text:
Should I drop out of grad school?
I have just completed my first year of grad school. I am currently in a enormous amount of debt from undergrad. I want to continue but I am afraid of accumulating too much debt! Yes I did know this going in about the increasing of debt. I have exhausted many options as far as looking around for financial resources. I am interested in the healthcare field.

Did this not occur to you before starting grad school?

Can you expect a better salary with a post-graduate degree? Can you get any funding?

Perhaps, if you rephrase this question, it might be on topic at personal finance & money stack exchange. But you should ask in their chat or on their meta first.

No you should not drop out of grad school. The words "grad school dropout" doesn't fare well on any freshman CV. But, it must also be noted that after the initial slog, it also doesn't matter as much.
I have been told this statement many number of times by professionals who are at much better positions than me (a newly graduated PhD) in terms of both earnings and academic positions.
There is a real dearth of hard-working professionals in every profession.
I know it comes across as a bit philosophical, but I take it as a ground reality after having observed the same. Notice that I do not say talent, because talent seldom makes a person successful, hard work on the other hand almost always does. Also, a freshman with a degree always has more value than one with none.
Having said that, If you are worried about covering your debt after school, you should ponder these thoughts

Are you in a graduate course which makes for high employability?
If not, can you transfer to a course which offers high employability? CS and Informatics, are some examples of fields that offer very high employability.
Can you learn skills or enroll in courses which may increase your value in the job market?
Maybe try enrolling in one of the many free courses available online through portals like Udemy and Coursera to increase your value?

Invest as much time as possible towards learning as much as you can with employability being the focus. Furthermore, only learn that which you would love to do yourself because to get ahead in any field you need mostly determination and perseverance. You can only muster these two things if you love what you do. I do not make any mention of money here, because money generally follows people who get ahead in their respective fields.

I don't think there is nearly enough information for such a strong response. There are in fact plenty of fields where there are way more PhD holders than jobs. OP could get themselves into so much debt that they will never recover. The first three bullet points are definitely things that OP should consider; the key point is to have a firm plan for what happens after graduation...time passes faster than you expect, and "I'll become a professor" is not a realistic plan for most applicants.


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How to find gaps in mathematics/theoretical physics/mathematical physics ? How to proceed after that? (Undergraduate research and Publications)
How to find gaps in mathematics/theoretical physics/mathematical physics? I am interested to do independent research in physics though a purely mathematical/theoretical (pen and paper) approach with or without some programming.
How to proceed further (with which methods) after finding a gap?(Undergraduate research and Publication)

It seems that you ran into the problem independent researchers have: you don't have colleagues to spar with or mentors who can help you with those steps.

Generic answer is to either get a PhD, or find someone in research to mentor you in how to do research (generally done by getting a PhD).

Could you narrow the question? As it is, the question is basically "how do I do research?", which is far too broad for us to cover here (if we could answer it in a couple of paragraphs, there would be no need for PhD programs).

@cag51 Actually I was asking about undergraduate research and publications.

@SayantikaBose That doesn't really narrow it down much with respect to the questions you've posed, research is research whether you're an undergraduate or not. Step 0, though, is to find a research advisor because these are all questions to ask your research advisor, and not limit yourself to this idea of "independent research"; having these questions is exactly the problem with trying to do this sort of thing independently, it's like saying you'd like to fly without wings and your only remaining question is how to go up and not down - that's the entire problem in the first place!

@BryanKrause Thank you very much sir!!

You can only be an independent researcher, i.e., a researcher without an affiliation with a research institution, if you are already a researcher. For this you should enrol in a PhD program to be trained as such. After that, you will be acquainted with the basic tools and methodologies to pursue new research directions and find the knowledge gaps to be filled. If you want to become a researcher independently, then you have a different question.
Even as independent researcher, I believe you should be part of the community. Getting inspired by others plays a big role on creativity and learning. It helps you look at problems from different perspectives and understand where you can expand the current knowledge.

You have asked two questions - how to find gaps and what to do when you find one.
If you know that a gap you have found is real (not just something known that you do not happen to know) and you have found a way to fill it then you write it up and submit it to an appropriate journal.
That said, it is unlikely that you can do "independent research in physics" without connections to current practitioners to share ideas with.

The sane answer is as already suggested get a PhD in the subject you want to do research in. Doing useful research is really hard. (Getting a job in doing it is even harder!).
But I know someone who took an unusual route into a PhD (at a prestigious institute) by first performing impressive original research that was a direct follow up of a well-known paper. The best way to do useful research and to be recognized for this despite having affiliations/degrees to vouch for you at least a little bit is to solve known open problems (preferably one where you have some hope of succeeding). These can often be found in conclusion/discussion sections of recent papers.
Note that you will likely be trying to solve problems that people with a much more appropriate background did not find easy to solve (or they would have done so). So this will probably be very very hard. (And you will probably at first not even understand any of the papers let alone the open problem and a good strategy for solving them.)

The story of the "independent researcher" I knew did not end that well. Their unexpected impressive result was not followed by more such results and they left their PhD without completing it or publishing much more additional original research.

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sort: votes


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What are red flags when it comes to choosing a PI?
I just finished my first postdoc and I had a terrible experience with my PI. Unfortunately, he is known in the field and I worked with him for two years and half. I've been to hell and back during this time. I don't want to repeat this experience ever again. He is not a bad boss. He is the enemy who tries to ruin everything, literally he was the only obstacle that I was facing during my postdoc. I can't count on his recommendation letter at all.
I worked with two other PIs during my PhD and I don't like to work with them again. They only think about how to take advantage of me without offering anything. It seems to me that this postdoc-PI relationship is very abusive in its own nature.
My experience with PIs so far hasn't been well. However, people say there are good PIs and I just were unlucky.
I talked to a new PI as a potential PI for my future postdoc. I thought he is nice but I realize that he is not easy to handle. He is not willing to listen to me and he only cares about his goals and his work which seems like a red flag to me.
Is this common or I'm unlucky in finding good PIs? Where should I draw the line while choosing a new supervisor? How much of abuse is normal in academia?
Edit: It seems that my question is not clear. By abusive behavior, I meant: lying, fabricating rules, stealing credit, humiliating in public, blame shifting for what is actually PI's fault, yelling, lack of open communication.
So the main question is: What are red flags when it comes to choosing a PI? What defines a toxic work environment?

There are (at least) two kinds of post docs. One in which the individual is very independent to follow their own course, and one in which you work for a "boss": the PI. This varies by field. I assume you are in a field with the latter expectation but you can't accept that. In such a field, I find little objectionable about the PI behavior you describe. You ain't the boss in such a situation.

Added after your edit: And were your previous PI experiences like that also? Lying, yelling, etc.

I don't think this post contains a directly answerable question. A good PI fit for one person may not be a good fit for another; there is no single line. What is an "average nice PI", anyways? What should a non-tautological answer to the question "what does an average nice PI look like" be?

My last postdoc was with a boss who lied about rules to prevent me from doing things. I have to check rules with a third party all the time. I even tried to submit a complain. The other postdoc in our group left in the middle of his contract. He is known for being a problematic PI. Thank you for the answer. I think I had incompetent  PhD PI and I learnt to be independent and it probably is inconsistent with my last workplace.

If a PI is known for being a problematic PI, don't work for them. Very very few people would lie about rules to prevent someone who works under them from doing things. There's just no logic to that: why would you hire someone that you want to impede? Instead, there are likely other explanations for the behavior you describe. Some might be selfish, some might be benign, but it's pretty hard for us to tell what's going on except to notice that you're upset.

When all three PIs you've had were "abusive" and so is the fourth, one must start to think about what connects them all ...

@BryanKrause We probably assume the OP is in the US or a country where there are controls about PI abuse. Maybe, however, that is not the case. In which case, OP probably needs to move to a country where the PI does not have unlimited power.

It is in Europe and PIs usually have unlimited power due to lack of systematic way to address problems. My PI lied and I double checked it with secretary to make sure he lied. Then I went to report it. Ombudsperson told me it is common in academia. Let it go.

If you find yourself repeatedly the victim of "bad" PIs perhaps you should also look at yourself. What is it that you are expecting that is not being met? Why was your prior advisor your enemy?
"unfortunately, he is known in the field" I should hope so otherwise why would they get funding for a postdoc, and why would anyone want to waste a postdoc working with them otherwise?
Why does your new potential PI need to be "easy to handle"? What does that mean? Why are you trying to handle your advisor? What is wrong with being goal and work driven within the context of explaining ones work to a potential postdoc? That is the role of a PI running a research enterprise. What do you want them to listen to you about? Have you advocated for yourself or are you expecting someone else to guess what your needs are?
"How much of abuse is normal in academia?" Depends what you describe as abuse. There is actual abuse which is wrong, and there is incompatible personalities and expectations. The latter doesn't feel great but is not abuse.

Thank you for your time but it wasn't answer to my question. It was just critisizing me. My question was how to draw the line with a new PI. Also, it is obvious what abusive behavior means. I want an enviorent that foster a postdoc growth, give them opportunities and help them advance their career. Not doing labor work and others get credit for it.

@Apostdoc This response was not a criticism. If you are unhappy with 4 PIs by now (I counted the ones you criticized), the question is really who needs to adjust their expectation. There is the occasional nasty PI. But if you encounter more then 2-3 in a row, then you may be doing something wrong, and that's what you have to find out - if you want to fix the issue, that is. "He is not willing to listen to me and he only cares about his goals and his work which seems like a red flag to me" - sorry, but that's perfectly legitimate behaviour. Of course the PI cares about his goals and work, as...

@Apostdoc .. as you do about yours. So, you need to find a PI whose goals are aligned with yours, especially if you are very specific about what you want to do. Note that if the PI gets funding from external funders, they may actually not have that much leeway anyway, as they have to fulfil their contract with the funder. So, you need to see, where are you willing to compromise, where is a red line you want to protect? You cannot have it all, unless you are absolutely brilliant, and even then it is difficult. Good luck.

@Apostdoc: imagine that someone asked you: “I’m trying to dig a hole, but I bought four different shovels and all four shattered within five minutes. Is this normal for shovels? How do I draw the line when I buy my fifth shovel?” Your question may be about shovels, but the answers will rightly focus on your unusually high shovel attrition rate. If you don’t want this, you might edit your post to better describe the specific problems you faced (not all the details, but more concrete than “he is the enemy” and “I went to hell and back.”)

I edited my question in order to clarify it. Also, I haven't got the answer yet. Thank you for your time. PS: It is very common to blame victims. People learnt not to blame rape victim by saying you dressed inappropriately or you were drunk but they haven't learned not to blame other types of victim. I understand the meaning of abuse, victim and a PI perspective. I hope I get a right answer this time.

@Apostdoc I don't think you'll be gaining yourself much support by equating your situation to rape.

I answer a lot of questions here and think about a lot of others, including this one. But I can't come up with a better answer than this one. I could only add: evaluate the likely compatibility before you accept any job.

I was not looking for support. I was looking for answer. However I think I got enough of answer here

The only answer is you get your own fellowship of postdoc, then you can control everything. You worked with 3 PIs and all of them are 'bad' in your mind, including one that is very famous. Did you consider that you are the one that is difficult to work with?

Thank you for your time. I consider that. I'm not the problem. I just didn't see red flags. So I wanted to know what are red flags when it comes to choose a PI. Abusive behaviors are well defined. I don't think it is my fault when my PI lies. How can it be my fault? There are many abusive PIs in academia. I just wanted to know how to spot them. Instead I got lots of criticism which is very disappointing.

It is because based on your question and response, most people here think that you have unrealistic expectations to advisor. Why don't you try to answer the question 'What is wrong with being goal and work driven within the context of explaining ones work to a potential postdoc?'

@Apostdoc It is not a question that there are abusive PIs. And they may lie, too. The question, however, indicates that you have a series of extraordinarily unlucky choices, which means that you somehow end up choosing the wrong ones. More surprising is that you didn't like them setting goals and expectations for you. Was that not agreed beforehand? Did they bait and switch you? I think this needs to be clarified in the question before we can help you. And yes, we would like to help you. One other thing may be the area you work in. Some communities are toxic overall.

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Posting commentary papers to preprint repositories
Short version:
We noticed a problematic but influential preprint, wrote a commentary paper to criticize and rebut it, but were not able to post the comment to any public preprint repository.  In this situation, what can I do against bad science?
Note: Some focus on our wording being too harsh, even accuse us of "personal attacks".  In fact, we enlisted the help of many proofreaders to ensure that we did nothing like these, especially when the situation was so politically sensitive.  Most feedback says that we were too friendly.
Long version:
Background
On 8 Jun 2020, a preprint is posted on Havard institutional repository "DASH".  It suggests, based on satellite imagery of hospital parking lots and internet search trends, that COVID-19 outbreak started in Wuhan, China in August 2019.  The officially documented first case was on 1 Dec 2019.
This study attracted significant media coverage and political attention (cited by Trump).  But from a scientific point of view, its method and argument is really ridiculous.  It is criticized by many, but mostly on social media.
We decide to write a commentary paper to criticize the study.  To explain our concern and motivation, here is a summary of the conversation between me (A) and a colleague (B) when they tell me about this study:

A: So did they submit the paper to a journal? It will be rejected.
B: They don't need to if the purpose is media attention.
A: But we do have things like PubPeer that allow people to
criticize anyway.
(checking PubPeer)
A: OK ... DASH does not assign DOI, so the paper is not indexed by
PubPeer ...
B: Yeah, that's how they announce shitty studies now.  Post online,
news release, then who cares about publication.
A: Not necessarily.  We can always write a manuscript criticizing it,
and post it to arXiv.
B: Can we?  Let's do it.

So I organized a team and drafted a paper.  We fact-checked many information, rerun the statistical analysis to spot the main fallacy, and asked many people (academics and journalists) for proofreading.  We identified many problems, including statistical fallacies and cherry-pickings.
Our attempts
Our original plan: posting our commentary to arXiv so that everyone sees it.  Then we wait for the original paper.  If they get published in a journal (to my surprise), we will submit our comment to the same journal.
As a mathematician by training, I'm a big fan of preprints, and a heavy user of arXiv.  I usually post to maths category, occasionally to condensed matter physics category.  I know that arXiv accepts commentary papers like ours.  Since we are criticizing a paper about "digital epidemiology", I checked related arXiv preprints, and determined that "stat.AP" is the most suitable category.
But to my surprise, our submission is put on hold by arXiv.  Then the major category is changed to "None".  So I wrote to arXiv moderators to explain our choice of category.  Then I get the following "rejection letter":

Our moderators have determined that your work would benefit from additional review and revision that is outside of the services we provide. Our volunteer moderators are not referees and do not provide reviews or other detailed feedback for improvement of submissions with their decisions.
As a result, we have removed your submission. Please instead send your paper to a conventional journal for the necessary reviews.
Please do not resubmit this paper without seeking permission and obtaining a positive response. Resubmission of removed papers may result in loss of submission privileges. We will reconsider this decision if your work is published or accepted with a resolving DOI (Digital Object Identifier) or link to the journal's website showing the status of the work.

This was very shocking to me, but I will refrain from commenting on this decision.
We then think about medRxiv and bioRxiv, but they made clear in their policies that they do not accept commentary papers.
We ended up posting the commentary on my personal academic website.
My question
Announcing scientific studies by press release is becoming a trend now.
Imagine someone, out of malicious motivation, decided to post misinformation in the disguise of an "academic paper".  To avoid peer review, they do not plan to submit the "paper" to any journal.  To avoid PubPeer, they intentionally avoided arXiv, medRxiv, or anything that assigns a DOI.  Then they promote their "paper" in media, and gained significant attention.  They might receive critics, but only on social media.  The critics are mixed up with other misinformations and conspiracies, and will not be taken serious.
In this situation, what can I do as a concerned peer?  If I made effort to write a detailed critical analysis, how is that helping if no preprint repositories accept it?

Did you consider the possibility that the original authors tried to submit to arXiv or similar, but were rejected on the same grounds as you? That simple turn would explain the full story, without assuming any intentional dishonesty by the original authors.

@nabla Yes we considered this possibility, but did not take it serious.  They might have been rejected, they might not, but the authors did have an media campaign for their "study".

You stated that you "wrote a commentary paper to criticize and rebut it" in order to do something about "bad science".
However, your preprint does much more that that: it does not solely focus on the content of the manuscript, but it attacks the authors!
The most striking instance of that is found in your Section 6:

The authors do not show an adequate statistical literacy.  They
misused statistical tools on insufficient data and misinterpreted the
result, leading to premature claims that only bring media popularity
but harm academic reputation.  It is a pity that a field at such
an early stage already gets plagued by statistical fallacies.The
cherry-picking of search keywords for internet trends is a very
questionable research practice [21]. We understand that digital
epidemiology suffers from insufficient data, as the authors admit in
the manuscript.  This does not justify the abuse of statistical
methods and the suppression of evidence.  In the case of insufficient
evidence, the only right thing is to refrain from making any claim and
simply stop writing a paper.

Personal attacks on authors instead addressing the shortcomings of a manuscript is widely seen as bad science. This could have contributed the rejection by arXiv.

Here is Wikipedia page about "no personal attack".  Can you tell me which category do our "personal attacks" fell in? https://en.wikipedia.org/wiki/Wikipedia%3ANo_personal_attacks

The first and last sentence of the quoted paragraph above essentially say: "stop wasting everyone's time and go back to school you idiots."
This is just the most striking paragraph, similar innuendo is spread throughout the manuscript.
E.g. "misuse of statistical tools", alluring to "self-promotion" of the authors, title such as "Internet epidemiology done right", alluding that their paper is a "source of misinformation and conspiracies",  that the authors make "premature claims that harm academic reputation", questioning the "academic integrity", etc.

How would you point out a misuse of statistical tool?  If the authors did not justify something as they should, how would you say it?

"As outlined in section 3, the results of Ref. [3] regarding the observed variances in the performance of underwater basket weavers can be traced back to a monofactorial analysis and an flawed statistical approach. Taking into account the necessary decompression stops during the ascent of the weavers and fitting with a more suitable U-distribution, the observed correlations in the weavers performances and their work schedules can be completely accounted for. "
Does that sound nicer than "the authors cherry pick data and misuse tools that will only harm their reputation"?

Let me be clear, you talked about personal attacks, but in fact, you were saying that we are too straight and harsh, not diplomatic enough.  We are saying "they are wrong" and you suggest something like "their result can be traced back to some faulty practice".  But being straight is not equivalent to personal attack, do you agree?

"You are wrong" when one actually means "the manuscript has flaws" is being not very diplomatic. Writing or alluding that "Chen et al. are illiterate and should stop writing papers and learn statistics, they will only ruin their reputation by self-promoting their misinformation on social media" is a personal attack. If you can't safely convert every instance of "author" or "they" into a "Ref. [1]" in your comment (and maybe that would be a good idea), that particular sentence should probably not appear at all. There is no such thing as "too friendly", your results should speak for themselves.

Let us continue this discussion in chat.

Arxiv normally accepts commentaries. But your commentary is not just a technical criticism of Nsoesie et al. Starting with the abstract, you include non-technical considerations such as "This claim received widespread
media coverage despite the lack of validation from peers.",  "This review serves as a pre-
publication evaluation of the study.", "We also reflect on scientific publishing in a time of public emergency."
This might by why arXiv rejected your commentary. In this case, the solution would be to rewrite it in a technical style, and leave the sociological comments for another venue. (Interviews with the press?)
Also, it would probably not hurt if you framed your commentary less as a denunciation of the errors by Nsoesie et al (since their paper is unpublished, and not even on arXiv), and more as an assertion of your own conclusions regarding the pandemic, even if you only have negative results.


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Pursuing a Masters from a low ranking university? Will it reduce Phd opportunities
I belong to a south asian country. I got BS Electronics Engineering degree from a Leading Government Engineering University of our country almost 10 years ago. Now I am 33 and I am considering to pursue masters in Bio medical Engineering  from a low ranking private university (despite the fact that it is private and low ranking, it is still approved/recognized by Higher education commission of our Country) . I am considering this university because it is near to my job place but if I consider high ranking universities I will have to travel a lot which may not be easily possible keeping in view my current family and job commitments.
So my main question is that if I pursue Masters in Biomedical Engineering  from this low ranking private university, will it reduce my chances of securing Phd scholarship/funding especially when considering Phd in Europe and US? Or does the ranking of university not matter in such a scenario, as it is mainly research and thesis of a Masters that determines chances of securing Phd scholarship/funding?
Update: Please note that I am already currently doing a teaching job for the last 5 years and I am a Lab instructor/teacher in a BS Electrical Engineering program of a good ranking university, but my university doesn't permits you to study for a Masters while you are on the job so I have to consider other universities for Masters.

My close friend is a professor of biomedical engineering / biomedical physics in Boston. His personal position is to ignore college rankings, but to take into account candidates' motivation, knowledge of physics, and the ability to work in a lab. Send me an e-mail, if you wish. I shall direct you to his website, and you will be able to talk to him directly, if you choose to. Such personal contacts are of utmost importance in the search for a grad school. This said, I fully agree with @Spark in that you will have to publish at least one good paper while doing Masters -- and in a good journal.

@Michael_1812thanks for your detailed comment. Please let me know your email id

Please go to my profile here in Stackexchange and click on a link to my personal webpage.

I actually spoke to that friend, and he may have funds to support an MS/PhD student starting January or February. (In many US schools it is possible to hire graduate students in mid-year.) So you may want to write to him.

All things being equal, yes.
If during your masters you manage to publish a breakthrough result in a top journal, do some truly remarkable outreach or teaching work, you will probably improve your chances, but you will need to do something like that to be considered, whereas an applicant from a well-known university would not.
I sat on many admissions committees and we always get a lot more applicants than we can admit. We’re looking for a signal that this person will be able to finish their PhD successfully. If they got in to a prestigious program they send that signal by default. Others need to send it via other means.
If you want to improve your chances, I suggest you try and work with people in universities that you’re targeting for PhD. See if you can collaborate with them so that they want to advise you later on.
One caveat- I’m in computer science, don’t know about other fields.

That being said: wouldn't starting (and I imagine finishing in regular time) a masters at 33 be a significant indicator of motivation?

Of course, but again- if I had to pick between two similar candidates where one came from a top-10 school and another from an unknown university, it’s pretty clear who gets picked. University prestige matters.

Motivation is great, but it’s hardly the only factor. Prestigious universities often offer better education and training, more opportunities to interact with good researchers etc.

Dunno, I did my undergrad in a tiny uni in Spain with no research output and then went to do a PhD to quite a decent uni and my research career is going well. I don't think it's as bad as you make it sound.

I’m glad it worked out for you. I did my PhD in a low ranking university and am now in a top R1 university. The general statistics say this is an exception, not the rule.


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Changing author's affiliation after a paper is submitted
I worked on an article when I was with University X . Now I am with University Y.  I submitted the article in IEEE access with University Y email and affiliation as corresponding author. However, with University X affiliation as corresponding author I would receive some benefits in terms of article processing charges since the University X is in their list. With university Y affiliation I will have to pay the APC from my own pocket. So I want to change my affiliation. If my paper comes with major/minor revision, will I be able to change my university affiliation?

Does this answer your question? Can I change my affiliation after re-submitting the manuscript before acceptance?

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

You can even change your affiliation at the galley stage.

I have edited the question I hope its now more clear

This is no problem.  The only thing you cannot change is the list of authors, and order.   Other than that, affiliation can be updated.  You may need to note that the work was done when you were at your previous institution.

Even the authors can be changed, you will just need to explain why. For example, the revisions might involve running additional experiments with new collaborators, in which case it would be fine to add them to the paper.

@avid in my discipline that's not allowed because there have been cases where authors sell co-authorship to others upon receiving a revision.

Changing authorship depends on the journal and the discipline. Some journals allow, some don't. In any case, the reason should be provided (taking note of the rule/norm of authorship)

yes I worked on the article when I was at my previous institution. Do I need to email the editor for change of affiliation?

@user7341333 no.  There will be opportunities for you to update your affiliation at a later time, e.g., upon receiving a recommendation or if it's already accepted, then you can ask for the change when they show you the galley proof.


text:
Am I likely to struggle in a high-ranked PhD program, if I struggled to get GPA of 3.5 in my master's?
I want to be realistic whether I am a material who can complete PhD at top universities such as Stanford, Princeton, Berkeley or Caltech. Grad school courses were hard. I scored 3.5 GPA in my specialization for MS with thesis. My overall GPA was 3.42.
Whether I will get in these universities or not, that is different question. My concern is: If I get into one of these universities, say because of other achievements like research, LOR, SOP etc., it will be harder to maintain this GPA at these universities. Given the fact that U of Michigan has its Electrical Engineering Grad program is ranked 6th in US.
Any suggestions? Reason I want to apply to these universities is because of my area of research.
Course directly related to my research: I have A-, A.
Closely related to area of research, but in my specialization: I have B+, A-, B+, B.
I do not want to talk lot about my MS thesis, because I want to focus more on rigor of the course and qualifying exam at these universities.

PhD GPA matters basically not at all. Your question shouldn't be about trying to maintain your GPA.

@Azor Ahai : Thanks for your input! I agree, but there is a minimum expectation, and then there is qualifying exam. It is not about minimum number, say 3.4, but more about that course expectation. My doubt is, I may not be top university material. So, I am stuck at this point whether or not I should try to get into these universities. Even if I make it, will I be able to meet the academic requirements.

Don't worry about it, it signifies nothing. The challenge at the PhD level has very little in common with master's level coursework - if you can pass from any reputable institution, you are fine for that. The challenges you face in a PhD is far more about organization, self-management, interpersonal skill (with mentors esp.), mental health, motivation, and perseverance. The meaning of the prior GPA ends upon admission. Don't confuse University brand marketing with rigor or difficulty.

Changing the title to something like "Am I likely to struggle in PhD coursework if I struggled to get GPA of 3.5 in MS?" might help clarify that you aren't asking about admissions. And then someone can convert @BrianH's comment to an answer and you're all set.

I edited your question to move the list of schools to the body because it a) clutters the title and b) makes people think this is a "shopping question." Would you please edit to add what "EE" is? I assume it's electrical engineering, but I can't read your mind.

Michigan's EECS department is basically in the same tier as the others you cited.  If you struggled but succeeded at Michigan, you should probably expect a similar experience at any of those other schools.


text:
Copy pasting definitions and theorems from other papers to my own paper
I am writing a mathematical paper.  Since my English is not perfect, i am borrowing sentences from English-speaking authors. I have some questions about copy and paste from other papers to my paper. As you know, one needs some definitions and theorems from other papers. I cited all of papers that i used either definition or theorems from them.
1)Can i copy and paste the original either theorems or definition from the papers to my paper or i have to change them?i mean writing somehow that is not as same as original one.  Because i have seen English-speaking authors often change original theorem or definition in their papers. On the other hand, i have seen someone does not.
2)As i mentioned, i am borrowing sentences from English-speaking authors. When i look it my introduction, i see this sentence from that paper, that sentence from that paper and ... It makes scene. My supervisor read it and he said it is okay( it is not ambiguous) but i'm scared that referee rejects my paper.

I take a somewhat hard line on this: usually lifting whole sentences from other people's papers is, in my view, plagiarism. Not the worst kind, but plagiarism nonetheless. However, this does not apply to statements of standard definitions (e.g. what it means for a group to be residually finite, etc.) but more to sentences where some opinion or insight is being stated

In particular, I do not think it is appropriate to construct your introduction as a collage of sentences from other people's work. You should try to communicate in your own words what it is that you think your paper is about, and why it might be interesting, not why Professor X thinks it is interesting

(This question, and the answers to it, may also be relevant https://academia.stackexchange.com/questions/20414/ )

One possible concern, as well as the plagiarism, is that if your paper can be described by taking the intro from other's papers then your paper material has already been covered and it does not add much...

Please do not borrow sentences
Instead, borrow sentence structures. If the original sentence is, "Our results also have implications on the study of öhkömönkiäiset.", you might write "Our main result also has implications on öhkömönkiäis-studies."
First, this way you are not copy-pasting. Second, this forces you to think about the language and therefore learn it, thereby reducing the need to copy and making writing a lot easier.
Also, go ahead and improve your English. There are many free resources online, but simply reading a lot is a great help. For more specific advice on how to learn the language, https://languagelearning.stackexchange.com/ is a fine place to ask. For specific questions about the English language, maybe ask at https://ell.stackexchange.com/.
(The easiest improvement to the English in this question would be to capitalize "I".)
Quoting definitions and theorems word-for-word
For many basic definitions, there are only a small number of ways of writing them clearly and compactly. Just use an established way of writing.
Sometimes, if a definition or result is complex or not yet established, there are better and worse ways of writing it and maybe even several variations that define slightly different things. In this case, cite the source, since the exact definition matters.
Usually you are somewhere between these two cases, in which case I would recommend you to write the definition or theorem by yourself, so that you are more likely to write it in the same way as your other results and to use the same notation.

Thank you for your good advice. I did it, but you can not do it for some theorems, because Authors write very short.

I have another question. what about same notation? because in mathematics it's not common to use some different notations.

@Michal If the definition is very short and standard, just use it. If it not standard, use it and refer to the source. Feel free to use the same notation; if there are several alternatives, maybe write something like "We use the same notation as~\cite{source}.", if the notation comes from a book or a significant paper.

I am sympathetic to the problems in writing effectively in languages other than one's most native language.
Still, you should never just copy-and-paste. Period.
Nevertheless, yes, if/when you know well-enough some standard definitions/concepts, you will appreciate their highly optimized forms, and see that it is best to essentially say the same thing.
Yes. But don't "say the same thing" by copying-and-pasting. It should be that "the same thing" is what you yourself say, simply as the optimized description of the thing.
If the optimization is recent, yes, cite. If the optimization is 50 years old, and the idea is universal in your milieu, don't cite, unless you are making historical points.
Summary: never copy and paste, in any case.

"you should never just copy-and-paste" - +1. It's just bad practice.

Thank you. I am trying to do as much as i can. But, some Authors write as less as they can, so i can not optimize them.

I have another question. what about same notation? because in mathematics it's not common to use some different notations.

Always use standard notation, yes.

There is nothing wrong with something like:
'blah' was defined by R A Fisher [reference] as 'blah blah blah', in this paper we adopt that definition. - You give credit to the author of the definition, you do not give the impression that it was your idea.
If the definition is very well known in your field you might get away with 'blah' is usually defined as 'blah blah blah', but only if that is actually true.
Or you could equally justifiably say, 'we have restated Fisher's definition of 'blah' as 'blah blah halb' to take account of ...'
But there is something very wrong with:
The definition of 'blah' is 'blah blah blah'. - You give the impression that you thought up that definition when in fact you just copied it.
The simple question to keep in mind is: if I wrote that, would the reader assume that it was my own work? If it isn't your own work then don't write it in a way that might mislead a reader into believing that it is.

Thank you for your advice. I'll do it. I have another question, what about notations? if i use same notation.


text:
How to pick masters topic?
I asked a professor I had taken a class with to be my supervisor for my project in 1-2 years. He agreed. I overlooked that, typically, students apply for projects directly with professors or proposition them with an outline for a project (our project component is similar to a master's project (but on a smaller scale with a 3 month timeline)). (I can provide more info if needed, but typically it is similar to a publication with a period of testing/data collection and then a conclusion that supports a thesis).
I directly asked him to be my supervisor. He agreed and has offered that I propose some topics and he will provide readings to me.
I am a bit overwhelemed with topic research, but I am interested in starting early and establishing a foundation for my chosen topic ahead of time, as the timeline proposed by the university is far too short. I recognize that he was immensely generous in agreeing, so I do not want to bother him.
Would any students who have completed this process already inform me about what timeline to expect and how they chose a topic to focus on throughout their undergrad?
Thank you. (I am in computer science)

Talk to your professor about this exact issue.

publication with a period of testing/data collection and then a
conclusion that supports a thesis

This is very little to go on, but generally speaking, try to choose something that is actually of interest to you. This will help you through the inevitable roadblocks. Maybe some other coursework of yours got you interested in an area of your field? In my experience, the data collection is the hard part. If you are required to gather data yourself and are not allowed to use datasets that are available (many institutions offer free access to datasets for research), try to avoid anything where you need human participants, this is a time sink that you can not control.
Also, realize that "No" or "hard to say" is a totally acceptable answer to your research question. You don't have to publish it. It's about you learning to apply the scientific method.

I recognize that he was immensely generous in agreeing, so I do not want to bother him

Firstly, he was not. This is literally his job. Nothing wrong with respecting his time, but he is doing his job.
Talk to other students that allready did their project or the students' representation of your program to see other people's opinion and experiences. I found it useful to see examples. This really comes down to how your specific institution, what "a research project" means in terms of size and depth. I understand not wanting to waste the Professor's time, but most prefer you asking instead of never submitting anything or something completely off the mark due to not understanding the task at hand.

certainly, thank you for your insight. I'm planning on getting into contact with some TA's and gleaning some insight from them. Overall, it's very daunting, but I appreciate your reply. What did you study?

@mike Stack Exchange discourages using comments to chat. But I'll interpret your question as a clarification question, so you can gauge if my experiences apply to you. I did try my hand at several programs, including stem and humanities. So I did experience how different the culture in the fields are. I have a bachelors of sociology and a computer science master.


text:
Is it normal for journal reviewers to reject submissions based on non-scientific reasoning?
Is it normal for reviewers to use nonfactual statements as reasons to reject journal submissions? Here, nonfactual statements will be defined as statements that are in contradiction with verified textbooks. Has anyone else experienced this?

Backstory/details:
I have recently submitted to and appealed a physics paper at a very well known journal. For anonymity, the journal will not be named. In both cases, the initial decision and appeal were rejected by separate reviewers. Neither reviewer addressed any direct issues with the submitted work. One of the reviewers acknowledged the work for its novelty and originality.
Reviewer 1, had rejected my work based on their misinterpretation of a well renowned textbook (General Relativity - Wald, as a cross reference every other textbook agrees with Wald) and made up their own "fact" behind this misinterpretation and used it as a reason to reject. It was a completely false claim.
I applied for an appeal with a new reviewer. The initial false statements of Reviewer 1 were tossed as reasoning to reject as they were not used again. However, Reviewer 2 brought up another point which they used as justifications to reject my work. This point also did not have any direct objection to my work but addressed the foundations of my work. Again, this claim was also false and in disagreement with what textbooks say. Unfortunately, after the appeal attempt I am no longer allowed to further fight the decision. I will be going to another journal.
In both cases, the reviewers were proven to be wrong by direct textbook citations. The foundational reasons they used to reject my work, if true, would invalidate entire branches of serious research in gravitational physics as well as the textbooks themselves. My research is a specific case scenario within a well established and pre-existing branch of physics.

It seems a lot of you have concerns for the specific details. I will provide some more insight below:
All reviewer concerns did not touch the main section of the paper and were all focused on separate topics of the "Background and Introduction" and "Conventions and Refresher Section" at the very beginning.
Reviewer 1 had rejected the paper due to a choice of convention with definition X. The reviewer went on to cite the textbook General Relativity - Wald Section Y stating that the textbook said we had to use definition Z. Upon reading cited Section Y, it is apparent that there is no mention of forcing definition Z. Reviewer 1 made up their own statement. This journal publishes works frequently using definition X, so this should not be an issue to begin with.
Reviewer 2 had rejected the paper due to an "erroneous" derivation in the convention/refresher section. In this section, we provided useful definitions and derivations to derive the framework used in the paper. The "erroneous" derivation is almost word for word copy and pasted from the original literature as well as cross referenced to every textbook for consistency and correctness. Because he deemed this step "erroneous" he deemed everything else after to be incorrect. As with above, this journal as well as every other journal frequently publishes papers using the same framework given by this derivation.
In both cases, the reviewers did not present an argument against the actual works and methods in the submitted manuscript.
Upon inspection of the final email communication, both reviewers are part of the editorial board and it was not sent out for real peer review evaluation by independent reviewers.

I think everyone here can sympathize with being on the receiving end of a disappointing rejection. A Q&A site isn't the best venue for venting about it, though. If the rejection was really on such weak technical grounds as you say, though, what more can random people on the internet advise than to resubmit it somewhere else appropriate?

@user176372 I'm asking if this is a common issue that others has also experienced (non scientific opinions being used as facts in academic journals). Is so then this is a discussion to be had as a scientific community.

This isn't a discussion site, it's a Q&A site.

The discussion doesn't need to happen here. But answers confirming or denying having this specific experience would fit into Q&A.

Welcome to Academia.SE! Your question receives many downvotes in particular because of its emotional tone. You may consider rephrasing the title and question in a more neutral tone that translate more information than emotion. I think that your question raises an important issue and deserves attention.

Thank you @DmitrySavostyanov I will revise it promptly!

I agree with Dmitry here, for what it's worth. If this question were edited down, included the possibility that the author is incorrect, and removed the auxiliary discussion-based "How can this be avoided..." part, I think it's within scope. We probably have a dupe target somewhere for "Do reviewers or editors frequently reject on incorrect technical grounds?" though.

Yes, it's all-too-common for referees to be hasty or prejudicial, partly due to wanting to get the job off their desk. Yes, all-too-often leading to mistakes.

@user176372: We probably have a dupe target somewhere for "Do reviewers or editors frequently reject on incorrect technical grounds?" though. – I doubt that. While that question can be theoretically be answered within the rules of our site, it will practically only attract opinions and anecdotes. There is no way to properly study this question: You cannot collect peer reviews and have them peer-reviewed and you cannot conduct a meaningful survey, because either side believes to be correct.

If so, how can we as a scientific community avoid this issue in the future? – This site is about how academia is, not how it should be.

@Wrzlprmft and user176372 thank you for your input, I will revise the question again.

Is it normal in physics to cite textbooks? Are you also citing the original source material the textbook is drawing from? If so, why do you need to also cite the textbook? If not, are you sure the material in the textbook isn't just a simplified summary that leaves out some details for educational purposes?

@anjama Yes, it's quite common to cite a small number of textbooks in physics papers, particularly graduate level textbooks. Some such books are genuinely standard resources on a topic or technique. Other textbooks may be cited for various reasons, including "we adopt the convention/notation used in book X that's probably on your shelf". Other textbook citations can come in the intro, and play a role similar to citations to review articles.

A recommendation to accept or reject is an opinion. As such it is very normal to be based not only on facts, but on general impressions and subjective beliefs, by definition.

In my experience it is not uncommon for reviewers to state wrong claims in their reviews. My submissions received the following criticism from reviewers:

Manuscript claims X, but X is wrong, so reject (yes, X is indeed wrong, no, the manuscript never claims X).
It is known that X, but manuscript says Y, so reject (yes, X is well-known, yes, manuscript says Y, no, X does not contradict Y)
The proof of theorem T on page N is too hard to understand, so reject (there is no theorem T, and actually no proof on page N)
Obviously, from X it follows Y, hence Z, so reject (all statements are true, none are related to the submitted manuscript).

Having reflect on these experiences, I made the following notes for myself:

Academic publishing relies on unpaid work of reviewers and sometimes editors.
Unpaid work has low priority. It can be done well, but often it is not. People are too busy.
Reviewers are rarely held responsible for the quality of their reviews. Since they are not paid, it is not even clear how they can be held responsible for it.
Some reviewers are power-hungry, and some actively attempt to delay publications of their competitors and hurt their academic career.

As a community we can do the following:

Light is the best disinfection. We should evolve the publication system towards much greater transparency. For example, make all submissions publicly available, make all reviews publicly available, made authors' responses and rebuttals publicly available, make reviewers' and editor's names publicly available after the decision is made. Keep all submissions and all peer-review process publicly available, whether the submission is accepted or not.

Treat peer-review as work. Compensate reviewers financially and attach responsibility for the timeliness and academic quality of their reviews.

I don't have anything against your answer per se, I just don't think it's great to encourage rant questions with responses.

@user176372 I do not see the question as rant. It is a serious issue in academia that is rarely discussed. There is a serious power imbalance in author-reviewer relationship, that can and often does hurt early career researchers.

We'll have to disagree on whether the question was a rant as originally written then, but it has been updated. I'm locked on the downvote unless you edit, unfortunately.

@user176372 I did not intend for the post to be a rant, and apologize for any emotional wording. I am genuinely trying to see if this is a common issue.

@user176372 What edits do you suggest for my answer?

I have had a paper rejected twice because the referee didn't read past page three or so when the issue they presented had been directly answered and addressed on page four or so. Sometimes people don't referee papers in good faith. There's not much that can be done about that.

I'll answer the title of the post: "Is it normal for journal reviewers to reject submissions based on non-scientific reasoning?"
Empirically, no, it isn't. As editor-in-chief of a computational mathematics journal, I read every review that ever comes across my desk, which is ~150 per year. At least in my field, and for this journal, I would say that 90% are well informed and carefully written (though occasionally too short) and the remaining 10% are so short that they don't contain much information. I have not come across any over the past 6 years for which -- to the degree that I understood the specific topic -- the reviewer was just plain wrong or used non-scientific reasoning. I have had a single case where an author complained about a biased reviewer and in that case think that perhaps both reviewer and author insisted too much on their perspective.
In summary, having seen perhaps 1,000 reviews, I don't think what you describe is "normal".

I recognize, of course, that that's not really what you were asking. But I have nothing to say about your specific case.

There’s a catch though: Part of the asker’s problem is that the editor followed the reviewers’ decisions and thus probably considered them correct or couldn’t check due to lack of subject knowledge. Likewise you cannot know whether you just missed cases where “the reviewer was just plain wrong or used non-scientific reasoning”. Now you might say that nobody even complained about this, but then most authors are wise enough to not phrase their rebuttals like this. (And just to be clear: This is not about your actual editorial qualities; I think the question is fundamentally unanswerable.)

@Wrzlprmft Perhaps. But I also have conversations with my associate editors about the reviews they receive, and they do not report these sorts of issues either, even though they are much closer to the subject matter of the papers. I've also published ~70 papers myself, getting ~150 reviews, and have not had had this experience myself. I just don't think that it is "normal" or even "happens frequently".

I think this question is difficult to answer without knowing what the exact disagreement is. After having seen hundreds, perhaps thousands, of reviews, I've never seen a reviewer espouse crankery. However, I have seen reviewers disagree with authors over more subtle issues that can nonetheless resemble what you see.
Example: suppose there's an important parameter in your field, and two different methods to measure it are giving two different results, A and B. Your new work uses this parameter as an input, and you've chosen to use A. Your referee is strongly convinced, however, that B is correct. If your referee is right, then your entire work is wrong, and deserves to be rejected. Of course, you chose to use A because you think it's correct, and you think your reasons are well-grounded in textbooks. (Your referee surely thinks the opposite.)
Example: no referee is ever going to say "this paper claims 2+2=4, but 2+2=5, so it must be wrong. Reject". If you ever get a review of this sort, it would be highly abnormal. A reviewer could, however, say "this paper claims 2+2=4, but they also make this assertion that, if true, would lead to 2+2=5. The paper is contradictory. Reject".
Therefore, depending on how serious the disagreement is, the answer to this question varies from "it is absolutely abnormal" to "it is completely normal".

No, it is not normal. Usually reviewers are experts in the general area in which they review, and they should be familiar with textbook material. So, first of all, consider the possibility that you might be in the wrong, especially if this happens more than twice.
In any case, reviewers are your first prototypical readers. If they have major concerns about the groundwork of your paper, then the paper should be amended, even if it is 100% correct as it is: you should add explanations that make the tricky points clearer and address their issues. If you dismiss their feedback and continue, other future readers will have the same concerns about your paper. I suggest you to adopt the mindset that "reviewers are always right, even when they're wrong": address their doubts, and add more explanations. See if you can find an illuminating example, for instance. Sometimes you have to convince people that you are right.

Although I agree with all your points, it is easy to see how the mindset "I am right even when I am wrong" coupled with lack of accountability can lead to exploitative, dominating and power-hungry behaviour of reviewers towards authors

@DmitrySavostyanov Agreed; I myself find particularly obnoxious "plz cite my work" requests from reviewers. But here I was assuming that OP observed a genuine technical mistake, not a malicious false statement made in order to get the paper rejected.

@DmitrySavostyanov It could lead to this kind of behavior, but the empirical evidence presented in the answers here says that it doesn't actually lead to this kind of behavior, at least not frequently.

@WolfgangBangerth It may depend on your perspective. As an editor-in-chief, you are at the top of academic publishing hierarchy. As an early career researcher, I experienced abusive and unprofessional reviews coupled with factually incorrect statements. I can not say it was frequent (about 10%), but sufficient to have a severely demoralising and traumatic impact on my perception of academic publishing, as well as damaging my academic career. I should add that editors in my experience did not interfere with such behaviour, and anonymity protects the reviewers.

@WolfgangBangerth You also should acknowledge the survivorship bias. Here on academia.SE you collect opinions of active academics. They are people who so far survived the "publish or perish" academic game. You should not take the word (or "empirical evidence" as you say) of survivors as an unbiased estimate.

@FedericoPoloni In this case, I am only wrong if the well established techniques and conventions are wrong. I have provided more details in my most recent edit. If the two separate concerns were found to be true, the entirety of gravitational physics would be upended and these two reviewers deserve to immediately be awarded with Nobel Prizes by invalidating thousands of rigorous publications by many well renowned researches who have even received Nobel Prizes for their works!

All jokes aside, I agree that we should always consider the possibility of being wrong. But in this case, it is not even my works they are arguing with.

@DmitrySavostyanov This is a useful observation about my own publications, but as I mention in my answer, I see a lot of reviews and these are for papers of all kinds -- good ones, bad ones, for established researchers, and for junior researchers. Surely not all of these authors are going to make it in academia. Yet, I don't see the reviews in my practice that would discourage these authors.

In short your papers can and will be rejected for every possible reason you can imagine, fair and unfair, true and false, scientific and unscientific. I've had paper rejected in all these circumstances.  No journal has an obligation to publish any of your manuscript  and can decide not to for whatever reason they want.
Get used to it. Always assume when you submit a paper that it will be rejected. And be thinking of where you'll submit next as soon as you've press go on a submission.

Indeed, among the many reasons one might get a rejection, I might actually be happy with a completely off-base review - if you really believe there's nothing to fix, you can just send it elsewhere immediately without a single edit.

@NuclearHoagie I share the same sentiment as you. I view it as a good sign that they couldn't find any real and valid reason to object.

Without addressing the details of your submission, I would like to point out a few details of a functioning review process.
First, reviews are always an educated opinion of peers, hence the term 'peer review'. The value of peer reviews depend on the quality of the editors choosing the reviewers, hopefully educated peers that can evaluate the manuscript from an unbiased point of view. So a few questions here is whether the review selection has been performed according to appropriate guidelines. Note that this does not preclude the selection of reviewers that may express negative views of your work as little as selection of exclusively positively inclined reviewers. There is always a little room for randomness in the inclination of possible reviewers here. That said the role of an editor is always to convey the main points of the feedback to the author.
Second, and this follows on the first point, the role of the editor is to act as a moderator between the reviewers and the author, keeping the main role of the journal in mind. It is my (highly personal) view that editors tend to skip their responsibility in favour of reviewers comments. In an ideal world the views of reviewers and authors should be seen as views in an educated debate and not favouring one or the other side. Editors not engaging in the possibly conflicting views between author and reviewers is not doing their work. Unfortunately this seems to be be an increasing point of dissatisfaction that I deem is die to a lack of resources (time) on behalf of everyone involved in the  review process (editors, reviewers and authors).
In the case of ending up in perceived conflicts, I would strongly advice to consult the Committee on Publication Ethics COPE and browse through their cases. The Committee is intended for editors but is equally of value to authors.


text:
Reapplying to Ph.D. Programs: Ways to improve?
This year, I applied to Ph.D. programs in history, hoping to continue my research. Unfortunately, I discovered that, despite a "strong application," I was not admitted to any of the programs to which I applied. While I was told that it was not because of my application, but rather a school's lack of focus on my particular field of study, I cannot help but think about how a gap year will look when I re-apply next year.
In the gap, I intend to teach in a high school (and potentially community college), but I am unsure of what I can do to improve my application for future applications. A year-long gap is frustrating, personally. I would appreciate any advice on what I can do to increase my chances. How might the gap year look to programs? What, exactly, would help me improve/enhance my application? Thank you, in advance.
Brief Outline of Background:
B.A. in history, magna cum laude with distinction (Honors Thesis), Conferred 2016
M.A.T in History Education, awarded Hattie M. Strong Fellowship for teaching excellence, Conferred 2017
MA in East Asian Studies, awarded two travel grants for conference presentations, Expected May 2020
I have continually presented in academic conferences since my sophomore year as an undergraduate  and am currently working on a book review article and journal article for publication
I maintain a strong GPA from all institutions attended, despite working a full-time job, serving as a Graduate TA, and taking a full courseload (sometimes more).
I have strong references from well-known scholars in the field, all of whom I keep in constant contact.
The only area I could see a need to improve is my language acquisition. While I know Japanese, I would like to add Chinese (and perhaps Korean) to my list of languages. This is currently in progress.
While this is by no means an exhaustive list, and it is difficult to judge without all the available facts, I would appreciate your insights.

"While I was told that it was not because of my application, but rather a school's lack of focus on my particular field of study" - and what is that particular field of study? Is it something likely to be controversial or very niche?

Actually, I think your suggestions aren't likely to help much. You are suggesting making your CV more diverse while doctoral research requires more focus/specialization. You've already been told what is lacking, and you have a lot of breadth already in your CV.
Either find a program that matches what you want to do, as the places you've already applied to do not, or match your short term goals to some program(s) that do exist and are taking students. I think the latter is probably more viable.
Write a SoP with the knowledge of what is supported by the places you apply to. If they have no way to move outside their range of expertise they have little incentive to accept you, no matter how good you are.
But it is only a short term twisting of the path to success. A doctoral program in a field somewhat related to your long term goals will give you both the skills and the credential to research in the future as you like. The specific topic of your dissertation need not be limiting.
But you've got to get in the door first. And specialization is the name of the game played in that space.

Thank you for your advice. I also think that the latter option you suggest is the most probable. I don't necessarily want to make my CV more diverse, in fact, it's just the opposite. For future applications, I intend to discuss my specific, specialized interest within a larger context (which ties into my second interest). For example, my research in Japanese history and memory fits well with my interest in Japanese history in a global context. Thank you for your advice, I appreciate it.


text:
How do I differentiate between addressing two professors with the same last name?
I am currently taking an online course (at a university in the US) in which once a week I am in the same virtual meeting room as two professors, one male and one female, with the same last name. I am unsure in how I should go about directly addressing one of them when I typically address all my professors as "Professor <lastname>" . As a second-year undergraduate student, I have been told it is inappropriate to address both professors by their first name if they have not stated this is okay (e.g. my past professors have typically said "you can call me <firstname>" on the first day of class). Additionally, when I took a course with one of these professors last year, I (and all other students) addressed them as "Professor <lastname>". If addressing them by first name is inappropriate in this context, how would I selectively address one when both professors are in the room?
With the exception of myself and another undergraduate, all other students in this course are graduate students, and address the professors on a first-name basis. So this has not a common cause of confusion in the course.

Did you ask them?  It's up to their opinion.

Our Head of Department was also a Knight of the Realm. So he was a Professor and a Sir. When addressing a Knight, one should use first name (Sir John), but when addressing a Professor, it's Professor Gunn. Had us undergraduates utterly baffled...

@OscarBravo What was settled on?

Don't forget one or both could have nicknames they prefer.  This is fairly common in these situations.

@AzorAhai--hehim: I'm guessing Professir Gunn...

I would refer to them both as Professor X. The comedy of the situation will soon play out, with one or other of the professors (or preferably both) insisting that you call them by their first name.

@AzorAhai--hehim He was officially called Professor Sir John Gunn (the Sir takes precendence). We usually called him Professor Gunn because we wanted to talk to him about professor-stuff rather than knight-stuff.

This is a simple problem, compared with regular communications with three different medical nursing specialists (all with the same professional title) called Diane Smith, Diane Smith, and Dianne Smith. (Yes, really. I'm not making this up).

There are few things you can do.

Call each by their full name like 'Professor Ann Smith' or 'Professor Bill Smith'.
Ask whether you can call them by 'Professor first-name' like 'Professor Ann' or 'Professor Bill'.
Continue to use 'Professor last-name'. They'll either decide who will answer or ask you to clarify which person you wanted.
And the easiest, as pointed out by Buffy, ask the professors if there's an alternate, unique name you can use so you can differentiate between them.

Even simpler, just ask them what they prefer. Maybe first names is fine, even for an undergrad.

Very true, @Buffy! Thanks for pointing that out. Let me add that in.

That is really helpful advice, thank you! I will reach out to them; I thought this might be one of those things I should know already and was worried it would be a bit embarrassing to ask.

@mkennedy Further to Buffy's point, you don't need to ask them privately beforehand.  It'd be better to ask in the open room at the start of the session, because that'll clear it up for everyone.

@Proxentauri Unless it's really embarrassing or really inappropriate, it's usually better to ask if you're uncertain about something.

In addition to the other great suggestions, you can address them as "Professor X, Sir" and "Professor X, Ma'am". That's so over the top formal that they might cringe and tell you to use their first names.

This seems unnatural, since one would (or at least I would …) never address someone this way—"Professor X" or "sir/ma'am" separately, but never together.  I think that, if one were to go this way, then "Mr Professor X" or "Mrs Professor X" would be better (but still worse than asking them).

was "seeming natural" among the design criteria?

At my school, there are several married professor couples who we refer to as "Dr. Mr. Last Name" and "Dr. Mrs. Last Name". This would probably be less appropriate if they are unrelated, and is informal enough that you would need their approval first, but it is both unambiguous and obvious in meaning.

Sounds a bit weird in English, and grotesquely formal in German. Herr Doktor Meier, that's how letters from your health insurance company start. ;-)

@Karl: In German, wouldn't Frau Doktor Meier be Herr Doctor Meier's spouse?  It's been decades since I took a German class, but that was one of the things that struck me as odd.

@Flydog57 That may have been the case 50 years ago, but would be considered odd if not even offensive today.

@Flydog57 Being an academic herself, Mrs. Meier could take offence if you referred to the couple as Herr und Frau Dr. Meier, instead of Dres. Meier.;) Today it usually means that she has earned her own doctorate, but I'm pretty sure show knows which is the case.


text:
I switched PhD programs after a month, do I mention this on my CV?
More detail: After a failure of communication, I turned down other funded offers to accept an unfunded PhD. I had some money saved and tried it out anyway, but after one month quit and went with a previous offer (after telling them I'd made a bad decision)!
I worked for 3 months specifying my skills for the defaulted PhD, do I mention the experience on my CV? On one hand I don't want the blip recorded as it leaves a little time gap between finishing MSc and entering PhD and records my bad decision making, on the other the institute name is a major buzzword for careless recruiters. Thoughts?

If you just state years, and not months, surely you can omit the first PhD position without there being an evident gap?

I think you should not bother mentioning the first (unfunded) PhD program.
From your post (emphasis added):

After a failure of communication, I turned down other funded offers to accept an unfunded PhD. I had some money saved and tried it out anyway, but after one month quit and went with a previous offer (after telling them I'd made a bad decision)!

Since you only spent a month in this PhD program, I can't see how it is really relevant to your experience, nor will it result in a significant gap in your CV if you omit it. Moreover, you probably do not have many achievements from this month, so it is more likely to just result in unnecessary questions when people read your CV.

I worked for 3 months specifying my skills for the defaulted PhD, do I mention the experience on my CV?

What do you mean by "specifying my skills"? This could be a good thing to mention if you were working on, e.g., online coursework, but you don't need to mention that it was for the PhD that you quit.
On the other hand, if it was just you working on skills on your own, then it won't help to mention it.

On one hand I don't want the blip recorded, on another it leaves a little time gap between finishing MSc and entering PhD

How long is the gap of time? If it's just a few months, it will be ignored. If it is a full year, it may be something you will want to explain to someone if they ask, but I don't think it will be necessarily critical.

and the institute name is a major buzzword for careless recruiters.

I am not sure I understand why it would be a "buzzword" -- is it a poorly regarded institute? Anyway, combining this concern together with all your other reservations, I think it would be fine to leave it off.

"Buzzword" in the sense that oxbridge holds amplified weight in prestige focused industry and some startups

@Jordan OK, I see. So you take that as a reason to include it, not to omit it?

A frail reason, sure

My personal experience says don't.
Similar to you, my CV included a semester of irrelevant PhD studies. It helped me a lot to find a position after I removed that part completely.
If you mention some unfinished business, then the question

Why did you quit/dropped off?

is inevitable. This is not because people want to come down on you, but the thought is

If the candidate mentioned this piece of information, which is
  obviously useless, it must have a reason.

Then, it is not very helpful for your interview process if you don't give a satisfying answer. So, in my personal opinion, I suggest you leave that period out, and answer only if you are asked about what you did in that month.

While it is a bit of a grey area, I'd suggest that it isn't necessary to do so as it hasn't contributed to your qualifications for the future.
You need to be able to give an explanation for the gap if asked, of course. But not everyone's education trajectory is a smooth and unbroken upward curve and people understand that. As people we aren't perfect and we suffer setbacks. Having made a poor decision isn't career ending and you have wisely found a better path.
People change programs for lots of reasons.
However, if you decide that you should list it, I doubt that there would be any downside. It will probably guarantee a discussion about why, but that is fine also. "I made a mistake and worked to correct it" is a pretty human response.
While it isn't precisely the definition, a CV normally lists accomplishments, not setbacks. Long gaps are suspect, of course and can be explained or not.


text:
For how long afterwards can you publish papers based on field research?
In 2010 I did field research for my Masters Thesis in International Peace & Conflict Resolution (i.e. multi-disciplinary social science and international relations) in Bolivia interviewing indigenous judges. The interviews focused on the structure & function of their indigenous judicial system and its relationship of the state system. After graduation, I had wanted to publish a version of my thesis but never got around to it. After a while, I assumed too many years had passed for any of it to still be relevant to publish but then I was reading an anthropology methodology book that mentioned how anthropologists will publish papers based on notes from field work for years after finishing the field work.
I still have all my notes and recorded interviews. Could I still publish a paper in a journal based on 10 year old field research?
(Note: I haven't decided on a specific social science field I'd want to publish but does it make a difference? I am also not a academic associated with any university.)

If you prove a theory or find an interesting or useful relationship using 100 year-old data you can publish, that is send to a journal for review.
It is not the age of the data but the results / analysis / conclusions.


text:
How do you cite a paper that you found online?
I found this paper online and would like to cite it. I've looked up the rules for citing conference papers, but this is not a conference paper. It's also not a book and not a website and not an essay. It looks like this image may have the correct format, but I can't tell exactly what information is what.
How do I cite any paper? (MLA is preferred, but multiple citation styles would be ideal.)

I threw the title in google scholar and clicked on the "cite" button -> "Harrison, John, Josef Urban, and Freek Wiedijk. "History of Interactive Theorem Proving." Computational Logic. Vol. 9. 2014."

Several people have found a published source for this paper, but if the online paper were the only available version, I'd cite it as "[Authors' names], [Title of paper], (date if known), available at [URL] (accessed on [date])." People who use some official bibliographic style can, I hope, incorporate the same information in that style.

Worth noting that if the paper really isn’t published in any other form, then the answer is field-dependent.  In some fields (e.g. pure maths) it’s quite normal to cite preprints, public-but-not-formally-published work, personal communications, and so on.  In other fields (e.g. many experimental fields, I’m told) it’s considered very bad practice to cite anything except peer-reviewed publications, and many journals don’t allow such citations at all in their articles.

@Fábio Dias nice approach, but never rely on Google Scholar's cite button. The citation you mention is incomplete at best.

@henning but probably enough so anyone (or any automated script) can find/match the paper. Which is kind of the point of citations anyway. Volume/page/etc aren't really as necessary nowadays...

The first step is figuring out if it has been published in some form elsewhere. Recognize that people often put some draft version on their personal website to make the full text available, especially if they're not allowed to host the published version.
In this case inspecting the URL gives some hints*. Consider omitting the "joerg.pdf" part, and go to John Harrison's Complete publications list, which further links to this page. Both these pages can tell you that this document is a chapter in a handbook:

History of Interactive Theorem Proving
John Harrison, Josef Urban and Freek Wiedijk.
In Jörg Siekmann (ed), Handbook of the History of Logic, vol. 9: Computational Logic, Elsevier, pp. 135-214 (2014).

(The last link even provides a citation in bibtex form, but it uses the InProceedings form. I would probably use the InCollection style instead. Elsevier seem to agree.)
In MLA, book chapter references can be written

Last, First M. "Section Title." Book/Anthology. Ed. First M. Last. City: Publisher, Year Published. Page(s).

For this document, you'd have something like

Harrison, J., Urban, J., and Wiedijk, F. "History of Interactive Theorem Proving." Handbook of the History of Logic, vol. 9: Computational Logic, edited by Siekmann, J. Elsevier, 2014, 135--214.

*In cases when the URL doesn't reveal anything, consider searching for the title and authors in a search engine. This can often lead you to a more official version.

Use Google Scholar with the title in the search box to find:

Harrison, John, Josef Urban, and Freek Wiedijk. "History of Interactive Theorem Proving." Computational Logic. Vol. 9. 2014.

That's a good method, but an imperfect result. It shouldn't be Vol. 9 of Computational Logic, but Vol 9 of Handbook of the History of Logic, where the volume in question happens to be named Computational Logic.

@Anyon none of the google entries refer to a Handbook of the History of Logic... :( ? :(

I think Google Scholar must have some error in their database. If I search for it in Google Scholar, and click through to the Google Books link, it's clear from the cover picture and the "About this book" section that they've only identified the volume title, and not the series title. If I search for just the title of the document on regular Google, I do find the link to ResearchGate corey979 linked in a comment, which indeed references the Handbook.

Google Scholar can't be relied upon for citations. This is an example why. The citation looks like an incomplete citation of a journal article while it should be a book chapter.


text:
Can figures and tables go past page limits?
I'm writing a paper for a conference, and the tables and figures go past the page limit, but they end up in the references section. That is, our text does not go past the page limit, just a few tables.
Is this usually acceptable? Is there any standard guidance on whether or not this is okay, or does it often differ between conferences?

What exactly do the formatting guidelines say? You probably don't need any other information.

The answer to this question will depend entirely on where you are submitting the manuscript.

This is conference specific. I have seen calls for abstracts that explicitly say two, period, I have seen calls that say one page text, one page figures, plus references, so on and so forth.


text:
Lord and Prof titles
Someone has a title Lord and is a Professor.  How will I address a letter?  And what will the correct manner be after Dear?

https://www.debretts.com/expertise/forms-of-address/professions/ deals with exactly this case when it gets down to "professors"

Looking at this link, Professions, as provided by erstwhile editor in the comments to your question, the answer would be Professor Lord [Such-and-such]:

If a professor is also a member of the peerage, or a knight or dame, the academic style and title may be combined as ‘Professor Lord Ryder’ or ‘Professor Dame Elizabeth Pulteney’. He/she may prefer to be known by title alone.

The "correct" form of address, as noted by another answer is "Professor Lord". However, the person in question is likely to use a less unwieldy title. Given he is a professor and a peer, there are probably ample press releases, news articles and interviews with him, and you should also look at his biography on his institution's page.
Most likely, he goes by just "Professor" in an academic context. Most likely, his reply email to you will just be signed with his first name. British academics are for the most part quite relaxed about titles. You shouldn't worry about it too much.


text:
How can I present the significance of two statistical tests in one table?
I am working on my first independent publication and am unsure how to report the significances of two statistical tests in one table.
My professor has recommended that I should perform two statistical significance tests for robustness and present them in my article.
So far I have only done the t-test.
(If the value is significant according to the t-test, asterisks are added indicating the significance)
But I should add the significance of the Wilcoxon test as well.
The problem is that my tables with the t-test are already big enough and I can't expand them any more.
What can I do to also report the significance of the second test in the same table?
Should I perhaps write the values in bold if they are also significant according to the second test?
Or does anyone have a completely different idea?
Adding columns to the table or creating a new table is out of the question.
Here you can see an example of a table:

Many thanks in advance!

Those stars (three on all but two entries) use lots of real estate and are very distracting. Footnotes for just those two would help whatever else you do.
Without the stars you might be able to report the second set of results this way:
xx.x (yy.z)

with the caption explaining the parenthetical numbers.
You can also format to make better column width choices.
Please align the columns on the decimal points.

Use a different symbol.
You're reporting your t-test p-values using asterisks, just use crosses or daggers or any other symbol to denote the Wilcoxon p-value. Alternatively, just list the p-value itself in the table - the way it's formatted, it would actually occupy less space than the asterisks. I'd also recommend cleaning up the table a bit - there's not really any reason to include the single asterisk in the legend since it's not used anywhere in the table (although you might want to keep it if some Wilcoxon p-values are between 0.1 and 0.05). You can also tighten the spacing between the asterisks, as they currently draw more focus than the values themselves, and take up a lot of space.


text:
Addressing selection criteria
I am applying for PhD scholarship and there is selection criteria and I have to respond to each of them. One criterion is given below.
•   willingness to collaborate and engage closely with industry partners.
The question is, how can I respond that criterion. Not to mention, I have no experience with industrial partners

"Addressing selection criteria" is a bit vague, can you think of a more descriptive title for your question?

A possible suggestion is: "How can I answer 'willingness to collaborate with industry partners' if I have no experience with industry partners?"

It asks for willingness, not experience. A simple statement that you are, indeed, willing to work with people from anywhere, industry or otherwise, if it advances the art and the science is enough. Provided that you believe that, of course.
But you also need to be aware that industry partners have their own agendas and they aren't always aligned with dissemination of knowledge. But, as a student, you should be able to get good advice from advisors about how to deal with such things.
Collaborative relationships are generally good as long as they aren't exploitative. So, the advice is to be open, but keep a certain wariness.

This answer seems to forget that every statement must be supported with evidence, preferably using a S.T.A.R. model for success in job applications and interviews.

@DmitrySavostyanov, perhaps, but then the question was badly posed. It is easy enough to ask for a history of collaboration rather than a willingness. But, I'll guess that in this case, they thought such an expectation would be unrealistic to ask of a potential student.

@DmitrySavostyanov In this particular case, the statement (a willingness declaration) is the evidence.


text:
Two of my potential PhD referees are married to each other – is that a problem?
Note: By Referees, I mean individuals who can support and validate my application for a PhD; for example, former lecturers or supervisors who have worked with me in the past and would be able to say whether I am suited for a research role.
I have been taught by a former associate professor of my university in one module for my undergrad degree, and his spouse taught two of my master's degree modules and co-supervised my master's degree dissertation. I am thinking of naming the both of them in their separate capacities as academic referees for my PhD application.
They are were not involved in teaching me at a joint capacity at any point in time and neither of them had to review the other's work with me.
However, I'm worried that an external reviewer of my application might think that they would influence each other outside of work, and that if one of them thinks favorably of me, so will the other. I don't think that is the case, as they are people of integrity with a strong moral code, but someone whose job is to review my application with trained skepticism might not see it that way.
I could adopt an 'if they don't ask, don't tell' policy, but that wouldn't be very honest, and even if it did work initially, having it resurface at some point in the future might land me in a lot of trouble if this behavior is considered questionable at best.
Can I ask them to be my referees, and will an external reviewer treat them as a single referee? Obviously the best outcome for me would be if:

They are treat as separate referees, as I think they should be.
I am not obliged to disclose their relationship anyways.

What do you mean by "referees". Letter writers for your application or something different?

I don't think anyone would care.

Hi, Dr. Buffy... By Referees, I mean people who provide references regarding my academic credentials; for example former lecturers or supervisors who have worked with me in the past and would be able to say whether I am suited for a research role.

@AnonAnon I believe the term you are looking for is "reference," not referee. Referees enforce rules in a sporting event. References provide support for your application.

@Vladhagen "Referee" is also used to mean the people who advise editors about whether a paper should be published --- also called reviewers, but in mathematics "reviewer" more often refers to people who write reviews for MathSciNet (= Mathematical Reviews). Of course, none of this affects your essential point that referees are not the people who write recommendations.

@AnonAnon After looking into it a bit more, it does look like "referee" is sometimes used in Britain in the context you have used it in. I guess I learned something new.

I don't expect this to be an issue.
I have been at departments where two spouses were faculty members. I have also received and evaluated applications where there were references for the same candidate from academics who I know are close collaborators and friends. In each case, the natural assumption was that they have their own careers, working style, students, collaborators, and -- of course -- opinions.
In this case, it is clear your exposure to them is in different contexts, and presumably their letters will make that clear. It is perhaps more likely than average that they will talk with each other about their letters as well (given they have more opportunity to do so!), but that happens all the time anyway.


text:
Can a Guest Lecturer be my Referee?
I have a guest lecturer who taught me one module for one semester and graded my work. He is willing to be my referee. Would he be counted as an acceptable referee if I were applying to be admitted for a PhD (graduate admission)?
Edit: I would like to mention that I asked because I was just worried because I don't know if it's standard practice to accept such referees even if they have taught me for one full semester, and some bureaucrats who may act as gatekeepers to academic staff might err on the side of caution almost to the point of inflexibility.

Probably, but I have no idea what you're applying for.  I don't see how we can help without knowing who will read the reference.

You mean for graduate admissions? (From the tag) i mean, why not? What leads you to believe that it could not be the case?

Hi, Anonymous Physicist and user 111388; yes, for graduate admissions. I will amend my question accordingly. Thank you for pointing that out.

Could you amebd you question to write why you think this would be not possible?

Can a Guest Lecturer be my Referee?

Yes, they can. To determine if they are the best referee for a graduate application, try answering the following questions:

Can this person attest for my strong research potential? (Not just performance in coursework) (e.g. did you talk to them after lecture about ideas outside the scope of the course? Did they seem interested in discussion research-level topics with you?)
Will this person's name (or at least their University affiliation) be recognized by the admissions committee or by the professors whose groups you apply to?

If the guest lecturer satisfies one or both of those criteria, they could be a good choice. If they don't satisfy them, see if there is someone else who would satisfy them. It is still a trade-off here -- someone who knows you better is more likely to give a good letter than someone who does not know you as well. It may be that the guest lecturer is the best choice even if they do not satisfy these criteria, in the case that no one else really does either.