's still a good principle — and this answer explains some of the reasons.

The obvious problem, as noted in another answer, is monochrome (black) printers. Yes, you can get a color printer for very little money (not much more than the cost of the ink cartridges), monochrome printers are still far more common for those who need to print a moderate amount (hundreds to thousands of pages per month) because the cheap color printers tend to cost a lot per page (inkjet) and the expensive color printers (laser) have a high upfront cost.
But there are other problems as well:

Screen readers for the visually impaired. I'm amazed (my evil twin has told me all about it) how many people rely on screen readers to read email, web pages and everything else on a computer. The colors would either be lost altogether or would add a lot of extra time to the reading ("white a blue x squared").
Copying. Even if the journal is published in color, someone might make a photocopy (yes, an actual photocopy, not a print from a PDF!) and that will very often be only (or default) in black and white.
Readability. In addition to true color blindness, color text can be harder to read on paper than black text simply because it has lower contrast.

Re color printers for "not much more than the cost of the ink cartridges", it's often less.  And for many of us, the cartridges dry up long before they run out of ink.

If you are trying to publish in a journal which has printed issues, you will (at best) eventually run into the problem that these (even ones which normally have no publication charge, which is pretty much all the ones in my field) typically impose a significant charge for every page which needs to appear in colour. Normally that might just be one page with a particular diagram, but in your case it sounds like it will be most of the pages, and there's no way for you to argue that colour printing isn't really necessary.
However, I very much doubt it will get to that stage, for the excellent reason Alexander Woo gives. I can't print in colour at work, and I doubt that's unusual. That means I wouldn't review your paper, since I always make notes on a printed copy when reviewing. And the editor might veto this idea even before trying to find reviewers, since readers will want to print.

Since your profile avatar mentions physics as an interest of you, I assume you either possess, or know someone with working knowledge of LaTeX. (If not yet, learnlatex.org is an entry, and tex.stackexchange worth a subscription.)
If so, you may consider underbraces, e.g.

which define the terms contributing to the global function in mind.  In the paper/poster/presentation, you may focus on each of them on a one-by-one basis (minima/maxima/symmetry and other peculiarities).  If the equation spans into a second column, you equally may split the equations over multiple lines, too.

The MWE of above was generated on latex2png.com (no affiliation, your TeX editor of choice likely equally offers a .tex to .png/.pdf conversion) with this snippet:
%
% syntax of an underbrace:  \underbrace{content to underbrace}_{underbrace label}
%
i\hbar \frac{\partial \Psi}{\partial t} = - \frac{\hbar^2}{2} \bigg(%
%
\underbrace{\frac{1}{m} \left( \frac{\partial^2 \Psi}{\partial x^2} + \frac{\partial^2 \Psi}{\partial x^2} + \frac{\partial^2 \Psi}{\partial x^2}\right)}_{\text{contribution a}} + %
%
\underbrace{\frac{1}{m} \left( \frac{\partial^2 \Psi}{\partial x^2} + \frac{\partial^2 \Psi}{\partial x^2} + \frac{\partial^2 \Psi}{\partial x^2}\right)}_{\text{contribution b}} + %
%
\underbrace{\frac{1}{m} \left( \frac{\partial^2 \Psi}{\partial x^2} + \frac{\partial^2 \Psi}{\partial x^2} + \frac{\partial^2 \Psi}{\partial x^2}\right)}_{\text{contribution c}}  %
%
\bigg)
%
%
+ V_1\Psi + V_2\Psi + V_3\Psi

You should not "get away with" anything while trying to publish your work. You comply with the rules/guidelines, and everyone will be happy. Less headache for everyone (you, the editor, the publisher, the readers) - there's already a lot of headache in publishing a paper.
"Could I use color...", yes you could, in theory, depending on the rules imposed by your publisher. But you probably shouldn't.
The guidelines are there for their reasons. In some conferences or journals I sent papers too, they even highlighted that I couldn't/shouldn't use/rely on colors in my charts, let alone for the text content (like the variables). Instead of using red column, blue column, etc. which is discouraged, they suggest using texture patterns to fill the columns. The extensive use of (verbose) description using colors in the Figure captions or in the text body is also frowned upon: e.g. "we can see that the red line diverges significantly lower from the blue and green lines", instead use markers on chart lines, and the legends in the chart should be sufficient enough (a picture is worth a thousand words, no?).

If it helps to convey meaning and the advantages outweigh the disadvantages mentioned in the other answers, do it.
The answers make some good points about the usage in your example, but I honestly think that using color in equations is a good idea. Inventing new notation to declutter equations has certainly been done before. I think color could really help make complex equations easier to understand. The common use of color for syntax highlighting for programming languages supports this idea.
Honestly, I can't believe the most highly voted answer makes the argument that people won't be able to distinguish it if they print it out in black and white. Literature from recent years is full of images and graphs that are useless in black and white. For instance, I see a lot of biology papers that include fluorescence microscopy images like this:

Fluorescence microscopy image from Slater et al. (CC BY 1.0) https://doi.org/10.1371/journal.pmed.0040164
You won't get much out of an image like that in monochrome. In the graph below from a recent PLOS ONE paper, color and shape both carry distinct meanings, so you won't be to get all of the information in the plot without color:

Zhao et al. (CC BY 4.0) https://doi.org/10.1371/journal.pcbi.1009345
Let me address some criticisms in the other answers.

Not accessible for people with colorblindness. You can avoid ambiguity for people with the most common types of colorblindness by choosing your colors carefully. This Nature Methods paper has some good suggestions. Some will argue that you should never represent information purely with color, but in the era of "big data" you really need all of the tools available to synthesize complex information into a plot. At the end of the day, we have to make some compromises. Most plots are not accessible to people with visual impairments, yet we still rely on them heavily for the enormous benefits they have in imparting information.

The publisher won't let you. You could include the equation as a "figure" or "diagram" rather than a pure equation. If they don't let you do that, then find another journal.

Extra charges for color pages. Many journals used to charge extra for color pages, but, increasingly, journals are all digital and these page charges have gone away. I haven't published in a journal with such charges for 10 years. Journals used to suggest using different patterns for different data rather than colors, but high contrast patterns can be distracting and difficult to distinguish.

As you've seen here, you are likely to experience some backlash when introducing a notational innovation; however, if it truly enhances understanding, others may pick it up and it may become more standard despite initial misgivings.

Part of the difference here might be differences in working patterns between fields.  If you're a biologist, you're probably in your lab when reading a paper, and that means a computer with a good screen is available.  As a mathematician, if I'm seriously reading a paper (rather than just looking up a reference), I'm at a coffeeshop (without my laptop), if not on top of a mountain or at the beach.

Or I may well be reading it on a tablet, at night, with the screen in dark mode.  The examples here work (at least for me) because the background colors of the images are specified.  But in the OP's example, the background is not specified, which makes the dark blue basically invisible on my black background.  Those of you who prefer light backgrounds would have similar problems seeing my highly visible yellow text.

@jamesqf I suggested that the equation should be typeset as a diagram or figure. In this case, the background of the diagram could be fixed to be white.

@AlexanderWoo It sounds to me like different people and different fields have different ways of reading papers. When I'm seriously reading a paper, I usually want internet access, because I often end up downloading and skimming references, as well as googling chemical structures and unknown terms (often protein names).

With regard to those two examples that you chose, the first actually seems separate the images by showing the first of each set of colocalized structures on the left. Further, when the image is converted to grayscale, each set of structures has two distinct brightnesses. Although the image uses color, it does not seem to rely on it as much as you say. Also, note that it is a paper from 2006, so it should perhaps not necessarily be taken as guidance on best practices in the field today.

As for the second image, I would have to say that while color certainly adds something to the image in terms of interpretation, it is far from ideal because it is an unreadable mess in grayscale (and undoubtedly for people with some types of color blindness). With the image already being quite busy in color, it would probably be advisable to consider an alternate means of presenting the data.

@Obie2.0 "It is an unreadable mess in grayscale." This is exactly my point. For better or for worse, much current literature includes figures that rely solely on color to convey information. It's not hard to find more examples like these. For the first figure, including the green image on the left helps, but the image on the right has red, green, and blue, so some information is definitely lost going to grayscale (the blue and red things can't be distinguished).

The blue and red structures in the middle picture actually do have different brightnesses, as well as different textures, so they can be distinguished even in the grayscale image. The green and red parts, on the other hand, do become hard to distinguish.

"This is exactly my point. For better or for worse, much current literature includes figures that rely solely on color to convey information."
That's the reason slavery lasted so long: it was the state-of-art of cotton picking! Which does not mean it was the most effective way, nor the best way.
Especially reg. the second plot, it is quite sloppy visualization, to the point that same data are plotted separated in inserts B-C-D, making the different shapes of marker useless.

@WaterMolecule re "I suggested that the equation should be typeset as a diagram or figure" but typesetting an equation as an image (even a vector image if that's supported by the journal) plays havoc with other assistance technologies.  I don't know if any screen readers could handle this example but simpler equations can be read out.

Even in colour the points are so dense in the "gut" region that distinguishing the shapes is hard.  I don't know whether that matters, but the use of different shapes implies it does.  I really don't think that figure is a great example, but not for the use of colours. Actual photographic images as in the fluorescence micrographs are harder to deal with, even if composite, because displaying the channels separately doesn't show (anti-)correlations anything like as clearly as overlaying, and combining colours where 2 emissions occur requires a CMY or RGB colour set

my opinion in 2 parts:
part1. bad since confusing even for non-colourblind.
besides having to read the thingy as like 'red-x', 'green-x', what's hard is reproducing the equation like when we write the equation in our notes we'll write $(red-x)^2$? (as mentioned in a comment above this is the same with those cases where multiple fonts like mathfrak, mathscr, mathcal are all used in the same thing)
part2. BUT i think a good idea for certain cases, but most probably just informal cases of explaining things directly to students or other colleagues, where you have show certain details in proofs

BUT as much as possible no using different colours for the same letter... here i had to use different colours for the same letter y to show where each y was going. (I forgot the exact context, but I think $y_0$ would've been weird to use. But right now I'm screaming at my past self to use $y_0$ instead somehow. idk.)

The problem with colors in an equation, is suppose I don't believe your calculations and want to re-derive the equations myself with pen and paper. Do I need now need to find a set of color pens to work with? and hope I don't pick up the wrong pen at the wrong time? Just make your readers lives easier and just use different symbols (or subscripts) for different variables. Or if the equation is still too complicated break it up into smaller chunks and use intermediate variables.

As others have said, color is fine as an aid (so long as you select more sensible color combinations than dark-blue on black), but it is useless on its own
Something I haven't noticed mentioned yet: if someone wants to quote or discuss your work, whether in speech or writing, they'd be unable to do so without circumlocutions like "the blue m".
No form of OCR would be able to read the expression. MatLab would not understand it.
You could not even ask this question without using an image.
So it's not just about "black and white printing" or "e-readers" or "colorblind people" - it's about people being able to apply the expression you have written.

Existing answers make a lot of different points, but there’s an overarching summary point that I think hasn’t been highlighted: You’re approaching the question a bit wrong.  Your main question shouldn’t be “Could I do this?” or “Would this reduce the chances of publication?” — it should be “Is this good scientific writing?”
As other answers amply show, the answer to that is “Certainly not, in most people’s judgement” — it has many clear and serious drawbacks, and not much advantage.  But what I want to emphasise is that all these reasons aren’t arbitrary rules or conventions of publishing — they’re about making your paper clear and useful to readers.  Asking “will publishers be willing or able to accept this?” is only useful when you’re already confident that something is good writing style, and able to make a case for that to people who disagree.

The general consensus is to not use colors.
However, this also depends on the field.
Some fields, particularly in computer science, have accepted the use of colors for sake of readability.
The following does not only hold for papers, but also for presentations, since accessibility at conferences or workshops should also be considered.
If you really want to add colors to your work, some care must be taken.
As the other answers have indicated, using colors to convey important information can seriously impede the experience for the color-blind.
It really depends on what colors you choose. You can choose colors that any type of colorblind people can still distinguish.
To make sure you use the right colors, use a tool like Sim Daltonism.
In order to distinguish on black-white print, it's advisable to add additional emphasis/use different fonts, e.g. the blue one is bold, the other, green one cursive, the next, orange one is underlined.
That way, people with monochromatic vision and people who read your work on a black-white printout can still benefit from your highlighting.
That said, depending on how adopted the use of colors is in your field, you might have more trouble than good if researchers, and ultimately referees, are not used to it and strongly oppose to the use of syntax highlighting, despite its benefits and, if done rightly, accessibility. To try to remedy this, you should add a line to your paper that says "This paper uses colors. While still readable as a black-white print, for an enhanced experience, view this paper in colors."
Concluding, yes you do can use colors in your paper. However, do so in a sensible manner that keeps the accessibility. Nevertheless, you should really ponder whether the inclusion of colors+font diversification is actually beneficial to your work after all.
As a personal judgement from your screenshot, the current choice of colors and fonts makes it much more difficult to read than without colors. You should abstain from using a hard blue or a hard red on black background.

"...computer science, have accepted the use of colors..." Not in the way OP is proposing, no. Code terms are distinguished by grammar, naming, capitalization, and enforced uniqueness. Color/font are additional aids by the viewing software, never consciously applied by the developer as they work, and never solely used to distinguish between unique items of the same type, as OP is proposing. Instead, all languages are legible if printed monochrome and monospaced, because we have not accepted color as syntactically meaningful, and would not. The only exceptions are toy langs like Whitespace.

I do agree with you. Nevertheless, especially with e.g. POPL papers, authors really do seem to consciously choose to use color + font alteration to distinguish between syntax of multiple languages within one development, e.g. true in language A and true in language B. As I've explained, the use of colors + font alteration in such a scenario still renders the work as legible even if printed monochrome or when read by colorblind. Here is an example: https://www.ccs.neu.edu/home/amal/papers/fabcc.pdf

@DewiMorgan: most modern programming languages use reserved words and keywords that are distinguishable without color or font. However, Algol 68 allowed identifiers and keywords to be spelled the same way, distinguished by font bold/nit, or .stropping. This history may indicate that font/color is a bad idea, although it might purely be that color printers and displays were not available back in the old days. Going back to this would avoid the excesses that C++ goes to to avoid breaking old programs as it adds new features.

@KrazyGlew That's fair comment: I thought that using bold for stropped identifiers was only used in print, not when writing code, but maybe editors/compilers allowed coders to strop ( https://en.wikipedia.org/wiki/Stropping_(syntax) ) using control characters for bolding rather than, say, apostrophes? Algol was WAY before my time, so if you say they were a thing, that's good enough for me. Plus, those were the days of hand-compiling to punched cards with no IDEs, so I admit the distinction between "code for print" and "code for compiling to punched cards" must've been fuzzier.


text:
Can one get a degree in a field one has not formally taken any classes in?
If one hadn't taken formally taken any classes relating to a field but was able to demonstrate sufficient competence in the field could one get a degree in that field?

Do you mean a honorary degree like a honoris causa doctorate?  Depends on what your local school defines as convincing expertise/engagement for your profession/a group (an example) instead of passing written/oral exams.

How would you display sufficient competence in the field?  How would you have acquired sufficient competence in the field?

I feel like "relating to a field" is vague. I know a person who has a PhD in microbiology but has never taken a microbiology course. They have, however, taken courses in molecular biology and biochemistry. Are those classes sufficiently related?

Academically, yes.  The problem is demonstrating you are competent (as judged by the academic unit) in the topics required to get the degree.
In other words, if you can find a school that will let you meet the requirement of all the classes without enrolling in any of these classes, this school might let you get a degree.  This is unlikely to be limited to taking final exams in terminal courses since final exams are usually only one component of the final grade.
On the practical side, I doubt university administrators (including academic chairs) will let you get away with something like this.  If anything, they’d probably want the income (or whatever other form of recognition or metric) associated with 4 years of study, so it wouldn’t make much sense to allow people to get degrees without studying in their program (at least in reputable institutions).
One could envisage a scenario where a unit would waive the pre-requisites and invite the student to enrol in upper year courses, thereby requiring the student to complete some of the coursework required for the degree but still getting the full degree.  I’ve seen this done once in 25 years (not at my institution), to allow a gifted student straight into graduate school.  However, this cannot be done in every area: you can imagine that in some discipline with labs (for instance chemistry or biology), demonstrating competence in the experimental aspects of the fields is not something can be done so easily.
I must admit that the most common and unfortunate scenario I’ve seen is with  people who think they are competent, and dismiss the lack of knowledge in this or that aspect of a discipline as inconsequential.  In other words, people claiming competence in a cherry-picked narrow subfield.
My near-universal experience with such cases is that the claimant are factually rarely competent even in a narrow area.  This is why people asking to get degrees without taking classes are rarely considered seriously, and why administrators are not inclined to waste time on such people.  In all but one of the cases I know, these people were not able to complete the requirements for the degree they sought.

source: Stack Exchange

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

sort: votes


text:
Why are scientific publications generally not in cartoon, video, or other forms different from paper documents?
The advantage of looking at scientific publications is that they tend to be the most reliable source of information as they are produced using the scientific process.  I think the disadvantage of scientific publications is that they are at least generally in the form of a paper document, which while it doesn’t impact their accuracy I think it makes them more boring to read and harder to understand, and might partly explain why a lot of lay people end up trying to learn from less reliable sources of information.
I think if a scientific publication was in a different form, such as a cartoon, or video it would make it easier to be motivated to study it might also make it easier to understand it without sacrificing accuracy.  Also on the face of it it would seem like it would be possible to have a scientific publication in cartoon or video form be as accurate as one in paper document form provided that it went through the same peer review process.
Is the reason for scientific publications generally being in paper document form as opposed to something like cartoon or video form just tradition or is there a more practical reason they have the form they do?

Why not give it a try, see how it works out. I suppose a reason would be similar to the reason there are books and movies and plays: different kinds of expressiveness.

Rob Ghrist wrote a calculus comic book. And it's very good.

admittedly, very many publications are cartoonish, albeit not in this exact format.

FWIW, I would really challenge the assertions made on the second paragraph. It might be a matter of age for me, but even for the stuff available in video format (say, programming tutorials) I still prefer text; that’s not to mention that a cute video does not remove the need for vast prior knowledge that many domains science inherently demand. The point about accuracy just seems entirely baseless, unless we are talking about making a video showing text; stuff like math or technical descriptions do not translate well to pictures.

I do not find writing boring to read and harder to understand.  Indeed, it is so frustrating that my HR department forces me to spend an hour watching a video whose content I could read in twenty minutes.  And I am a slow reader.

When the iPad generation reaches grad school, I guess.

Plenty of scientist also try to disseminate their work in other forms, in addition to papers.. Otherwise I agree with @MisterMiyagi , most people won't be able to grasp the full content of a paper outside their field, no matter what the format.

Scientists make written documents because the purpose is to be an archive of knowledge, with very precise meaning of words, notation, and figures/tables. Other forms of expression like videos and cartoon are not so appropriate for archival, specially over a large period of time. Video in particular is a relatively new technology that was not available in 1800s for example. And you do not know if a video will be watchable in the future. Technology rots.
One thing that people forget is that writing is one of humanity's greatest achievements, that is how we know of ancient civilizations and their records, we barely know about of human history before the invention of writing systems.
And more importantly, scientists are the ones that produce the knowledge, but its not the final form, there are other people in society that can interpret a scientific publication and provide videos, cartoons, etc. This is clearly exemplified with many youtube channels that specialize on describing papers. Scientists often do not have training to present knowledge directly to the public.

Technology of course rots, but that also applies to papers only delivered as PDF files today. Historically, of course, papers were printed -- and libraries burned on a regular basis (-> Alexandria!). I don't think technology is a particularly good argument to make here.

You can get a good idea what scientists communicating their work through videos would look like from scientific talks at conferences, colloquia, etc.
Almost every scientist I ever talked to about this agrees with me that a high percentage of such talks are a waste of time to them, and the only reason this format still exists are the remaining good ones. One of the main problems is that these talks are impossible to follow because they assume too much familiarity with the subject, central things are not explained, the speaker is not intelligible¹, etc. And talks have the advantage that you can ask questions when something is unclear. In videos, you can rewind hoping that the information is there somewhere, which has its pros and cons compared to talks, but then this is clearly easier in text.
Moreover, even the best scientific talks only give you a summary of a piece of work. For most papers, a talk that is equivalent in information would take hours (and would not be accessible to lay people at all). While the same applies to thoroughly reading the corresponding paper, in many cases, scientists engaging with a paper don’t do that at first. They want get a quick overview whether it contains the information they need, either by glossing over it or searching for certain terms of interest. They may also only ever read a particular result or a particular passage that is hopefully sufficiently self-contained. Now, you might say that we can make good automated transcripts of videos that allow for searching, etc., but then everybody is working with transcripts all the time such that we might as well make those the main format – and we are at papers again.
Now, what are the underlying reasons for this?

A good and clear audiovisual representation requires more work and skills than writing. This particularly applies if it should be accessible to lay people.
Text is much easier to consume at different intensities, from a thorough reading for peer review to skimming for an overview. You can only speed up a video that much.
Writing is much easier to navigate.
Writing depends much less on the English skills of the speaker and consumer.

¹ And I am in a scientific community, where most people have little problems with the listening comprehension of English.

I am not sure which domain you are in, but in Computer Science, it is expected that talks are understandable in principle. And most, while not necessarily brilliant, are. A talk is not a full exposition of a topic, but a showcase, inviting people to read the details in the papers. Otherwise, I agree with your response.

Most scientists can write adequately. Only few scientists can create videos or cartoons adequately. Only very few people can create good videos or cartoons that get hard facts across.
So aside from all the problems that having information in moving pictures brings, it is generally just not practical to create them in the first place.

"Just about every scientist can write adequately." This seems like an overly optimistic assumption to me...

@JochenGlueck There’s a lot of mileage in the first two and the last word. FWIW, I certainly wouldn’t think that these people are better at making videos than they are at writing…

"Just about every scientist can write adequately."  Hard disagree.  I know what you're trying to say in comparison the second and third sentence.  But still, hard disagree.

@Anonymous "adequately" is the lowest passing mark. And yes, that's about it. I think it is the correct choice of word.

One might argue that many journals and publishers do support hybrid formats if you add multimedia content:

eg. PNAS embeds supplementary videos directly in the HTML version at the place in the manuscript where they are referenced.
a number of journals encourage video abstracts (e.g. IoP or Cambridge University Press)
there is also JoVE, which tried to establish peer-reviewed video content, but I don't think it really took off. Partly, as argued by
other posters here, because making videos is hard: part of JoVE's
package was to handle the video production and hardly anyone in
academia has money for that.

Let me add an example. There was a "popularizer of science", Carl Sagan, who had a knack for making difficult concepts accessible to non-professionals. His talks were informative, for the lay audience, and were usually good introductions to the fields and the concepts he discussed. He had previously made his reputation in the advancement of science (writing papers) and so had credibility in addition to showmanship.
His talks make good videos and would be amenable to a cartoon presentation, either video or print.
But, he didn't present new ideas in that way and he wasn't speaking primarily to professionals. He wasn't, in those talks, advancing the state of scientific knowledge with the required precision, but explaining what was already well known in the field.
Different formats are appropriate for different things. The printed word (along with equations) seems best for presentation of new scientific (and other scholarly) ideas. But it wouldn't work very well for Tom & Jerry or Calvin & Hobbes.
And, at scientific conferences, it is fairly common for some attendees to take notes on the talk, perhaps even writing those notes on a printed copy of the paper that underlies the talk. Those who only require an overview probably won't bother, but those with an intense interest will want some things captured in print.
Moreover we learn to read and write from a young age and are comfortable with it. Creation of videos or even artwork in cartoons is a different skill, mastered by fewer people, and probably a distraction to a scholar.
If it worked, we would use it, but print "feels" right for presentation of new and difficult concepts.

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


text:
Is it considered academic misconduct as a tutor to help your student with homework that is for marks?
I am a private tutor and some of my students are in university with homework assignments that count for marks. Is it academic misconduct to help them with homework that they will be submitting even if I am using Socratic questioning and making sure that what they produce is mostly of their own thought process?
I was also a teaching assistant for a 100 level physics course and we would hold homework help sessions and directly help students with graded problems, but somehow because it's not part of a course I'm just not sure if it's still kosher.

It is unethical to do their work for them. It is certainly ethical to teach them how to do their work. But somewhere in between those is a dividing line so it takes some finesse.
Ideally, as a professor, when a student asks for help on an assignment, I'll try to determine why they have a block that is holding them back and then try to clear that block with some minimal hint that lets them have an insight. Of course, this requires a back and forth conversation to discover what they have tried and why they have taken the approach they have done. It also assumes that they have made some initial effort before you start.
For a tutor, especially one who could be in contact with the professor, it is actually easier than for the professor or a TA, since the scale is 1-1, rather than many-1. A professor may not have time to follow through with each needy student according to the ideal.
But, as long as you stay focused on the learning and unblocking then you should be fine.

This took me a while to get used to, as my "back and forth" conversation almost always ended up with me walking them through the problem.


text:
Masters' advisor uses my work without citing it - Journal decided to intervene
About a month ago, I read a new article published by my previous advisor and three other researchers in a top journal. I noticed that part of it uses part of my master's thesis, only written as if they are the ones who did it.
It is the second time he is doing that, only that last time I didn't know my rights.
I wrote them, asking them to add a citation to my thesis. My advisor refused. He was claiming to "forget" citing me and that it was too late to make any changes. When I reminded him of the first time he "forgot" to mention me, he said that he paid me a scholarship, so my work is his (meaning he will do it again and again).
Of course, I was not very happy with this disrespectful answer. I was also very unhappy to understand that he didn't let me finish my masters (he kept me for 4 years!) because he knew that my work will become "his" one day.
Just a little background - I come from a small country, and my field is very specific. One bad word from this professor can ruin any chance to build a career at a local university.
My current head of the group (I am doing a postdoc in another country) told me to write to the journal editor, but she also said she doesn't think I will get any reply.
I wrote to the editor, along with a link to my masters' thesis and the parts that he copied. I didn't expect any answer. However, he replied very quickly and told me he and the other editors see it as a very serious case – They want to contact my advisor and change the article. I got panicked and asked him not to do that, explaining that it can ruin my possible future career. He proposed a Zoom meeting. Then, he proposed that I speak with other past-students of his, and that we write a letter together, so it will not be personal, only from me. He emphasized that he can't leave the article like that because it is a significant plagiarism (3 paragraphs + graph). I agreed.
The problem is that most of his students did not finish (they either changed an advisor or left before finishing). The one who did finish managed to do it because another professor pressured this advisor, so there was nothing serious he could use.
I am currently in an advanced stage of getting a research position in another local university. I try to postpone the action from this journal as long as possible, hopefully, to be after somebody from the other university will surely ask him about me. But:

It is not serious not answering for such a long time
I don't know if I can postpone their letter to this past advisor long enough

I know I should not have written this message in the first place. However, I did, and now it is too late. So the question is – what can I do?

"I know I should not have written this message in the first place." Incorrect, you did the right thing.

What is it that you fear? Is it that this professor will try to subvert your chances and has the power to do so?

@AdamPřenosil, you are theoretically right. In reality, this professor is much more powerful than me, and he can ruin any chance of me getting a job in this country

@Buffy, yes. After all, his reputation is already bad in this specific journal. He will be very upset to discover it, and I will pay the price.

Can you visit the university in person? Is it close enough? And, do you judge the administration there as honorable?

I just came back from a visit. The other university invited me to meet the people in the lab, give a seminar and participate in a conference they organised. He came to the conference as a guest, and we spoke a bit. BUT he doesn't know I wrote to the journal. For the moment, everything is going on behind the scenes, and I try to keep it like that as long as possible. The university is considered high-ranked, but the professors have almost unlimited power, and I suspect there is also some corruption. The big issue is how I can prevent him from making the other university not hire me.

Ethics aside in your f-ed up situation, what did you hope to achieve by contacting the journal? I can only see two outcomes: what happened which was quite likely as it sounds like serious plagiarism, and to be ignored. If you haven't yet, discuss with the PI who made you do this, and ask her for advice as she's surely closer to the situation than people here.

Perhaps the rogue professor will have less power when their actions are revealed. Bullies need to be stood up to.

Thank you for your answers! Perhaps I should speak with the PI who advised me to do it in the first place. On the one hand, she is not familiar with anything going on in this country, nor the politics within the academia. On the other hand, she is much more academically respected than this ex-advisor. Maybe she can save me with her recommendation when he says (and he will, after being contacted by the journal) something nasty about me.

@gnometorule > "what did you hope to achieve by contacting the journal?" sounds an awful lot like victim-blaming. Maybe the OP needs to make the situation clearer to the editor - these days all sorts of things are on-line (including theses: "a link to my masters' thesis"): the journal doesn't need to identify the complainant to the perpetrator, maybe it was flagged up by a plagiarism search-bot...

Are you sure that your adviser will be able to trace the journal's action back to you? If your thesis is publicly accessible, in principle anyone (perhaps even an automated plagiarism checker) could have noticed the plagiarism. You could ask the editor of the journal to keep your involvement confidential.

Maybe being proactive with the new university will help. If you tell them not to contact your old advisor due to you being involved in the revelation of a case of academic misconduct by ppl near him and offer that the editor confirms this (ask them prior), that could significantly reduce their power.

Yes, can't you just say that your previous advisor cannot be contacted regarding job applications because he was involved in a case of academic misconduct with colleagues and this is confirmed by an editor of a journal, is that not enough to get him away from your other applications?

@ajd Since the OP contacted the adviser pointing out the misconduct, the adviser would very likely assume the OP has "responsibility", even if the issue was in fact spotted by a plagiarism checker.

Agree with Martin here, since OP has talked about this issue with the professor, any actions against the professor from the journal would likely be assumed to be linked to OP, regardless whether it's true or not. Buffy's answer is great, as well as DonQuiKong's comment above.

This is a truly evil modus operandi: (1) Get students and exploit them (2) Once they have interesting results notch it up until they leave without graduating or published evidence of their progress (3) Use their unpublished work and claim as own (4) Repeat. This is awful and you should feel proud to stand to this abuser. Best of luck!

@LouKnee why the hyperbole? OP asks what they can do. It is obvious that we need to know what they want to achieve in order to give good advice. OP can do a lot of things, including giving up on academia and opening a restaurant. If we know what their goals are, we can avoid irrelevant advice.

It blows my mind that this behavior is somehow foreign to some commenting academics. That, somehow, this dishonesty and abusive behavior is an exception and not the rule. This is standard behavior in my experience --unacceptable-- but standard.

Do provide an update once the dust has settled.  :-)

First, I think you have done the right thing in bringing this to the editor. A serial plagiarizer and abuser of students should be stopped.
Second, you can't control the situation anymore. The editor might not be convincible to delay an update and the article needs to be corrected.
Third, the only people that can protect you from this professor either have the same power over them that the professor has over you: a department head or dean, perhaps. But you would need to bring the case to them forcefully.
Fourth, while the power of that professor might be enough and the system corrupt enough to deny you a career at that "local" place (which is what I think you are concerned about), I'm guessing that a career there would be one of your worst options. If they have power to  stop your entry, they still would have power afterwards. The best case is that you are mistaken about that, but no one here can say.
Finally, your best option might be to explore options elsewhere using resources such as the PI you mention in a comment. If an institution is made aware of the entire situation from people (the PI, the editor...) that can be trusted, then the professor's attempts would probably fail and they would face disgrace. Their actions can only succeed in darkness.
Good luck with this. You are, at the moment, a bit stuck. Use what options are open to you and don't depend on things that you don't have control over.

Thank you so much for your great comments! As you recommended, I will get in touch with the PI tomorrow morning. I believe she will support me. I also spoke with the editor-in-chief again, and he promised to talk with the steering committee about the potentially retaliatory behaviour of this advisor. I believe this can solve everything.

Important:  Before you take this further (and I also believe you should!) make sure that you have all relevant documentation securely archived, and easily at hand.  This includes not only the links to, and copies of, your thesis and other work, and the plagiarizing articles, but also any relevant e-mails or other archived communications with this professor.  Specifically, if the conversation took place in e-mail, any comments to the effect of, "I paid you, so your work is mine."  That is an extraordinarily incriminating statement.

@Anonymous I believe the professor in question is more likely to double down on that stance than to hide it when openly confronted. If this view is widely acceptable in OP's country, one simply does not get to both be ethical and not having their job security threatened by this kind of people. Good advice though.

Can you comment on the part "I paid you for your work, so the results are mine", is this not true?

@AndrewSavinykh, it can be true if the person worked under the close supervision and the "worker" added no intellectual content to the work. You can hire people to gather data, for example. Universities "pay" professors who do research, which is quite different. The university doesn't add intellectual content.

... but even in those cases where the worker transfers the IPR, I would expect it to belong to the university (corporate) not to the individual professor, even if it did come out of their grant.

@LouKnee, transfer of rights (by contract) isn't the same as the situation here. It doesn't confer the right to plagiarize. It is about who controls the economic benefit - usually patent owner rights. And even this is much to the benefit of the creators due to the legal expense of filing and defending patents.

Yes - I didn't explain myself well as I'm in a rush, but I'm trying to point out that the professor personally owning some data - let alone alone a report - is very unlikely, compared with the uni owning it (at least this side of the pond). Most of the stuff I've done as a postdoc is technically owned by the Uni, even if I've later persuaded them to release it OA somehow.

@LouKnee, the uni doesn't own "ideas". It may control copyright, etc, but not ideas and not "creatorship" in the plagiarism sense. If you create something that needs to be respected. I'm pretty sure even Disney recognizes its "creators" properly.

What then is a spreadsheet that tabulates data? It's not an "idea", and it's clearly an expression that requires some level of "creatorship" which may/may not be covered by a clause in the employment contract.. Getting off topic though: my opinion re. @AndrewSavinykh 's question is that unless the professor paid from his own pocket, then "I paid you for your work, so the results are mine" is false; the results are the university's. And the OP's context is that the professor is making this claim whilst signing the journal's copyright assignment form...

(As usual for me I've written this off-line, so not taken into account your later comments. I hope it's still useful food for thought!)
I believe you have done the right thing in the bigger picture, by trying to expose your former advisor as a plagiarist and exploiter. Unfortunately, as you are finding out, the system treats juniors that raise such questions as disposable footsoldiers giving them no protection and minimal support. Thus these situations can turn into a nasty mess...
I'm afraid I can't add much to the other answer, beyond a few things to think about:

You say it is a Master's thesis, and that you are now on a postdoc;
what is the state of your PhD? Until that is completed (submitted,
graduated, certificate in your hand) then protecting that should be
your first priority.*
Consider carefully and calmly what power this guy actually has over you - bullies will bluster and exaggerate. His position is probably much weaker than you think. I agree your PI is
probably the best person to turn to - as sympathetic and available -
but you will need to share clearly the whole situation with her. I
assume she is your first reference for the position you are chasing; maybe she can mention that your former advisor cannot be relied on to provide a fair reference for you? (That's a whole Academia.SE question right there!)

I've no idea what the journal is playing at: they have his manuscript, and the thesis is online, hopefully with the proper timestamp, so they have all they need to demonstrate plagiarism. Similarly, other students (published) theses are presumably also accessible on-line, so it should be easy for anyone, including the journal, to check for any plagiarism from those. The editor of any "top journal" has no excuse for being unaware of the way things are (What researchers think about the culture they work in, 15 January 2020), so I'm gobsmacked that he's apparently trying to expose you as the complainant, opening to victimisation (retribution).
I doubt that's malice, more likely a badly thought-out procedure by the publishers, but the upshot seems to be that not only are you at risk of retaliation yourself but are also being used to entrap other former students. I'm not sure I'd trust the guy.

* Because even if this whole business makes you go off and do something completely different, you still don't want a multi-year gap (or worse, multi-year failure) on your CV. You don't want it and you don't deserve it.

"the difference between theory and practice is that in theory, there is no practice." The post did the theoretically the correct thing. My personal problem with academia is theoretical and practical "right things" have almost nothing to do with each other. This is a perfect example. Perverse incentives, perverse power structures nepotism, tribal warfare... It's rampant and it's disgusting.

Sometimes the right thing to do is hard, but it must still be done.
The right thing to do is report this, which you have already done, and allow the editor of the journal handle it from there. You may well end up being victimised for that at your current institution, which is a terrible situation I have been in in the past for bringing malfeasance to light. Unfortunately, you should still aspire to do what's right, and you will come out the other side all the stronger for it.
However, this says far more about the institution you work at and those other local universities who you believe would deny you work based on this. Any respectable institution would see a young researcher taking such a difficult action in the the defence of academic integrity a huge, green tick at interview stage - as long as they handled it properly.
Given that, I don't think aiming for a position at these local institutions serves your long term career well at all. If they tolerate this sort of behaviour, and even try and suppress reports of it, then they likely have, or will develop, a terrible reputation internationally. At which point your reputation will suffer by osmosis.
Get out at the earliest opportunity and try and get a job with a respectable institution. I know for some people this may not be easy, but in the long term I think anyone would be better leaving acadaemia than working at institutions like this.

The institute I work at right now is beyond incredible. I feel fortunate to work here.
After finishing the Ms, I left the country and did my PhD abroad. The university I aim for and even the department are entirely different from the one I left. But still, as the country is small (6 universities+ one academic institute), you can't avoid knowing everybody.
But of course, if I cannot get the job I want there, I can stay abroad and come only to visit every now and then.

@CatededUr - I don't want to invalidate your lived experience, but any university that would let this behaviour go unpunished is far from incredible.

I left the university in which I did the MSc, right after finishing. Since then, I haven't gone back to my country. I try to get a post at another university with completely different people, which I think are more honest.
My current PI, who had never even visited my country, is the one who advised me to write to the journal. I am now in Europe, where such things can't just pass and be ignored.


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Copyright confusion - scientific paper
Currently, we have a discussion in our work group as to whether one may use images from WikiMedia Commons in Case Reports. I have a general understanding of what types of CC license one may use or not. However, this specific case is confusing me:

Said file has been uploaded under multiple licenses. How is this possible?
Is it correct that I can use that image for a scientific paper (provided I give proper credit) which is going to published under a "NonCommercial 4.0 International (CC BY-NC 4.0) " license?
Any input is greatly appreciated.
Background: the image is necessary for a case report in Medicine. Regrettably, it is about a plant that is not growing in winter. Thus, I need to find an alternative way of obtaining a picture of that plant.
I know there are related topics: Can I use images from Wikipedia in my paper?
Yet, in this case, the image has multiple licenses.

Screenshots are not a great way to share the details of your problem

@user2705196 I am sorry - it won't repeat in the future.

If you want you can go and copy the text and then quote it here!

Said file has been uploaded under multiple licenses. How is this possible?

If you own something, you can license it however you want as long as you haven't agreed to some terms that prevent you from releasing it under other terms (usually referred to as an 'exclusive license'). A fairly common scenario would be releasing something under a fairly permissive license that lets others use the content for anything except commercial purposes, and then also licensing to specific users for commercial purposes for a fee.
Often journal publications occur with terms that either give the full rights to the journal and then re-license the content back to the others allowing them certain privileges, or keeping the ownership with the original authors but offering the journal an exclusive license that promises A) That you haven't already licensed the work for certain purposes, and B) That you can't in the future.
It seems unlikely to me that this image under either of these licenses will be useful for your purpose if you plan to submit your paper to a typical medical journal, and I don't see compatibility with CC BY-NC 4.0, but I'm not going to pretend to provide legal advice on that, I'm no lawyer. It also doesn't seem like it is truly necessary to have an image of a plant for a case report - I'd look for something in the public domain or something you can obtain directly from the rights holder.

It looks like this SE Q&A disagrees with me, suggests it's fine to use a CC-BY-SA image in a work released as CC-BY-NC, and references a dispute of this that led to a court case. Personally, I'd still probably want clearer permission for something like this (as it seems it was still unclear enough to have a case over) or to work around the issue entirely.

Dear Bryan Krause, Thank you for your comment. It is a very difficult matter. May I ask how you judge the following issue. A paper in frontiers (which is also open access; https://www.frontiersin.org/articles/10.3389/fpls.2021.720171/full) also used numerous CC-3.0 images. Based on my understanding and your comment, this is not legit either.

@Dr.M It doesn't look like that paper is released as CC BY-NC 4.0, but yes I think CC-BY without the SA would not be compatible. It hinges (like the Q&A I linked) on the interpretation of the courts of "remix", "transform", or "build upon". If you do those things, then you have to comply with what the licenses say about sharealike. If that's not a derivative work, then you don't. In any event, "someone else did it, too" is not a good legal argument. In practice, the vast majority of these things never see any sort of court action taken.

IANAL, but I don't see any issue with your use of the image, provided you keep some things in mind. First, once a license is granted it can't be replaced by a more restrictive license. Both of the licenses permit what you'd like to do.
Just note, however, that your "non commercial" restriction won't apply to that image, since it already has a permissive license. The NC clause will apply to other things in your work, however, but others are still free to use the image "commercially" due to the earlier license(s).
You have to attribute the image to its source, of course. And, if you modify the image you have to adhere to the "share alike" clause which you agree to in using the image. It would be proper to put a note in the paper concerning the license on the image which both gives you rights to use it and notifies others of their rights.

Caveat: I can (barely) envision a situation in which that image is so essential to your larger work that you would need to apply the more permissive license to your own work. That seems unlikely, however, but would apply if the report you write could be fairly considered to be a work derived from the image.  Unlikely, but not impossible.

Thank you Buffy. Our report discusses plant intoxications of 2 potentially similar looking plants. Thus a picture is essential but hard to find on the internet.

@Dr.M Why is the picture essential? "We present here two case reports involving potentially similarly looking plants, Plant A and Plant B". Then you describe what happened to the patients. No picture needed.

Being "essential" to your paper isn't the issue. It is whether your paper constitutes a derived work. I think that is unlikely but it is a judgement call.

@Dr.M have you tried botanical books/journals as an alternative for the image source? And/or asking a research librarian?

@Lodinn Thank you for your idea! Our library is closed for personal shortage / COVID reasons these days. Luckily, I found some freely available pictures on the internet that may be used.


text:
Supervisor pressures me to co-author his paper
The title says it all: my supervisor pressures me to co-author one of his papers.
The paper is based on a study which was performed by a student in our department. In the very first weeks of the project, I was supposed to support the project and the study. The student had her own ideas of the study, and although seeking my advice on a frequent basis she would never follow it. At a later stage, numerous problems occurred (which I anticipated). The problems were the consequences of the student doing whatever she pleased to do. My supervisor gave her the freedom to behave like this. I informed him that I could not support a project like this. He was fine with it. In the meantime, I informed the student about it. She ghosted me for one year and then came back seeking my help. I refused to support her after she always neglected my advise and made a lot of predictable errors. Still, my supervisor was fine with it. Now the student under discussion produced a paper based on the study. The paper is of low quality and will not get accepted in a reputable journal. In fact, the paper is poorly written and the methods (statistical analysis) lacks rigor. I am sure my supervisor knows about this and this is exactly where he wants me to polish the paper. This cannot be done in a few days but requires several weeks because everything has to be done from scratch.
How could I escape that situation?
Background: my supervisor is my boss. He pays 50% of my loan (I pay the other 50%). I have my own projects and publish on a regular basis and work independently from him these days. I work as a clinician scientist, seeking tenure this year.
Any help would be appreciated. I feel that said paper would look bad on my CV.

What sort of position do you hold?

@ Buffy, Thank you for your inquiry. I am a clinician scientist. I will update / edit the question.

Any chance to drag it out? Some papers take years to polish to publication level (even good ones). This one just needs time. A lot of it. It is surprising how long things can take when one does not work on them.

Dear Captain Emacs, Thank you for your hint! I thought about that but the issue is that the student under discussion ghosted me about 1 year and so nobody really worked on the paper. Now my boss realized this and "prioritized" it but pressuring me to work on it (although I do not want to co-author). I may apply your strategy!

How are you being pressured?  Have you already tried politely declining?

@Kimball he argues that I supported the study and should thus co-author it. He knows I am good writer and pay attention to details, thus we asks for a deep edit of the paper. If it was my work though, I would not publish it. Another co-author, who did the statistics for the paper, is also refusing to coauthor.

You'll have to judge whether this would be safe, but to me, the best solution is to explain to the supervisor and the student if necessary that a poor paper will benefit no-one and that you'll take on the task if (only if) you are given enough time to do a proper job.
Even if you do a lot of the work but end up not as first author it would be preferable to producing cruft and having your name associated.
That said, it is risky to oppose supervisors as I know you are aware.

@ Buffy, Thank you so much for your insights. I regret that the paper can only be improved to a certain extent. The paper itself contains a fundamental flaw that makes it to some extent invalid. I would spend months for a non-important mid authorship...

In theory, every author vouches for the quality of the papers published. In practice, just the reviewer vouches for its quality.
If the paper won't get accepted, let it be. A proper review process should hide the names of authors during review so if the paper never gets published, you get the chance of saying "I've tried" or "I've told you so" without anyone outside your department ever knowing you had a part in it.
That being said, life is not fair and doing what people in power positions want often provides better outcomes than antagonizing them (in this I mean your advisor). Regarding your colleague, treating people fairly is not always what produces the best short-term outcomes. I'd advise you to provide a review of her paper, as if providing her with a fresh start as a person. See how she reacts, try to get responses in written, not in personal talks. Give her some space to redo her work herself. You can them just tell your advisor you are waiting on her.
Don't just say a hard no to your advisor, also don't commit at once to do the hero saving the day role: Aling (small) step by (small) step with your advisor. First just a reading, then changing insights on the fundamental flaw, proposing a new introduction and so on.
If all goes well, you'd get tenure before this paper is finished. If all goes bad, you've stalled working on this as much as you could without antagonizing your advisor.

Whether authors are anonymous or not during the review process is very field dependent.

@Anyon ... and journal dependent. The reviewer can be a gatekeeper, but the reviewer does not vouch for the quality. It is the responsibility of the authors to ensure the quality of the paper. The reviewers are just a second line of defense.


text:
Do editors check your submission history?
I was wondering whether one's submission history to a particular journal plays an important role / is considered by a handling editor? Let's assume that one submits to a particular journal multiple times and gets rejected in the majority of cases. Will this adversely affect the handling of your most recent submission, e.g., does the editor think "oh no, not again this guy"? Do handling editors have access to an authors previous (rejected) submissions?
EDIT: Previously I did not find this related post: Strategy for submission of articles to highly ranked journals
I am sorry for opening and the inconvenience.

Journals have a finite number of editors.  If you've submitted many times before, probably many of them will have been handled by the same editor, who may simply remember your history without any need to "check" or "access" it.

"in the majority of cases" is very ambiguous. Some top journals have a rejection rate of 90% and if you managed to publish 20% of your stuff there, you're above average... I don't think it will play out against you if you submitted papers of good if sometimes too low standard and got rejected a few times but also accepted at some point.

No. ............ :)

I assume that editors normally have better things to do than researching the submission history of an author of a new submission, even though they probably could. But a submission should be treated on its own merits and the submission history shouldn't play a role, so I don't see why an editor would invest effort into looking at this.
The editor of course may remember you. They shouldn't be biased by this, but there is unconscious bias so it cannot be ruled out. However I'd believe this will only be the case if you submitted extraordinarily bad or extraordinarily many papers that got rejected. If we're talking top journals, many people hope to get published there because of the career boost, and this means it's fairly normal that some people submit a lot there even if often rejected.

+1 ... they shouldn't be biased ... and ... submission should be treated on its own merits

As an editor of Elsevier and IEEE, I see no option to check an author's submission history.  All I see are the author's publications.
Having a high quality publication record helps, but each paper is judged on its own merit.


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Why are mega journals so popular?
I would like to ask why mega journals (large journals designed to be much larger than a traditional journal and with a very broad audience, e.g. Scientific Reports, PlosOne, BMJ Open, Heliyon, ... to name a few) are so popular / receive so many reputations. Why do people choose such journals over field-specific journals. As for me, I would never go to the homepage of Scientific Reports, Heliyon, etc. to screen the most recent articles because the subject span is to broad for me. I understand that their acceptance rates are a crucial factor - but is there anything else I did not consider?

could you clarify what exactly your idea of a mega journal is? Is it simply one with no specialization?

@ Sursula - Yes, a large journal designed to be much larger than a traditional journal and with a very broad audience, e.g. Scientific Reports, PlosOne, BMJ Open, Heliyon, ... to name a few.

Lose lost a loose 'o'. Choose chose to be different.

@DanielHatton I think most visits to journal websites occurred well after 1960 :)

I never go to e.g. Nature to skim through it in hopes to find the paper that matches my field, however, I tend to be aware of such papers. They tend to be quite public at least within the research field communities.
Which leads to what I think its a conflation of concepts you are making in your question. They are not reputable because they are a good source of information for all fields, on the contrary, they are reputable because they only publish "groundbreaking"* research, from any field. Prize-deserving research. So it is reputable to get a paper in Nature because you got in, not because other people from your research field will read it. Its the exclusivity that makes them reputable, the "stamp of approval" that a publication in these journals gives you as a researcher, and to your field, because its considered "important enough" to be on Nature. In some way its a lesser form of a price, as very little people get in.
This does not mean I agree with such "reputation-based" system for academia. But the truth is that academia works a bit like this, and the above paragraph describes how many people see publications in these journals.
*In theory, of course, not saying this is necessarily true.

It is the Matthew effect.
A reason some people select a journal to try to publish in is prestige. A reason some people judge a journal to have prestige is the famous articles published there. This provides a positive feedback. A famous article makes the journal more prestigious. Being more prestigious attracts more attempts to publish by people doing interesting work. If the editorial process is handled with care this can produce a journal that becomes more and more prestigious.


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Can I accept a review invitation after prior email contact with the author?
A few weeks ago, we (2 authors) published a hypothesis paper in the medical sciences.
Some days after the manuscript was published online, a researcher wrote me and asked for the full text. I did not know said researcher at that stage. We exchanged some emails back and forth about the content of the paper. I encouraged said researcher to publish his own ideas on that topic in a comparable hypothesis paper. Subsequently he wrote a draft and submitted it to the same journal. He informed me about that step and sent me the manuscript to have a look (after submission). Now the same journal where we published invited me to review the manuscript of the aforementioned researcher. We work in foreign countries and never published together before.
However, we had contact prior to his submission and he sent me some of his ideas.
Should I decline the review invitation in this case? I would love to review this piece because it is my main research topic. On the other hand, I feel it may be inappropriate that he sent me the piece after submitting it to a journal.

Did you ask the editor? It is part of their role.

@ Marc Glisse - based on the comments, I accepted the review invitation and intend to explain the background in my comments to the editor in ScholarOne.

This is a great question, but i recommend to rename the title to something like: "Can i accept a review after prior email contact with the author. " That makes it a little better search and findable, and it covers the question better than the current very general title.

@ Hijan. Thank you! I changed it.

Yes, accepting the review invitation is fine. Having discussed an idea with a researcher before they wrote it up in a paper, and having received that paper in private communication, does not constitute a conflict of interest.

Dear lighthouse keeper, thank you for your opinion and quick reply. Should I inform the editor about this ?

@Dr.M It's absolutely not necessary, but if you want to feel safe about it, you can inform them.

It is not terribly unusual to be a referee of a paper (co-)authored by someone you know somehow. The scientific community is small in some fields, and discussing ideas is common enough. That alone is no problem by itself. However, I would return the question to you: Do you think you will be able to judge the manuscript based on its scientific merit alone? If so, go ahead. If you think that there is a chance that you would give the manuscript a preferential treatment, for example due to a personal connection with the authors, it would be advisable to take that into account, and maybe decline to review the manuscript.

Some days after the manuscript was published online, a researcher wrote me and asked for the full text.

That is normal

I did not know said researcher at that stage. We exchanged some emails back and forth about the content of the paper. I encouraged said researcher to publish his own ideas on that topic in a comparable hypothesis paper

Subsequently he wrote a draft and submitted it to the same journal. He informed me about that step and sent me the manuscript to have a look (after submission)

However, we had contact prior to his submission and he sent me some of his ideas.

Your contacts appear to be more than mere contacts. It tilts towards engagement.
Ethics kicks in here. Irrespective of you not being a co-author, there're contacts between you; sufficiently so.
This call for you to reflect deeply and honestly.
Before you hit the decline (or accept).

be transparent by contacting the editor about the degree of contacts and engagement between you and the author
indicate willingness to remain unbiased if requested to go ahead and review the manuscript
consider how small or broad the field (or subfield) is
you may then accept to review or not

PS: in some subfield, there are only a handful of researchers!

Engagement in the form of discussion does not lead to a conflict of interest. Researchers regularly discuss their work with other experts in the setting of conferences and meetings. If that would generally lead to a conference of interest, it would be impossible to find expert reviewers for most papers.


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Journal forces me to provide figures in .pdf format, what can I do?
Approximately one year ago, I submitted my manuscript to a Wiley Journal. The submission was in full adherence with the submission guidelines. Upon submission, the journal requested color figures in TIFF format with at least 600 dpi. Back then, I generated these figures using Stata. In the meantime, the journal was transferred to Hindawi. My paper was now accepted and the journal does no longer accept my figures. They requested color figures in PDF. I have no longer access to Stata though. I tried to convert the existing figures using various converters / software, but I always experience a loss of quality / resolution. I guess this happens because I asked Stata to generate them in a very specific format/dimension. I explained the situation to the journal and they stated that they could not proceed without PDF Figures. They would not proceed with my accepted manuscript. To clarify, my figures are mainly contour plots, for which I do net understand why a PDF conversion is required. Could you provide insights in how to handle this situation?

@Daniel Hatton I have them in TIFF. Sorry, I did not mention it. I updated the question.

Do you want to meet the implicit expectations of the journal as well? They may expect vector graphics without saying so, and indeed translating from pixel graphics to vector graphics is not so easy. However, translating TIFF to PNG, and including the PNG in a LaTeX document, followed by running pdflatex will give you a lossless path to a PDF containing the original image in a pixel-perfect way.

@DCTLib Thank you for suggesting a path! I will try that. Do you think this would work for contour plots, as well?

@Dr.M If the Figure was nice and readable in TIFF form, it will be nice and readable as a pixel figure embedded in a PDF. Note that however some PDF readers will use non-pixel-perfect rescaling for showing the image, which may affect how it looks. Experiment with using "\includegraphics[interpolate=true]{}" and "\includegraphics[interpolate=false]{}" - in this way, you can ask the PDF reader (nicely) to interpolate or not interpolate your image when displaying the PDF.

Re: "I guess this happens because I asked Stata to generate them in a very specific format/dimension." Surely you can extract the aspect ratio and resolution from the TIFF file and then use that for an informed conversion with, e.g., tiff2pdf?

You might be able to use Stata at a university library. Of course, that depends on what universities are close to you and their policies. For example, “visitors may be issued guest credentials that allow them to use Library computers” at the University of Chicago (see https://www.lib.uchicago.edu/thelibrary/computers-and-wireless/ ). I would imagine many other universities have similar policies.

Hopefully, you will find a solution to their satisfaction by merely repackaging the tiff inside a pdf container file.
If you absolutely need to not only provide in pdf format, but at a resolution that is incompatible with your current raster file, you can try rescaling it to a different resolution. In my experience with cartographic images (admittedly not quite the same thing) Image resize... in paint.net (Windows) followed by some sharpening (with trial and error...) provides much better results than merely rendering a raster at a "wrong" resolution in a pdf viewer. It is free. If you are willing to consider paid solutions, Topaz Photo AI or Gigapixel will upscale images with AI; they are primarily for use with photographs but with some tinkering do a decent job with lineart and text labels in simple fonts.
Finally, you could vectorize the raster images with some effort. The old way of doing this used a drawing package like Inkscape to redraw curves and was timeconsuming. Now there is software like https://vectormagic.com/ and https://www.vectorizer.io/ which offer free trials to see if helpful, and then will cost about U$10 for an access pass.
All of this is suboptimal versus recreating the image at source, or just packaging the raster tiff as pdf to keep the publisher happy (which should be fine if the resolution is high). But I'm trying to outline the options if you are stuck complying.


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Ethics of staying at my a pre-doctoral research fellowship
I accepted a pre-doctoral fellowship at University A with the expectation I will pursue a PhD there. After 3 months into the fellowship, I realized that the program doesn't exactly spark my interest and I cannot see myself spending the next 4-5 years doing this type of research.
Unfortunately, it's hard to bring it up with my current potential advisors since my background is a perfect fit for this topic. A professor at another university B reached out for an interview and if I am successful with my application there, I would be more inclined to go to University B as I believe it is a better fit and the research topic there would be much more interesting.
Am I misleading my current advisors by continuing my fellowship at A? Note that at this point, I have not received an offer yet at B, and I'm afraid to leave A in case B doesn't push through. On the other hand, PhD is a major commitment, and I'm afraid I might have ended up committing to a PhD that I'm not all that interested in. What are the ethics of staying at fellowship A?

If you delete and re-post your questions, you can be at risk of system-imposed restrictions on posting future questions (if this happens, even moderators can't help you). Instead, you should [edit] when you want to make changes, rather than deleting.

Many times at StackExchange, esp. in Academia people come with questions that are critical for them. Their question might be phrased poorly or might be opinionated or may have other flaws. But downvoting the question in those scenarios is mean and might hurt them more. (Not referring to OP here)

In general, you can leave a position, even a generous one, as long as you fulfill the requirements. Accepting a fellowship isn't normally signing away all your future choices. It might be problematic if you leave some projects unfinished when others depend on you.
But, it would be wise, just so that you have all options before you, to discuss your plans at some point with current advisors. That need not be immediately unless they need to take some action on projects to assure continuity, but that probably isn't the case.
It isn't the "leaving" per se that has ethical implications, but the other factors around it as noted above.
Ultimately you shouldn't commit to something that you feel isn't in your best interest. In particular, continuing into a PhD there after the fellowship, even if you complete it, is probably not a good idea.

I think Buffy answered really well. But just wanted to add that you also want to reflect carefully on how you were attracted to the program at University A in the first place. The grass is always greener on the other side. No matter how exciting the project at University B sounds at the moment, there are always boring and mundane tasks involved in the pursuit of a Ph.D. degree. Just the fun should outweigh the pain somehow. And it is easy to dislike something when you are working on it day in and day out. So it is easy to have a bias towards your current program now. Just make sure that you will not come into the same situation at University B. If you ever want to hop to a University C, people will start questioning why you keep hopping.


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Do journal editors/referees expect relatively unknown authors to provide evidence of counsel from an expert when submitting a paper?
The reason I've brought up this question is due to the following observation.
Let's say, for instance, there is some field which is called "Specific Grand Theory".
The field is quite minor and only A,B,C are the reputable experts regarding the field.
Reading some published papers from young researchers concerning the "Specific Grand Theory", someone observes every of those young researchers shows a gratitude to one of those A,B,C at the 'Acknowledgement' section.
So that 'someone' begins to suspect that whether there is an implicit rule in that field which demands for a young researcher to consult one of the experts before publishing his/her own paper to the field. Otherwise, that 'someone' should worry about the acceptance rate of his/her submitted paper for not getting stamped with authentication by the experts around the field.
The hypothetical situation I described above is similar to what I'm facing. I think that even assuming this kind of custom do exist in some fields, it shall vary field by field. The field I'm particularly interested is one of discrete mathematics. However, if you have your own experience with my question in your field, I would also like to hear your opinion.
Added:
I have an additional question. I may assume that the hypothetical situation I've described above exists, leaving aside whether it results from the custom in that subdiscipline or just a coincidence by the closeness of network.
Then, in the eye of journal editors, would not getting some authentication mark by the experts affect the credibility of the newly submitted papers compared to other papers which got its stamps from those experts?
I'm particularly concerning this, in mathematics, many of the papers are left unread if they give some air of crackpots.
I wonder the opinions from journal editors or reviewers whether not having some authentication mark unlike others will have possibilities to affect the credibility of the submitted paper in some minor fields.

This is not how the refereeing process works. Such acknowledgements are irrelevant when evaluating a paper.

@MoisheKohan: Thank you for your opinion.

are left unread if they give some air of crackpots --- Regarding mathematics at least, I think you're vastly over-estimating the influence of "authentication by experts/authority", and vastly under-estimating how obvious actual trite and/or crackpot results/writing are to detect by someone even the least bit knowledgeable about the subject matter. On the other hand, don't mistake difficulty of concepts/proofs and correctness of results with "worth publishing".

@DaveLRenfro: I think your comment answers my additional question. Thank you.

Acknowledgments simply do not function as a seal of approval. I am grateful to Prof. Bigname for their useful comments on an earlier draft of this manuscript says literally nothing about what Prof. Bigname thinks about the paper and could in reality mean anything from I exchanged two emails with Prof. Bigname about the topic and am erring on the side of being polite to Prof. Bigname loves my paper to I showed a messy draft to Prof. Bigname and they provided some feedback while also politely indicating that the results might not be very significant or even true.

@AdamPřenosil: Thanks. Now I feel comfortable since I was too shy to email Prof. Bigname.

@user1851281 If you genuinely feel that they could provide useful feedback and that they might find your work relevant and interesting, then there is no need to feel shy. Circulating manuscripts among peers is what scientists do. But don't do it in order to get some fictional stamp of approval. Of course, this works much better if you have some pre-existing relationship with them (for example, they know you from seeing you around at conferences).

@AdamPřenosil: Thank you! Maybe I should bring up with another hypothetical question later regarding the strategy to approach them,,,haha,,

I don't quite understand the way that you've used the word "counsel" in this question. To counsel is to give advice, and I don't know why a young researcher would need to give advice to an expert. Did you mean "seek advice from" when you wrote "counsel"?

@TannerSwett: Oh yeah it was meaning "seek advice from". English is not my first language so I sometimes just translate things by looking at the dictionary without distinguishing the context. Could you recommend some more decent word? I also wonder whether the title makes sense when I substitute the word from 'counsel' to 'consult'.

"consult" might be OK, and "demanded" should probably be another word, maybe "expected". Also, "the expert" should be "an expert" -- use of "the" tells the reader there is only one expert, or there is a single previously mentioned expert that "one expert" refers to, neither of which is true here. But rather than trying to band-aid the current title, maybe use something like the following, which more explicitly conveys what you want to know: Do journal editors/referees expect relatively unknown authors to provide evidence of counsel from an expert?

@DaveLRenfro: Wow, thank you very much. I liked your title than mine so I've edited following your advice. Really appreciate the details!

I think the meaning is clear without "when submitting a paper", and removing these last 4 words improves the title by decreasing its relatively large number of words.

Mentioning somebody in the acknowledgements is no evidence for anything.

Short answer: no
Longer answer: in small fields many of the junior researchers will be PhD students or postdocs with either expert A, B, or C. Since the advisor often comments on articles before they are published or are in another way helpful, they end up in the acknowledgement section.
Maybe there is a really supportive culture in that subdiscipline and the experts are really generous with their time, and thus often end up in the acknowledgement section.

Research funding may also have an effect - in a minor subfield, there aren't that many funding opportunities, and established experts have better chances of acquiring such, so a lot of the research happens in their groups.

For the record: My area is math, I had served as a managing editor for 3 journals, currently just for one. I also edited proceedings of several conferences.
As an editor/referee I pay very little/no attention to acknowledgements when evaluating a paper (with one exception that I discuss below). As an editor, I either know the specific research area of the paper well enough to evaluate if it is at the level of the journal after a quick look through it (which includes eliminating crockpot papers) or I ask for an "expert quick opinion" instead.
Now, for the exception. In general, I prefer to receive a quick opinion or a referee report from a person who is not too close to the author(s) of the paper, to ensure impartiality. If the author thanks all three main experts in the area, my job, as an editor, becomes more difficult.

Thank you very much! And yeah I'm confident that I won't be in the exceptional situation you've mentioned!!

Recently I've been getting asked to evaluate papers because I'm in the acknowledgements.

@Kimball: Oh, dear... I guess, not everybody shares my concerns about impartiality.

Well I wasn't a mentor/advisor in these situations (except once, which must have been an accident).  If I haven't been that involved with the paper, I think I still can be relatively impartial.

I suppose this means that, if there is anyone (other than @Kimball, apparently!) whom one particularly does not want to have as a referee, then one should thank that person in the acknowledgements.    I see this has also been mentioned by @yarchik.  (Not, by the way, that I would have any problem with @Kimball as a referee, except that I wouldn't want to inflict that on him.)

Do journal editors/referees expect relatively unknown authors to provide evidence of counsel from an expert when submitting a paper?
No, but ...
No: Whether there is evidence of a mentor is not considered by the editors.
But: Whether the paper shows understanding of the field is important.  One way (not the only way) to learn the ins and outs of a field is through a mentor.
And a corollary:  "Name dropping" a famous person will not rescue a bad paper from rejection.

Thank you very much for the answer!

I agree with the No answer above. Adding names to the acknowledgment section will not alter your acceptance rate.
However, some authors do play games with acknowledgments: assume one is in conflict with profs. A, B, C. One does not want them to review the manuscript as it would reduce the chances of acceptance. Therefore, one acknowledges them! Next, the editor reads these acknowledgments and does not consider A, B, or C as potential referees (see the last paragraph in the answer of @MoisheKohan). After the manuscript has been reviewed by other unproblematic referees and already accepted, one removes acknowledgments while in the proofs stage.
It remains to be said that I do not support such practice.

lol, I would not practice it. But just note it,,,! xD

I did not say that I would not, just it would not be my first choice. However: In the case of a conflict of interests, the right thing to do for an author is to write a separate letter to the editor(s), mentioning a conflict and asking that the paper not to be sent to some experts for a review/quick opinion. Such wish is normally granted. The same for grant applications.

You often don't even need to write a separate letter: some submission portals ask you for the names of suggested and opposed reviewers.


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Can we use past exam solutions during an exam if it's authorized to use anything
I just did an exam where we could use anything (online exam).
On the exam page it's written; authorized material : everything.
During the exam, i noticed a question was exactly the same as an other question of a past exam. So i almost identically took the same answer, but there was multiple answers possible.
Before the exam, the teacher gives us access to 2008 to 2020 exams with all the solutions to practice.
(the solutions of past exams are given to us, so i had the right to have em.)
Is it plagiarism ? It's the first time he's giving the class, did he also commit plagiarism ?
Am i in the wrong ? Or the fact that the teacher gives us those solutions he wouldn't care if an answer is the same ?
This is at university level, so it's kinda odd to me that he did this. If he was to report someone for plagiarism, i am not sure the dean would be really proud of him for doing this...
Thanks !

I suppose the devil is in the details. Using "anything" doesn't seem quite the same as "open book", which in turn isn't the same thing as, say, "open notes".

@prets i mean it's written authorized marerial : everything. Also, what if i practiced this exam and when correcting my answer i wrote their answer. Then i look at my notes and i take the answer, i am not sure it's plagiarism idk..

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.

This may be subject to explicit rules set by the instructor, of course, in which case, follow them.
But, given the situation you describe, I'd suggest that you just cite/reference anything you use from an old exam. This saves you from any charge of dishonesty.
But, you also suggest that there can be multiple correct answers to the questions. Unlike math where 42 might be a correct answer and 43 totally incorrect, in philosophy, say, some questions require interpretation and it might be important to introduce specific elements into an answer. In this case, you would be wise to supplement any old answer you draw on (with citation) with your own (hopefully correct) thoughts and interpretations. Use the old answer as a base, not as a complete answer.

for example the answer in practice exams was P = a->b \ {d} and in my exam i have an equivalent which was A = a->b {f,g}  but the a->b pattern could"ve been many other answers.. I am dumb to have taken this one, but i am not sure it can be called plagiarism, it's a way to solve the problem...

@dfgg it looks like you think they are equivalent, however they are completely different ...

The interpretation  is up to the instructor. But you can make a case that you used approved sources - perhaps. After the fact it becomes a local issue.