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Supervisor appears to have a different scientific attitude
I'm a first year PhD student in the life sciences. So far, my PhD has been going well. I meet my supervisor regularly and he is interested in the project and generally supportive.
A couple of months ago my supervisor encouraged me to start writing a draft for a paper, incorporating the results I have so far. We regularly meet to discuss parts of the draft, mainly figures and main statements.
The problem I noticed once we started working on the draft is that my supervisor has a different attitude towards the project. Very often I try to emphasize that I am uncertain about a statement, a method or whatever but I feel unheard and ignored. I feel as if my doubts are not taken into account when we work on the draft at all. It appears as if my supervisor has this grand idea already fleshed out in his head and appears unwilling to hear that some statements might have to be toned down a bit. I feel uncomfortable and depressed as of late, as it is me who is ultimately responsible for producing a piece of scientific work that adheres to the standards of scientific rigor that I think are correct. I feel pushed into doing something that is wrong.
Could it be that I overthink this? Are there different shades of scientific rigor? 'Selling your story' is part of the modern scientific world, right? Do young PhD students tend to be overly defensive and critical of their own work? Is this just 'how the game works'? Should I just trust my supervisor?

Are you uncertain of your results? Uncertain what they mean in the context of your research? Unwilling to make definitive statements about them? What are your doubts about?

Related: https://academia.stackexchange.com/questions/68735/do-academic-reviewers-have-a-duty-to-critique-authors-who-submit-questionable-re

From on your key statement "It appears (...) my supervisor has this grand idea already fleshed out (...)[and is] unwilling to hear that some statements might have to be toned down a bit" my understanding is that you are perceiving potential flaws in your supervisor's thinking.
Firstly, my congratulations, as you seem to be maturing as an independent thinker, ie. a scientist. You are probably what I would call a 'true' PhD student, which (I am afraid) might be not so common nowadays.
I believe being skeptical towards colleagues' ideas is fundamental to healthy scientific logic. This is discussed in the invaluable books from Bachelard, Popper, among many others. The problem is, this is not in line with the practice and expectations of modern academia, where a sense of "collegiality" and smooth political connections are valued over traditional logical and scientific rigor. A main message here is: a maturing PhD student ought to understand the dividing line between scientific practice from academic practice. Contrary to what ivory tower inhabitants preach, science is not contained within its walls. I discuss the two sides of this coin below.
Side 1: Questioning your colleagues and being skeptical until convinced otherwise is healthy for your scientific formation. Constantly debating with your peers should be an essential part of your formation as a PhD student, towards becoming an expert in your field. In this line, I encourage you to politely push your advisor into discussing your project with you in open terms. Bring in papers, seek the opinion of others in the field. Come up with your own hypotheses and encourage others to question you.
Side 2: It is common practice in today's academia that institutions compete for available resources within a logic akin to the corporate environment of companies in the real-world market. Departments try to impress an internal sense of political unity focused at short-term materialistic goals (e.g. authorships, grant proposals, equipment, etc) for institutional survival. This favours a mentality where criticism and judicious thinking are counter-productive. Disagreement becomes an impediment to fast publication instead of the origin of new ideas. Advisors are seen as office heads and staff managers, and students/technicians/postdocs jointly regarded as employees to generate quickly the assets. Questioning an advisor equals insubordination which in corporate logic leads to micromanaging and firing (i.e. alienating the student and failing his degree).
My personal experience furthermore suggests your advisor (others here might say "your boss") has quite personal ambitions regarding your line of research that he would like to see published on paper. Under his name. However, unable to achieve this personally from his bureaucratic seat, the supervisor expect "his staff" to produce in his behalf. That would explain why you're not allowed to question his will, against any logical thinking. Because this person wishes his ideas published as such.
Finally, my advice is that you weigh inside yourself whether you value science over academia or vice-versa, and what is the current tradition in your institution and among workmates. Prioritise your objectives as strategically as possible to minimise conflicts of interests. Stay aware that successfully acquiring PhD training does not equate to successfully earning a title. Consider postponing the open reasoning and publication of your ideas if you wish to work as a true scientist inside the academia, while already being conscious of the necessity of finding the best like-minded colleagues and collaborators.
Sorry for an intricate answer, and good luck!

Very insightful

I think you may be attempting perfection (though you may
 not define it as such), but the reality of research is that it is constantly evolving, and may never mature into perfection.
Conflict, rejection and skepticism are all indeed 'part of the game'. If not your guide, then an editor, a reviewer or a fellow-researcher will (almost certainly) at some point refute your ideas. Many times they will not (and may not need to) justify themselves, which will add to the discomfort.
If an idea is wrong, it will be pointed out at some stage, maybe before submission, or during review (and sometimes after publication). Even if this happens, it will not blot your career as a researcher (unless the mistake is very fundamental, targets other researchers wrongly or involves some kind of trickery). So you should do your due diligence and rest assured after. By due diligence, I mean being thorough, verifying and re-verifying until you are satisfied that your work is technically and logically sound, in all aspects.
Also, never forget that the work is a partnership between you and your guide. Any responsibility for mistakes is held jointly between both. The more junior you are, the greater is the guide's responsibility.

Yes, if this disagreement is about tone of he paper and it’s claims, a peer reviewer is likely to catch it. Just make sure the tables and numbers are accurate.

In my experience the attitude towards expressing uncertainty and hyperbole in manuscripts varies a lot between disciplines. Some fields (notably math, as far as I know) tend to be extremely conservative, while in other fields a certain level of confidence in your own experimental design and results is basically expected by peers and reviewers. In my field (applied CS), uncertainty about methods is virtually never explicitly mentioned in papers (that is, it is very rare that an author would write a variation of "we used method A, but method B would be promising as well but we did not try it"). Expressing a certain caution about results is common, though ("the results appear to support hypothesis C, but further research may be required"). My community is also very big on describing limitations of experimental design in a dedicated section, but many other CS fields don't do this either.
It is very honorable that you try to be truthful and conservative, but I suggest that you trust your advisor's experience on the expectations of the life science community on how manuscripts are typically written. Note that this does not mean that you need or should throw scientific rigor out of the window, but as a PhD student, you are most likely not in a position to change the general culture of how the community likes to write papers. Frankly, it's also not like a lot of harm is done by not describing obvious alternative methods or limitations. A qualified reader will typically be able to read between the lines - if you don't write anything about alternative method B, they will infer that you did not do B and judge your results accordingly.
If you are really unsure about this, you can get feedback from a trusted second senior person in the community, but in general, in the context of a PhD study, it is correct to trust your advisor's experience more often than not, and learn what you can until you have your own lab. This is the time to enact larger changes that you would like to see in your community.

You may be overthinking it. Or not. Certainly your supervisor has more knowledge and experience than you. (One sincerely hopes, anyway.) On the other hand you are right to be skeptical and cautious. After all it is your reputation that is at stake here.
If your supervisor is correct he may be willing to provide you with some references that have led him to his conclusions. I hope your relationship is good enough that you can ask for that.
Your dissertation gives you a chance to say many things in support of your theses. In particular you can have a section listing non-supporting evidence. That is, things that seem contrary to your main ideas. You also can, properly, rebut these - with appropriate evidence.
Skepticism is an excellent trait at your stage of development. In fact, for a scientist, at any stage.
If time and effort permit, consider, at least mentally, two versions of  your paper, one in which you accept the assurance of the professor and one in which you don't. You needn't contradict the prof, but you may be able to simply sidestep the issue. I don't suggest completely developing these two versions. It is just a mental experiment. See where it takes you.
However, a solution that angers your supervisor won't help you, but you understand that already, of course.

I think this answer is on the right track, but I would like more discussion of the role of peer review in this dispute.

@Dawn, Say more. I don't understand. Where does peer review come in at this point? After submission, certainly.

If the advisor is overly optimistic about the importance of the results, a reviewer will likely point this out. So it does not need to be only on the judgement of the student.

@Dawn. Perhaps. I worry, though, that if the advisor is actually going beyond what is really known and accepted that the paper will simply be rejected. And the rejection will come to the OP, not the advisor. Your comment, though, made me think about "peer" review as coming from a more local source: other students or faculty. The might be impossible, of course, and likely risky.


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Anything we could do for abusive PhD advisor?
I have wasted 6 years in a bad lab in some biomedical sciences PhD program in the US. Basically the PI is a MD with no training for science.  I felt treated like a slave. In spite of significant discoveries meriting publication my project got stagnant for at least 3 years.
The PI is famous and powerful in academia. I spoke with the dean and learnt almost EVERYONE in my lab has come to complain about my PI. But graduate school won’t do much, as he's influential and could bring benefits to the school.
I have switched to Computer Science Master program and now as a software engineer. However, many of my ex-labmates are still struggling in This lab. No one has graduated from this lab since he came to this school 10 years ago. And it seems no one would dare to protest against him.
I feel like something ought to be done. Perhaps expose this situation somehow? What could we do?

Recently there has been a number of people in my field go public about abuse they suffered during their PhDs. Since you have left the field and are presumably safe from his influence, have you considered going to the press?

You are obviously upset, and airing that can be good for you, but this is not the place to do that. I suspect that that is where the down votes come from.

Sorry you had a bad advisor. However, as written, the majority your "question" (points 1-12) is a rant. Would you please try to edit your question into something we could answer on this site.

I totally agree I'm just airing out my anger. There's nothing we could do. It's the whole system's problem. I myself couldn't challenge the whole system. But I'm simply too angry and feel unfair why such a science-ruining liar could stand on the top of world?

"such a science-ruining liar could stand on the top of world" -- This guy probably doesn't, this is just your impression. A PI's position is much more delicate than you think. Not helping him already makes a big difference.

@astronat have you got links to their public testimonials?

@scientist see e.g. https://www.buzzfeed.com/amphtml/pascalemueller/guinevere-kauffmann-max-planck?utm_term=.qbve1d4d5&__twitter_impression=true or search the #astrosh hastag on Twitter.

I am answering here before this question gets closed.
I understand your position as I have seen and been through much in the academic sphere. Unfortunately there is a number of such cases in modern Academia where too often the main priorities have shifted away from bonafide scientific investigation and betterment of society.
My main advice is that you move on. As mentioned, you have changed your professional settings and found greater peace and enjoyment. There is nothing stopping others from doing the same as you did, so do not think you are entitled to rescue your ex-colleagues. A parasitic supervisor can only thrive where there is fair availability of dedicated minions.
Surely you feel like you ought to somehow stop this person. This is quite possible to be done. That depends on how much time/resources/reputation you would be willing to sacrifice. I strongly advise you to keep a safe distance and save your peace of mind. I list a number of relatively sane measures you can take which would help others in the place you just escaped and reduce this PI's power.

Science self-corrects from peer approval and high technical standards. That means the bad publications will eventually show. When negative exposure of publications happen in the short term, the responsible PI loses peer support and soon finds it harder to collaborate and publish more (rubbish). Surely the reputation of some "powerful" PI of today relies on a number of recently published papers, some of which in high impact (=highly visible) journals. Are these papers truly substantial, scientifically sound and useful? Take a careful read. In case there are glaring inconsistencies or obvious misconduct, do objectively expose those to others in the field. I recommend resorting to technical discussion websites such as Pubpeer.com, and contacting journal editors directly.
Give lectures to younger students and colleagues and describe objectively what befell you. Most victims of an abusive PI did not foresee those problems, nobody told them anything. Information is key to avoid being scammed.
Contact academic organisations empowered to defend students' rights. Warn them against this institution.
Find out from where this PI is recruiting victims and then better direct your lectures, contacts.
Consider writing a blog, even if anonymously. Perhaps even some Youtube channel with short explanatory/warning videos. Do not directly reveal the names of this PI or University. There is a lot of abuse going on in modern academia, and we need more victims talking about it. You may get a lot of attention and make a point.

I believe with trivial exposure you will weaken this person. However fixing the system relies on a lot more. Hopefully your divulged materials will help in that sense.
Good luck, and move on.

Many thanks. I've already moved on. Even if I'm intended to do anything I won't find time. I'm just airing out my emotion. But my pity for all my other friends in the lab, they are still suffering. I'm only one of lucky person who eventually survive from this academic hell. What about others? Why a hypocrite liar could stand on top of world so many years keep ruining young students without being punished?

Also I'm not entitled to rescue my ex-colleagues. It's simply they are still crying and complaining to me about my ex-PI. I'm the only person who could take care of such issue to comfort them. The whole point is, EVERYONE in the lab suffers and never graduates, and we victims can do nothing.

"we victims can do nothing" -- the point is , you can. But you won't.

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Do I need to cite an artwork? How would I do it? Is permission needed?
In my academic paper, I have well over 100 figures, and would like to use an artwork I found online in one of my figures - it is not published in any book, it is just something they made and posted online. I would be using 1/6th of the author's artwork figure, and it would be so heavily modified it would barely be recognizable. The modified artwork would take up 1/40th the space of 1 such diagram (out of 100+) and used once only, it is a minor element of my figure.
(1) Do I need to cite the artwork in this case?
(2) Can you give any guideline on when an artwork citation is needed?
(3) Am I required to get permission from the author, or is it a courtesy to the author only?
(4) How would one cite an artwork in their dissertation?

Is the artwork accompanied by a license? (For some artwork-publishing sites, there might even be an implicit one stemming from "posted here."). If so, that should tell you what you can do with the artwork and how you should attribute it (cf. various flavours of Creative Commons licenses).

Simply contact artwork's author (since the artwork wasn't published, the author is copyright holder, otherwise it usually would be the publisher), requesting permission to adapt the artwork. I suggest sending the author planned version, so that any potential issues can be assessed and addressed.
(1) I'd say Yes. The citation is usually located below or above the figure in the following form:

(Adapted from “The DeLone and McLean model of information systems success: A ten-year update.”, by DeLone and McLean, 2003, Journal of
  Management Information Systems, 19(4), p. 24. Copyright 2003 by M.E.
  Sharpe, Inc. Adapted with permission.).

(2) Since artwork is someone's intellectual property artifact, protected by copyright, it is usually (for an exception, see fair use in the next point) required to cite the artwork (as any other such artifact) to properly credit its authors. The format of citation depends on the publication style you're using (my example above is based on APA Style).
(3) You're required to get permission, unless you want to risk by using the fair use legal doctrine.
(4) If the artwork is part of a figure, see example above; otherwise, other relevant standard citation guidelines for visual elements apply, based on the publication style you use.

+1 but actually, the artwork was published: it was made available to the public (which is what "published" means) by being placed on a website. That's how the asker, who has no connection with the artist, was able to find it.

You are conflating the copyright and academic etiquette issues. Unless the copyright license explicitly states that a mention is required (e.g. CC-BY), citing the artwork is purely for giving proper academic credit.

@DavidRicherby: Thanks. Good point, however, when I said "published", I implied publishing in a peer-reviewed outlet, which usually transfers copyright from the author to publisher (I noted that specific aspect).

@Mangara: I'm conflating them, because both issues are present and should be addressed. Moreover, IMHO, using a copyrighted material (in original form or adapted) is not only an academic etiquette issue, but a legal one. Authors' attribution is a part of authors' moral rights, which are protected by copyright law.

@AleksandrBlekh Moral rights are not recognized everywhere (despite their inclusion in the Berne Convention), in particular in the United States.

@JeffE: OK, point taken. I guess, then I'd call this issue soft legal.

You have two issues I can recognize, neither is of how much space a figure takes up.
First, you have an issue of copyright.  This applies to any work that is being disseminated in public, especially published or monetary work, yours the former.  For copyright, there are certain laws (based on country) that you must follow.  This relates to how much of an original piece you need to modify before you are not infringing on the artwork.  This is hard to discuss online and without an expert.
The second issue is of academic publication.  It is better to be on the safe side, but also taking the risk of not citing some work can look very badly on you, and also be considered plagiarism.  Most often, if you would like to use someone elses image with some modifications, you should be citing it as 'Modified from X'.  Unless you are using some photograph, and tracing over it to make some line drawing for a particular outline of some device, I would always use the 'modified from' citation.

"[Copyright] applies to any work that is being disseminated in public, especially published or monetary work" Copyright has nothing whatsoever to do with money changing hands. The only connection is that somebody who profits financially from violating copyright is more likely to be pursued through the courts and more likely to be punished more severely.

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How can one prevent a co-author from publishing without consent?
I have been reading about several cases in which a co-author submitted a paper without the consent of another author (for example in  What to do after I was named as co-author on a paper, without my consent?).
Consider a situation where one co-author goes on to publish without my consent when I am the first author.
I know the rule for most publishers would legally prevent a co-author from doing this as the submitting author requires consent from all authors.
However, it seems that in practice many journals have no practical processes in place to prevent this. The co-author would likely submit to an Elsevier journal. It seems that the Elsevier submission system (EES) would allow them to submit and go through the whole process by themselves without informing me if they wanted to.
Moreover, it seems that for Elsevier journals, only the submitting author is informed of advancements through the process, so that the co-author could indeed go through the whole process without other authors knowing.
If I only find out when it is published, it also seems that I have nothing to do about it. It seems that a retraction would only do more damage to my career as the paper will just stay online with my name and also be tagged as retracted. There seems to be no way if disassociating yourself with a published paper.
I am a bit worried to see that in fact there seems to be no real barriers to a co-author doing something like that.
Note again that I am referring to the Elsevier process, though there may be other publishers with a similar process (and potentially the process is not like this for all Elsevier journals).
To summarize, it seems that, at least for certain journals:

A co-author could submit a paper without the consent of other authors and the journal would not inform or ask explicitly for consent from other authors.
The co-author could go through the entire process, even up to publication, without any other author explicitly being asked for confirmation.
Other authors in such a case would not even be informed of the submission or status changes of the paper
If eventually the paper is published, the only option unaware authors have is retraction, which is likely to do even more damage to their career than the fact that the paper has been published prematurely.

Am I correct in my assessment? it seems like if this is true for even some journals, then the publishing process for such journals has been designed quite poorly.
I would like to know how, as an author, I could prevent such a thing from occurring to me. How can I prevent a co-author from publishing without my consent?
I am aware that the best means is having a good relationship and communication with the co-author in the first place and I will do the best I can in this regard. But I would like to know what other practical means I have of preventing this.

Just to clarify, the situation is that you really are a co-author on this paper but you're worried that one of the other co-authors of the paper will submit it before you all think it's ready?  And not that you're afraid that some random person will add you as a fake co-author without your consent?

@DavidRicherby, Coauthorship is a grey area in academia. For example you write some code for a lab. After leaving that lab, someone else in that lab uses that code as a core part of thier paper. Somepeople would view that as coauthorship situation (others wouldn't because the paper that describes that code has already been published). It is completely concievable that the student using the code could add you as a coauthor without your permission, even if you don't think you should be a coauthor. This example fits neither of your 2 scenarios

@WetLabStudent Sure, so add "Or something else entirely?" to my comment.

@DavidRicherby I am mainly worrid about a scenario where one of the other co-authors will submit before I think it's ready. But I intentionally phrased it in a general way as I hoped to have a solution to the general problem for the future

@proggie45 That makes sense. But the different situations may have different answers. For example, the UK Copyright, Designs and Patents Act (1988) explicitly gives the right not to be listed as an author of something you didn't, in fact, write. (This is the complement to the "moral right to be identified as the author of this work" that you sometimes see in books.) That deals with the case of somebody adding you as a fake author but not other cases.

@DavidRicherby Yes, I understand. I'd prefer to focus then on the situation I described, where one of the other co-authors will submit before I think it's ready.

Write an email to the editor.
As you said, submission needs formal aproval of all coauthors so if you tell the editor or publisher that this is not the case, the paper will not be published.
Publishers usually assume academics are grown ups and the likelihood of person naming people as co-authors against their will is very low and thus the hassle of sending multiple emails or having everyone involved in the online submission is not worth the trouble. Keep in mind that some articles have up to 1000 authors.

I do not understand this.  For example, If I am one of the 1,000 authors on a paper of which you are lead author, do I have the right to prevent publication? If I am being unreasonable can you drop me from the authorship list? It seems if I made a contribution worthy of being on the authors list, then you can not drop me.  But with 1,000+ authors, there is bound to be some unhappy person at any point in time.

This sounds quite unreasonable. That is, the non-publishing part. If one person wants to publish something and the other person objects, he has the right to remove his/her name, and to suggest reasons to refuse publicaiton. IMHO anyway.

I haven't had any bad co-author experiences like this (thankfully), but have friends who had, and have had some "less than optimal" experiences of a similar nature.
The best single piece of advice I've come up with (for myself) is to address co-authorship expectations early and often. If there are plans to turn an analysis into a paper, talk about who will be on it, the order, the expected roles, etc. the first or second time you meet about it. That gets expectations out in the open. If it's a multi-person project with several papers, talk about that (who will use which variables, co-author which papers, etc.).
Then, stay connected with the group (particularly if you're junior). Check-in with the leads often, do whatever work you can with/for them, etc. So they know you're still interested, active, and available. Sometimes, people fall off papers because they just lose contact with their team. Other times it's for poor performance. So don't hesitate to ask your seniors and peers what else you can do to help (and if what you did was helpful). For example, you might feel like you're being helpful by giving a lot of comments on a draft, but if none of them are useful, and all you do is comment (not edit), you might start to be seen as the person who just drags out the writing process without adding much to it. If you're senior or the money-getter, you can do that and stay on the paper. Not so much if junior or in the middle.
Another thought is to make yourself indispensible. Learn one part of the data, one technique for analysis, one lit area better than everyone on your team. That will make you the go-to person for that element for all papers to come.
I hope this is answering your question. I've been assuming that your co-authors are all working in good faith. That is, that if you get dropped it's because they accidentally dropped you or you really weren't doing your job well. There are malicious people out there, too though. Short of literally holding their hand, there's not much you can do if they wan't to publish without you. If that happens, take it up with the journal immediately. If you're at the same institution, take it up with your department head or other ombudsperson. If you have a close friend on the paper, ask them what happened. You may find out it's an oversite, and they add you to the paper. But it's better not to let these things fester.
Good luck!

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IEEE referencing : Acceptable reference format for personal work log
I’m writing an academic document and I can’t seem to find any specific mention of how to refer to a personal work log. Work logs are essentially to be published journals documenting what happened when in a computing project (but not published in an official journal).
The closest thing according to IEEE referencing style guide from the University of York is possibly a weblog. What is the best citation type for such a work log?

Would you really cite your own unpublished logs? I'd think you should just describe what you did.

What do you mean exactly by "non-published"? Is it online or otherwise available to the general public? Can you send a copy on request?

amended for clarity

It seems to me that you are describing the kind of content people often publish as tech reports, so that they can then reference them in "regular" publications.  In which case, you could consider doing just that.

it could also be described as an informal log of everything that happened in a project.

If it's not published anywhere, be it in a peer-reviewed journal, conference proceedings, some book or whitepaper, then don't put it as a reference.
You could write,

According to our work log, we first frobnicated the machine, …

The idea of including references is for interested readers to follow up on them. If it's some internal document nobody will ever see, then it does not qualify as a reference. It also makes it impossible for peer review to happen: you could claim anything and back it up with a reference to your internal document—and nobody could ever (dis)prove it.
The APA blog has an entry on that subject (emphasis mine):

Likewise, if you have other nonretrievable sources (personal communications, like personal e-mail and phone calls), these do not get reference list entries either (although they do receive in-text citations, because they involve other people than just yourself).

seems irrelevant to the IEEE standard.

A weblog is publicly available. Your work log is not. If it's not published somewhere, it's not suitable as a reference--regardless of which style guide you follow. The link you added even says, "Only published works, those due for publication and unpublished work available in a library or archive are included in citations".

There are other citation styles where personal communications do appear in the reference list.  I occasionally see this in mathematics papers, though mostly in older ones.  But I agree that citing something which isn't publicly available and doesn't involve other people seems unnecessary.

In this case it will be submitted with the main report as a separate submission. I guess that's not publicly available per se but is it possible to reference it ?


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How can I gracefully exit my current post-doc position for a new one?
I'm a post-doctoral research fellow and I've just been offered another post-doc position at another university. I still have a year and a half left on my original contract, but it's not going as well as I'd hoped and ultimately is not going to lead me to a place I want to be in my career. The new position is at a better lab with many more PhD students to work with, somewhat less research freedom but more resources and support, and also genuine guidance to prepare for life as a professor. As an added bonus, the new position is in the same city that my partner lives in, and we will be able to live together.
The problem is, for the sake of professional etiquette, I can't tell my current advisor that this position was offered to me, as my new advisor doesn't want to be seen as poaching a post-doc from another university. I don't want to burn any bridges or cause ill-will at my current position. I'm at a bit of a loss now, trying to figure out how to approach a conversation with my current advisor to tell him I'm leaving, and I would really appreciate some advice!

Is the other Prof. poaching post-docs? Or were you looking around?

I was looking around as I am not particularly happy at my current position.

Can you clarify how long you are required to keep your new position as a secret from your current employer? If it's indefinitely, then that is obviously an absurd restriction. And if it's only for a few months, then I'd say it is still an absurd restriction, although for a different reason. Either way, I see some serious ethical problems with what your new advisor is asking you to do.

"my new advisor doesn't want to be seen as poaching a post-doc from another university" -- what's the plan, are you supposed to pretend that you first quit the old post (with no job lined up at all), and then later applied for the new one, when in fact the sequence was the opposite? Sounds like a tough lie to sell, just so your new supervisor can't be accused of the supposed crime of offering a job to someone who already has a job but applied for a different one. That's what happened, and it'll probably be fairly obvious that's what happened to anyone who thinks about it.

I changed from one unfinished postdoc to start a new one.  In your list of reasons, there is one that easily trumps all others:

the new position is in the same city that my partner lives in, and we will be able to live together.

Tell your current advisor that you are moving to another postdoc so you can live with your partner.  Any remotely humanoid advisor will understand and accept that.  The reason for my move was exactly this.
All your other reasons are less important, and may be interpreted as implicit criticism of your current place.  Since you have the two body problem, you can move without mentioning any other reason.

@WoolyJumper I think it is generally accepted that people can change their minds based on people they love, just as easily as jobs they thought they would love.  Different people have different priorities, and I think @ gerrit answer is reflecting well the understanding that this happens

@WoolyJumper - over the course of a year or more, people have been known to decide that they really want to be in the same city rather than remain separate. Priorities change, people move, and it does sound like this aspect was important, even if not the sole reason.

It is not sure if being unhappy with the position and being unhappy with being away from the partner are entirely separable.

One could also suggest that the OP does not have to provide any reason at all. And, certainly, not a laundry list of all the things that bug him/her (I hate the color of the fridge in the lab...). So, are they trying to provide feedback (does the current place want the feedback?), or be polite and leave on good terms? Only the OP can answer that.

Ideally, I'd like to be polite and leave on good terms.
Also, I'm not satisfied with the position now, but I may have stayed longer before moving on if she were not a very important factor in the decision. I should mention that I've already been in this current position for a year.

@JonCuster my feelings exactly. One good reason is good enough. You do not need to go and make a laundry list, or worse yet, do wash that laundry.

"All your other reasons are less important" -- well, the phrasing in the question, "as an added bonus" suggests that in fact they are not less important, and that the questioner at the moment would be prepared to live away from the partner if it was a significantly stronger career move to do so. But even if it's an exaggeration (or an outright lie) to claim this as the most important reason, as you point out it's nevertheless effective because it's highly plausible and it's untestable by the current supervisor.

@DanRomik I think the "ideal" would be to give no reason at all - but since people generally expect one, giving the reason that it's closer to their partner has the advantage of being (a) true and (b) not a criticism of the current employer and thus is more advantageous to the poster's future prospects. The old employer may still take offense, but that's beyond our control. Perhaps it's a sin of omission, but that's life in the business world.

Unless you are living in a country I've not heard of, post docs are employees like an other and are under no obligation to work until the end of their contract. Just hand in your notice as soon as, but not before, you have a new job.
By all means give your current boss a reason for quitting but if you don't want to don't sweat it, they'll have some plan to spend the money.

But surely you recognize that academia is not exactly a workplace like any other (which is why the question is posted here rather than on Workplace.SE), right? So, I'd say your answer, though it contains elements of truth, is too generic to be very helpful to the OP.

Actually, I spent 20 years in academia as a postdoc and PI trying to convince people that academia is just another job and that it must work properly in the modern world.

I would suggest talking to your current and future supervisors about a solution that works best for everyone. Trying to keep the new position secret from your current advisor is silly since he/she is going to figure it out when you start the new position. For example, it might be best if you split your time between the two projects for the next 6-12 months. This way you could wrap up your current work and get a head start on the new project. You might be able to work in the new location with only occasional visits to your current lab (thereby solving the 2 body problem). Maybe your current advisor or the new advisor has no flexibility, but if you do not ask, you will not know.


text:
Is the Psy.D. degree (US) equivalent to the "Licenciado en Psicologia" degree?
I am not sure about this. In some scenarios, seems like a "Licenciatura/Licenciado" degree is equivalent to a Bachelor's Degree, or sometimes to a Master's Degree.
Nevertheless, in some cases "Licenciatura/Licenciado" seems to correspond to a Doctoral Degree. Examples:

Pharm.D.="Licenciado en Farmacia" (https://en.wikipedia.org/wiki/Doctor_of_Pharmacy#Spain)
MVD/DVM="Licenciatura en Médico Veterinario" (http://www.vets-net.com/other/GlobalVetSchools.pdf)

The equivalence between a Doctoral Degree and "Licenciatura/Licenciado" seems to be particularly the case when the later "allows to practice the profession".
A closely related question would be: what is the equivalent degree of PsyD in the Spanish-speaking countries?

@TommiBrander Why Spanish-speaking countries are equivalent to Europe? I thought there are a lot countries in Latin-America are Spanish speaking.

I've edited that; switched "europe" tag for "translations". Yet, "europe" might still be appropriate.

It's not unheard of for functionally equivalent degrees to officially be at different levels in different countries. For example, a US MD is a postgraduate qualification titled "doctor", while the UK equivalent is officially a bachelor's degree (or, rather, two bachelors' degrees earned concurrently: MB BS).

I can not be 100% certain here but to my understanding the 'Doctor' degree (as in a PhD) is always post-graduate. The licenciado degree is a graduate degree and can therefore never be equivalent. I think that what is the cause of the issue described in the OP is a translation issue (where a Licenciado en Farmacia is translated as a Doctor of Pharmacy, while Pharmacist may be a better translation).


text:
Post-doc application: references not requested?
I have seen that some post-doc ads (in the US) do not explicitly ask for contact details of references. This is more or less common on LinkedIn, even for academic post-docs.
Is it ok to not provide those contact details initially, and just send a cover letter with the standard "please do not hesitate to contact me for additional information"? Or will it harm the application?

By "offers", do you mean job ads?  I'm puzzled by the reference to LinkedIn, since I've never heard of academic postdoc positions being advertised there.  It might help to specify which field you are in (since advice from someone in a field that works differently could be counterproductive).

Yes, job ads. There are many "Postdoctoral Research Fellow" and similar on LinkedIn, Glassdoor, etc. [I've edited the original question to state 'ads'.]

If they do not request references, you do not need to provide them. In that case, they may still ask for your references later if they need them (for example, if you are selected for an interview).
It is always better to mention the names of people who can provide references in your CV. But I assume that you do not have good references since you are asking that question. If you have some good references from top researchers in your field, it is better to mention them in your CV. It would make your CV look better perhaps. If you do not have good references, and do not want to mention them, then it is ok. But expect that they may ask for your references later.

+1, good answer. You're partly correct: since I'm switching fields (neuroscience to genomics), I don't know many people in the new area.


text:
Applying for (externally-funded) postdoc position: how to follow-up after 1st email?
I would like to get a postdoc fellowship grant that is addressed to a specific department (in a particular top-tier university). Now I just need to get a professor there to accept to host me.
While I think that my chances of getting the funding are high, I've emailed a professor to ask whether I could work at his lab (with this funding), but got no response after an email a week ago.
I do believe that I'm a good match for the lab and a good candidate to get the fellowship, so... should I call/email this professor to follow-up? Otherwise, is it fine to just email another professor (in the same department)?

I would call this "externally funded".  Self-funded would mean you are a volunteer.


text:
Whether to share at thesis defense where I have submitted pertaining papers to
I have submitted journal articles that come from my thesis.
When defending the thesis, is it a good idea to give the names of the journals to which those pertaining papers were submitted to?

What details to you want to provide to whom? Your sentence structure makes no sense, sorry.

I need to provide the name of journal which I submitted the article resulted from my thesis. In my defense time.

I submitted a paper from the work done in my thesis. By details, I just mean "The name of Journal which I submitted the paper to that".

Why haven't you asked your colleagues or your advisor?

And if it gets rejected, and you submit to a different journal. Then what?

@user40491 I have substantially edited the question to capture what I hope you meant to ask in more understandable English. Please check whether I have succeeded. If this is not what you meant to ask, please edit it back or comment here.

No, when defending your thesis there is no reason to give the names of the journals to which you have submitted papers based on it. It would not benefit you in any way (since they have not been accepted) and you will be embarrassed if the papers are rejected.

I agree, although I think that there’s a bit of a difference between advertising this and responding to being asked. I think this answer is correct wrt unsolicited sharing. If being asked, I would consider sharing.

@StellaBiderman I agree with you.

From my experience of defending my own master thesis and supervision of some others, I can conclude that it is always a good idea to present the papers that you submitted based on content from your thesis (in the main contributions slide), pointing out the details of the conference/journal, even when they are, yet, under review (just point out that in the presentation).
In some case it may be helpful to have a preprint version attached to your thesis document or in some repository such as arXiv.

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


text:
Does adding professors' names in the acknowledgement section influence acceptance of a paper?
I'm working on a research paper and two well-known professors have reviewed and commented on the paper. They have also accepted that their names be mentioned in acknowledgments section.
My question is whether including the names of prominent researches would influence the acceptance of a paper by a journal?

@corey979 I do that as well. Mainly because originally I did not think it was useful to peer review, and because I was waiting to add specific comments on reviewers' & editors' contributions.

@Scientist You can always add to your acknowledgments after peer review, so your second reason doesn't make a lot of sense.

@DavidRicherby Sorry if my comment is not clear: I usually add (or complete) acknowledgments after peer review partially because I wait to acknowledge some eventual contribution by reviewers and/or editors along with specific details, where available (e.g. Y anonymous reviewers and David Richerby provided useful comments).

@Scientist Sure. I'm just saying that you could acknowledge my useful comments in the submitted version, and then add the acknowledgment to the referees (and anyone else who might have helped improve the paper after its submission) to the final version. So the fact that you may want to acknowledge the referees isn't a reason to omit all acknowledgments from the submitted version.

@DavidRicherby I see your point (though in my example you are an editor). I first took on the habit of only adding acks to final version mainly because I believed they were irrelevant upon submission, as mentioned. Later I started mentioning colleagues' suggestions upon submission mainly because of grammar suggestions. As a native speaker of a another language I frequently got reviews based on "ms needs correction by a native speaker", which I believe is an easy way around a reviewer's task. Mentioning a colleague with an English name in the acks seems to stop that. But that's another story...

For reputable journals, including the names of prominent researchers should not influence the acceptance of a paper, and in the top tier journals I expect this would certainly be the case.
It would be easy (but not ethical) to include the names of prominent or famous researchers in acknowledgements or as co-authors in the hope of influencing a decision for acceptance but reputable journals will not publish something that does not meet their publication standard.
If prominent researchers have provided feedback or otherwise helped with the writing (but not to the extent that they would be co-authors) then it is appropriate to include them in the acknowledgements.
Also, some journals only forward the text (without authors or acknowledgements) to reviewers in the interests of having impartial reviews, so that the reviewers will not see names and then not be influenced to recommend acceptance for a paper they might otherwise reject.
For not-so-reputable journals, they will publish regardless of the names (and if a paper includes the names of prominent researchers, the journal will sit securely behind the declaration that the submitting author has signed).

I would only add that you can't account for psychological effects on reviewers who see a big name and say "wow". Hopefully an author doesn't count on that effect, of course.

I agree, but I think more experienced reviewers would have their "wow" tempered by some degree of skepticism whether the name contributed. Also, some journals only forward the text (without authors or acknowledgements) to reviewers in the interests of having impartial reviews. (I will edit this note into my answer.)

May I know what is a difference between reputable and top  tier journal?

A quick search shows https://academia.stackexchange.com/questions/68593/what-does-top-tier-mean-when-referring-to-journals-conferences

I really believe there is no such thing as absolute as a "reputable journal", but reputable editors and reviewers. And unfortunately these may not be the majority, even in the most appraised institutions and publishers.

I believe it does affect positively the acceptance of a paper.
Pre-publication peer review is biased by a number of factors, particularly the typically low number of reviews, their brevity and superficiality, the secrecy around what happens, field politics.
In fact, I believe my name is being recurrently added to the acknowledgements section of a number of papers issuing from a bad group I recently happened to work with. These people believe I am fairly well-known in our field of research, and probably seek to avoid me as a reviewer. They have first-hand told me other manoeuvres locally (nationwide) employed to skew peer reviews and papers' acceptance. Also I am aware of a number of "reputable professors" who actually secretly pass on their review assignments to PhD students and postdocs who just want to "be done with that" -- likely these are reviewers who will cling onto just anything to support accepting/rejecting a paper.
So, if you wish to use this as an asset to speed up acceptance of your paper, go ahead. The system as it is remains quite open to manipulation. However do fear a few judicious reviewers and readers that do exist everywhere, particularly after publication of your paper. The weaknesses of your manuscript might be so easy to spot and expose that a single easily-published paper might be your reputation's demise. A late public exposure that could be avoided with the help of a couple of good reviewers.
Good luck, and welcome to the Academia.
P.S. Please note that I am not saying that you ought not to add names of contributors to your acks section. These people must be acknowledged for their participation. Also I am not saying that you necessarily seek to game the system: you're just asking here because you're curious. I am warning you and other passersby of some reality in relying on peer-review and paper acceptance gimmicks as 'scientific career shortcuts'.

This answer is quite confusing for several reasons. The first paragraph obscures more than it reveals. The next paragraph seems to indicate a similar experience that you have had, but you also states your belief that the group in question was trying to avoid having you as a reviewer. This is a completely distinct motivation than what OP has asked about, so while it is not incorrect, I think it is irrelevant. Finally the link to the 'bad group' seems to talk about administrative issues rather than issues with the group. As such the link is unhelpful and distracting.

@user153812 I believe the OP is still young and may benefit from learning related facts.

That is a well-intentioned thought, maybe if you make it clear what issues are related but not directly relevant, it would be more informative..

You've described evidence that some people believe that acknowledging Famous People can have a positive effect, and attempt to game the system based on that belief. But do you have evidence that their belief is correct, that acknowledging Famous People actually does have a positive effect?

@JeffE Unfortunately not, apart from personal experience. It is quite hard gathering evidence of peer review potential flaws, mainly because a lot of what happens is kept secret. Accordingly, my answer starts with "I believe..."

@JeffE The research on double-blind reviewing strongly suggests that big names in the author list have a postitive effect on publication. If I had to guess, I would assume that also translates to acknowledgements, but maybe the effect isn't as strong.

Reading a paper takes several iterations. From a quick skim of figures and tables, to an in depth reading of the details. I only reach the acknowledgements in one of the later passes, if I ever bother reading them.
I cannot speak for others, but when I am reviewing, I take the same approach, but now I am trying to make up my mind about the merits of the paper. By the time I reach the acknowledgements, my mind is pretty much made up, and nothing you say in that section is likely to change my mind about it.
Who could be sway by this? Perhaps a lazy reviewer that just skims through figures? I don't know, but the review will show lack of effort, and one hopes the editor won't put too much faith on it.


text:
Sending a thank you e-mail to a professor as an external intern
I'm new to Stack Exchange and I apologize if my etiquette on posting a question on this platform is "wrong".
So I took a course last year with a professor who was exceptional on her subject that gave me a better perspective on the subject, and ultimately got me a really good internship in the same domain.
How should I write her an e-mail (without being awkward) with a thank you note, as I wasn't in touch since the end of that course?

I think the proper answer is "Just Do It." She will be delighted to hear from you. Tell her about your current success. Open and close with "thanks". That's all it takes really.
Of course the things you say here would be excellent to include in your thank you.
However, sometimes a more formal letter is called for, sent by ordinary mail. That is up to you, of course.


text:
Applying for a new doctoral program after expulsion
I am not prepared to give many details in a public forum - as such this posting will contain intentional generalizations that may be of interest to academia.se's research higher studies community help, in particular senior faculty members, if any.
I would like to ask for help in figuring out if there would be a pathway to return to the pursuit of a terminal degree sometime 2020++ in a field related to my accumulated research work and career credentials with publications and products. At present I  have a major blemish in my overall academic record at my last institution based upon an off-campus incident several years ago which ended in a sentence in a felony case.  At the time of my projected return as a doctoral candidate, the faculty committee recommended  suspension, and the admin decided on termination after it became clear I had failed to report it per student policy. Elsewhere on Stack Exch.  I have already described the good that came out of that research, and that chapter of my life is now finished.
Can I ask the community if there is any practical chance of pursuing a doctoral program again? If so, When could I approach that, and at what stage should I broach the subject to a new institution?
Thank you.
Added:

This is a US academic industry question, but I would think my research area would be useful for academic institutions of major space faring nations.
My felony is for a offense not related to any workplace or academic setting.
I was in the middle of my doctoral program when the inquiry began. Over a year I was encouraged to continue by the judge(s) to try to conclude the program as fast as possible. I continued work for the institution throughout (I tried to quit after some discussion but was asked to remain while trial was underway and the outcome not known). A sentence was imposed with reduction of all charges save a single one, based upon the admissions I made and material  I surrendered.
After completing my sentence, When I attempted to return, I was found to have violated policy for the crime conducted away from campus but while a student, and also that I violated another policy as I had signed a form for a leave of absence using a made up reason to explain my projected absence, the day before I left to begin my short sentence. The ruling was split: faculty recommended suspension and admin recommended expulsion.

Can you link to your related SE question, or do you prefer that they not be linked?  The reason I ask is that the answer to this question might depend on a lot of factors, including how far you were through your previous program.  If you were a long way through the previous program then you might have acquired many of the research skills from a PhD candidature anyway.

You haven't said anything about what country you're in or the seriousness of the offense (was it a felony?)

Your statement of "which ended in a sentence" is very confusing—are we talking about a criminal sentence imposed by a court of law or is it merely the expulsion in the title of the question as a result of the off-campus behavior? The range of potential answers may well hinge on the difference.

Wait, were you terminated because of the offense you committed, or because you lied to your university about being convicted of a crime? Or the combination of both?

I'm not used yet to the format of answering on stackexchange, so bear with me.

In reply to Ben's question about how far I was along my program, it was at the end of the research and in the dissertation writing phase. There was an opportunity to reduce our then current theories to practice and validate our models, and the research group changed track and to build a real world prototype.  For my topics, the results have just now been validated with a US  patent that I did not think would happen - a process that I described in https://academia.stackexchange.com/a/111700/94321 - with no formal publication.

This search turns up a number of related questions.

Do you know how your expulsion from the program is documented on your official transcript?  Presumably, it says something like "Expelled for disciplinary reasons/"  You can assume that any other program will want to understand something about these reasons before admitting you.

Also, would it be possible for someone to research what happened by searching using your name and the institution that you previously attended?

The felony itself shouldn't be a big problem. While university will often have rules that basically allow them to kick out students that commit crimes while in school, to my knowledge it is not common to ask incoming students about crimes they committed before starting school. To meaningfully screen for felons the university would need to require a criminal background check as part of the application, which is rarely asked for. Now some sources of financial aid may require that applicants have a clean record, but then again, some might not. In any case, you are asking about studying, not funding. Your former institution specifically might be committed to cut ties with you, so if you re-apply there perhaps they would not accept, but this is hardly an issue when there are hundreds of other universities you can go to.
However, wherever you end up applying, you will probably have to mention your past work. Whether you will be able to get away with only discussing your research work, and simply state that you were forced to abandon the program due to "personal issues", and if forced to elaborate, whether the committee there will be sympathetic to your situation, is impossible to predict. You will just have to try and see.

I don't think your goal is impossible, but it will be difficult to achieve. I assume that your past infraction was serious or you wouldn't be in the state you are in. You can do one thing now, and you must do another thing later, however.
Now, you can find ways to behave in a way that shows you learned from your experience, have paid for your sins, recognize them for what they are, ameliorate the bad effects they caused, and that it can never happen again. This is harder (even) than it sounds, as some acts might not be repeated, but an underlying attitude might lead a person to do other things, not exactly the same, but also quite bad. Narcissism, for example, can often lead to a lot of bad behavior of various kinds. Also, thing things you do should leave some visible record that clearly shows a change. Even better if other people can attest to your good character now and in the future.
The thing you must do later is to be completely honest with any institution that you apply to. It won't be enough for you to promise to behave better. But the things you have done in the interim should speak for your change without your comment.
Even then, of course, there are many who won't believe in your change. You need to make it real change, both for your future chances and for yourself generally.
Good luck.

Note that I mention narcissism as an example only. Lack of empathy is another. But I'm not trying to attribute either to you.

The easiest path is to apply as a PhD candidate abroad.
Whilst in the US and a few other countries & institutions there is a special demand for an official offence-free record, this will not be the case with so many others. For most international doctoral-degree programs you may not need even a recommendation letter.
Once you complete your PhD degree skilfully, this past issue will essentially have vanished while you will hold a new network of contacts for a new future ahead. Move on, physically.

Note that you should make sure a felony conviction won't interfere with things like an application for a student visa.

@Fomite That's a very good point. Dependent on country of destination.


text:
Bad relationship with PhD supervisor
I'm at the end of the second year of a phd in engineering. My project is going well: I'm involved in an international project and I submitted 6 journal papers and 5 conference papers.
The problem is the relationship with my main supervisor.
I have two supervisors. I'm working really well with my co-supervisor. He has always showed interest in my work and in me as a person. He provides me accurate revisions on papers, reports, oral presentations, and so on. At the same time, he leaves me free to direct my project as I prefer, as long as my work is coherent with the topic of my thesis and with the objectives of the project we are involved in.
Things are different with my main supervisor. He couldn't care less about my work. I hardly remember the last time he gave me any guidance or even corrected one of my papers. He requested I help other phd students and provide him with didactic material for courses.
I spent most of the first year helping another student, understanding that the work would be part of my thesis. At the end of the year my supervisor asked me not to inform the phd committee of my participation in that work, because it could damage the evaluation the student.
This year, something similar happened. One of his M.Sc students could not finish a job in collaboration with another professor. Now he wants me to finish that job, because he doesn't want to offend that professor. The problem is that he's not even in my research group, I don't have any experience with the subject and this is slowing down my work, as this job should be completed by the end of the year. My supervisor also gave me other extra work, telling me not to tell the other supervisor and not to add his name in my works.
The worst part came when my co-supervisor proposed me a postdoc position. My main advisor became arrogant, telling me not to f**k up things (litterally), that he's the boss and that if I want to go on working in research I have to stay with him.
I tried many, many times to talk to him, but his answers are always the same: "don't do s**t, remember who's the boss here".
Normally, I wouldn't ask advice from random people over the internet, but I really don't know what to do. Talking to him seems completely useless. Maybe I should talk to the other supervisor, but I'm not sure he would support me against a colleague. I'm afraid I could end up even more isolated.

In an ideal world, you would blow the whistle about your main supervisor at your institution's ombudsperson and do the right thing, not lending your name to clearly unethical procedures. In a realistic world, you probably keep your head down, do not signal any further rebellion to your main supervisor, write up as fast as you can and get out of their clutches, fast. Whether or not you postdoc with the other superviser depends on whether they have enough power. If not, go elsewhere, or your main supervisor (he has made it clear) will destroy your career. You need to get out of his reach, fast.

You got the problem. The only certain thing is that I'm running away as soon as I get the degree. Not only for me, but also for the other phd students of my group. Some of them are even in a worst situation than mine, since he changed their topic many times. All for his silly pride: everytime he doesn't like some collaborator, he tries to change topic (did I already say that he wants to be the only boss?). Unfortunately, we are in a realistic world and I have to cope. I just hope that he won't do further harm

My question is: will it be a problem for future employement? Since for suure I'm not going to have his recommendation letter.

"don't do s**t, remember who's the boss here" — You are.  Fire him.

Well, for now I've kept the ownership of my phd, and it's working (even if half my time is spent on other activities).

@JeffE All good and well, I think OP needs advice as to how to handle the references? My advice is: network as much as you can at conferences, you may find a referee there. The second supervisor may also be happy to write you a letter even if you don't stay. Good luck!

How are you being funded? If it's as a research assistant in his lab then you can be required to do research work apart from your own thesis project. Though denying you credit for your contribution may be an academic violation.

'Random people over the internet' or 'experts with specialist knowledge I would not normally have access to in my local area'? Anyway, I had a similar problem in my PhD, I went via the proper channels (head of school), we had a big in person meeting and sorted it out. You should do the same, with everything done professionally and documented.

I was in a similar situation with my dissertation director. After trying to resolve things with him (he became increasingly hostile and abusive with each attempt), I got other professors involved, including the graduate ombudsperson. One professor - the department chair - did nothing and sided with my director - but the other faculty (the graduate director and my other committee members) stepped in and separated us, and one of them took over as my new dissertation director. After that, I went straight to Human Resources and filed a complaint against that professor, since no one in my department made any attempt to hold him accountable for his actions. I also reached out to the Dean's office when HR was initially unresponsive, which I think helped because they may have leaned on HR to pay attention to my case. The investigation was recently concluded and apparently they "took actions against him," (a slap on the wrist, I'm assuming. But at least he has a record now).
Personally, as horrible as my experience was and as painful of a battle it was (from which I still haven't recovered), I have no regrets about standing up to that professor, making as much noise as possible in my department and to outside administration. At the end of the day, I stood up for myself, made it clear to everyone in my department that I could not be bullied into silence, and that I was leaving with a PhD no matter what.
One caveat to this experience before recommending you go down the same path: I realize that my situation could have been so much worse had I not lucked out in a few ways. I was lucky that the graduate director + my other committee members were willing to support me and not abandon me, even if they couldn't bring themselves to confront their colleague about his behavior. I was lucky that my contact in HR was extremely nice and sympathetic to my situation, and I genuinely believe he made every effort to investigate my situation fairly. Unfortunately, having people like that on your side is not always the reality, and all too often, faculty/staff turn against graduate students who won't "stay in their place."
My suggestion would be to not take this professor's horrible treatment, stand up for yourself, and expose his inappropriate behavior. But do so very cautiously. In light of my own experiences that I shared, my question for you is, do you have allies? Other students who can and are willing to echo your complaints? There is power in numbers. Are there professors (including your secondary supervisor) that you can talk to? And keep in mind, there are (or should be) resources outside your department that you might consult, though I think I would only do so if you can't resolve things within your own department:

the graduate ombudsperson: if your university has one, absolutely try talking to them. They're usually very senior, experienced professors, and they're meant to be available for confidential consultation. This is typically a very safe place to discuss your issues.
Human Resources
Dean's Office of your college
Dean's Office of the graduate college
the graduate student association might have resources

Ultimately, his behavior towards you - all of this telling you to not tell so-and-so about his actions and his insistence on controlling you and other students - is incredibly inappropriate and abusive, and none of you deserve to be treated that way. I hope that the dynamics in your department/university allow for a safe place for you to voice your complaints. There's nothing worse than silently suffering.

The worst part came when my second advisor proposed my a postdoc position. My main advisor became arrogant, telling me not to f**k up things (litterally), that he's the boss and that if I want to go on working in research I have to do it with him.

I don't understand this part? Why does your main advisor has so much control over where you would do a postdoc? The worst he can do for you is not to give you a LoR or worse, to give you a bad LoR. But I guess you don't need one from him.
Just complete your degree, and move to your secondary advisor's group. That's it. Or if you apply somewhere else, you can list only your secondary advisor.

At the end of the year he asked me not to tell the phd committee that
  I took part to that work, because it could damage the evaluation of
  the other student.

You should keep all evidences about your work on other PhD's student, including emails exchanged with that student or your advisor.
If I were you, I would not work for free any single day. You don't necessarily say NO. For example, if he says you need to help the other student before day/time. Just don't do it. How can he push you, via email? then you have some evidence then.

Hard evidence may make sense in a normal workplace when it comes to legal/formal battles. It is not clear whether OP has a chance here, we do not know the environment/HR/ombudspeople. The situation is abominable, but OP does a great job already (research!), so they have a good chance of getting out, if not unscathed, at least with limited damage if they play their cards carefully and close to the chest. Either taking the lucky pot shot and follow Ace's advice and go to HR or stay down until they can leave, but just refusing to work for free is not going to fly in the present constellation.

Regardless of the route taken, I agree with the saving all evidence of your work, your exchanges, etc, including oral interactions (make a note of what was said, and date it). You might not need to make use of such documentation, but you never know.

"I don't understand this part? Why does your main advisor has so much control over where you would do a postdoc?"      Actually, he doesn't have that power. My explanation is that he's just trying to frighten me, because he doesn't want to share my papers with the other supervisor. In fact, our full professor is near retirement, and one of them is going to replace him.

"Just complete your degree, and move to your secondary advisor's group. That's it. Or if you apply somewhere else, you can list only your secondary advisor." They are in the same group, so the only way to get away from him is to apply somewhere else. As you suggest, the best choice can be list only my second advisor in my future applications. Thanks everyone for your help :)

Just complete your degree, and move to your secondary advisor's group. — I would recommend both of these steps, but in the opposite order.

My instinct, since you already figured out bad advisor. If it is early period of your PhD work, there is nothing wrong to find another advisor. Here in US academics, your future career almost depends on advisor whoever he is, it does not depend on you and your ability and your explanation why you had tought time working under him.Change your advisor!!!! if you haven't wasted your years.

You have a bad boss - a situation common to all walks of life including academia and industry. This is temporary, and you’ll get through it, but you must be proactive.
One option is to just change advisors formally to the one you like. If that’s not possible, you are best off assuming the worst and treating this like a contract. Have a clear, frank discussion of what is expected to  attain PhD candidacy, and get in writing (or email for the record) all his/her requirements.  Make sure those requirements align with the official requirements of your institution. If you do this clearly and check in regularly, it would be difficult to hold you back.

yes, but I wouldnt say BAD; he is abuser!!! which is kinda worst than bad

‘Abuser’ is a strong term. If you mean that literally you have a pretty clear course of action.

@Alice yes, that is why I suggest to be more strick in describing them

The possibility of toxicity in your relationship with Ph.D. supervisor is not uncommon. My story is dated going back to the early 1970s in India when my supervisor published a paper without my name using 110% of my work. Later, I published a paper challenging his scientific thoughts and life continued. The difference is that I was doing it post Ph.D. The important lesson is to avoid any "toxic" elements in your relationship but the supervisor must respect you and your professionalism at all times.


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How to ask for employment help or referral from someone you don't know?
I will use fake names for the sake of anonymity. I have recently completed my PhD and applied to a professor position at University ABC. It has been almost 3 months since my application and I sent out an email to the Chair of the department (who presumably is the person in charge of recruiting academic/faculty members) but did not receive any response. There is another senior faculty member at University ABC, Dr. M, whose research is similar to mine and whose work I have referenced in my thesis. Moreover, Dr. M also attended the same university as my academic supervisor but they have never formally met.
Dr. M may not be involved at all in the recruitment process. However, I would like to ask for Dr. M's help in case he is able to give my application a push.
I am not sure how to write an email to Dr. M to ask for his help in such a scenario since there is no reason for me to believe that he is involved in the recruitment process. Nevertheless, I do want this job and I wan to do everything I can to make sure my application gets properly considered. How can I go about this task?

Was there actually a posted job opening? Your narrative doesn't make that clear. If there wasn't, your application is almost 100% likely to have gone straight into the rubbish can or spam folder.

@RoboKaren: Good point.  And if there was a posted job opening, it should have listed the appropriate person to contact - usually the chair of the search committee and not the department chair.

@RoboKaren My application was in response to a posting on their website. The name and email of the chair of the search committee was in the posting; however the chair has a different research area than mine. I sent an email to the chair but I didn't hear back, that's why i'm leaning towards sending an email to Dr. M.

The typical approach is to send an email saying something like:

Dear Dr. M.,
My name is ... and I am applying for the position of ... in your department.  (Brief summary of your professional background and research interests.)  I am particularly interested in the position because I would look forward to the opportunity to collaborate with you.  Please let me know if there's anything you want to discuss.  My CV is attached (maybe also a preprint).

This alerts Dr. M to the fact you are applying, so that he can get in touch with the search committee if he wants to support your application.
However, normally you would do this at roughly the same time as you submit the application.  You say you applied three months ago, but when is the application deadline?  If it hasn't passed yet, or if it was just a few days ago, then there might still be time for an email to Dr. M to have some effect.
But if it passed some time ago, then the search committee has probably already finished one or more rounds of screening.  If that's the case, and you haven't been invited to interview or otherwise contacted, then unfortunately, you probably didn't make the initial cut.  In that case there is very little that Dr. M can do, so not much point in contacting him.
(By the way, it's pretty much irrelevant that your advisor went to the same university as Dr. M, if they haven't otherwise been in contact.  That kind of relationship is roughly comparable to this one.  So I'd leave it out of any message.)

Thank you very much for your response! I found that Youtube link very explanatory haha.
The deadline for the application was around two months ago, and my application says that it is still active. So I don't think that it has been rejected. Do you think it is too late to send an email now?

@roland: The fact that it's still "active" doesn't really mean anything.  Common practice in academic searches is that you narrow down your candidates over several stages, but you don't technically consider anyone to be formally rejected until you've actually hired someone else.  You keep open the possibility that you might go back and look again at someone that you previously ruled out; but in practice it almost never actually happens.  We don't know what this particular department's timeline is, but I think it's likely that you're not being actively considered anymore.  Sorry.

I think it would be better to write a more targeted email, where you comment and/or ask a question about some paper the person has written.  Something that would pique his interest, and trigger a response.  Also, if you want him to push your application along, or you want to ask what the status of your application is (neither of which I personally would do in the situation you describe, but if you're comfortable doing that, go ahead), please be explicit.  Chances are that Nate's approach would not elicit a response.


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Is there a time limit after which you should cite a working paper as an unpublished paper?
I am citing a paper with the latest version being 2005. I checked some recent studies that cite this paper and some reference it as a "working paper" while others reference it as an "unpublished paper".
Is there a time limit or rule of thumb after which a working paper should be cited as an unpublished paper?

Well, what does "working paper" mean in your field?  (The terminology is not familiar to me; I think it is not used in mathematics.)  Does it mean something different from "unpublished paper"?  In my field we generally use "preprint" to mean either one, and I don't think there is any expiration date.  I would recommend putting more effort into making your that your citation is clear and making it as easy as possible on the reader to lay hands on the paper.

@PeteL.Clark Yes, I too agree with this.   Computer Science usually refers the same way.

In some fields, most papers are referred to as working papers even when they are basically preprints. And often they are explicitly in archives for "working papers," or published in a series of "working papers" (often if they were presented at a university for feedback).
After determining that there is not a newer or published version, I usually cite these papers, regardless of age, as a working paper if it is referred to as such. However, depending on the citation system, there may not be an official way to cite something as a "working paper", and so in that case I often default to citing it as an "unpublished paper." (A similar problem, or individual preferences, may be why different authors choose to cite it in different ways.)
I do not think time should change that classification, because "working paper" is a phrase indicating the general status of the work to those in the field. At the extreme, I might still refer to a "working paper" by someone who retired or died, even though it is certainly not still a work-in-progress. For instance, here is the official BibTex file for the first working paper in the NBER archive, a 1973 work by Finis Welch. The citation has type "Working Paper."


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Using a figure from a PhD thesis, but changed slightly. Copyright?
I am using a figure from a PhD thesis in an IEEE conference paper.
I have changed it slightly, mainly by adding text.
Though I will cite the author and publication, do I still need to pay the (what I am quoted as) $100 for rights from Springer? They have published the thesis under SpringerTheses.
How much can I use without paying the fee?

Also see: https://academia.stackexchange.com/q/138978/75368

If you use it at all you are at risk. Copyright is a matter of civil law. Springer's highly skilled and highly paid legal staff will have a say in the outcome. If they press it, you will likely lose.
Their position could well be that the figure is a "work" in itself, separate from the thesis and using it is copying an entire "work". Whether that is a valid judgement or not is less material than the fact that it has to be adjudicated if it is raised. That would likely cost more than the fee.
Your best options are to pay the fee or to reconstruct your own figure from the data that it represents. Small changes probably won't be enough. A third option is to reference the figure (cite it) without reproducing it. Let the reader chase down the image, which is less satisfying, of course.
Note that this is a very conservative bit of advice. But it is you who are at risk here.
But, it may well be that Springer will just let it go, being a small thing at their scale. I don't suggest they will, of course.

Note that grant funds or your university (or employer) may actually be able to pay such fees on your behalf.

So basically if it appears in a Springer Publication, I pay them for rights to use it. And I can potentially forward the bill to my university?

Possible, but ask first. Don't assume. Some places have a fund for that.

Indeed, ask. My university wouldn't pay for such an expense so don't assume you're will.

@GrotesqueSI, mine might have, if I debased myself sufficiently. Begging, etc.

We're encouraged/told to put a line in grant budgets for image rights and are out of luck if we don't :-/

If you were using the figure only for presentation you could likely use it under "fair use". However, I suspect that you are planning on having this published (I assume yours is a field where conference paper=publication...mine is not), and if that is the case you cannot use the figure or any part of it without proper permissions. A modification of a figure does not revoke copyright. Indeed, it might be a violation in itself. You can't use any of it in your publication.
While I am not familiar with the terms of SpringerTheses, you may find that the person who wrote the dissertation actually retains the rights to the figures. It wouldn't be the first time that a publisher tried to charge for something that they don't actually have the rights to. Why not contact the person who wrote the thesis and ask for permission to use (and modify) the figure? If they still retain rights to it, they can grant you the ability to use it for free.


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How to deal with corresponding authors not sharing submission steps? (E.g. Peer reviews & Decisions)
I am a 3rd-timer postdoc, and I often run into this issue. Over my career I have greatly benefitted personally of responsible peer review and participating in the elaboration of 'Response to Reviews'. Moreover I am very wary of publishing ethics, and open discussion of papers after publication.
This is often what happens: the 1st author of a paper where I am a co-author assigns a PI as last corresponding author. This PI is usually older and actually less invested in the project, but wishes to handle the submission. This person will however not share any correspondence with editors or submission files with authors other than the first (and I suspect even then not in full). I am thus left in the dark about discussions over papers where quite often I made a major part of the writing and experiments, and the only specialist about core topics being discussed.
I have tried asking for the details of peer review and was ignored, every time this happened. On a most recent case I received editorial notification of submission of same paper from two different journals within the time span of just 5 days, and now I fear somebody pulled a duplicate submission! This kind of attitude has made me reluctant of handing the position as corresponding authors to others, particularly to PIs, which is politically not good.
Thus I ask: How do others deal with such a situation?
UPDATE 1 (24.01.2018): I have just sent an email to the PI politely asking again for the peer reviews stating I will follow up with the journals if there is no reply.
UPDATE 2 (25.01.2018): First author responded informally providing the dates of all submission and general reasons for two rejections. The details didn't really add up, but given a casual tone perhaps it wasn't precise (e.g. I suspect this person is not aware of the difference of editor x reviewer). I still asked again for the Reviewers reports, and was left with the impression the 1st author did not (care to) see them either. She said she'll ask the PI.
In case I get no response I am not sure on how to proceed (e.g. if I want to see peer review from a previous journal).

"Is this widespread?" Hopefully not, it never occured to me, and I'd probably state very clearly how submissions should be handled. I'd stop collaborating if the problem persists.

I am already planning on stopping collaborating but have had already with three different groups. Either it is rather common or somehow my behaviour leads to such communication disruption...

@Scientist Were those three different groups at the same department or institute? I observed one department where this is common, but not in other places. For what it's worth, after this happened repeatedly with the same PI I not only stopped collaborating, but also informed the editor that manuscripts had been submitted without my (co-author) approval (amongst other problems). The editor too found the PI's behavior unacceptable.

With respect to the duplicate submission issue, while that's certainly possible, some journals engage in an "editorial review" process where the editor reads the paper and immediately rejects it based on some criteria (quality, relevance etc.) without ever sending it out for a full review. I don't know if this practice is common in your field but that might explain it.

@Mark Three different groups spamming two very distant countries. I am not adding too much detail to avoid an exposure but all are medium-tier institutions at 3rd-world countries, two in Latin America and the other in Asia. I get the feeling this is widespread and nobody says anything, and -- yet again -- I am the 'troublemaker'.

@TPM Yes, I think it is indeed quite possible. But I would not want to get penalised or badly exposed for sth I wasn't informed about, in case a duplicate submission was pulled. A relevant detail: I tried linking my ORCID number to both submissions via the Elsevier system using the submission notification emails, and found no submissions in the system. Why both seem to have been cancelled, and without any communication? Feels uncomfortable.

@silvado I am editing out then my more personal doubts and leaving just the question on how to deal with such situations.

Reputable journals often require a formal consent to publication (and sometimes a copyright agreement) from all authors.  This could give you some leverage - you can make it known that you won't sign the consent unless you have had a chance to read all the reviews and approve the final version.

Based on this experience, have you tried having a conversation about submission process before beginning the collaboration?

@Nate Eldredge Regarding signed documents, whilst I’ve seen it It is not common in my field. Usually it goes as “by submitting all agree in that” on a tick box. Regarding discussions prior to collaborating, I agree. However the work culture in such places is informal. In reality I settle collaboration with another postdoc who’s younger and friendly and get briefly introduced to the PI. Orders of authorship are usually not settled before having the results (may not develop), and sb may chose to rever a PI by making this person corresponding author. I don’t like it but it’s how it works.

@NateEldredge I do wonder how common it actually is for such a form to be required from all authors. I think I have only once had to sign such a form when a coauthor was the one submitting (this was for Transactions of the AMS), though I may just have forgotten about it again.

@NateEldredge Many reputable journals (e.g. IEEE and IOP journals for engineering and physics) require the copyright form to be signed just by the corresponding author, on behalf of all authors.

I have decided to post my final update on this as answer to anyone arriving here in the same situation.
The following line of response worked: I have written a formal email (in English, which is not our language of choice for communication) to the first author and PI asking again for the results of previous submissions and to be duly warned of future submissions. I implied (by stating I could just contact the journals but 'felt that was the role of the corresponding author') I'd contact journal editors if ignored for more than 5 days.
Within less than 12h the first author responded informally describing generally what had come out of previous submissions. I still asked (informally) for the peer reviews and she said she had to ask the corresponding author for it (PI, last author). By that I understood this 1st author had also not seen the result of peer review, and told her this was not fair on her as well.
Finally after 5 days the PI contacted me formally, and in English (unexpected because it is not easy for him to write in English) excusing for the time taken, informing any future submissions would be correctly reported, and attaching the results of previous peer reviews. I am formally thanking him for the attention given.
I cannot say how the PI feels about this (I now live on the other side of the planet) nor whether there will be further collaborations. Whatever the reasons, his response was appropriate, thus I am recommending this line of action. On a personal note, I would not have escalated this to the journal editors unless I was sure there was something else out of place.
Thanks to all for the suggestions given.


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Can one prevent a co-author from publishing on arXiv without consent?
This is very much related to a previous question I posted here: How can one prevent a co-author from publishing without consent? It is not the same question though.
Consider a situation where a co-author submits a paper without your consent to arXiv. This seems to be more problematic than them submitting it to a journal, because on arXiv it is published (almost) immediately and there does not seem to be an easy way to stop it, and also arXiv does not ask about consent from all co-authors.
It does not seem to be illegal to do this because the co-author has copyright as well and so it seems that legally they could grant a non-exclusive license to share the work. However, it does seem to go against the principles of academic honesty to publish without the consent of all co-authors (and that would include IMHO publication on a non-refereed source like arXiv.)
It does not seem possible to remove papers from the arXiv.
The question is then if there is a way to prevent it beforehand. Assume the co-author is not malicious, but simply a bit slack, so they would be willing to cooperate after it is found out (though if there is a way to prevent even malicious actors from doing this that would be even better).
If it is not possible to prevent it, is it possible to remove one's name from an arXiv article if one does not endorse the paper submitted?
I am aware that the best means is having a good relationship and communication with the co-author in the first place, but I would like to ask what other practical means there are.
To show this is not a completely made-up scenario, here are two examples of papers withdrawn from the arXiv due to this issue: http://arxiv.org/abs/0810.4310v2 and http://arxiv.org/abs/1307.4296

I might be missing something, but don't your two examples contradict "It does not seem possible to remove..."? A co-author contacted arXiv with their concerns, arXiv withdrew the paper (permanently or temporarily)

In the cases I have shown there is indeed a notice of withdrawal. When I mentioned it is not possible to remove the paper, I was referring to removal of the paper from the website completely. https://arxiv.org/help/withdraw mentions that a paper cannot be removed completely. To clarify, when I mentioned the possibility of removing the author name, I also meant removing it from the website completely rather than just having some kind of notice.

@Andrew: you can still access the version that was initially submitted if you look at the v1 page, so it's not completely gone.

While this is a good question, it is not one a bunch of random gals and dudes on the 'net can really answer. You should contact the people at arXiv about their policy, or even ask them to revise it.

i am voting to close since the author seems to have answered their own question in the question, and I am unclear what the actual question is.

Once an author has put their work into the public domain, it is very difficult to rescind it. All of the authors still have rights to the works, like attribution or trademark, but not copyright since that was given up as part of uploading to arXiv. So it might be impossible to force arXiv's hand with any legal tool where both of you are co-authors of the works. You do have one option though, but it's not pleasant...
If the co-author claimed joint-ownership over some part of the paper that you can prove (or they will agree) that they do not have rights to, then the works was illegally shared with arXiv, and arXiv have a duty to take it down if you DMCA it. The key is that you have to be sole owner of the copyright, and not shared ownership. Since you never personally signed off on the publication, that should be fairly easy to put forward. I don't know what arXiv says about this though, since their may be a fee for the co-author for retracting the paper - which I suppose you could both share, and i think you should, since arguably you should have done more to prevent a communications error like this ever arising in the first place.
Finally, may i just add, that this would not be illegal, but it would go against the principles of academic honesty...

arXiv offers a variety of license options.  Public domain is not relevant.

"For a licence where the author's retain copyright, they can pull it down whenever they like!" not necessarily

The page http://arxiv.org/help/license explains that once you submit to arXiv you give them an irrevocable license. So as far as I understand, whichever license you give them, it would be irrevocable, so you could not pull it down.  I do think it is still correct though that if the submitter did not have copyright (or more generally, the right to distribute) for part of the work and you could prove that, then they would take it down

@proggie45, that license is null and void if some of the authors didn't agree to it.

@vonbrand: That's not actually correct. If several people jointly hold the copyright to a paper, then any of them can license it non-exclusively, with no legal need for permission or even notification. The only condition is that if they make a profit, then they need to share it with the other copyright holders. In particular, if any one copyright holder authorizes the arXiv to distribute an article, then the license is legally binding. It would be unethical to do so without the permission of coauthors, but not illegal.

@AnonymousMathematician: who has to agree with multiple co-authors seems to be one of the points where copyright differs widely between countries. E.g. German copyright requires all coauthors to agree (though it sets limits to whether one can block publication) - vonbrand would be right over here.

I'm glad people still read this answer even if it was downvoted for being unpleasant :)