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Potential ethical concerns on advisor's advice on publication venues
I can't be sure, but my instinct tells me that I am about to step in a minefield. I want to seek your advice on how to handle the situation. Here is the brief story:
The background: my PhD thesis is almost ready for submission and I am now working on turning it into several publishable papers. I have identified a few potentially suitable outlets, with one of them a special issue in a prestigious journal in our field edited by my advisor's ex-student (who he has been close with and has influences on). One of the essays in my thesis fits perfectly the scope of the special issue that has a deadline 3 weeks. I want to revise my essay to fit the requirements and submit to the special issue, but my advisor has been trying to stop me using three reasons: (1). It takes a long time to write a paper for a top journal and I wouldn't be able to make it; (2). The journal usually publishes highly technical papers and my multidisciplinary mix-method paper does not at all fit methodologically (actually, the special issue calls openly for these types of papers); and (3). If I rush to submit my paper, it'd certainly be rejected and if I then revise and re-submit it to other less prestigious journals, I'd likely run into the same reviewers and be seen very badly in this community. When I told him that I felt comfortable meeting the submission deadline, that I understood the possibility of getting rejected and would take it as a learning experiences, and quoted the section of the "call for paper" that shows my method actually fits the scope, he seemed to lose his temper, became quite upset, and sent me a message saying something like "it doesn't work this way" and another journal (similar level of prestige, but he does not publish there often, and it is edited by other scholars) would be a better fit. His arguments obviously are not convincing to me.
More background: I sent him this essay 6 months ago and he seemed to start working towards this direction since then. Actually, the idea of that special issue might be from him (he as a highly influential academic in this field organized a workshop soon after with many people from different disciplines coming to talk about this topic, and he mentioned back then that he'd write a few papers based on the workshop, probably planning to publish in this special issue). And I also asked for his advice on selecting journals for the other four papers from my thesis, he pointed me to those lower-ranked journals which I think is not a fair evaluation of my work (I have received very positive feedback on my thesis from other academics in our field), neither a good-willed gesture an advisor would show to his students. So I now have the strange feeling that he might be trying to slow down my progress as a young and promising scholar in the same are. He is seen as a world renowned so-called "guru" in this field. I am also concerned that he might have already used my ideas (interesting and new) in the essay that I sent him 6 months ago to write his papers and might have already submitted them to the same special issue.
My question: what should I do now? I feel it is a right thing to do to submit to the special issue. But I am afraid that might expose him if he'd done something unethical (he is about to retire and it is certainly not the most graceful way to go). I am also afraid that he might sabotage my job search for tenure-track positions as he will be one of the two key references for me. However, I also feel strongly about standing up for what I believe is right, and not to tolerate unethical behaviors around me. I think tolerating such exploitation (if it actually exists) would only reinforce such behaviors and empower these human sharks.
Please share your thoughts and offer your advice. Thank you in advance.

It sounds like he doesn't think your work is good enough for whatever journal you're talking about and doesn't want you to leverage his connections to get it in anyway. You are in no way in the right here.

Is your advisor a co-author on this or no?

Please avoid vandalizing the content of your posts.

In essence, you're peddling in conspiracy theories: You're claiming some dark motive in your adviser's response for which you have no real proof. You also claim that he might sabotage you, without actually having any concrete evidence nor do you show any reason why he might do so. Moreover, your adviser actually gave you three quite sensible reasons why he thinks that your current plan isn't good that you dismiss out of hand.
Here's the thing about life: If (i) someone says something that actually makes sense, then (ii) that's usually what is actually the case. In your case, I very much believe every reason your adviser gives you: It genuinely is hard to write a paper in 3 weeks; I'm going to claim that it's impossible. If he says that the journal generally published a different kind of paper, that's something that can be checked by why not just believe an experienced researcher and author? And finally, if the community is small, you do risk running into the same reviewers and your adviser is correct that there is a stigma attached to having reviewed someone's half-finished manuscript. Nearly every other statement by your adviser in your question also seems totally reasonable to me.
So I see no good reason to believe any of your conspiracy theories. I think you fundamentally need to adjust your assumptions about people indeed meaning A when they are saying A.

Look, your adviser has many years of experience in (i) figuring out where papers are most likely to be accepted, and (ii) how long it takes to write a good paper. Why are you arguing? I too agree that writing a paper in 3 weeks isn't going to work, even if you can adapt from other sources. In your case, it takes 2 authors multiple rounds of proof-reading even if you were essentially ready -- that alone is going to take a couple of weeks.

@user13399399 -- I'm not sure where you're going. Posting questions here implies that you are looking for answers or opinions you don't already have. I gave you mine. It's of course your prerogative to disregard them.

I am inclined to agree with Wolfgang on this in general. However, it can sometimes happen that senior scholars don’t fully appreciate the career stage of being a junior scholar. Here, it may make sense for you to try for the best journal you can and risk getting rejected as not a good fit. I think there is a distinction between getting rejected for fit and quality. It is not clear if this is being fully considered.
You might try negotiating in one of two ways: you could propose that you spend a week working toward the deadline and see if you get far enough that he agrees you will be able to produce a quality manuscript. And/or you could propose sending it to some third party for a “friendly review” and recommendation on which of the journals to try for. Basically, I would recommend you get to work (rather than make accusations) and the “winner” of this argument will become self-revealing.

I see no reason to think that anything unethical is happening here. I'm not saying you are definately wrong, these things do happen, but I see no reason to think this is the likely explaination. Unless you have other evidence, i'd be very careful about saying anything to anyone else about these accusations, as you risk turning what is now a slightly irritable difference of opinions into a major breakdown of your relationship with an importnant source of support.
I agree with others. If this journal really is a "top" journal, there is no way you can write a paper in 3 weeks. I say it takes at least 3 months to pull a paper together for a glam journal.
For the fit, I guess it would be possible to do a pre-submission enquirey as to fit. Paritcularly if you already have some professional connection to the editor in charge.
Re-review is a real problem. You don't want to just chuck something in on the off-chance as at best you are burning the people best qualified to judge the work as potential reviewers.


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Can a person who once supported pseudoscience or conspiracy theories ever be considered a credible source again?
All the sciences come across as merciless to me. If you make even one statement that turns out to be false, it seems you have no chance of recovering your career. I have heard of plenty of stories of accomplished scientists and academics losing their credentials after making claims that were either rejected from the start or later disproven. I have never heard one story of someone 'redeeming' themselves and gaining respect in any intellectual field. This all makes it look like even so much as a simple mistake can destroy your career forever.
So tell me, is there any route for someone who at some point in their lives supported conspiracy theories or something else obviously false can take to regain respect? I've noticed a lot of psychologists claiming that conspiracy theories are hopeless and impossible to 'cure'. Are the sciences just completely intolerant of imperfection or do they express some mercy?

Could you clarify what you’re meaning by “conspiracy theories”? If it’s the GM streetcar conspiracy that’s a different kettle of fish than if it’s that Queen Elizabeth is a reptilian.

-1 Half this question is about making "statements that turn out to be false" and half is about pseudoscience/conspiracy theories. A lot of it doesn't make sense. Please focus on one or the other.

Comments are not for answers nor for extended discussion; this conversation has been moved to chat.

Agree with @Azor Ahai. The question should focus on either conspiracy/quack theories or theories/statements that turned out wrong. Unfortunately my comment was purged, but the question should be edited for clarity.

The existing answers are mostly about scientists coming to false conclusions, making errors in mathematical analyses. Pseudoscience and conspiracy theories are particular kinds of falsehoods with different dynamics, and often attract very smart people.

Let me answer this by turning it around: just because somebody hasn't supported obvious bunk doesn't mean they are even vaguely right.
One of the beauties of science is that, at the end of the day, the people don't matter to the validity of the material.  As long as a document presents a clear argument, you can evaluate it for yourself, no matter whether it was presented by a known crackpot or  a heroically revered elder.
That means that somebody can be ridiculously wrong in one area---even to the degree of crazy conspiracy theories---and still well respected in another, through the magic of mental compartmentalization and cognitive dissonance.
I had a direct experience of this as a young graduate student: one of the early conferences that I attended was a complex systems meeting with a very loose policy for acceptance: you basically had to be sane to give a talk, but even crazies could join the poster session. I was all charged up from earlier listening to keynotes from seriously famous luminaries, when I walked into the poster session and met a respected mathematician with a poster explaining the connection between fractals and peace, supported by poems pleading for one to use the hypotenuse and not the legs of the triangle for the sake of peace. Complete gibberish.  This person, however, is apparently a well-respected researcher in their own field---they just go off and let their crazy flag fly in certain other places.
That said, if you know that somebody has gone to crazy-town, you certainly would be well advised to examine their arguments and citations quite carefully.  Still, at the end of the day, the only truly unrecoverable stain is falsification, because then people can no longer evaluate your arguments without wondering whether the data is simply fictional.

William Shockley (invention of the transistor) and Robert Lee Moore (American mathematician) come easily to mind.

Jack Parsons is another.

"One of the beauties of science is that, at the end of the day, the people don't matter to the validity of the material" - that would be the ideal. But in real life, humans are not perfect, and science itself is sometimes plagued by ideological and political biases.

@vsz And under their influences, sometimes the day is long indeed, eppur si muove

Isaac Newton also studied the occult and alchemy. In his defense, that wasn't quite as crazy then as it is now, but even then there was a wide gap between his studies in math and physics and some of his other pursuits.

@RobertColumbia Jack Parsons was a devil-worshiping occultist, but I'm not certain if having non-standard religious beliefs would qualify you as "crazy".

@TimothyAWiseman the connection of Newton and the occult does not surprise me at all, as whole foundations of mathematics in ancient Greece were treated as a somewhat esoteric mystery by Pythagoras et al. Maybe it is the same exciting feeling of mystery is what drives both rigorous science and outright occultism.

@vsz To suggest that scientists are people, who are subject to ideologies and biases, is seen as heresy by some people. Ironically, science has achieved a religion-like status for some people where anything that is published "in a study", no matter the quality, is considered as "the one and only truth".

Pseudoscience and conspiracy theories are one thing, but your opening paragraph reveals a much deeper worry...

All the sciences come across as merciless to me. If you make even one statement that turns out to be false, it seems you have no chance of recovering your career. I have heard of plenty of stories of accomplished scientists and academics losing their credentials after making claims that were either rejected from the start or later disproven. I have never heard one story of someone 'redeeming' themselves and gaining respect in any intellectual field. This all makes it look like even so much as a simple mistake can destroy your career forever.

...which is false. Check out the doing the right thing category on RetractionWatch. For example,

“I was shocked. I felt physically ill.” And still, she corrected the record.

Strand tells Retraction Watch that the response to her self-lustration has been:

incredibly heartening. I didn’t know what kind of reaction this would get, and it has been great to see such support. I wanted to share the story so people could see that admitting a mistake doesn’t necessarily end your career; it’s an added benefit that now people can see the outpouring of support for transparency. This experience would have been less trying if I’d had models of what might happen and how the scientific community would respond. Although this has been a difficult experience, I’ll be very glad if it makes it easier for someone else to do the right thing in the future.

“Commendable”: Researchers retract a paper when they find gene sequence errors

Oliver Pybus, the editor of Virus Evolution, praised both the authors and the researchers who generated the original data and then corrected the sequences:

[T]heir openness and responsiveness was commendable.
GenBank seqs do occasionally get updated.  But it’s perhaps unusual that the seq changes led to such substantial alterations to the conclusions of the paper.
My take is that the benefits of genomic data sharing vastly outweigh the occasional costs, such as this. Everyone acted in good faith and the system self corrected quickly.

“This is how science works:” Error leads to recall of paper linking Jon Stewart and election results

As the Twitter feed reflects, Porter and Wood received praise for their handling of the mistake. Here’s a response from one follower, Michael Spagat:

Seeing this is the best moment of my day so far. It seems that everyone involved in this has has done themselves proud. I wish this kind of thing were routine.

There is a difference between making a scientific mistake if you are trying to honestly follow the evidence and pure intellectual dishonesty. Pushing conspiracy theories is hardly valid science but somehow 'mistaken'.
Lots of people make scientific mistakes and are honest enough to admit it and accept scientific evidence when it emerges.
Lots of other people push (what they call) "theories" with no evidence, but with some sort of political, economic, or societal agenda.
Mistakes don't need "forgiveness". A person just admits that their science was flawed. Perhaps a non-representative sample. But pushing things without valid evidence because of some agenda does require that the person seek forgiveness as they can do great evil. Should we inject Clorox to "cure" covid-19? Evidence? People die for such stupidity. Forgiveness may be slow in coming.
Follow the science and don't worry too much about the fact that mistakes do occur. But you need due diligence in your scientific pursuits. Sloppiness isn't a virtue. You can't just expect to be honored if you are sloppy.
That said, there have been a few people who have "seen the light" after a period of misadventure. They may be able to find a road back to respectability. Some have done, but it is a hard road.

Agenda is the word here. Most conspiracy theories have a layer of agenda which has nothing to do with the underlying truth. Once one is tainted with the reputation that one sacrifices scientific insight to drive their agenda, that's very difficult to get rid of. As it should be.

I like to think that if a researcher were to make embarrassing claims, and then sought mental health treatment and subsequently repudiated those same claims, that the scientific community would not reject later research out of hand.

Most soft sciences have a layer of agenda behind them also but those researchers are not discredited. Unfortunately, even science has been taken over by politics or money. Someone who supports the current consensus is not challenged too hard but those who offer alternatives to the current consensus are routinely branded fringe and conspiracy theorists. The fact is that the overwhelming majority of science throughout history has been disproved,  many times proving the nut job correct. As a matter of fact, science has NEVER proven anything to be correct. All science can do is prove things wrong.

@Dunk: mathematicians prove all the time that something is correct.

@Dunk, "Most soft sciences have a layer of agenda behind them". Is that your area of expertise?

@Buffy, if you've ever read a gender studies paper, you'll know this very true of that discipline. But I also think it's untrue of most branches of psychology, from my own experience at least. More important, it's worth noting that merely having an agenda doesn't (or shouldn't) disqualify anyone's  intellectual contributions. The basic thing we all have to do in a scientific context is say low-ambiguity, testable things, and honest about the evidence. We're allowed to have an agenda as long as we follow these two basic principles. I think that's very important.

Also, a third very important principle is to try to distinguish between descriptive and normative claims and not mix the two. If I think sexism is bad, for example, that's okay, but if I then start mixing the assumption that sexism is bad into sentences that are about descriptive questions, like whether a pay gap exists, that's bad. I should break my points into two different sentences, so a reader can agree with one point but disagree with the other more easily. I think it's important to talk in a brittle way and not mush things together in a way that undermines proper criticism.

@Jan True, though many people do not consider math to be a science. Much to my frustration, the patent bar in particular does not view math as a science at least not for purposes of the patent bar.

@TimothyAWiseman, applied math can be a science, but not pure math. The processes are completely different. Patent is involved with inventions. Math is involved with ideas. That is the key distinction. And "inventiveness" isn't the same as "inventions".

@Jan Only if a certain set of unprovable axioms is correct!

@MatthewWells Actually, that isn't even strictly necessary a lot of the time (somewhat confusingly!). Indeed, mathematicians tend to prove results of the form "if [this] then [that]". So the validity of [this] isn't needed for the implication to be true -- in fact, if [this] is false then the implication is trivially true! (a false statement implies any statement). Such assumptions aren't usually stated explicitly (one does not derive everything for each paper!), but they are implicitly there. Just, of course, statements which rest on incorrect assumptions are not so useful/helpful! =P

@MatthewWells, axioms are neither correct nor incorrect. They are simply the base statements upon which deductions can be made. They are "assumed to be true" for the purposes of an argument and are outside the world of verification. You can change the axioms if you like and come up with different mathematics. Explore Nonstandard Analysis for example.

You can make honest mistakes, and that is fine. You can do everything right, but based on later data your conclusion could be wrong. This is perfectly fine to. What is really problematic is cheating, either plagiarism or making up data. That is a career killer,  and so it should be.
As to pseudoscience or conspiracy theories, it depends on when you supported them and how. If you did that in your teens, then it will raise some eyebrows, but that is in all likelihood all that happens. If you supported them when you should have known better, well then you should have known better...

Nobody cares if you make wrong claims, only if you make fraudulent claims. Wrong is part of science. Fraud and pseudoscience nonsense isn't.
As for the effect, it depends on how well-placed the scientist is when the nonsense hits the fan. Many professors will be able to handle committing a moderate amount of fraud because they know people. It's not good for a career, but it's only really hard on early career researchers.
It's hard to prove fraud at all. It took like 3 years and a ton of work from dozens of people to get Brian Wansink force-retired from Cornell and his entire stupid career was fraud (and he was dumb enough to blow the whistle on himself by accident). We all have to put up with Jim Watson being in the news for his idiotic racist nonsense even though he hasn't been a scientist for 20 years.

Do you mean James Watson for his idiotic racist nonsense?

ermm, are not these the same names? The Star Trek pilot was 53 years ago. I can understand people not knowing Ian, John, Jan, Jack are the same name, but Jim and James?

Not my field but a high profile example of an academic mess-up is that of an economic study that turned out to be faulty because the authors made an mistake in MS Excel.
And it was not just an academic mistake either because the study was used to base policy on.
As far as i can find on scholar.google.com, the authors are still publishing. Probably their reputation took a dent but it was not the end of two careers.
And it should not be as it was an honest mistake.

No, not until they have been checked and shown to be credible many times in the future. No-one should be accepted as totally credible-ie check the source and the science behind the claim.

I'm not quite so pessimistic. Normally I agree with you, but there are cases of clear conversion and a clear trend away from quackery. Maybe "trust but verify" is appropriate in some cases.

Yes, but it will be much harder for him.
In science, you should judge a source by objective criteria and not by authority (who is the author). This means when someone who talks a lot of nonsense writes a good article, this article can be a good source.
But most people will not bother to evaluate an article in depth, when they already know that the author supported pseudoscience and other nonsense in the past.

Well, a person who has been wrong will be at a disadvantage in a debate in which ad hominem argumentation is allowed.

@EvilSnack This isn't a direct ad hominem attack. Ad hominem is purely personal and unrelated to the point made. If the personal properties being used are previous experience of this person's papers using cherry picked data or dismissing arguments they couldn't address then it isn't unrelated to be more cautious of their results.

Actually, it is. "P is true because X." "Don't give me that. Mr. A says that, and he said Q because Y, and we know that's wrong."

Due to the difficulty of science there are unfortunately many examples of people who made substantial contributions in one field and then threatened to undermine their reputation (or actually undermined it) by espousing nonsense in some other field.
Jordan made fundamental contributions to QFT and quantum mechanics whilst also spouting theories of geology which were nonsensical.
Broca is known for his discoveries in anatomy and also spouted racist nonsense in his pseudoscientific work on anthropology.
Henry Heimlich famously invented the Heimlich manoeuvre and then undermined his reputation by promoting a treatment called malariatherapy, in which people were intentionally infected with low doses of malaria in the belief that it would cure them of cancer and AIDs.  His reputation was so undermined that the American Red Cross now apparently refers to the manoeuvre as the 'abdominal thrust'.
Also the infamous example of Linus Pauling who did Nobel Prize-winning work on chemistry and then went on to promote pseudoscientific views on the disease-curing properties of large doses of vitamin C.

This answer doesn't seem to be answering the question? You're mentioning people who lost their reputation as a result of pseudoscience, but not any people who rehabilitated their reputation afterwards.

Genetics, computer science, black holes and extraterrestrial intelligence were all called "pseudoscience" in various places at various times of the history of science. I think it should not be "forbidden topics" in research that ruin the honor if just mentioned.
The only activity that ruins the reputation of the researcher is the intentional falsification of the experimental results. If the work does not follow scientific method in general, the reviewer should care. Publishing something strange in a non scientific press is not a science but just a hobby activities of the researcher and normally should not impact much the reputation.

Genetics, computer science, black holes and extraterrestrial intelligence were all called "pseudoscience" in various places at various times of the history of science — can you back this up with evidence?

See https://en.wikipedia.org/wiki/Lysenkoism, https://en.wikipedia.org/wiki/Cybernetics_in_the_Soviet_Union and https://podcast.sjrdesign.net/shownotes_150.php.

I'm aware of political campaigns against genetics in the Soviet Union, whether that is the same as calling it pseudoscience is a matter of interpretation.

History exists so we could learn from it.

I would like to provide a counter example showing that belief in crazy ideas doesn't always mean the end of your career.  I did my PhD research in the Stanford Biochemistry Department, which was home to Arthur Kornberg; Nobel laureate for his discovery of DNA Polymerase.  In his later career, he became obsessed with inorganic phosphate, which he felt was the key to understanding the origins of life.  His evidence for this was far from convincing and every year when the faculty would introduce their research to new grad students, you could see all the other faculty cringe as he would introduce his lab.
Despite his eccentric views he was still well respected and frequently asked to speak at other universities.  When he did, he refused to talk about anything other than inorganic phosphate and if anyone tried to get him to talk about DNA Polymerase, he would call it a "former distraction" and refuse to talk about it any further.  This meant he didn't get a ton of repeat speaking engagements, but he still gave lectures, still was an active researcher in the Biochemistry Department, and still found students willing to research in his lab to have a Nobel laureate on their CV.

I think we have to distinguish between what what we mean by reputation and credentials:
Science doesn't really rely on creditentials or reputation. At least in thoery, papers etc are judge on the merits of the material contained within them, not on the identity of the person submitting them (granted, big names are sometimes given an easier ride, but the problem here is that its too easy for big names, not that its too hard for everyone else).
All science is only an approximation to the truth and any paper will be proved wrong in some aspect, given enough time.
Make a mistake, or support a crazy theory - you will still be able to publish, apply for grants, teach  students (as long as your crazy theory doesn't give the impression of wanting to make students unsafe).
But that is science. Scientists also enjoy a certain reputation and authority outside the actaul performing of experiments. They might be asked to weigh in on policy decisions, or speak to the media, or ask to give speeches or write books for the public. They might be asked to move into the senior management of a university to be a head of department, or a dean, or a president etc.
Here supporting pseduo-science, or making serious miskates in your scientific work probabaly does do lasting and difficult to recover from damage.
The difference is, in the first case your authority to make a claim rests on the data, while in the second case you are deriving your authority from your reputation.

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Photoshopping label onto graph
For a project, I noticed really around an hour or so before my deadline was due that some of my graphs lacked units when I labeled the axes. In the interest of time, I decided to add units to the plots manually using photoshop. The deadline has now passed, and I’m worried if this is considered academic misconduct or something. The data I used complies with the labels I gave the graphs manually, and I haven’t done anything to change my data in any way with the image editing program other than to simply add the units of some of the labels. The only thing I’ve done is to write the axes labels myself instead of telling Python to.
I can’t find any policy on this on my university website. Should I be worried? Could this be considered falsification of data or some other form of academic misconduct), even if the units I’m adding are literally the appropriate units?

I'm not sure why you think it would be. Photoshop is a tool like any other. Unless it was a pure python programming assignment, of course.

@Buffy The assignment was coded in Fortran with plots meant to be made in Python. I made all the plots, but forgot to add units when typing in the x and y labels for a few of them. Some plots have them where I remembered (as it’s not like I simply don’t know how to add the labels), and for the ones that didn’t I added it manually. I literally just added “(m)” next to “x” and “y” for the few plots I did this to. It’s not like I’m getting around the fact that I don’t know how to label the plots or something.

Best to be upfront about it when you submit, I would think. Safer.

@Buffy The idea of that scares me greatly in case it would result in me being punished.

Just guessing, but the penalty for doing it and not noting it could be worse. But I don't know your prof.

I’ve decided to resubmit the report without the photoshopped axis labels just to be safe. The submission is now late so I’m asking for leniency with that. It will not mark as well because of the lack of axis labels but I’ll have peace of mind.

I applaud your choice.

Anyone care to explain the close votes?  This is clearly generalizable.

My interpretation of the question is:

I was told it is unethical to photoshop my data.  Is it ethical to use Photoshop software to make a graph?

The choice of software used is completely irrelevant to the ethics of any scientific image.  You can use python, Photoshop, or crayon.  If the image is drawn correctly, it is okay.
If the contents of the image is false, that is never okay.  It is much worse if it is deliberately false.  When people say it is unethical to photoshop, they mean that it is unethical to lie.  They do not mean you cannot make truthful images using the Photoshop brand software.

From a practical point of view, Photoshop is not a good tool for working on graphs.

My interpretation of the question was different. It was that OP was asked to use Python to make the graph (the assignment was assessing his proficiency with Python), and he was worried that altering the output in Photoshop would be viewed as academic misconduct.

@PersonX Maybe, the question does not indicate.  If the goal is to teach python, judging students by the units on their graph labels seems misguided.  If the goal were to teach data analysis, it would be make a lot of sense.

It depends on the nature of the assignment. If the assignment required you to use Python to produce these plots, and you were being evaluated by how well you used Python, then yes, altering the output later in Photoshop and not disclosing such could be considered academic misconduct. Based on the comments to your post, it sounds like you did disclose this to your professor, in which case you haven't committed misconduct.
If the assignment was just to produce plots, but you weren't being evaluated on your proficiency using a specific software, then I would completely agree with this other answer that there is no issue here.

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Can a PhD student co-supervise master students in Germany?
In Germany, is it possible for a PhD student to be co-supervisor of a master thesis?

what does their department chair say?

By and large, yes.
The conditions for master thesis supervision are specified in the examination regulations of the considered department. Generally, there is a big variety between the regulations of different departments, so it's always worth having a look at them.
In all cases I'm aware of, PhD students can act as co-supervisors of master theses. Usually it's required that a professor is formally specified as the main advisor, both in the formal proposal and on the title page of the thesis document. The PhD student can be specified as an co-advisor on the title page.

Yes, with some notes on terminology here (from a viewpoint of computer science, in case there are differences by discipline):
Prüfer: In Germany, the person who is formally in charge of the thesis on the university's side is typically called the "Prüfer" (literally: the "examiner"). This is usually a professor. They are the one who are logged as the official person supervising and grading the thesis in the exam office.
In practice, it is well possible the student never has any contact with the Prüfer except during the final presentation/defence.
Betreuer: Then, there typically is a "Betreuer" (literally: the "adviser" or "tutor"). They have likely had some influence on the thesis topic (if it wasn't them writing down the task description in the first place - to be greenlit by the "Prüfer"), will regularly be in touch with the student (e.g. by means of weekly status meetings), and has a deep understanding of the topic the student writes about.
This "Betreuer" may very often be a doctoral candidate whose own work (either their doctoral thesis research or some project their position is funded from) is in some way related to the Bachelor/Master thesis - as in, the Bachelor/Master thesis could be seen as a sub-project of the "Betreuer"'s topic, which the "Betreuer" may then be able to cite in their own work.
Authority of the "Betreuer": Behind the scenes, the "Betreuer" will write a brief report and grade suggestion for the "Prüfer" at the end of the thesis, often including not only aspects from the resulting thesis document, but also the general impression of the student's enhusiasm and skill level when it came to driving the Bachelor/Master thesis forward. Other than that, the "Betreuer" will take little "administrative" action on their own in that if anything goes wrong (student refuses to communicate, thesis task proves unsolvable, ...), they will usually consult with the "Prüfer" on how to proceed.

The differences are not only by discipline, but by department. I'm in CS, too, and the two German departments where I worked did not have the role "Prüfer". Instead, in both cases, there was "Erstgutachter" and "Zweitgutachter", who wrote two independent reports. One department allowed the Zweitgutachter to be a PhD student, whereas the other department required a PhD graduate. In both departments, Betreuer and Erstgutachter were the same person by default (exceptions were possible), and PhD students involved in the supervision could be specified as additional Betreuer.

In the departments I know (in chemistry), there is a distinction between the formal supervisor (i.e. the supervising professor or similar) and informal supervision: the exam regulations mean that a PhD student cannot be the official supervisor, but the supervising professor can delegate day-to-day supervision to whomever they trust to do this. The formal resoonsibility stays with the supervising professor, though.

@lighthousekeeper: in the faculties I know, the Gutachter (reviewers) are a subset of the Prüfer (examiners): examiners are also the ones who do the [oral] Master exams.


text:
When a professor takes an affiliate appointment in another department, do they get an increase in salary?
Let's say an associate professor of Math makes 120k per year USD in a United States university and takes an affiliate professor position in the Quantitative Biology department.  Would they get additional salary for doing so, or is it simply more responsibility for no incremental salary, kind of like service work?

I assume you mean at the same university. Yes?

@Buffy yes same university

Then I think the answer of Dan Romik is excellent.

I have never heard of a joint appointment in a second department being tied to a salary increase. It’s possible that in some rare situations such an increase will be negotiated as part of the deal for a professor to take on a joint appointment, but generically, the answer to the title question is “no”.
On the other hand, the answer to “or is it simply more responsibility for no incremental salary, kind of like service work?” is also “no”. Being a joint appointee does not involve “more responsibility”, rather it’s more accurate to describe it as a shift in responsibilities. Professors without a joint appointment already have a full time job, so they cannot increase their responsibilities (at least in a formal sense, and to a large extent also in a practical sense). If a professor takes on a joint appointment in another department, it’s likely because the professor simply likes the idea of being involved in the other department because their interests are aligned with that move, in the sense that the professor wants to have collaborations with other people in that department, wants to advise students in that department, wants to teach courses offered by that department, or similar things. But they had a full time job before the change in appointments, and they have a full time job after the change in appointments, so the total amount of work they are expected to do overall does not change.

Also the synergy that might come from such work. Hopefully it extends beyond just teaching a course or two into some collaborative research.

It is probably taken as part of their contracted teaching load, but as you don’t have the details of that contract you won’t know for sure.
We had a professor from the maths dept teaching in our engineering dept...


text:
What should you do if coauthor refuses to work on paper and refuses to consent to submit it?
My old PhD adviser and I had a falling out. We wrote a paper together, it is done at this point in my eyes. He "disagrees". Near the end of revisions the edits became more and more banal and even flip flopping. "Do it this way, no change it back, no change it back, no change it back etc" endlessly. I have shown the paper to other faculty and they think it looks fine.
We got into an argument about this, the paper has been done for well over a year at this point. I have a new adviser. At this point the old adviser flat out refuses to submit the paper, he refuses to make any edits to the paper, he refuses to even talk to me.
The grad head has been notified, other professors have been notified. My current adviser is really pissed off about the whole situation and is planning on talking to the old one.
Can he just not submit the paper? Do I have any recourse? I wrote the paper, I did the majority of the work (other than his idea etc). Can I just submit it myself? I feel like he would email the journal and complain about it. But I don't see any other choice.

"I didn't the majority of the work"? You did or didn't? This is critical.

@captain I did, sorry

'I have shown the paper to other faculty' - I would be pissed with this.  Students should never use other people or papers to justify that their work is good.  This is no different to saying, look, Bob killed Jane, so it must be ok I kill Tarzan too.

@Prof.SantaClaus I, on the other hand, would be pissed off if my students didn't show their work to other faculty.  I have no idea what your Tarzan comment means, or what showing your work to other people has to do with murder.

@JeffE So it would be ok for a student to undermine you with the help of other faculty members?

@Prof.SantaClaus It is not entirely clear from the question, but my reading is that OP showed the work to other faculty after it had been dragged along by the old adviser. If my reading is correct, the undermining is not coming from OP.

@CaptainEmacs that is indeed the case.

@Prof.SantaClaus "Undermine"?  I think you misspelled "solicit critical feedback for". Yes, I absoutely do want my students to get advice from other faculty, even if—or perhaps more accurately because —their advice sometimes contradicts my own.  Research only counts if it is subjected to public scrutiny; advisors own neither their students nor their students' work; and academia is not Game of Thrones.

@JeffE If it's just to solicit constructive feedback I'm all up for it.  However, if the intention is to use another faculty's words against mine, then it's undermine!  Students act like kids at times; playing one parent against the other in order to get what they want.  It sounds like the questioner is doing exactly that.

@JeffE One other point.  You must work with colleagues who can conduct high quality research and write well.   Would you want your work criticized by a colleague who can hardly publish anything or write poorly?

No, you probably can't just submit it yourself if the prof is validly a co-author. You need his permission, just as he needs yours.
But I suggest that you let the two professors fight it out among themselves. That could result in a good result for you, and probably not a worse one. Professors sometimes don't mind behaving badly in front of students, but are less likely to with colleagues. Collegiality is still valued in most places. If it needs to get escalated, let the new advisor do it also, on your behalf.

+1 for "Professors sometimes don't mind behaving badly in front of students, but are less likely to with colleagues."

@Buffy "Professors sometimes don't mind behaving badly in front of students, but are less likely to with colleagues." [reference required]


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Simultaneously submitting, one paper got rejected, other didn’t - what to do?
There is a result R and teams T and U.
Team T submitted into a journal result R, but not on Arxiv. Team U then submitted result R to Arxiv, without knowing about the submission of Team T. Team U also submitted to a journal after publishing on Arxiv but got rejected. Now the paper of Team T is already published, but later than the Arxiv submission of Team U.
What should or can the Team U do?

And "published" isn't the same as "submitted". The published version may have been the first, actually. But there are anomalies in hot fields. No one can know of everything simultaneously.

@GoodDeeds sorry typo

@Buffy Yes, the submission to journal was before the submission to arxiv, but submission to arxiv was way before accepting in journal

I suppose arXiv could be used to try and scoop a paper unethically with this method. Color me worried.

In a reasonable world. both teams would get credit for independent discovery.  (Whether the world is reasonable or not depends on your research community.)

If this was dissertation work, say so. There may be solutions for that situation.

Some journals publish on which date papers were (a) first received, (b) revised, and (c) accepted. Could help.

Is Team U suspicious that Team T was among the reviewers of Team U's submission that got rejected?

@Buffy Where is the problem? There is a priority stamp on both T's (through the journal) and U's (through arXiv) papers. Since it was U's paper that was rejected, it is also not likely to suspect that one team tried to scoop the other, since this really would only properly work if U blocked T's publication, but not the other way round - U's work was already public. Unless T copied from U, but that is easy to verify and date.

Team U can genuinely claim the following in a future version of their article:
"After making our result publicly available on arXiv, we became aware of a similar result obtained in \cite{teamTresultPublishedPaper}."
Team U can congratulate team T and ask the following:
"Dear Team T, congratulation on your result R in journal J. As you may be aware, we have been working independently on a similar result as your recently published paper; our article was available on arXiv on Sept 2019. We were planning on acknowledging your independently obtained result in the next revision on our article, and we were wondering if you would agree to do the same." As pointed out in the comment, this is potentially obnoxious, and might not have any benefits.
Team U can submit to paper to the same journal that accepted team T's paper. "Dear Editor, we have noticed a recently published article by team T in your journal on result R. The same result was obtained independently by our team and made public on Sept 2019, a few months before team T's result was publicly available. We are wondering about the journal policy regarding publication of two papers that prove the same result, when the public record shows that the results were obtained independently and contemporaneously."
Alternatively, instead of asking the Editor on the possibility of such submissions, Team U may directly submit the article to the same journal with a cover letter asking to be considered.
If members of team T were referees for the paper of Team U (the paper that was eventually rejected), this may constitute a conflict of interest. If a reviewer reviews a paper that proves the same result as an article written by the reviewer not yet public but currently under review, the reviewer should at least declare this as a conflict of interest during the review. Of course, reviewers are anonymous so there is no way for team U to know. Team U may contact the Editor that rejected the journal, saying     "Dear Editor, thanks for your consideration for our submission XXX that was rejected on $RejectDate. After the submission of our article to your journal, the same result was published and made public by Team U in OtherJournal. We are wondering if you could double check that no conflict of interest among the reviewers hindered the review process." this is potentially obnoxious, and might not have any benefits.

Beyond these, team U should try to have their result published. Team U can certainly claim the result in their CV, research statement etc.
There are numerous cases of independently obtained results in hot fields and many papers actually include a sentence as in 1. above. When that happens, curious readers and historians can lookup arXiv or other public repositories (e.g. PhD thesis, etc) to check the actual timeline.

1, 2, and 4 are potentially obnoxious, and might not have any benefits.

I agree that 2 and 4 are potentially obnoxious but I am not sure about 1? The authors will be expected to cite Team T's result in some ways when revising. The sentence in 1 sounds neutral and factual to me. If you still find 1 obnoxious, how do you think team U should describe the relationship with team T's result when they revise? (I have simplified the wording in 1. and added warnings about being potentially obnoxious for 2 and 4. Thanks)

What should or can the Team U do?

Team U should improve their paper and try to publish it again.  Be sure to cite your competition.  It would be an ethical obligation, even if their paper had also been rejected, because the citation will make it easier to understand your paper.
The value of being first to publish is exaggerated.  An ethical journal will publish replication studies without regard to claims that the replication was developed first.  Most authors will cite papers because they are helpful, without regard to which paper was first.
Disputes about priority are petty and best avoided.
The fact that both teams got the same result is very good for science.

I'm guessing here that the team T finished first and submitted. The fact that you (assuming "you" = U) didn't know about it doesn't give you priority. The paper might have been in the works and under review for a long time.
Team U seems to have been later even though their result was visible generally earlier. I doubt that a journal would want to retract based on an arXiv version by someone else. Almost certainly the journal editor and, possibly, reviewers saw T's work before the arXiv version of U.
Congratulate team T. See if there are opportunities for collaboration on future projects since you are on the same trajectory.
But this is one of the dangers of working on hot problems. There is likely to be other work going on simultaneously.
Get your follow-up paper submitted STAT.


text:
If a journal requires "Article Processing fee" does that make it a predatory journal?
If a journal take article processing fee then does that mean the journal is predatory? or there are some other criteria to tell a journal as predatory?

This answers your 2nd question: https://academia.stackexchange.com/questions/83764/with-bealls-list-gone-how-can-i-tell-if-a-journal-is-spam

No, not all journals that charge to publish are predatory journals.  Some genuine open access journals charge article processing fees.  For example, the journals by Copernicus, by the European Geophysical Union (EGU), charge moderate article processing fees.  These cover the costs of the publisher, which then makes the articles available open access free of charge.
To label a journal as predatory you need other (additional) criteria.

Some journals charge a "page fee" even when open access doesn't happen. Costs need to be covered somehow if a journal is to remain viable.


text:
Is peer review process totally theoretical?
Does the peer review process involve only theoretical analysis or it contains some practical components?

The question seems a bit vague. Can you clarify what you mean?

@6005 the question title says it all, literally. not anything more

Well I do not know what it means. I don't know what "totally theoretical" means or what a "theoretical analysis" means in the context of a review.

There are many reasons that peer review generally "works" but isn't perfect. In some fields, such as mathematics, a paper is normally expected to contain a sufficiently detailed proof of any claims (theorems) that a specialist can check the validity.
In other fields, this isn't possible within the time frame or the resources available within the review process. As your first version of the question suggested, the best way to verify claims made using, for example experimental or statistical methods, is to replicate the study independently. This takes both time and money and so is infeasible if results are to be made available in a timely manner.
But there are several safeguards that tend to weed out the garbage, though they don't eliminate it with 100% certainty. While an author may not know who the reviewers of a given paper are, reputable journals use reputable and experienced reviewers. Typically a paper is reviewed by more than one person and most will have some expertise in the specific subject matter. They will know what is reasonable to expect and what is not.  A reviewer will first ask whether any claim is at all reasonable. Unreasonable claims either get rejected or get extra scrutiny.
Reputation in general is a check on bad results, though, again, not absolute. If an author is associated with a reputable institution, they want to protect not only their personal reputation but that of their institution. A reviewer seeing a paper from an independent researcher, associated with no reputable institution, won't have the automatic confidence that the study was carried out properly and so might reject it, or give it extra scrutiny. But many such papers don't pass the "smell test" and get quickly rejected.
There is, in fact, a "web of trust" in the research community. An assumption that people, generally, do honest work and try to avoid error. An assumption that they check their work and try hard not to publish things that later turn out to be wrong.
For an academic wanting to build a reputation, there is very strong incentive to get it right. It is one thing to have a paper rejected by a good journal and quite another if it is learned later that there was intentional misconduct, even sloppiness. An good academic reputation is easier to break than it is to build. And much harder to rebuild.
Also note, that incorrect science is sometimes published even when everything is done correctly and ethically. Unseen factors and even statistical anomalies do occur in work even when it is done carefully. There is no absolute guarantee in an imperfect world.
But, yes, it is possible to fake data. It is possible to assert that procedures were followed when they were not. But people doing that get a reputation that will follow them.


text:
Having trouble responding to professors' emails due to anxiety,
I have crippling anxiety around "authority figures", and I'm irrationally deathly afraid to the point where I will cry in a room when alone with them, likely due to my upbringing, namely, always being afraid of my verbally abusive, but very loving and well-intentioned, father.  And so I tend to leave very important and very kind emails from professors unanswered.  This is unprofessional of me, and so I was wondering what some of you here have successfully tried doing to counter this level of anxiety.
The authority figure can be a professor, a fireman / police officer looking to help me, my basketball coach.  I've experienced similar with all of these people.  I am sometimes just mute.
I see a doctor and take meds already, but I am looking for other ways to cope.
Is there a cool, fun strategy to try to implement, say, respond to emails within 5 minutes of reading them, even if my response is incomplete?  Aim for a one-sentence reply?
I don't know, I'm just thinking, but I know I need a lot of help.

would it be helpful if I were to share some e-mails I wrote to authority figures (such as a professor I know, a professor that I do not know, a department head) and try to break down what my personal approach is?

@BoatyMcboatface Sure, I'd be happy to read it.

Who are you? An undergrad, grad student?

@AzorAhai PhD student

If your doctor cannot help you with this question, they should be able to refer you to someone who can.  I do not think you should take advice from internet strangers who might not have any experience with severe anxiety.

I’m voting to close this question because it is not within the scope because the question is about anxiety relating to all authority figures, and not specific to professors.  Futher, this site is not suitable for treating health problems.

The critical point is: authority figures are humans too. And, unless they are overgrown children who abuse authority like toys, they are no different than you and me. Treat them with respect (as you should every human, anyway) and you're fine.

I would recommend OP to ask this question in Academia Reddit and not here. Because moderators here don't allow personal information

@SSimon good suggestion, I didn't know there was an academia reddit - thanks.

You are doing the right thing seeking some medical advice. But the way to become more comfortable in this, as in most things, is:
Practice. Practice. Practice.
The first steps are painful and you may fall. Eventually you learn to walk and probably to run.
My doctoral program took a few years longer than it might have because I was too afraid to speak up on my own behalf at a certain point and got stuck (really stuck) with an unhelpful advisor.
Later, I took on the issue head on and taught myself to look people in the eye and to speak up. It was very difficult at first. Now I do it without thought or worry.
It is just a skill. Learn to apply it. Haltingly at first, but it is extremely unlikely that bad things will happen if you speak up. If people don't know your needs they will not be able to assist your academic growth. Just. Do. It. Grow into the person you want to be.
Sometimes you need to just pretend to be the person you want to be.

As I mentioned in the comments, I will try to explain how I go about writing emails via breaking down some of my older ones. Hopefully this can help a bit. I am not boasting my writing skills (or of the lack there of). This is what works for me. Note that there are some reductions and italic text are the censors.
I) A professor that I expect to remember who I am.
Here I am asking for a professor for the homework questions he prepared for a class that I have attended. I also have a good rapport with him. So I try to keep it brief and on point.

Hello,
Can you please e-mail me the algebra homework sheets you prepared for your courses (if you have them)? My friend is retaking algebra in another university and it appears they don't give decent, constructive homework. I also think I can benefit from redoing those and repeating some of the basics with her. Finally, I intend to send you a some other matter draft tonight hopefully it is not too late.
Regards

For something like a small request, I would simply briefly say hello, state my request kindly and explain why I am asking for it. Thank them for their time and end with regards. If it were something more time consuming I would use phrases like, "would it be possible" or "if it is not a problem". Brief and on point usually works great.
II)A professor that most likely does not know who I am.
This is a more complicated issue. I am asking for a proffesor (to whom I have never talked before and that I will be working with) if he would be okay for me the apply for a grant for another project relating to his project in order to fund my participation.

Hello,
I am writing to inform / check with you something. I will be participating your program and as you might know along with the usual expenses your university demands a payment around ... I have been looking for financial support options for a while and I could manage to find two small ones. The part that might concern you that one of the support option comes from some institution and the only way to get the program funded is to declare the program payments as "cost of education" for another project that will be done in my country. Hence, I will be doing a senior project next semester with another advisor on a related or correlated topic to justify the declaration and get funding. I acknowledge that the any result or material done in the summer is the program's intellectual property and I ensure you that any result will be used only with the appropriate citation and reference. I also acknowledge that your program is the more important between two and that my total attention and concentration is and will be on your program. Aforementioned senior project is only to make the program financially less crushing. I hope that this is alright with you.
Regards,

For a longer e-mail I find it useful to state its purpose in the first sentence. What are you asking/saying? Then introduce yourself if it is necessary. Finally make your point. It is usually a good idea to keep it as brief but complicated issues have naunces and it is important to adress them. In the case above, I try to answer why am I writing? who am I? what is the issue at hand? why is this issue at hand? why it might concern them? Why shouldn't they worry about obvious issue?.

Several of the techniques here could help, but here's another angle to consider: Use your email's delay send feature, and schedule for, say, half an hour from when you hit send.
That takes the pressure off of actually hitting the send button, because hey, if you think of something catastrophically wrong, you can go back and fix it. However, it's entirely possible that when you step away for a moment, it'll take a backseat in your mind. So, the half hour mark will pass, the email will send, and you won't think twice about it.
Maybe worth a shot?
(Your mileage may vary. The trick is taking your mind off it in the half hour, if that's at all possible)

What helps me reply to emails from professors is to have a lot of "template" sentences; things that you would pretty much say to anyone in a professional setting without much attention to context. That way it removes a lot of the personal interaction that brings anxiety to me and luckily this sort of attitude is more or less preferred in an academic setting because everyone is busy and all they want is a kind and concise email. Once you develop a habit you can write emails faster and consider it more of a task than an anxiety-inducing social interaction.
My emails frequently contain some of these phrases:

Hello, Dr. _
Thank you for getting back to me/Thank you for your help/advice. Yes I
  agree with you/I appreciate your comments/I would like to ___.
I look forward to meeting/discussing/hearing from you.
Regards, Cell

I very much agree with Buffy's answer, but I believe there needs to be a slight change in emphasis.
What you are describing is not a lack in some skill that you could overcome by practicing. It sounds like the textbook definition of an anxiety disorder, specifically a subtype of social phobia.
Anxiety disorders are quite amenable to behavior therapy. I would very much recommend that you talk to a psychotherapist, not just a medical doctor or psychiatrist. Your school may be able to help you with finding a good therapist.
Your therapist will likely recommend a form of exposure therapy, which consists of performing the anxiety-inducing actions in a controlled and safe environment, essentially to unlearn the anxiety response by learning that the action is indeed safe. For instance, you might write email responses in a therapy session, under the therapist's supervision and help. You will start with small messages and work your way up to more confrontational ones.
Yes, this will take a lot of practice, just like Buffy writes. However, professional support will be invaluable in doing this and in reflecting on what is happening in yourself as you write your mails.
Good luck!

Please do not accept medical advice from people you do not know who have unknown qualifications.

@AnonymousPhysicist: do you consider my advice to see a psychotherapist as medical advice which the OP should not accept? Or my personal opinion of medications as a second step after behavioral therapy? To be quite honest, a diagnosis of social anxiety seems sufficiently likely to me here that I would consider any advice not to see a professional and to essentially work only through a self-help program as dangerous. Incidentally, I may actually be best qualified in this thread about social anxiety, having collaborated on a couple of papers some years ago.

"I may actually be best qualified in this thread about social anxiety, having collaborated on a couple of papers some years ago."  If that were true, surely you would have ethics training telling you that you cannot treat patients you have not examined personally.  Your advice is very dangerous because it might cause someone reading it (not necessarily the asker) to stop taking their prescribed medication.  Further, this answer is inappropriate for this site.

@AnonymousPhysicist: I do not quite see how my advice to see a professional constitutes treatment. I have removed the sentence about medications, as you are right it could be misunderstood. I do not see how my answer is inappropriate for this site as long as the question remains open. (I see that you have voted to close this as a "boat programming" question, and I am inclined to agree.)

Thanks.  .......

@AnonymousPhysicist You protest a lot against this site, as of late.  I can understand though.

I know such problems very well.
My advice is: Do not put yourself under pressure. This makes your fears worse.
You do not have to answer within five minutes. Unless it is something really urgent, you even do not have to answer the same day. Authorities usually are quite busy, they do not just sit there and wait for your answer. So take your time.
I myself start by writing a draft. Not the real answer, but just a draft. I make a list of items I want to mention in my e-mail. I collect some phrases I might use.
Then I start writing and try to finish a first draft of the text. I save this draft and do something else.
When I get back to my e-mail after an hour or so, it is not so terrifying any more, because I already have a draft. Perhaps it is not so bad, and I can use it. Very often, at a second glance, I quite like my text, and I send it as it is.
If not, I go over it again and tell myself that it is still a draft. Then I wait again for some time, and then I send it. In very difficult cases, I sometimes wait until the next day, but not longer.
This works fine for me, and I hope it is of some help for you, too.


text:
Given name versus nickname at work
During an instant message conversation with my supervisor, she brought to my attention that I am using the given name of an employee instead of the preferred name this person wants people to call her.  My supervisor claims that this is a professional courtesy to call this coworker by the preferred name and it would eliminate any tension in our group between me and this person.  This coworker's given name is Maria and she wants people to call her Mari.  In Spanish the two names sound very different.
My question is should my supervisor had brought this to my attention?  Also I don't see how it could be unprofessional  I am calling this person by their given name.  I am not calling her out of her name.  I don't see how it's unprofessional.

Your supervisor brought it to your attention because, frankly, it is rude to not call somebody by their preferred name, particularly if they have asked you to.

Is this a joke?

Could you tell the reasons for not using her preferred name?

Note that this is a problem a lot in high schools where students want to be named by their nickname and many teachers say "This is not your name!"

This seems like something you should clearly do. You should even welcome the "hint" from the supervisor that Mari has preferences and that others are honoring them. In general, I believe, we should take a bit of care with our co-workers and go along with things that aren't clearly evil and might do a bit of good.
Maybe you are happy with your given name and never thought much about whether used it or not.
The opposite problem is probably worse, where someone decides to give you a "nickname", like Mich, that you don't appreciate.
After the "hint" it would be a serious error to use your preference, rather than hers.
In my case, my spouse is pretty much the only person with permission to use my given name. Everyone else uses the nickname I grew up with. My given name sounds harsh to me when used by others.


text:
Are there other evaluation processes besides traditional to evaluate disabled person at university based on their understanding of the subject matter?
Say there is a disabled person who wants to have B.Sc degree in Computer Science.
He knows he has the option of college and other manual jobs.
I want to know are there any other easier evaluation processes for that student who understands the subject matter but cannot answer the traditional questions on the paper like other ten students because these questions require creativity and he doesn't have that talent?
If there are other evaluation processes why aren't they implemented in real life? And if they are implemented which university allows such implementations in Canada and USA?

I am confused as to the nature of the disability - a lack of creativity?

What is the end goal for this person after achieving a BSc in comp. Sci.? For many people the degree is a certification for job recruitment so I wonder what the job prospects will be for this person if they can't even compete at the exam level? One can still learn as a hobby without spending thousands on tuition.

Most universities have policies to handle students with learning disabilities. I think your best bet would be to contact the institutions you are interested in and ask them about those policies.

Hmmm @Cell, would you say that to Stephen Hawking?

I, too, am confused by your use of the word "creativity". And a disability could be purely physical, not a learning disability. Cerebral Palsy is an especially difficult case.

@Buffy Why would I say that to Stephen Hawking? Was he unable to answer exam questions despite claiming to know the material? And did he not use his degree to become a lecturer?

@Cell, actually he was fine in younger life, but toward the end it would have been impossible for him to sit a timed exam. A person with cerebral palsy likewise has a lot of communication difficulty (possibly) but no mental disability. And you have to judge whether Hawking's physics was a profession or a hobby.

@Buffy That's totally irrelevant. This question involves someone claiming to know the material, but not being able to demonstrate it through answering exam questions. There is no mention of physical disability or psychological disability unrelated to cognitive thinking/problem solving. If you get paid to do something, you're definitely a professional.

Both Buffy and Cell seem to very confused about what the topic at hand is.

Are there other evaluation processes besides traditional to evaluate disabled person at university based on their understanding of the subject matter?

Yes, they are called accommodations.

I want to know are there any other easier evaluation processes

If the student is assessed using accommodations, the assessment will be different.  It will not necessarily be easier.  Typically, the student is required to demonstrate the same course-specific skills as the other students.  Example:  a test is checking to see if a student knows about widgets.  Most students will answer writing by hand.  A student receiving accommodations might answer verbally.  The accommodation would be easier with respect to writing, but the same with respect to knowledge of widgets, because that is what the assessment is about.

If there are other evaluation processes why aren't they implemented in real life?

They very often are.

And if they are implemented which university allows such implementations in Canada and USA?

In the USA, universities are required by law to provide accommodations to students with disabilities.  I am not familiar with Canada, but I am sure there is something similar.

I am confused by the downvotes here. This seems like a very reasonable answer.


text:
Is asking practice exam questions on the web cheating?
Is asking practice exam questions released by a professor on the web cheating?
If you asked questions from a past exam, that was already released, and graded, is that cheating?

Don't burn the practice questions by getting some other person to solve them. Buffy's response below is on point! You can sit down with a friend and try to solve them together, though if that helps.

No, if you aren't going to be graded on them it isn't cheating.
But it is foolish.
The point of the questions is to give you practice in solving them, not to obtain answers that the professor already has.
If you don't practice your craft you will never get very good at it.
Moreover, just seeing an answer will very likely give you almost no insight in what it takes to actually solve such problems when face with them in a more important context. You may actually be doing yourself harm by reading answers.
Much better is to work on the problems yourself, and, when you get stuck, ask the professor for help. They will, I hope, give you just enough of a boost to get you going again, rather than so much that it denies you the insight. Strangers on the web are not the best source of your education.

@Numbers: Having someone else do them is a bit like asking someone to practice basketball free throws for you or asking someone to practice tennis serves for you or asking someone to weight lift train for you. Of course, sometimes if you're completely lost (analogous to not knowing how to shoot a basketball free throw or serve in tennis or lift weights properly), then you should probably seek help, but because this is a much more mental activity than the sports analogies I gave, you should of course put forth more mental effort before seeking help in such cases.


text:
Should I admit to cheating when it appears I cheated but I did not?
One of my TAs is accusing me of cheating.
The professor had shared a 2-question quiz through our online portal (Google Meet). One of the questions contained a 9-digit sequence. Somehow, I misread this sequence and ended up solving the problem using a different 9-digit sequence. My incorrect sequence exactly matched the sequence used on a different version of the quiz, which had been administered to a different section of the class several days before. I do not know how similar the two sequences were; I assume they were very different.
I understand how bad this looks, but I actually did not cheat. I am baffled as to how this could have happened given how careful I normally am about reading the question. I have no history of cheating in other classes.
I don't understand how I can prove that I did not cheat. The other question of the quiz was, of course, exactly as given on my quiz, so I'm thinking I may argue along the lines of "if I were to cheat why would I do it on only 1 question", although this seems slightly weak to me.
One complication is that the professor said that anyone suspected of cheating will be required to take an incomplete on the class and do the exam whenever university resumes. This is not ideal, as I am bound to forget a lot of material. On top of this, the classes I am taking next semester require this one as a prereq and this will derail by entire class schedule. I don't think there are any classes I can take for my major without this prerequisite filled.
The professor is offering that I can admit to cheating and then he'll give me a warning for the final and get a 0 on the quiz. Assuming the warning for the final does not come with the above requisite of webcam, should I falsely admit to cheating?
While I am normally against false admissions, I need to resolve this quickly, as the final is the day after tomorrow. Also, given how bad this looks, if I don't accept this and am found guilty, then I will probably fail this class and have to retake it anyways.
Update: For anyone who finds this later, I requested the Prof to let me take the exam without a webcam, given that it may be dropped later. He agreed and also stated there would be no need to drop it later. After the exam, I laid out many of the points given below, which the Prof said he would take into consideration and look into overturning the decision. I had an easy out, where I could take the 0 on the quiz and still get an A in the class, but there is a lot of good advice below for those who are still stuck.

Note this user has asked a series of questions about cheating.  This answer might make more sense in context with those questions.

@AnonymousPhysicist You mean it might indicate retaliation?

@CaptainEmacs No idea.  But I think the asker should be more patient.

There was a ton of useful info in the comments, so I edited the question to fold in this additional information.

I don't know how you resolved it in the end, but can you "prove" you didn't cheat somehow? Go step-by-step with the professor and show how you got each intermediate part? So for the sequence, show how you mixed up the pieces?

@eurieka Nope. I just wrote the step before the answer and the answer itself, so I imagine I messed it up somewhere before there. I ended up laying out most of what was said on this thread in one email. The prof seemed to receive it well and said he will look into overturning the decision.

I'm panicking right now, as I was supposed to be studying for finals

If you did not cheat, you do not need to be panicking.
I recommend these steps:

Tell the professor that you did not cheat.
Tell them that right now you need to focus on studying for your exams.
Tell them that you look forward to straightening the matter out after the exams.
Request to take the exam at the normal time.  Point out that the professor can always require you to take the in-person exam later, so it is possible to resolve the accusation later.
Go back to studying.

After you have taken your exams, then learn and follow your university's procedure for resolving these disputes.  Keep it calm and logical.
If you are still feeling panicky when you need to study, talk to your university's counseling service.

I thought this was brilliant and followed exactly this path, but the professor flat out refused #4 and would like to straighten this out right now but also is responding to my emails with significant delay. I'm concerned about taking this to the university because realistically who is going to believe a student who says "I promise I didn't cheat and the fact that my numbers are exactly the same as the same quiz given a day earlier is just a coincidence".

I suggest you go back to studying for now, and think about this after your exams.

I think you can later get good advice from someone who has seen the quiz question.

"If you did not cheat, you do not need to be panicking." ..it would be a great world if inncocents would never be wrongly convicted..

@user111388 Indeed. Though, I still agree with the answer that - if indeed the student did not cheat - not to admit fault. However, they should ask themselves how they can explain such a rare coincidence. Having a good alternative scenario is the strongest case they can make.

@CaptainEmacs The problem is I have no explanation for why this happened beyond mixing up numbers. It was a fairly intensive computation that I tried to fit into my head, just for speed purposes, and I suspect I switched numbers then. But again, this is such a ridiculous coincidence to the point where I am starting to question if I did cheat, even though I know I haven't.

You say you didn't cheat. I have no reason to disbelieve you, so I start at that assumption.
My position would be to refuse to go along with any coercive suggestions about "admitting" to cheating. I would say something like "You have the power to punish me for something that I didn't do, but you don't have the right."
I wouldn't try to explain how it might have happened that some answers were as they were. The paper stands for itself. The paper may lead to suspicion, but not proof, but I wouldn't even say that. You can't prove a negative. Don't even get into any conversation where you try to do that. You answered some questions incorrectly. End of discussion.
I would escalate it to the department or dean's level. I would demand a retraction, even an apology. "You don't have the right. I did nothing improper."
If they don't back down, talk to a lawyer. Don't threaten to talk to a lawyer. Just do it. It will cost you money, of course, but might save your reputation.
YOU HAVE NO RIGHT.

Background: The current pandemic situation has left many courses in chaos with instructors not yet having any valid way to evaluate students. People are falling back on things that (sort of) work in face to face situations and trying to adapt them to a new situation with no evidence of validity. I find this maddening. The system is now broken and more broken in some places than others.

Another worry I have is that admitting to cheating in these circumstances might (though I don't know) result in a notation in you permanent record.

While this would be the solution I would normally take, I am inevitably stuck at a position where I must defend myself. Given the ridiculously low probability that I mess up numbers and I mess them up to exactly the same form as the other quiz, most reasonable people would probably think I cheated. On the other hand, this prof is not escalating the issue, simply giving me a 0 on this quiz; thus, this does not go outside this course. However, if I want to dispute it, I must ask the prof to officially report it, in which case it would go on my record if I lose the case.

as the professor has said that anyone suspected of cheating will be required to take an Incomplete on the class and do the exam whenever university resumes

The university is likely to have standard procedures in place for handling cheating allegations. Look online for an "Office of Academic Integrity" or something similar.
If you decide to not falsely admit to cheating, you could contact this office, say that you've been accused of cheating when you didn't cheat, and ask for their advice. The professor's policy seems likely to be against the rules.
Moreover, I'd try to think about how you produced exactly a list of nine numbers which you presumably hadn't seen. For example, did this come from a homework question which you had solved, and which was reused for the quiz? Although you won't have to prove your innocence, you'll have an easier time if you can explain this coincidence. Good luck!

This answer is very good!  Certainly better than my answer.

This is the main crux of the issue though. I have literally no idea how I got 9 completely different numbers from the problem and that those 9 numbers were the same as in a different version. Even if I do escalate the issue, how many people are going to believe "I promise I didn't cheat it was just a coincidence that I messed up my numbers and wrote down those 9 numbers that are exactly the same as in another version"

First, some background. I think the larger context to your story is important and potentially gives you a fighting chance, not to prove your innocence (that sounds impossible), but to make the TA understand the very real possibility that they are accusing you falsely.
The context is, of course, the covid-19 pandemic. The issue is that professors and other teaching staff are now deathly afraid that with the transition to online teaching, the spread of student cheating is undermining the whole enterprise of higher education and their ability to meaningfully assign grades. I can tell you that I and all my colleagues are deeply worried about this and have spent a huge amount of time and energy discussing this and thinking what can be done. There have also been numerous discussions on academia.stackexchange on this topic in recent weeks. (If anyone wants to edit this answer and add some links to relevant posts, please do so - I don’t have time to do this currently but I think it could be a really useful resource for people in OP’s situation.)
The flip side of this coin is that some instructors have become so hypersensitive to cheating and so determined to fight it that we’ve also seen a number of complaints just like yours by students claiming that they are being falsely accused of cheating. Here’s a recent example (again, anyone, feel free to edit the answer with other examples if you have time to look for them). Faced with an instructor convinced that they are guilty and with little idea of how to “prove their innocence”, these students are, like you, faced with the Kafkaesque and unpalatable option of admitting to cheating they did not commit as a way of minimizing the damage.
Now to my actual answer: I suggest that you collect examples of stories posted online like the ones I pointed to, from academia.se, Reddit, or anywhere else you can find them, and send an email to your TA with links to these stories, to help make the case that in their zeal to punish cheaters they may unintentionally end up punishing some completely innocent students, and that they need to reconsider their approach. Tell your own story and include a link to this discussion as well. I don’t know if it will work, but it’s worth a try. The main point is that the fact that there are other students in your situation is strong evidence that instructors are overreaching in their (well-intentioned, of course) fight against cheating on online exams. Good luck!

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I think the other answers that emphasize not worrying about this while you study have a lot of wisdom, but if it were me I’d be trying to figure out what actually happened.. It’s frankly completely implausible that you “misread” the numbers and got all of them exactly as in the previous version.  If each question has 5 reasonable answers the odds are 1 in 2 million, and if each has 10 answers its 1 in a billion!
So what actually happened?  One possibility is you cheated and are lying to us.  One possibility is this isn’t actually about a sequence of 9 numbers, maybe only 3 changed and then it’s plausibly bad luck.  Or maybe the TA actually gave you the old quiz.  If this were an in-person quiz it’s very plausible that the last quiz in the stack was from the wrong pile.  But I don’t know how these were given out.  I’d hope the actual truth had a better chance of clearing up the confusion.

I think the point of the post is moot if I was lying. Let us go on the assumption that I am not. I'm not sure how many numbers were different. I was just told that my sequence of 9 numbers was exactly the same as the other quiz's numbers. I no longer have access to either version of the quiz, so I cannot say for sure how many changes. However, I am assuming all 9 were changed.

Please note that "investigating" the issue can be (depending what you do, e.g. aquring the old exam and presenting it) dangerous since the standards for "proving" you cheated are probably not as high as in a court of law. Depending on your university, the standards for "proving someone cheated" might be "the instructor's gut feeling says so".

@user760900 "I think the point of the post is moot if I was lying" I think it's fair to assume that you might expect a benefit from lying: People will be more likely to give you effective advice if they assume you didn't cheat. I support this answer, as I find the whole story absolutely implausible (you assume that you messed up all 9 numbers - really?!) and it's likely that the professor will do the same.

Let us "assume good faith" and accept OP's premise that no cheating occurred. That said, it is fair to point out that their story (even if true) may seem highly implausible to the professor or other judges.