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What channels do people use to challenge or provide criticism for newly developed theories?
I currently not in academia, but I am an undergraduate alumnus with no graduate experience.
What are the normal processes for academics to challenge each other’s theories or findings, or to support them.

The primary way to refute a theory is to do the research necessary and publish a paper (or papers) with a (more) correct theory. the primary way to support a theory is to (positively) cite it in future work that embraces it, especially to extend it.
The theory of the aether was refuted when Einstein published the theory of relativity. But it took years for confirmation of Einstein's ideas to become firm - it is still happening, actually.
Every paper that cites another is supporting the earlier work.
It isn't my field, but I've heard that the ideas of Freud are slowly being replaced in psychiatry.
This is the normal process of science, actually. Old ideas are replaced by newer and more supportable ideas. Think Galileo.

Minor channels, are discussion groups and arguments at conferences. But the "refutations" need to be backed up, not just claimed.

I'm not sure about "every paper that cites another is supporting the earlier work". There are plenty of citations that say "In this work our findings contradict A. Author 2019".

@astronat I made a small change, but I'm surprised you missed the clear implication of the sentence as a whole.

Specifically, try to find a point of divergence, such as the observed orbit of Mercury.

I imagine if a theory is already widely contradicted by existing work (and/or if it's based on flawed data or research methods), then the primary way to refute it would be through public discourse (and maybe an eventual retraction) instead of by publishing yet another paper.

I have the same objection to Buffy's response as @astronat . You have to cite things you disagree with in order to refute them.

If the theory has not been published, usually one does not bother challenging it.
If the theory was published, most journals allow other authors to submit a "comment" or "matters arising" which can criticise it.  This rarely occurs.  Usually the comment is peer reviewed.

As stated in the answer by Buffy, the major road to criticise published results is to publish something yourself. There is a problem with this, which is that the academic publication process is slow, and may be held up even further if supporters of the criticised work recommend rejection when they are reviewers of critical papers. In particular, reviewers and editors often demand a better original theory or results than the one criticised. This can be counterproductive, as this requires new research which may be more difficult and harder to do than correctly finding problems in somebody's work. There is a handfull of journals publishing plain but well justified criticism; the majority, according to my experience, will demand additional original work, which obviously is a problem if the criticised work is wrong and will be used and cited as if true in the meantime! (I have occasionally criticised related work as a side remark in a published paper the main aim of which wasn't to criticise that work.)
Another major avenue for criticism is open to only a few, which is being a peer reviewer. You need to be invited, so this is not a way to criticise whatever you find wrong, but rather to criticise something specific you were asked to assess. However, if you establish yourself in science, you will be asked to do more peer reviews than you can do, and also young and relatively unknown scientists are asked (because much peer review is needed), so being a peer reviewer isn't very exclusive, also it is often effective as you can ask the authors to repair certain issue or recommend to reject the paper, but of course it's not a path to criticise stuff you are not invited to review. (Occasionally journals also publish discussion papers where either a chosen view or everyone interested is invited to write discussions.)
It is important to have in mind that human psychology is important also in science, and hardly anybody likes to be criticised in public. One should think that scientifically minded people are actually happy to learn from having errors pointed out by others, but careers and funding depend on this, so it is often not that easy.
My first channel for criticism will always be to contact the criticised authors directly. Most journals allow the authors to publish correction notes if they themselves realise that something is wrong in their work. Also, rather than straight away accepting that they were wrong, they may be happy to collaborate and come out with something that corrects the original issue but can be sold as an extension or at least as inspired by their earlier work rather than just admitting openly that "we were wrong". Chances to have an effect are probably better before work is finally published in a journal, as long as it is still only on preprint servers such as arxiv, privately circulated, or presented in preliminary stages at conferences.
I have pointed out issues at conferences but mostly this didn't have much effect. Authors may defend their point, or even agree with me, but may not change it anyway. Maybe the odd author learnt something and changed their approach at least in their next work, but this is rather the exception than the rule. (Obviously we also need to take into account that when criticising others we may be wrong ourselves, or the issue may have potential for genuine controversy, so we shouldn't expect anyway that everyone criticised by us says "you are right and I was wrong".) Obviously one can always criticise work by talking to others, and quite a bit of this is going on, but it is hard to know whether and how much of an effect this has.
On top of that there are more or less well visited blogs and open forums where stuff is discussed, probably also things like facebook groups (which I don't do). Chances are for criticism in such places to have any effect, the blog needs to be popular and the writer a "big name". However there is a number of such places where it is at least possible to write criticism without going through the peer review process, and some of this is read and even responded to by the authors.
In my field, statistics, Andrew Gelman has a very popular blog, which he uses to criticise work, and also to reflect about how difficult it is to criticise work effectively in science. Unfortunately it is very normal that criticised work continues to be cited and used and taken as "true". Searching for "criticism" and related terms on his blog brings up lots of stuff.
Gelman's blog on Statistical Modeling, Causal Inference, and Social Science, example entry on "A ladder of responses to criticism, from the most responsible to the most destructive"

Gelman's blog is not peer reviewed. He often uses it for angry personal rants as well. It's really not a model of how criticisms should take place. Gelman is often the poster child for the "proof by twitter follower count" activists as opposed to the "proof by peer review" practice.

You don't like it, fair enough. It still has a number of interesting postings on how criticism in academia works or doesn't work. I haven't cited it as a "model" (everyone interested can read stuff there to make up their own mind), and sure it's not peer reviewed, but the question wasn't for peer reviewed channels only.

Intro
One way to look at a theory is to treat it like a model. Models are simplified versions of reality allowing analysis and making predictions about reality. However, no model or theory is perfect, thus the limitations of a model are as important as the model itself.
Some time ago, the theory of a flat earth was good enough. People did not travel very far, there was no need for precise time measurements, movement of celestial objects was explained with divine intervention. Indeed, if all you want is to measure your own small crop field, it does not matter if on a grand scale surface of the earth is not flat.
A globe is a model of the earth and shows that the shortest path from Europe to the US is actually over the north pole. Something that is not evident from a flat map. However, a globe is a really poor model to say anything about earth's composition, core, and atmosphere.
Back to critiquing a theory.

You can present a better theory in some way outperforming the earlier one. However, there is nothing to say that the earlier theory was bad. Merely, your theory is slightly more complete. Round earth orbiting around the sun explains the day/night cycle, seasons, lunar and solar eclipses, and enables much more precise distance measurements over long distances. Thus it outperformed the flat earth theory.

You can demonstrate the constraints of an existing theory, or identify a contradiction suggested by the theory. Here is a good example: https://www.youtube.com/watch?v=d_XuFkVdAYU Doing so invites more research into the area.

A good start to evaluate any theory, especially yours if you aim to propose one, is to use the 7 criteria:

scope - what does the theory can predict and what it cannot?

logical consistency - does it makes sense, is not self-contradicting?

parsimony - is it simple and elegant? This is connected to the Occam's Razor, "The simplest explanation is almost always the correct one"

utility - is it useful?

testability - can we demonstrate it, and more importantly, can we disprove it? This is an important one in the light of fake news. There is no way to prove (or disprove) that the world is governed by a large pipe-smoking rabbit or lizard people. Luckily, this theory fails at logical consistency.

heurism - does it provide a good basis for extension and further research?

test of time - Do the above criteria hold true over time. Einstein's theory of relativity was criticized at the time. However, it turned out to be one of the most elegant and useful theories ever.

In academia, the accepted way to disseminate results is to publish them in journals and conferences proceedings.
Outside academia, you can make use of a new theory by creating a new product and bringing it to the market. It is somewhat common that companies do their own in-house research to advance their products and business.


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What is the difference between hypothesis, thesis statement and research goal?
Can someone explain the difference between hypothesis, thesis statement and research goal based on an example?

You should mention which subject you are in. 'Hypothesis' has opposite meanings in maths and physics.

I had this same question recently and did some research on it. The definitions I found weren't consistent, but from them I derived the following.
Thesis statement -- A definitive statement about the way the world (or your system of interest) works, especially what is most important in causing or influencing the behavior of the system.

"Family expectations has primary significance on the performance in college for Latino girls in the Western US" is an example of a thesis statement.

Research goal -- Expresses what you hope to learn or shed light on in your research.  Specifically, the goal should specify what type of results you are hoping to achieve. It contextualizes your work in relation to other research, especially theory.  It also feeds into your choice of method.

"My research goal is to develop a theoretical model of cultural influence on college performance, contextualized by gender and ethnicity" is an example of a research goal.

Hypotheses -- What specific conditions or relations do you aim to test or evaluate in your research.  Any research that does not include a method for hypothesis testing should not claim to test hypotheses. A hypothesis statement must be specific enough that it is testable by the methods you choose, and also it should be falsifiable -- i.e. it is clear what evidence might prove the hypothesis false, and such evidence should be plausible and possible.

"Low family expectations has a detrimental effect on the college completion rate and time-to-complete for high-achieving Latino girls" is an example of a hypothesis statement.

Notice how there are specific, testable conditions and metrics -- "college completion rates" and "time-to-complete".  These conditions should appear as metrics in your research methods -- i.e. instruments and analysis methods.

A thesis statement usually helps guide the research paper. It is a short sentence or summary containing the central idea of the research paper. It helps a reader have a clear glimpse of what the paper is about.
The Hypothesis statement comes in different format but with the intent to help prove or disprove a phenomenon. The hypothesis can help defend, support, explain or disprove, argue against the thesis statement.Usually the hypothesis measures specific issues or variables-two or more and therefore should be testable. The thesis statement creates a background while the hypothesis creates a means to measure the interrelationship.
The research goal takes a look into the future of your study or research paper. |It tries to help you state what the outcomes you seek to achieve by the research work. With a research goal you can set specific milestones to accomplish at the end of the research work.

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How to use a case study in a literature review?
I am writing a literature review and I may need to include three case studies. What is the best way to go about it? Am I allowed to include the whole case study for the reader's review and then analyze the points made?
Thank you for your advice in advance.

What do you mean by 'include the whole case study'?

To copy and paste it as it is, word for word. Then reference it.

I don't know about your field, but in mine, case studies are full-length articles. These you couldn't cite verbatim from beginning to end.

Noted with thanks! For clarity, I'm looking to use mini-case studies which are not that long. Hence why i am using three.
But I do see your point.

Why would you include a case study in your literature review?

I am by no means a master when it comes to research work so maybe it's not common/acceptable to use case studies in literature reviews. Please let me know if this is the case.
But I feel that it is a source of material that can be used to perfectly illustrate how a problem exists in the real world with an example.
The case study does this and gives perspective on what still needs to be done in future to address the problem better. This is why I have included them.

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What is a 'classic paper', and when do we refer to a work as a 'classic work'?
I have come across a few times in research papers or in books, where the authors refer a past (mostly an old) research paper as classic paper. For example, in a book Bratko refers the following:

The procedural meaning of Prolog is based on the resolution principle for mechanical theorem proving introduced by Robinson in his classic paper (1965).
  [1]

In another example, the author mention such a statement in the abstract itself,

Notes that the stimulation from a classic paper in the heuristics and biases tradition does not come only from the insights provided into processes of judgment and decision making; ... [2]

What is a classic work? Can we say a work as 'classic work', if it cited more number of times? Or, it is a breakthrough work? Then, how do we define a breakthrough work?
[1] Bratko, Ivan. Prolog programming for artificial intelligence. Pearson education, 2001.
[2] Sloman, S. A. (2002). Two systems of reasoning. In T. Gilovich, D. Griffin, & D. Kahneman (Eds.), Heuristics and biases: The psychology of intuitive judgment (pp. 379-396).

Related: https://academia.stackexchange.com/questions/5369/how-far-back-should-one-go-in-citing-classic-works

For me, I think it probably has something to do with if it is regularly read in a graduate level class.

@StrongBad Okay, so can we claim that all the works that are published and cited more often are 'classic'?

Some professional groups, like the Ecological Society of America, have books of complied "classic" papers. (I suspect these books were more popular before online articles made finding the classics easy). Inclusion in a books like this one would be way to id classic papers (but doesn't help for paper that were not included).

Related: When to refer to a paper as “seminal”

Whenever we feel like it can bolster the prestige of our own work ("we answer the following question posed in the classic paper by ...").

If people are still reading it 100 years after you wrote it, it's a "classic" - even though you may never have known that in your lifetime!

This isn't something that is decided based on objective measures - it's a statement of the author's opinion that history has shown the paper to be very important.
If you, in your professional opinion, believe that the paper has had a major influence on an area of research, for a considerable period of time, then you could call it "classic".  If you don't believe that, or you're not sure, or you don't think you have enough experience to judge, then don't use the word.

This is a classic answer.

@JiK It's too new! Maybe someday. =p

I don't think there really is any one definition of a 'classic' paper, but I think features that might contribute to the label include:

being an old paper that still gets used (or just referenced) a lot;
introducing a big new idea;
having been built on substantially (in a good way);
being well known as a good survey/suitable for learning the area from;
dating from and using methods from before a paradigm shift took place.

Note that some of these use the word 'classic' with slightly different meanings.

Your last bullet is "classical" rather than "classic". For example, in physics, "classical mechanics" refers to mechanics prior to the paradigm shift of quantum mechanics. There are many humdrum papers about classical mechanics and many classic papers about quantum mechanics.

It is really just a mild expression of reverence by the author. It has no set meaning beyond that.

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Asking Thesis examiner for guidance
I am currently writing my undergraduate final year thesis. It happens so that I have to consult papers written by my thesis examiner on a particular topic. My question is is it appropriate to seek clarification from him on parts which I'm unsure of in his paper even though he is my examiner? I tried asking my supervisor first but he is unsure about it as well as this is not within his area of expertise. (I need some results from other branches to prove something.)

I think this depends on the country in which it happens and the regulations around thesis examination.

This is perfectly acceptable.
Caveats:
I would be wary about asking questions you should know the answer to.
I would also avoid anything that might be interpreted as a criticism. I know this sounds obvious but its an easy mistake to make. If you are not a tiny bit careful, "Please clarify X" can easily be read as "X wasn't clear".

If your advisor isn't clear you're covered that it's not a 'trivial' or stupid question.
If you are careful about how you word the question, you shouldn't be in any danger of offending anyone. Explaining things can be tricky and if you are outside the immediate field, it doesn't look bad for anyone that you didn't follow.

Conversely not asking could end up reflecting badly on you. He will in all likelihood: understand the issue, see how it applies to your situation, and will be interested in your response/use of his results. If you don't follow it will probably be clear. If on top of that you missed (what he will see as) an easy step to rectify the situation - ask, exactly as you suggest - he may well see it in a negative light.
Finally if for some nuanced reason - and I really can't think what this would be - there was a reason he wouldn't be happy to discuss this with you: if you ask in a way that doesn't demand or expect an answer no harm will have been done.


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Listing in reference section, but not quoting
Can we list papers/Journals in reference section, but do not quote them in thesis. It may happen that I read some papers which are close to my area of work, but I may not use any idea from that paper. So in such case, I may not quote anything from that paper. But since I have read that paper, can I list that paper in reference section?

The references section is not supposed to list every paper you have read; only those which you think the reader needs to know about.

What is the merit of listing a paper that you don't use in your argument? The reference 's purpose is to help reading your argument, not a list of your accomplishments or general recommendation for reading in the topic. Also, you should note that many regular references are just pointing important papers or reviews in the field, which may be your original purpose here

Many journals require you to reference every entry in your list of references somewhere in the paper. That is probably also a good rule of thumb for a thesis.
The reason for this rule is that people do not typically just read through the list of references by itself. They read through the text, and in places where another publication is referenced, they will look it up in the list of references at the end. If the list of references contains entries that are not in fact referenced anywhere in the text, nobody is likely to ever look at that entry.
In practice, if you think that a paper is relevant for your thesis, then there ought to be a place in your text where you should cite it. If you cannot find a place where it would be worthwhile to cite it, then the paper is likely not relevant.

"The reason for this rule is that people do not typically just read through the list of references by itself." - I think that is a questionable assumption. I have met plenty of researchers who saw "take a paper related to your research interests, jump right into the bibliography and, one-by-one, check whether the referenced works are relevant to you" as one of their primary methods of maintaining a wide overview of all the interesting ideas published out there.

@O.R.Mapper -- I don't doubt that some people do it some of the time.  I'm among them. I doubt that that's the majority situation when people read papers.

Can't you make some sort of remarks like "This work is closely related to [1], [2] and [3], that investigate [this other issue]"

@Ant -- clearly. What I wanted to point out that if it is possible to make such a remark, then that remark should have been in the paper to begin with because the references are pertinent to the place in the paper where you want to put the remark.

The correct answer for you will depend on your field's citation style. In styles more common in the humanities, you might have a Works Cited section, a Works Consulted or just Bibliography section (MLA style), which together work quite different than APA/IEEE/ACM styles.
The Works Cited section works as the Reference section does in APA/IEEE/ACM style, and only the works cited section needs in-body citations. If you do not cite and properly integrate the work into the body of your paper, you do not include it in the works cited/reference section.
However, some styles and fields use the concept of a more general "Works Consulted" or "Bibliography" section, and listing here does not require you to cite it in the body of the text at all. Here you are explicitly required to include any materials you read, consulted, or which may have materially contributed to your work, even though they were not explicitly cited, quoted, or more directly referenced. This style of work believes in acknowledging much more generalized/abstract "indebtedness", and proponents of this practice often argue that it is more scholarly honest. In fields that don't use it, the argument tends to be that it's overkill, unproductive, and unnecessary, and thus is not used. The fields that use this style also tend to allow secondary sources, and thus both primary and secondary sources end up being listed somewhere even if you only cite the primary source.
You should refer to your own field's style guide and norms, or other explicit rules of your program and institution, to determine what is required of you in your work. In fields where you must actually reference the work directly in the text, it is not appropriate to "stuff the references" with work you did not cite directly. In fields with works consulted/bibliography sections, it can be considered plagiarism and scholarly dishonesty to not list items that you did not even explicitly reference in the text body.


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Is a copied acknowledgements section considered plagiarism?
A friend of mine has told me that his Master student (Chemistry) defended his thesis sometimes ago and everything went alright and he graduated.
He recently realized that in the acknowledgements part the student has copied practically (word by word, line by line) the acknowledgements of another thesis available on the Internet by replacing the name of my colleague with the name of the supervisor of that thesis. He added that he was hurt by the fact that the student has not tried to say his 'thank you' words by his own words.
My first question is that can this be considered as a plagiarism?
My second question is that is it necessary to inform the student about this possible (if any) misconduct?

I would say that your friend is "making a mountain out of a molehill."

It seems to me that the number of reasonable ways to thank one's thesis supervisor is far smaller than the number of theses. So I would expect lots of theses to contain the same formulation of thanks to the supervisor.

@AndreasBlass Of course, many acknowledgements (just like love letters) are conceptually similar. However, word-by-word copypaste is still quite different from taking an effort of saying the same things in your own words.

@DmitrySavostyanov: Unlike love letters, however, acknowledgments are both public and meant to be lasting statements about someone else. A statement that could be, for lack of context, interpreted the wrong way by a 3rd party, or a miswritten statement that should better be forgotten and can be corrected in a follow up are not an issue in a love letter, but can seriously distort the intended impression about the person referred to in the acknowledgments of a publication. Therefore, in the acknowledgments case, it's maybe better to play safe and restrict oneself to standard formulations.

I would be more worried about the possibility of other parts of the thesis being copied. The student in question might just have been uncomfortable with writing the mushy part on their own - or it could be just one instance of a more damning pattern...

He recently realized that in the acknowledgements part the student has copied practically (word by word, line by line) the acknowledgements of another thesis available on the Internet by replacing the name of my colleague with the name of the supervisor of that thesis.

I'm slightly confused: I assume that in order to discover this, the advisor must have run the entire thesis through some plagiarism-detection software.  But the question indicates that this took place after the student's graduation.  I don't understand that: two reasonable times to run your student's thesis through plagiarism detection software are (i) at some point before you sign off on it and (ii) never.  Would one really do this after the fact out of idle curiosity, or did the advisor have some other reason to suspect that plagiarism took place?
Is line-by-line copying of someone else's acknowledgments a form of plagiarism?
Well, plagiarism has a sufficiently precise definition that I don't see how the answer can be "no".  The better question is whether this is viewed as unacceptable enough to do anything about.
I think that part of that question depends upon the writing quality and originality of the purloined acknowledgments.  As @Andreas Blass points out, if you've seen 10 different thesis acknowledgments, you've seen 1000 more: such acknowledgements are formally part of the thesis but they are not part of the academic / intellectual content of the thesis.  So they are not vetted in any way, and there is no expectation of intellectual originality.  There is more than one way to phrase "Thanks so much to my parents, my friends and my thesis advisor", but the number of standard ways to phrase that is so much smaller than the number of theses that the pigeonhole principle applies to show that many people are writing the same sentences in their acknowledgments.  If the purloined acknowledgments contained many clever and original turns of phrase, then it looks worse: the fact that what you stole has nothing to do with the intellectual content of the thesis cannot excuse the fact that you are taking credit for someone else's distinctive writing.  That's a really icky thing to do in acknowledgments to your own thesis.
Unless the purloined acknowledgments contained several paragraphs of poetry or something similarly egregious, I would not consider a formal plagiarism inquiry.  This runs the risk of getting the degree rescinded, which to me is clearly too harsh.  But there is a real problem here:

He added that he was hurt by the fact that the student has not tried to say his 'thank you' words by his own words.

Ça y est.  The student's former advisor has discovered that the student has cut corners and compromised some academic integrity just to get out of thanking him in his own words.  What a slap in the face!  I think that if something like this happened to me, I would have to bring it up with the student (though it would be painfully awkward) just because I would feel like I have to be honest with them about the change in my opinion of them resulting from this discovery.  Without some kind of sincere apology / explanation of this, the future of this professional relationship is at risk.  The student, alas, may need to be informed that he should look elsewhere for future recommendation letters and so forth.
Added: A lot of people seem to be suggesting that parts of this answer are an overreaction.  I tried to make clear that I don't find the premise of the question completely plausible or understandable, but after discussing that I did what I think is the appropriate thing on Q&A sites like this one: I assumed the premise, in some form which made sense to me.  Yes, if the "word-by-word, line-by-line" copied acknowledgments constitute five lines thanking the student's family, friends and advisor, I see no problem at all -- and I  don't see it as a reason to run the text of the acknowledgment through an internet search.  Nor would such a search turn up a unique antecedent; it would turn up hundreds or thousands of cognate passages, as Andreas Blass pointed out. Thus to assume the premise I had to assume that the purloined text was much more substantial and distinctive. To be more specific, imagine the text was:

I feel greatly honored to be able to add, in some small way, to a subject founded
by so many [Field Xers] whose work I so deeply admire; among them are
[My Advisor], [Person A], [Person B] and of course [Person Whose Name Appears in the Thesis Title], the richness of whose ideas seems undilutable by time.

I thank [Professor C] and [Professor D] for suggestions directly relevant to the material appearing in this thesis. I thank [Fellow Student E] for helping me – quite a while ago now – with some results of [Somewhat Technical Theory] that appear in the appendix.

I thank [Postdoc F] for helping me calculate a fistful of [Something] (I regret that none of these calculations appear in this thesis)
and for generally being so free with his technical and [Field X-ical] insights.
I am grateful to [Recent PhD G] for making his own as yet unpublished thesis
work available to me.

The graduate students in the [University Y Department of X] have been without
exception intelligent and friendly, and it has been a pleasure to learn from them and with them over the years.

Thanks to [Old Girlfriend H] for providing comfort in the sad days of [a few years ago]. Her kindness will never be forgotten.

I am indebted to my thesis advisor [My Advisor] for more things than I can list
here, but most recently for a careful reading of an early, ugly draft of a certain lengthy [Field X-ical] document.

My father would have been proud of this thesis beyond all moderation. My
mother has long made and continues to make me proud of her strength in the
face of all the challenges life has to offer. I thank them both with all of my
heart.

Imagine that the advisor read this the first time around and was happy to be thanked along with so many other people who made a difference in the student's life.  Then later, for whatever reason, he does an internet search on or including this text and discovers that it is lifted word-by-word, line-by-line from this 2003 PhD thesis.  The specificity of the stolen text would be downright creepy.  Is it really an overreaction if the advisor is upset by this??

Yes, many peculiar premises to the question... I am still wondering how it happened that the copy, if it was so, was observed. The sameness of more things than acknowledgements are inevitable, as you say, by pigeon-hole, if nothing else, and/but the detection requires effort... For that matter, one could argue that taking the trouble to find a really compelling acknowledgement wording is better than writing one's own crappy one. Do we want one of the great symphonies, or an all-new one? :)

"... the advisor must have run the entire thesis through some plagiarism-detection software." Not necessarily. He might have just read the text and found it familiar, especially if the phrasing was distinctive.  Or the style of writing may have changed dramatically, prompting the advisor to do some Googling.

@David: Certainly anything is possible, and my "must" ought not to be taken literally: I was speculating aloud on what "must have happened".  But I find your alternate explanations rather peculiar as well.

Is anyone feeling what is described in the last paragraph not a gigantic overreaction? Such that I would actively worry about them having a normal reaction to anything. Not to mention misinterpreting the action; your own slap dash acknowledgments is almost certainly easier than looking through templates to find one that sounds right (much like buying a birthday card; a scap of paper with "today is birthday" written on it is definitely easier)

Plus one for concluding that this is not part of the academic/intellectual content. Almost minus one for taking it so personally. When I read "Ça y est" I thought you were going to criticize the motivation, not jump on the bandwagon. Too much thin skin in academia.

@Aaron: This is not a situation I have ever found myself in or imagine that I would: I have never  searched my students' theses for plagiarism and I'm not sure what would motivate me to do that.  But if one accepts all the premises of the question it does seem a strangely unpleasant form of ingratitude.  I assume you have directed graduate theses  so as to be able to characterize the behavior as thin-skinned.  Have you ever had a student react this way to your hundreds of hours of work?  What did you do?

Without wishing to exaggerate my psychic powers, the author has probably thought "what's a formal, polite, appropriate way to phrase this?", and plagiarised another thesis in much the same way that one might look up how best to phrase a wedding RSVP. Sucks, but I strongly suspect not that the author has tried to "get out of" thanking the advisor in his own words, but that the author has overlooked the opportunity to write something personal. As do many others, since as you point out these things are generally bland and samey. Which is why RSVPs sprang to mind.

Also, if collisions really are inevitable by the pigeonhole principle, then this may not be plagiarism. If it is just an unfortunate coincidence of clichés, then the offense is that of someone who feels their acknowledgement ought to have been more interesting, not someone whose student has taken steps to avoid composing one at all :-)

Formally, the copy-pasting of the Acknowledgements section is stealing the other author's language, expressions and maybe even ideas, that fits into the common understanding of plagiarism. Therefore, it might be a good idea to discuss this with the student.
However, before you do this, you may wish to double-check your internal motivation. Do you do this to help student realize that even if they copy a small piece of text like this (not directly related to the academic content of theses), it still can be considered as a breach of ethics and negatively impact their future career? Or do you do this because you feel for your friend and have some hard feelings about the ungrateful student?
The situation is definitely very delicate, and should be carefully dealt with. It touches the field of academic ethics in two separate points: copypasting the text, and expressing gratitude. It is crucial to separate these two in the discussion with student.

It is very unlikely that there's much more than one or two lines of text per acknowledgement per person. A google result "author wishes to thank * for his help" gives more than one million hits. I'd say any discussion with the student would be absurd, unless the acknowlegment text is a whole paragraph.

@mmh We do not know how long the acknowledgements section in question is. You may wish to check with the author of the question, whether it is a whole paragraph or less.

You should really take a step back and put this into context. This is just the acknowledgement section.

My first question is that can this be considered as a plagiarism?

The acknowledgements are not really part of the academic work. In general, it's the only part of a thesis where the writer has a larger degree of freedom regarding style and content. This should certainly not be academic plagiarism per se.
There's also the secondary question of copyright infringement, but in all likelihood, the text is too short for this to be clear cut. I'm not a lawyer, but I suspect this could fall under some sort of fair use (although some form of citation would be good I guess). Nevertheless, the one who could be upset about this should be the initial author of these acknowledgements, if they care. Of course, if a court of law decided this was indeed copyright infringement, this would have an impact with respect to the plagiarism policy of the institution.
I'll just assume that no one felt this issue had to go outside the scope of academia.
It sounds like this is more an issue about causing offence than about actual plagiarism.

My second question is that is it necessary to inform the student about this possible (if any) misconduct?

You can have a quick word with the student, since he or she visibly caused offence, but I wouldn't call this misconduct.
Putting things back into context, the acknowledgement section of a thesis will be ignored by 90% of the 0.00000001% of the world's population who will have read the thesis (I might be generous there).
Acknowledgements are mainly a name-checking exercise:

You thank your parents so they can be proud when they exhibit the precious copy you gave them to their visiting friends shortly after the graduation ceremony, before gathering dust until eternity. You can also thank a few close friends for the bond of common graduation experience.
From a professional point of view, you also thank your supervisor and possible funding bodies who might have given you grants for the work. The latter are the points that really matter: the supervisor and funding bodies will be able to put the student's thesis as part of the achievements of their own careers and projects.

Besides that, I'm afraid to say no one really cares about the wording in general, as long as it's not offensive or outstanding in the wrong way (one should avoid things like "[...] Prof X was the catalyst that enabled this exothermic reaction inside me to produce this marvellous piece of work [...]", simply because it's ridiculous, not because it might be plagiarism). If someone takes interest in the work and want to find out under whom this was conducted, they'll have a quick glance at the acknowledgement section, look at the name of the supervisor, take note and move on.
Perhaps there is some cultural context at play here. You're not saying in which country you are or what your friend's cultural background and seniority are.
The student probably didn't mean to cause offence. Since it sounds like the text is sufficiently distinctive to be identifiable, it sounds like the student actually did make an effort to find something original to say, at least something distinct from the basic "I would like to thank Prof X for his (in)valuable advice". If anything, your friend should be flattered, by this attempt (sadly failed). The acknowledgements is probably one of the last sections that was written in a rush before the submission deadline.
As I said earlier, it doesn't sound like a plagiarism issue, but like someone who inadvertently caused offence. It's not so much about informing the student about a possible "misconduct", rather it's about defusing the situation, between the two of them. It can be tricky if your friend is seriously offended. In fact, perhaps you should have a word with your friend first to try to calm down this situation. If I was the student, I would feel really awkward having to work later (e.g. in a PhD programme for a number of years) with a supervisor who is likely to hold some sort of grudge for this.


text:
How do I properly cite the amount of times an article has been cited on Google Scholar?
I wish to properly cite the amount of times a paper has been cited according to Google Scholar. However, I couldn't find a proper answer to this question.
The paper in question is:

Blei, David M., Andrew Y. Ng, and Michael I. Jordan. "Latent dirichlet
  allocation." the Journal of machine Learning research 3 (2003):
  993-1022.

Hansen, S., McMahon, M., & Prat, A. (2014) note that

LDA is widely used (...) and has been cited over 8,000 times

But they cite no source! What is the proper source to cite here?
My first thought was something like this:

LDA is widely used (...) and has been cited over 10,000 since its
  publication, a search on Google Scholar reveals (Google Scholar,
  date).

edit: I e-mailed my advisor and ended up citing Hansen et al. (2014) saying that the paper had already been cited 8000 times. Not really a satisfying answer ... alas ..

In addition to Bill Barth's answer, the Google Scholar citation numbers can be terribly inaccurate in my experience, so I don't know what the meaning of this number would be anyway.

I would argue that if this number is from a source which only counts citations in other sources published in journals (such as ISI), then there is no need to specify a source - such a number would be a conservative estimate and pose a lower bound also on databases counting other sources.

I don't find such citations to citation counts very helpful in reading an article. Assuming such numbers are reasonably accurate, they only represent a snapshot of the popularity of a technique at the time you wrote your article. I would recommend simply saying that it is a popular technique and leaving it at that.

Maybe field-dependent, but personally, I'd find the citation of two or three otherwise unrelated papers from a diverse range of topics that indeed do use the technique in question much more convincing and interesting than a citation of a citation count (and also preferrable to just claiming it's "popular" without backing that up somehow).

@O.R.Mapper, agreed. Citing papers that cite the original is also a great idea.

I e-mailed my advisor and she told me to cite the paper that cites that is as been cited over 8000 times. So that's what I did, although I did not leave satisfied.

" it is a popular^[citation needed] technique" :-)

This is the correct answer if the paper is not about bibliometrics.

I would not give a formal citation, but I would mention something like this:

LDA is widely used (...) and has been cited over 10,000 times as of July 2020, according to Google Scholar (https://scholar.google.com).

Key points to note:

The URL to Google Scholar is sufficient as a reference. Nothing more is needed and nothing needs to go in the bibliography.
It is very important to specify the month and year of the search since, obviously, when the reader eventually reads your article the citation count will almost certainly not be the same.

One can get around temporal issues by saying “more than X” citations. Citation counts very rarely go down.

@StellaBiderman My answer says "over 10,000 times", which is exactly the same thing as "more than X".

yes, I understand that. Appologies for being unclear, but I was referring to the bullet "It is very important to specify the month and year of the search since, obviously, when the reader eventually reads your article the citation count will almost certainly not be the same." The OP appears to only care about demonstrating the topic is of interest, which means a lower bound is fine and the exact date they look it up isn't so relevant.


text:
Whether and how to thank a girlfriend or boyfriend in the acknowledgements of thesis?
How is it received by the academia if someone thanks to his/her girlfriend/boyfriend in the acknowledgements of the thesis?
I have seen writers including his/her fiancee in the acknowledgements, however I don't know if including an informal relationship in the thesis will be received well.
If it is acceptable, how should I refer to my girlfriend?

This strongly depends on your country. I know it to be quite common in my field and not worth a thought in Germany. In other countries you can get stoned to death for having an extra-marital relationship. I bet that there is some country in between where having a girlfriend is acceptable but acknowledging her isn’t.

Sometimes you can actually have a "Dedication" page other than you acknowledgement as well.

If you want to be a little more formal, write "partner". Most people write both personal and professional acknowledgements in at the end. @Wrzlprmft it's possible for someone to give love and support without yet having a sexual relationship. I'd be quite surprised if an acknowledgement as per jakebeal's answer would be a problem, even in ultra-conservative societies.

I think you dont see informal relationships not because it is not acceptable but instead because it can be regrettable.  In a few years, if your relationship ends, instead of having a persons name, you have an ex forever in your acknowledgment

@Moriarty: I wasn’t necessarily talking about a sexual relationship. Though I am no expert, I am pretty sure that publically stating that there is somebody who is just your girlfriend is at least pretty bad idea in Saudi Arabia, for example.

@user1938107 I'm very comfortable with the acknowledgement of my ex that is in my thesis.  That relationship may have ended, but the help I acknowledged still happened.

@user1938107: Also, there are societies where the formal relationship status is only mildly correlated to the stability of the relation.

Indeed, my thesis contains an acknowledgment of someone who was at the time of writing my ex.  As for @Wrzlprmft: I don't think we can be responsible for all the world's social mores on this site.  The question is "How is it recieved by the academia..." I think for any such question there is going to be a 1% where local customs differ from global academic customs.  Unless the OP puts their location into the question and asks for a specifically local answer (which may risk being "too localized"), I think answering "globally" seems only sensible.

I thanked a fictional dog in my thesis. Nobody cared. Or noticed.

I'm pretty sure that no one has ever read the acknowledgements page of my thesis (including my PhD advisor).  There's always the old joke about sticking a $20 bill into your thesis in the library and coming back 10 years later to find it still there...

@AndyPutman Perhaps those interested in the thesis are also so honest and altruistic, they leave the money for the next person ... ;-)

@JeffE I used all my Google skills, just so that at least someone cares (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.76.803&rep=rep1&type=pdf). But I can't find any reference to a dog ( at least if Nancy isn't a dog, which I do not hope because it would be a terrible dog name and the dog could speak, which certainly is spooky).

@dirkk: I think I found it in "Homotopic Fréchet Distance Between Curves". Not his PhD thesis but since even this paper was written five years ago I think we can forgive the memory lapse. :)

Dunno about thesis, but my BSc ticket is still taped inside its cardboard tube, 38 years after I received it. Nobody has ever asked to see it, so I never opened it.  I daren't open it now in case, instead of a degree certificate, it contains merely a 'You're joking, surely!' note from my prof.

@dirkk: You didn't read it carefully enough: "Thanks especially to Bob Hearn, Scott Holdaway, Scott Lindsey, Paul Lee, Ernie Pan, Syd
Polk, and my dog Bo-bo for their friendship and humor." Now, of course, the question is: "were the other people also fictional?":)

@Ajasja Yep, that's it.  And most of the other people in that list are real.

@LightnessRacesinOrbit  Nori and Kira were actual real-life dogs that four of us actually walked in the real-life woods.

@Ajasja Thanks for clearing this up. I swear, I read it three times - I must be Bo-Bo blind. If I am not the only one I guess JeffE could actually be correct that noone ever noticed it. Until no.

My own thesis acknowledgements are sadly very boring.  My wife, on the other hand, thanked people for mathematical discussions, for friendship, and for being fun at dinner parties; she thanked her department for paying for her to take ballet classes while she was a PhD student; and she ended by dedicating the thesis to the two rock albums that helped her get through quals studying.  Oh, and she thanked me, too.

Please take all extended discussion to [chat].

@JeffE wait, Bo-bo isn't real?!

The acknowledgements section is really yours to do with as you wish.  You can thank anybody who has been of help and support to you, no matter how formal or informal your relationship with them is.  You can make the relationship explicit or not, however you prefer.  Thus, for example, it is equally valid to write:

Thank you to Jane Smith, for all her love and support

or

Thank you to my girlfriend Jane Smith, for all her love and support

@keshlam's answer

Sadly, for a thesis this might not be the case. Check the rules of your institute! In my home country, the University of Leiden is somewhat infamous for forbidding "excessively long non-academic acknowledgments" and making a fuss about acknowledgments to deities, going as far as forcing people to reprint their thesis, or rip out the acknowledgment altogether.

Adding to jakebeal (and keshlam's comment about offensive text), I think the only negative consequence is when you leave specific people out, e.g., you thank one supervisor but not the other. And that includes people who did support you during your thesis but were not part of the formal structures, e.g., your partner, or your parents, etc. Not to argue with comics, but PhDComics put it best: "Acknowledgements" and "To you I dedicate this thesis".
To avoid forgetting someone, I found it useful to add a general thank you paragraph after the personalized acknowledgements for all those I did not mention explicitly (sums up other colleagues, extended family, etc.).

This is a very good answer. Actually, I think there is nothing wrong arguing with comics. Thank you.


text:
Is it okay to submit manuscript to arXiv after "revise and resubmit"?
I've read this question about how some publishers (e.g., Springer) allows authors to submit to arXiv before journal submission, but they make authors wait for a year after acceptance to submit to arXiv.
My question is: Is it okay to submit to arXiv during the time when the paper is under consideration by the journal, for example after it has been "revised and resubmitted" but before final decision?

This depends on the journal, and whether they consider articles posted on arXiv to be prior publication. See this list on wikipedia for some examples of journal policies.

@ff524 I guess the "prior publication" issue should not play into the question whether one can resubmit the revised version to arXiv. If it wasn't a prior publication before review, it shouldn't be one after. I think the relevant question is whether a journal can / does claim some sort of copyright or IP over the changes that have been made due to reviewer recommendations. My inclination is "no", but I am not a lawyer.

There are three separate questions: is it ok, is it legal, and does the publisher really care. The first one is a matter of opinion. The second one may depend on the circumstances (e.g. the country you work in; the country the publisher operates in; your employer and funder(s)).

@xLeitix you're right, I misunderstood the question

The version you mention is called a postprint. Publishers have various policies about them. You can use the SHERPA/RoMEO service to get a summary of the policy in place for a particular journal.
Here is an example of what you get for Lecture Notes in Computer Science, edited by Springer:

As noted in the comments, you do not necessarily need to abide by these policies, for instance if your funder has set up an open access policy.

I'm not referring to the final draft post-refereeing, but rather an intermediate version (perhaps after one round of refereeing).

Ok. Intuitively I would still consider that it falls in the "postprint" category as some input from the journal was included in the document, but IANAL… In doubt, just upload it, you should be fine.

you do not necessarily need to abide by these policies, for instance if your funder has set up an open access policy. – Those are not policies, those are what you agree to in the copyright agreement with the journal (which tells you in detail what you are allowed to do, i.e., what you did not agree not to do). If your funder has an open-access policy, this does not change what you are allowed to do by itself. It may affect the copyright agreements you can agree to, however.


text:
Posting master's thesis on arxiv?
I read this question, in which all answers recommend posting one's master's thesis online. My thesis is available from my university's repository, but I'm thinking about posting it on arXiv since it's more easily searchable. However, I don't think I've seen master theses on arXiv. Is this something that people typically do? Are there disadvantages that I'm missing?

If it is worth being read by many people, why not consider turning it into a publication?

Posting a master's thesis on the arXiv is uncommon, but not unheard of.  My feeling is that there's little point to it: if there's material worth publishing in your thesis, then you should turn it into papers and post them on the arXiv (in which case the thesis is unnecessary), and if it's not worth publishing then it's not worth posting to the arXiv.
If you decide to post both the thesis and the papers to the arXiv, you should indicate the relationship between them clearly in the comments so you don't look like you are inflating your publication record with duplicates, as well as in case you trigger the automated plagiarism detection in the arXiv.
One potential issue is coauthors.  If anything in your thesis is coauthored with someone else (either from a previous paper or to appear in a future paper), then I do not think you should post the thesis to the arXiv.  The problem is that you'd be pointing readers towards a version that lists you as the only author and relegates your coauthors to a brief note in the text, and you would be increasing the chances that they would cite the thesis rather than the coauthored papers.  Instead, it's best to emphasize the papers by posting them to the arXiv instead.

Any material in a (master or any other) thesis that has been published previously should be properly referenced. Any contribution from others should be acknowledged. Before entering common work into a thesis, the other authors should give their permission.
So none of these can be a reason not to submit the thesis to arXiv.

@DannyRuijters: I agree that it's not unethical to post a thesis to the arXiv that contains coauthored material, but I consider it unfriendly to the coauthors.  The thesis technically gives them credit (since they are cited within it), but in a way that is less visible to most readers and not visible at all if the thesis is cited.  Posting the thesis disadvantages the coauthors compared with posting the papers themselves, and I see no advantages that can outweigh this issue.

I do not agree with this "if it's not published but in a thesis, then nobody cares about it" attitude. (1) Theses are something we (still!) have to write and (2) there are plenty of introductory notes online which combine many papers into one coherent piece of information that are not only helpful, but have made their authors well-known and respected in the community. Why not combine these two things into one?

What about a "reading project" type of masters thesis? In that case, "if there's material worth publishing in your thesis, then you should turn it into papers" wouldn't be appropriate. In that case is it advisable to put it on the arXiv (solely for easy sharing with others/some prestige for young PhD students trying to impress potential advisors)?

Is this something that people typically do? Are there disadvantages that I'm missing?

There are NO disadvantages, but IMHO, this is not something that people typically do.
At least in my field, CS, nobody care about PhD theses, let alone Master theses. Because if there are any contributions in the theses, they should be published in conferences. That's the version that people want to read.

In my experience, the people who care about MSc or PhD thesis are the ones trying to replicate something, whether a lab result or an algorithm. So it sounds strange to me that no-one in CS cares about theses. Don't you replicate stuff? :)

@semi-extrinsic: very often, PhD theses are just long summaries of published papers as the majority of professors (I am talking only about CS) expect you to produce publications during your thesis. That's different to other tracks where you can get your PhD without any publications. So all replication will usually be done using your published conference/journal papers.


text:
Is there funding for non-research related projects?
Nowadays to obtain a PhD or a postdoc one needs to conduct independent research and present new results. However, at the frontiers of science there are many non-research related things that could still be done which are not being done by the professors since it would take a lot of time - examples include writing textbooks, translating a classical reference from one language to another (in some areas the classical reference is not available in English, for example), writing websites or programs which could assist one in learning the material.
I was wondering if there are any funding opportunities or academic grants available to hire a student/PhD/postdoc for those sort of projects. To me it would make sense to give such a job to a student rather than a researcher, as a student is learning that material anyway (and so can on his way adapt it so that the next generation can benefit from it) and it doesn't force the researcher to abandon research in favour of writing a textbook for a couple of years.
Paragraph removed by Dirk's suggestion

I would suggest to remove the last paragraph as it makes the question feel like a rhetorical question (and I think it is not one).

Some popular open source libraries also get funding from private and public entities because they are useful for many people.

Sure:

The DFG in Germany awards grants for projects to organize digital libraries.
The ministry of education and research in Germany funds large projects on higher education (one of them is the Qualitätspakt Lehre - you hire people (often at the PhD or postdoc level) to organize or develop new courses, course concepts or course material).
There are grants for projects on history of science.
Universities offer reduction of teaching load or sabbaticals for writing books (which is really some kind of a grant, you get paid with time not money).
In books you often see acknowledgements for some funding.

Granted, in many of these grants the money or time does not go to PhD students or postdocs but at least the first three things fit the bill.
Note however, that as soon there is no research involved, you can not get a research degree for this work. So these kind of positions are not attractive to some students.

Thank you! Do you know anything about the situation outside Germany?

@user45688: Note for future questions: It can be beneficial to wait for a while before accepting an answer in order to encourage other users to add possibly even more helpful answers. This is especially true if even your own (as the asker) desire for information has not yet been met.


text:
Audit or B in class when applying to grad school (mathematics)
Does a B in a class look worse for graduate school admissions than an audit, given I'm not expected to have the class in the first place?
More specifically, I'm studying abroad and taking five math classes. When I go back to my home institution, by the time I graduate I'll have exhausted all the math courses there, so the maximum math courses I'm "expected" to have is those plus four (four classes being a typical semester).
I have the opportunity to change a class to audit, even after I know my grades, so my question is, if there is a class I might get a B in (functional analysis, if you care), do you think having a B would look less impressive than not taking the course (or does audit risk the same sort of judgement)?
Does my question make sense? Does a B look "weak" when applying to grad school (even in comparison to nothing)?

My apologies, yes in regards to applying for graduate school. Question has been edited.

What would you consider an audit? Just sitting in on the class, no? I've done everything required for an audit, so I don't quite see the ethical complaint.

@Ryan you did take the class regularly, even if not required. Just give full details, particularly if somewhat unusual.

It's better to have documentable (whether in transcript or by letters of recommendation) exposure to more substantial mathematics. Especially in the U.S., the default undergrad curriculum in mathematics is far too thin for grad school. Without taking initiative, which necessitates not-the-routine channels, you'd not be ready for grad school. Naturally, the irregularities in the not-routine channels generate grades whose meaning is unclear, and so on. (And, no, summer "research experiences for undergrads" do not typically add much to one's scholarly preparation, although they may fire one's enthusiasm.)
So, for me, when I see "functional analysis" on a transcript, I don't really care what the grade is, nor whether it's "audit" or not. Just the  initiative to engage with it.

First, this depends on if you plan to apply to the #1 ranked graduate program in mathematics or a un-ranked program. Second, although the "audit" may not carry the burden of a grade associated with it, it is often associated with a student who enrolled in the course but did not do any of the assignments, tests, etc. So, this is a double-edged sword. Keep in mind that one course will not make or break a graduate school application!


text:
How much theory should be given in article?
I have created a software and the assisting methodology for its application to some kinetic studies. I used a lot of theory. E.g., I used kinetic model, reactor model, data analysis (about 7 methods to analyse the results totally). Now I have prepared an article where I report this methodology and demonstrate the results of its application.
How much theory should I include into the article? Can I only refer to other publications/books for the models/methods proposed earlier?
I have seen many publications where a part of theory is taken out from the main text to appendices (example with 5 appendices). In some journals appendices are not included into the article (supplementary, accessible online-only). Is it a good solution to include some theory in appendices? If yes, how many appendices would be OK (i.e., would the reader like the article with 7 appendices? As for me, I do not have anything against many appendices).

I'm not sure what you mean by "thoery", "kinetic studies" and most of the other keywords in your question. It sounds like the answer might be very specific to whatever field your research is in. If there's a Stack Exchange site for that subject, that might be a better place to ask than here. (In that case, please click the "flag" button below the post annd ask the moderators to move your question. Don't just copy-paste it to another site.)

Besides the already given hints I offer another guideline:
Give as many background as you yourself would have needed to get the idea and method before you have developed it.
In other words:
Write the paper to your former self (before you knew about what you've found out).
If you would have been happy with a paper that described the idea and references a lot to standard, readily available books for the background, then go for that style. If you had found it awkward to work through a paper that has a lot of references to papers/books that are hard to find, then don't do that. Note that different principles can apply at different places in the same paper.
These hint is in some way a simplified form of the general hint
Know your audience!
Oh, and also discuss this with your advisor.

My usual approach is based on two main ideas:

One new idea per paper
Each paper must be self-contained

So, if I create a new methodology for something that can be applied to something else, that's two papers, one theoretical, one application. Of course, that's computer science, not sure how it translates to your field.
The second is more important to the question. IMHO, you should include enough definitions so the reader can understand most of the paper without external sources, but not too much. You cannot waste space with derivations that are not your original work (unless you are writing a textbook). Explain the very basic, go straight to the end results, provide the references for further information.
Keep the focus on your contribution and make sure that it is very clear to the reader what is your contribution and what is not.

I forgot to say, it also depends on the length of the article. If it is a short article, I often just give the reference and nothing else.

If you refer to theory as derivation, then it is fine to refer to older/relative publications and only add the equations (in the manuscript) you have derived or those that are not included in previous studies. You do not have to derive/write every single equation! If the derivation is way too long, you can add the complete derivation (if needed?!) in an appendix. Or even, write two papers! One on the derivation, approach or theory itself and one on the application of such approach.
If you refer to derivation as solved examples, then you can always add a complete example in the appendix. The length of such appendix will largely depend on the journal's rules.


text:
Should I ask for a submitted recommendation letter to be retracted in order to submit another, stronger recommendation?
I am currently applying for a Ph.D. in Physics in the US. One of my recommenders has already submitted a letter to the schools I'm applying to, but I was advised by another faculty member that I should have gotten a letter from a different professor I worked with since the submitted one wouldn't be as strong. The latter professor would most likely write a stronger recommendation.
All of the programs I'm applying for require three letters, and most allow for four; would simply adding the extra recommender be sufficient or should I contact the school to remove the weaker letter entirely if possible? In other words, would having it there bring down my application if there is a stronger one I could replace it with or would it reasonable to assume that reviewers would consider all four and think of the weaker one as extraneous (since I cannot define a ranked order)?

You can't "retract" a letter.  This isn't done, and I think it would look weird and somewhat suspicious.  The committee might be inclined to read that letter more closely in case it contains something damaging that you were trying to conceal.  At the very least, it seems distasteful to be "gaming" your professors' supposedly well-considered evaluations in this way.
You certainly can have this other professor submit their letter in addition to the others.  For those schools that specify three letters, it will be up to the committee whether they read all four, or choose three in some arbitrary way.  I suspect that if three letters suggest you're a viable candidate, the committee will be willing to look at the fourth.

Could having four letters make the committee believe that I'm trying to make up for weaker parts of my application?

@SqueamishLizard: That seems unlikely.  Sheer number of letters doesn't particularly strengthen an application, anyway; what matters is the overall impression given by those letters collectively.

@SqueamishLizard I think the schools put a maximum limit on the number of letters b/c otherwise some candidates would attempt to snowstorm the admissions committee.  I think the danger is that if you send more than the limit, the committee will not feel obligated to read beyond the limit and they may choose the weaker letters.  But you should be fine to go to the limit.

No don’t do that. No better way to get everyone to read that exact letter out of curiosity. Plus you have no evidence it is any better or worse than any others.

There is an option if you have not submitted your application yet and most of your LOR writers have not submitted their letters: delete your existing application, make a new one and ask for letters of recommendation again. This time, do not ask for the LOR from the professor in question.

You can always ask if you can replace a reference letter or add a fourth reference letter. As long as it does not seem from your request that you are trying to hide something or cheat the process, you should be fine. Everybody knows that applicants generally try to submit strong reference letters if they can, so there is nothing wrong if you want to replace a weaker reference letter with a stronger one.

The writer of a letter should be able to retract if they discover something about you they don’t like.
You should be able to retract a letter if you discover that the author has credited you with accomplishments you know are not true.
But I say “should” for both because many things could interfere.

While this is certainly true, it seems like an answer to a different question; this one seems more focused on "strategy" than hiding/revealing malfeasance.


text:
Can I do bachelor’s, master’s and PhD at different universities?
Is it possible that I do undergraduation and post graduation from a university and Ph.D from other university?

yes it is possible

When you say "post graduation" do you mean a Masters degree? If so, yes. However, if you mean "can I do my postgraduate PhD studies at one university and get a PhD awarded by a different university" the answer is usually no.

https://academia.stackexchange.com/questions/149157/the-downsides-of-doing-undergraduate-masters-phd-at-the-same-institution

Not only is this possible, I would argue that it is generally advisable.

Yes, you can study for different degrees at different universities.

So I have another question, in my country cosmology is not available to study.. So I want to do Ph.D in cosmology from a university like Princeton, Standford etc, .. May you please tell me how can I achieve it?

@SawayamJha There's no need to go to Princeton or Stanford to study cosmology. Those universities are extremely competitive and you can get just as good an education at somewhere less well-known. For example, I did my PhD at the University of Portsmouth in the UK. I would guess that the uni is not at all famous globally, but the cosmology department is very well regarded. You need to look beyond the "brand name" universities. Then, you need to study hard, maintain good grades, get some research experience and apply to lots of places.

@SawayamJha this comment box is not the place for a long explanation but if you want more cosmology-specific advice, you are welcome to contact me directly (you can find my email address online easily enough).

Thanks alot for your kind support. I am sending you an email.

In the US, at least, it is very common to study at two or three universities on the way to a doctorate. Two is more common than three. Many undergraduate institutions in US don't have graduate programs or have only limited offerings. Some universities encourage their undergraduates to move on to another university just to get a variety of experience.
Again, in the US, one normally moves from undergraduate to doctoral study immediately. A masters degree might be earned along the way, but isn't always necessary. In other parts of the world a masters may be required to apply for doctoral studies. But changing institutions after each major milestone is permitted and common, though not universal.
If a student has worked very hard in a subfield and has worked with most of the faculty in that specialty, then the ability to learn from others, with different ideas, can be a plus. It can also be a plus to keep contact with the professors as you move on.

So I have another question, in my country cosmology is not available to study.. So I want to do Ph.D in cosmology from a university like Princeton, Standford etc, .. May you please tell me how can I achieve it?

Do they offer Ph.D degree if we have good research experience and good Graduation score?

The only way is to apply to an appropriate program. But applying to only the very top few universities is unlikely to result in success. There is a lot of competition. make a wider search if you want to get in somewhere. And "cosmology" can either imply a subfield of philosophy or of physics. They are very different.

Subfield of Physics ofcourse.... Like Stephen Hawking..... So okay, I should broaden my university interest... So on what basis I will get scholarship for my Ph.D from any university?

Scholarships in US are pretty rare. TA positions are the usual means of funding with some RAs available also in some places. But a TA or RA comes with both tuition forgiveness and a living (if minimal) stipend.

Speaking from the perspective of an American, it is certainly possible to obtain a bachelors degree at one institution, a masters at another, and a phd at a third, with all degrees being in the same field (or not).  Changing institutions between undergraduate and graduate work is quite common in the US.  I would even go so far as to say that it is preferable to complete one's graduate work at an institution different from one's bachelors institution.

Many colleges in the US do not offer any graduate degrees, and many of those institutions offer only masters degrees and not doctorates.  For example, most small, private liberal arts colleges in the US don't have any kind of graduate programs, and one of the largest public university systems in the country (the California State University system) does not offer doctoral programs (or, at least, there are only a very small number of doctorates available through the CSU system).  A student who completes work at any of these kinds of institutions would be required to go somewhere else for a phd.

Doctoral programs are extremely specialized.  To embark on a doctorate is to devote 5–10 years of your life exploring a tiny niche of human knowledge (this is very nicely illustrated here).  You want to make sure that you and your intended program are a good fit.  Do your research interests align with the institution?  Is there some faculty with whom you can get along?  How's the climate? and so on.  While students might find a faculty member at their undergraduate institution who is both a good mentor and studying something of interest to the student, it is more likely that you will find a good match if you cast a wider net.  Thus it makes sense for most people to go somewhere else after finishing a bachelors (or masters).

Admissions and funding can also play a role.  Any given phd program is only going to have a limited number of slots.  If you are close with a particular faculty member who wants to be your advisor, that faculty may lobby the admissions committee on your behalf, but even this is no guarantee of admission.  And even if you are admitted, there is no guarantee that the department will be able to support you—it is very hard to go to an institution where you are not admitted, or cannot afford a roof and three squares.

From a pragmatic point of view, moving from one institution to another exposes the student to a larger number of instructors, mentors, and colleagues.  This broadens the social network of the student, and makes it more likely that they will be able to find work in the future.  Faculty can both help a student locate promising positions, and provide recommendations for that student.  Fellow students may be able to open doors in the long run (e.g. a buddy from your undergraduate institution might end up in a position to offer you a job several years later, or to collaborate on a project).  The more connections you have, the easier it is to find work and research collaborators.  Thus it is beneficial (in my opinion) for students to leave their undergraduate institutions in order to pursue graduate work.

Finally, many institutions are understandably reticent to accept their own students into doctoral programs (or to offer post-doc positions to their own doctoral graduates, or to offer tenure track positions to their own graduates).  One of the major goals of the academy is to broaden the scope of human knowledge.  To do this, it is important to communicate widely with other scholars from other places.  Forcing students out of the nest is a way of spreading institutional knowledge to other places, whereas offering positions to one's own graduates can seem a little incestuous.  It is hard to explore the fringes of knowledge from an echo chamber.

So, again, it is not only possible to attend different undergraduate and graduate institutions, it is quite common in the US, and even (I would argue) advisable to do so.


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Should I include reference section on a conference poster?
I believe that including references is important, especially for a chemistry conference poster. However, I have more than two dozens of citations so it is way too lengthy.
Should I still include the reference section or should I simply explain when asked?

Biologist here.
I tend to be more careful to cite methodology on a poster rather than things that belong in an introduction or discussion section, and especially anything derived directly from a particular paper, such as an equation that is on the poster.
Sometimes there is a particular key reference - either a review or highly relevant original paper - to cite for background. Otherwise, if you find yourself citing a lot of things you probably have too much text on the poster.
(to be clear: if it needs to be cited, it should be cited; it just turns out that the type of content that needs to be cited should be at a minimum on a poster)

"it just turns out that the type of content that needs to be cited should be at a minimum on a poster" - yes, exactly.

Of course you should have references.  (Unless chemistry is really different from other disciplines.)  But it is probably acceptable to make it a pretty short section, and perhaps refer to another document if asked for more details.
In particular, are there 2-3 most important references you could cite in "short format" with "et al." to make them short enough to not distract?  That might be a good middle ground.  Alternately, you could do inline citations for the most important ones, with or without footnotes.

(But as always, different disciplines have different standards, so you might want to double check with a few other chemists with a lot of experience presenting posters in the event none of them post an answer here.)

I'm not in chemistry, but if I saw 5 citations on a poster that would seem too much

CS/AI: I absolutely don’t cite anything beyond the bare minimum and place citations in tiny font at the bottom. The point of the poster is to get people to read your paper. They need to get the TL;DR version of it on the way to get tea and cookies, and your poster needs to be more interesting than the robocup tournament. Put the main message in a few sentences, highlight the most interesting things in bold colors and large fonts (think accident lawyer billboards). If anyone asks you about references, give them a copy of the paper (print out a few copies to hand out on the spot).

Just as a commentary on the heterogeneity of academia, this wouldn't work in other fields, as posters are usually done on new or in-progress findings well before a paper is published.


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Can I use open-source code for a simulation for my research?
I am working on a paper and I found open-source code that I could use for running a simulation. Should I write my own code for that simulation? Will it be enough if I refer to the code in my citations/references section?

How is it licensed?

In particular, does it use a "viral" licence like GPL that would impact what you can do with your own code if you use it?

BTW Just be aware code on github with no explicit license isn't open source - https://opensource.stackexchange.com/questions/1720/what-can-i-assume-if-a-publicly-published-project-has-no-license

@DavidWayerworth On the other hand, using a copyrighted work for research purposes constitutes Fair Use, though claiming it as your own work would be plagiarism.

Yes, open-source code can be used for research if it is cited everywhere you use results from it. You may first like to verify that the code is indeed open-source by verifying that the license is one of these: https://opensource.org/licenses
This should be listed clearly on the website/repository/license/readme file. If this is not available, try contacting the author to verify that it is indeed open source.
Certain licenses additionally allow you to freely modify the code for your specific purpose; the link above contains details about this.

Open source software is used everywhere. For all example, nearly all of High Performance Computing, and the entire field of Computational Science and Engineering (CS&E) works with open source software, and does so very successfully. Furthermore, these packages are often at least as good or better than what commercial packages can offer. Many of these packages have been used in hundreds or thousands of papers. A few examples of packages just in my field that have very widely been used is here, here, and here.
So yes, you can use open source software. In particular, there is no reason to believe that open source software just by virtue of being open source is of worse quality.
In practice, nearly every software package has one or more paper that describe its inner workings. The right thing to do when you use a package is to cite these papers.

You'll need to conduct due diligence to ensure that the code generating the simulation is accurate and that you fully understand how it is working; otherwise other peoples' mistakes become your own.  Personally, I would take that code and deconstruct it to the point I understand how it works, then re-write it on my own.  That said, nothing prevents you from using open source code, just be sure to document accurately and be confident it is doing what you anticipate!

… which is the same as for closed-source software.

i have found incorrect computations in closed-source software.  onus remains on you regardless of the source

Exactly. I just want to avoid the impression that open-source software is special here.

I might not go that far - depending on the problem a simple black-box validation might be reasonable. But certainly you do need to take, and document, some way of ensuring that the code does the right thing.

There is so much excellent open source software out into which people have put tens of man years of work there that it's ludicrous to suggest that for the bigger packages, rewriting is even possible. Let alone for a single person. It's also silly to suggest that that might improve the quality: You'd surely introduce more bugs just because you don't have the resources to write test suites with thousands of tests. Evidence from software design research suggests that the big open source packages are of better quality than nearly all commercial software.


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How to verify a proof prior to peer review in mathematics
I think I have found that squared magic squares cannot be constructed which is an unsolved problem.
I have searched for months for any mistakes and I could not find any. I have sent this to Mr.Boyer who hosts the page yet I ended up not being able to regain contact with him after he stated he found an error in my paper. However, as I think I have been aware of the error (if clarification is needed, I will do so) and have resolved the error later in the paper, I doubt that it was, in fact, an error. However, I have no method of confirming this except by myself.
Hence, I think that the only method I have left is submitting to a peer-reviewed journal. Yet is there a method of verifying the proof prior to this? I have heard that the procedure of peer review may take years.
I am only a high-school student thus I do not have any connections to mathematicians.

Ask your teachers. They know you well, probably know math better than you, and are your closest connection to the academic world. That means they're the most likely to be willing to look through your proof, capable of finding an error you didn't spot, and if they can't find anything wrong, they'll know who to approach next (e.g. their professors from when they did their degrees).
You could conceivably approach math professors at your local university directly, but you risk coming across as a crank and being ignored. If you're able to get your math teacher to vouch for your proof, that would lend strength to your claim.

Thank you! I already asked math teachers and they said they could not find any mistakes. As for people to reach next, I could not get anyone from them. I'll follow your advise and ask my teachers to vouch for me. Thank you!


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Doing a PhD in sociology as a computer scientist – is it possible?
I am a PhD student in CS. I am also interested in the humanities and I would like to pursue a PhD in sociology. I know the traditional way is to repeat the cycle starting from undergrad studies but that would require a lot of time (which I do not have, given that I have other concerns).
Is this possible (ideally online)?

Have you talked to a supervisor to see if they are interested?

@SolarMike I couldn't find a program available in my country in that rergard! so I am just looking for any international program that could help me get what i want in less time. I did a lot of research but to no avail!

Why do you need a PhD degree in the humanities? An online program (if you could find one) would be of no use professionally (in any profession). Just study as much sociology as you like. Online courses are a possibility.

@Ethan Bolker "of no use (in any profession)". You can't be serious. Unless you think that secondary education and librarianship don't count as professions, to mention two obvious ones to start. On another note, sociology is not in the humanities. It's a social science.

Meta discussion pertaining to this. (CC@EthanBolker)

@Philly: This question was closed because it was what we consider a shopping question. However, the main answer did not focus on the shopping part, so I removed, generalised it, and reopened.

Why don't you get involved with research that intersects social science and computer science?

No, there's no legitimate way for you to get an online PhD in sociology (which is a social science, not humanities, but eh, lables are silly anyway), at least not with the profile you describe. You are also extremely unlikely to be considered for a normal sociology PhD programme. Speaking as a member of a sociology department, you quite simply do not have the background in the method and theory of the discipline needed to produce PhD level work. Just like I don't have the tools to suddenly do a CS PhD, you don't have the tools to do a sociology one. Successfully applying sociological theory and producing competent, critical analysis, not to mention data collection itself, is actually extremely difficult. You can't just casually pick it up. It recently took me 8 months and 40 pages of evidence just to get ethical approval to start a sociology project...
What you can consider is a taught one year masters programme in sociology, either in the UK or elsewhere. Some of them are available online and some are willing to admit students without a sociology undergraduate degree if they can articulate why they are making a disciplinary shift. Mine wouldn't accept you with an undergrad in CS without a strong focus of that CS research being sociological in nature, but others might.

It sounds like what you might be looking for is a PhD in the field of computational social science, which can best be described as using computing modeling and analysis to address social science questions. Unfortunately, the field is fairly new so there simply aren't a lot of PhD programs in it. The major reputable one that I'm familiar with is at George Mason (PhD in Computational Social Science) and UC Davis has a Designated Emphasis in Computational Social Science which seems to require admission it an allied PhD program (e.g., social science, economics, computer science, etc.). There are also some interdisplinary PhD programs out there that have extremely flexible requirements, but then you need to do extra work to have a committee and publications that establish yourself as a scholar.
Online PhDs are extremely rare, although it seems to be more common for PhD candidates to transition to remote study once all of the on campus requirements have been met (i.e., coursework, qualifying examinations, etc.).

I'm a sociology major, and I'll be beginning a sociology PHD in 2022. Most sociology departments prefer if you did a BA in sociology, but any Humanities degree would get you entry. If you apply with a STEM degree, then you can still get into a program — you just need to show that you have appropriate background knowledge in the area. I would advise you just buy books on social issues. Buy books on race discrimination, especially anti-black discrimination, since due to the recent BLM protests this is a hot topic. Also, read books on gender discrimination and read books on classism. If you have the time, write blogs with mostly academic references on sociological issues such classism, racism or gender. Since you're a CS major, writing about biases arising in A.I. machine learning endeavors would 100% get you entry, since that is a hot topic at the moment.

Made some edits to improve clarity. For example, I had to re-read the sentence "If you have the time right blogs with mostly academic references ..." because I thought this was suggesting the OP read the appropriate blogs, especially those with mostly academic references, and then the sentence ended in a way that didn't make sense until I started reading it over again, this time assuming "right" was intended to be "write".

I doubt this will suffice.

I know the professors in the sociology department relatively well for a student. They all told the  same thing depends on what university you go to


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How many papers per week does a professor typically read?
I'm curious as to how many papers one would need to read per week, in order to keep up with the latest research in a particular field. For example, how many papers on average would a typical tenured professor read in a week?
I am aware the answer might vary a lot between different fields, so perhaps answers could give a range or try to break it down by disciplines.

It really depends too much on the field: to give an example at the lower end, in my field, relatively few papers are published every year and I certainly read less than one new paper per week.Note also that, in many cases, if you're experienced enough you really don't need to read an entire paper to understand it, but you can go directly to the salient pieces and skip the rest: this means that when I need it (e.g. because I start working on a new experiment), I can read 10-20 papers in a day.

I'll expand on the comment by @MassimoOrtolano - the pace of reading papers is not constant. One might glance at the latest journals and if something looks interesting you will glance it over and put it in the 'to be read sometime' pile. If you are deep in an experiment, you might have not time to read anything (or lots of time if babysitting a long boring data collection run). And then there are weeks where you are just busy with other random stuff and nothing useful gets done.

But if you are planning an experiment or data collection, then you might be reading all the papers you can get hold of to see what has already been covered or just touched on...

The strong tendency is to specialize to the point that there are only a few deeply relevant papers every few months, and you may have heard of them or know involved people already before the paper even came out. In conference cultures, you then go to a few a year, look over the program, attend a few talks, and then pick out a few relevant papers if there are any. Depth of reading is...not always extensive. But I also know some professors who read at least 1 new paper every day, 5-7 days a week, no matter what and even if there aren't that many closely related ones, just because.

To me, the only sensible answer to this is "as many as required for the current task". This will vary from zero to some modest number, and won't even be an integer, unless you count skimming or reading the abstract as "reading". If you are creating a new grad course then it might be large. If you are near retirement with few responsibilities it might also be large. If you have a heavy teaching load it is probably small. "Whatever it takes."

There is no typical, even within a field, because different professors tend to find different "niches" in how they relate to the literature, and the depth with which they read papers.
I have known some professors who establish themselves as the "scholars" of a department and deeply read dozens of papers per week.  I have known other professors who rarely read anything, because they focus on construction of new gizmos instead, pick up their knowledge of the field through conferences, and make their collaborators and postdocs fill in the "related work" section of their papers.
Likewise, it's a mistake to think that "read a paper" has a single definition. At one extreme, sometimes one wants to spend a great deal of time working through the contents of a paper. At the other extreme there are times one just wants to check the "headline" conclusion and see if it can help you with your problem or not.
Bottom line: there is no good answer to your question besides "it depends".