Is it a good thing as a teacher to declare things like "Good! Things are becoming clearer already."

I started my academic career as a high school teacher.  As part of earning the credential to teach high school, I had to go through a semester-long "internship" as a student teacher---I taught in a classroom under the close supervision of a veteran instructor.  One of the first bits of feedback I got was that I had a tendency to say that a problem was "easy" or "clear".  In my own head, it was in the context of a universe of possible problems, e.g. "This problem is easy as compared to this other problem on a similar topic," or "Let's start with an easy example before moving onto harder examples." My supervisor encouraged me to avoid this kind of language, because

no problem is easy and nothing is clear, and
telling a student that a problem is easy destroys morale when they can't figure it out.

No problem is easy
There is a great Saturday Morning Breakfast Cereal comic which describes a view of how ideas come about in mathematics, and how we disseminate those ideas.  Essentially, modern mathematics is the distillation of several thousand years of thought.  The ideas and results were hard-won, yet we somehow expect students to master them in very little time.
I imagine that this observation is true across disciplines.  For example, I can't imagine trying to give a one-hour lecture summarizing Lewis Henry Morgan and the modern study of kinship, nor can I imagine how clear the ideas would be to students after such a lecture.
Ultimately, I think that this is a form of the curse of knowledge: as instructors, we might think that the ideas are easy because we are so familiar with them, or perhaps because we never had difficulty with them ourselves, but that doesn't mean that they are actually easy.  We have to figure out how to put ourselves back into the shoes of a novice, and remember how difficult the ideas were in the first place.
The impact on morale
Because mathematics is so often stigmatized[1], I think that mathematicians are (or, at least, should be) particularly sensitive to things which are likely to further drive people away or cause them to shut down.  However, I think that all instructors across all fields should be aware of how their style impacts morale, so this isn't really a math-specific observation.
If you tell a student that something is "easy" or "clear" and that student is still confused, you are implicitly suggesting that the student has failed to grasp an obvious concept.  This tells the student that if they admit to their confusion, they are admitting to being inferior, and that they might become an object of ridicule.  The student understands the failure to be theirs, and theirs alone, rather than a failure on the part of the instructor, or a blameless failure in the process of communication.  Such a student is not going to ask a question, is not going to seek clarification, and is likely to withdraw from the topic.
As such, I think that it is imperative that we avoid saying things that trivialize the work that we and our students have to do.  It is bad form to tell a student that a concept is clear, or that a problem is easy.
What might we do?
In the question, it is suggested that an instructor who makes a topic look easy might note how easy things have become.  I think that the reality is quite different:  the teachers who make things look easy are those who are most sensitive to how difficult things really are.  They lean into that difficulty, and explain clearly to students where the problems lie.  It is then up to students to come out the other end and say to themselves "Wow!  I thought that idea was hard, but the professor really made it easy to understand!"
I don't think that there is a one-size-fits-all solution to this, but there are a few things that I do in my own practice which, I think, help:

Ask Questions:  I don't assert that ideas are clear; I ask if they are clear:  "Is this clear now?", "Do you all understand?", "Do any of you have any clarifying questions you'd like to ask?", "Can we move on, or would you like to work through another example?", and so on.  Indeed, I often ask "Is this clear?" in a situation when I know that it should still be quite unclear to students.  Done often and early enough, this gives students permission to admit that things are confusing.

Provide Context:  To the extent possible, I like to give students some historical context for the development of ideas.  For example, we might spend as little as a week defining the derivative of a function.  This short period of time belies the enormous intellectual achievement it represents:  the ancient Greeks were the first to spot a problem (Zeno's paradoxes), Newton and Leibniz (both of whom "stood on the shoulders of giants") first put the ideas together, Euler (and Fourier and Cauchy) introduced the modern notion of "function", and late 19th/early 20th century mathematicians (Hilbert, among others) nailed down the formalism.  If the derivative looks easy, it is only because it took such a long time to refine and distill the ideas.  It is actually a remarkably hard concept.

Employ Appropriate Comparatives:  It is, I think, entirely reasonable to assert that one example is less difficult than another.  Logically, this is the same as asserting that one example is easier than another.  However, when one says that a problem is "less difficult" it could still be hard, whereas if one asserts that a problem is "easier" then a student might only hear the "easy".  I don't start with "easy" or "simple" examples; I start with "less difficult" or "illuminating" examples.

[1]  Speaking from the perspective of an American, it seems that no one has a problem with a person saying "I'm just not any good at math!" or "I'm not a math person!"  Fear and loathing of mathematics is considered appropriate, and mathematicians are seen either as god-like geniuses, or asocial nerds (or both, I suppose).  It is considered okay for a "normal" person to be mathematically illiterate.  A seemingly equivalent admission of illiteracy ("I'm just not any good at reading!") would be shocking.


What are the negative consequences of slacking off after attaining tenure?

I think the first question is, what does "slack off" really mean?  Many professors do change their priorities after tenure for a slower paced approach to their work more in line with their own intellectual values.  Many things that might be perceived as "slacking off" in a pre-tenure professor actually do have value and are much easier to pursue post-tenure, e.g., dedicating more time to students and teaching rather than research, or taking a slower pace to try to figure out an angle on deeper and harder to address issues.

But let's assume that our hypothetical professor is just saying, "I got mine, and I'm going to do the absolute minimum hereafter!"  Here are some of the non-firing consequences:

Not getting grants, it will be hard to have students.
Their professional prestige will plummet, and anything they do want to do will get harder.
They may get stuck with unpleasant scut-work tasks for the department, and will have more responsibilities foisted on them because "they have the time" that their harder working colleagues do not.
They will not get promotion to higher academic ranks, nor the accompanying pay rises.

Some people may actually be comfortable with this, and having a person who's given up ambition and embraced a comfortable position as the organization's reliable clean-up detail can actually be a good thing, as it takes those tasks away from others who have more ambition.

But what if the slacker professor really doesn't care, and does a poor (but not quite enough to be fired) job at all the tasks they are assigned by the department?
Well, every organization has ways to make a person's life hell without firing them.  In the next departmental reorganization, the slacker professor might find themselves getting moved to a small lightless basement office, the administrative staff may ignore requests for assistance, colleagues may simply treat the person as a pariah.  Few people last long in an actively hostile workplace, and it may be harder to fire a person than to make them quit...


Can I allow my personal life to influence where I do my PhD?

So I'm just some random stranger on the internet, but you asked for advice, so here it is.  Given only the information in your post, I think you have a difficult choice ahead of you:

Move or propose.

From a strictly professional standpoint, you make a very strong argument for moving.  Having a more competent and more supportive advisor, and working in a field that excites you more, will have a tremendous impact on your several-decades-long mathematics career.    As Dan C writes elsewhere, if you want to do math for a living, you should enroll in the strongest PhD program you can.  (I'm assuming here that you actually want a career in mathematics; otherwise, getting a PhD in mathematics is kind of stupid.)

From a personal standpoint, you make a much weaker case for staying put.  It's just another city; you'll be fine.  You can always find another apartment.  Do not listen to the Impostor Syndrome; everyone is afraid that they're not good enough.  Your girlfriend is OK with your moving.  There's some possibility that your current relationship won't survive the move, but the fact that you call her your girlfriend, and not your wife or even fiancée, suggests that you don't really think of the relationship as permanent anyway.

Yeah, I know, that's harsh.  And maybe I'm totally off-base.  Maybe your current relationship really is more important to you than the rest of your professional life.  If that's true, tell her so.

Who knows?  Maybe you can do both!

But whatever you decide, don't base your decision on fear.  Instead, ask yourself: What do you really want?  What really matters to you?  Fear of change and Impostor Syndrome are completely natural, and far more common than most people think, but they're just voices in your head.  Letting them control your decisions is not healthy.  You have people in your life who believe in you, who support you, who want you to succeed and be happy, and who know you far better than Some Random Stranger on the Internet—listen to them!


Different CV for university position and research industry position?

As a general rule of thumb, if the position you are applying for (1) has the term "researcher" or something similar in the position title and (2) requires a PhD (or research masters), definitely send the academic one. The fact they're looking for PhDs means they're interested in research experience, and your academic CV will highlight that much better than your industry one.

That being said, it is an industry position, so I would do my best to keep the resume two pages, and offer to send the full CV on request. Definitely include "Selected Publications" and "Selected Oral Presentations" sections, but keep it short.

One extra idea for consideration: I sent my (academic) resume to an industry position, and they sent it back asking for a short (one to three) sentence blurb describing each of my projects (at the time, my resume included work as a research assistant, graduate student, and post-doc). I ended up using that format for all the jobs I applied to, since most people have no idea what "Temporal Dynamics of the Cortico-limbic System" actually means. It's a good way to help them actually get a feel for what you accomplished and what your skills are.


How much can/should quotes from student evaluations be edited when preparing a teaching statement?

In general, quotes should always be edited as little as possible.

The only changes you should make are:

Truncations to remove sections of quotes that aren't relevant for your purposes.
Edits to fit the grammatical structure of the existing sentence.
Correcting small errors in the original text.

However, any changes to the quotation must be clearly indicated. Truncations should be marked with an ellipsis (" . . . "), while all other changes should be indicated using square brackets.


Should one list incomplete degrees on a CV?

Don't omit it. Changing your mind at some point during your education or your career is nothing to be ashamed of. Just make sure to put it in a way that does not imply that you actually got the degree.

Not listing it would be an error in three ways at least:

experience even in unrelated fields is always valuable;
if you omit that stint, there will be a hole on your CV, and you will have to explain it (so you'd better mention it upfront);
you got a publication from it, so it was actually a successful experience, even if you didn't complete your degree

In fact, my advice would be to always list what you've done on your CV, even if it is not an academic activity. Even if you spent two years traveling and selling onion rings on Australian beach grill house, put it in your CV. The pros outweigh the cons (and if that experience leads a potential recruiter to turn you away, ask yourself: would you have wanted to work with someöne who has such as narrow view of life?)


What style questions should I ask potential graduate students interviewing for positions in my lab?

I underwent an interview recently from a prospective adviser, and I found the questions he asked of me to be pretty insightful - hence I'm sharing them here.

Why do you want to pursue research in this specific area?

This would highlight the candidate's motivation in wanting to do research in a particular field - and would also tell the professor more about the candidate's exposure to this area.
What made you apply to this lab/university, as a continuation of the previous question?

The answer would tell you whether the applicant had simply browsed the rankings list of universities, or did he/she actually go through the research publications of the lab - and the application was done due to an intersection of the two!
What would you like to be doing post Ph.D.?

There is no "right" answer to this, but it also tells a lot about the candidate's motivation in pursuing a PhD.
Finally, you can ask the candidate to discuss any problem that he is familiar with in that field - doesn't have to be anything fancy/complicated, but that would serve to highlight the clarity of the applicant's reasoning, communication skills, and level of exposure to the field.


How to improve chances of admission to Ph.D. program for international student?

Here are some basics that can play a role and improve one's chances, from a U.S.-centric point of view:

Some assumptions:

Your postgraduate degree is reasonably recent (preferably immediate prior year or close, with relevant experience in between). If there was a lengthy break with seemingly unrelated work in between based on what you want to study now, this complicates things.
You are applying in the same general discipline as your postgrad degree (e.g. Marketing, Mechanical Engineering, Psychology).
You had good letters of recommendation. If they had any flags that might give cause for concern for admitting department, that is a problem that you need to iron out prior to sending out any more applications. If you have reason to think this may be the case, it may be best to approach your recommending faculty honestly about this and see if they can either share a copy of the letters they wrote for you, or tell you if they mentioned anything that might explain slow uptake.

Communication with faculty:
- evidence of "passable" English proficiency (if non-native), or (if native) ability to write in pretty much perfect English with no grammer or, punctuation errors.

Admission materials:
- Have all your applications been "cold," i.e. with no personal connection to / past interfacing with the faculty whom you contacted? In other words, have the letters of recommendation (which I am assuming

If so, this might explain reticence to respond. The Academe is a fairly tight community of several thousands or hundreds of individuals in any given narrow field. The "first order" professional networks tend to be on the order of a couple dozen past/present collaborators. Faculty tend to be more comfortable receiving a recommendation from someone they know rather than a complete stranger. So ask your professors who write your recommendation letters for contacts they would recommend, and tackle those programs as priority #1, gradually widening to "outer rings" of your recommenders' professional networks.

Maximally polished, edited, proof-read, 100% perfect letter of interest (cover letter/whatever they call it). The letter must show evidence that you have done your homework and are aware of the latest research projects of the faculty whose work most closely fits your experience and interests and who you would like to advise you.
High score on GRE or other applicable standardized graduate entrance exam.

Funding source:
 - As has been suggested elsewhere on this forum, I would avoid stating anything about the fact that you are not seeking funding. This self-qualification might come across as, "I am hoping the fact that I am a cheap date will sweeten the deal." This might work in some odd cases, but most reputable, large research universities tend to be more concerned with attracting high-quality applicants rather than affordable applicants.

If the department considers the applicant to have potential and leans toward admission, but there is no funding, they will communicate this though an admission decision without corresponding offer of Research or Teaching Assistantship. This leaves the ball in the applicant's court, and things work out through natural attrition. (For instance, I had no offer of support first year, so found a Research Assistantship with another research center on campus that was closely related to my field, and it ended up a good fit.)

Networking:
- Have you met, or at least read / cited in your thesis or research papers the professors you are contacting? Professors like applicants who do not only talk the talk (in a cover letter) but walk the walk, having used their theories and cited them accordingly in written work. Naturally these pieces also make for good writing samples, if the department and/or the Graduate School requests those as part of the application.

Finally, basic psychology suggests that applicants who behave like pests which, if not kept at an arm's length, would swallow all of a professor's free time and clutter his/her inbox, are less attractive, than applicants who communicate no more than necessary as part of the application process, and follow-up only with good cause and after first trying to get answers with the Graduate School and/or department's admissions office. Professors value their time immensely, and aggressively prioritize what emails they respond and do not respond to. They are not trying to be rude, it's just a professional adaptation to an environment with multiple competing priorities and limited time. So you want to come across as someone who recognizes this and helps them spend less, not more time addressing your inquiries.

UNLIKE THIS EMAIL, if you do email faculty, keep your email inquiries SHORT: 3-4 sentences, and get to the point in the first or second sentence. Begin with a question and request, and end with context. Professors often do not read to the bottom of every message.

Communicating through the appropriate administrative channels and only when necessary beyond the formal application process makes you appear confident, and confidence may be perceived as evidence of having other options. In a sense, you want to balance being courteous, excited, and a little reserved at the same time.

Finally, I would encourage to consider looking closer to home. Why apply to all continents if there might be a great program a few hours away in a neighboring town in the same country...but I recognize there may be other factors at play there.

I am sure I am missing some other important details, so extensions/comments welcome as always.


What did Grothendieck mean by "the capacity to be alone" in the context of mathematical research?

As this is a translation, the words "capacity to be alone" may not be the best way to phrase it. Perhaps this is a more literal translation, but from context I might write it as "independence".
He is saying that other people who he perceived as more capable individuals ("more brilliant than" he) as researchers were successful, and yet were constrained by doing work similar to others. Perhaps they worked on incremental solutions to problems within a general framework in the research community.
He implies that the status quo ("invisible and despotic circles which delimit the universe of a certain milieu") is a constraint on creative work.
He is suggesting that his own impact has been more profound or more revolutionary because he has been able to be more independent from others, to make his own path either in the problems he approached or in the solutions he found, and that he thinks the other people he talks about would have had similarly profound impacts if they had been less focused on the work or opinions of others.
Who knows whether he is correct that this is how researchers should think, it's just one opinion. I think it's somewhat dangerous to assume that because an approach worked for someone that you should take their advice that it would work for everyone. There is a lot of survivorship bias in that those who go their own path but are not successful are seldom heard from - who would read their book?
I'm not a mathematician and am not familiar with Grothendieck's work. Just from his Wikipedia page it seems he became a bit reclusive and didn't engage with the broader community later in his career. From Wikipedia which talks about the work that you quote from:

In the 1,000-page autobiographical manuscript Récoltes et semailles (1986) Grothendieck describes his approach to mathematics and his experiences in the mathematical community, a community that initially accepted him in an open and welcoming manner but which he progressively perceived to be governed by competition and status

It could be that he misjudges the ways in which his earlier work that became so influential benefitted from that of others around him, and misjudges the profundity or impactfulness of the work that he later pursued in solitude. Just because someone has a genius in mathematics or any other field does not necessarily mean they are good at assessing the reasons behind their own success; self-reflection is an entirely separate skill set.
For what it's worth in contrast, another famous mathematician wrote, "If I have seen further it is by standing on the shoulders of Giants", which seems to be a bit of a different philosophy (though I may be treating Grothendieck uncharitably, as it seems his quarrel is less with the work of others and more with the academic establishment, but it still speaks to the value or lack thereof of independence/solitude in academic work). Google Scholar uses the motto "Stand on the shoulders of giants" in recognition and tribute to this sentiment.


Is there some standard protocol to suggesting reviewers/referees for a paper?

No, the editorial board serves a different purpose from the reviewers. Typically, your paper will be assigned to one member of the editorial board, who will be responsible for managing the review process, and making a decision based on the reviewers' recommendations. However, the reviewers may be anyone with sufficient knowledge to understand and assess your paper.

So, feel free to list reviewers from the wide world! Note that there is typically no obligation for the editor to use the names you suggest; often they will make their own selection, based on their knowledge of the field.


Not sure if grad school was the right choice

You're experiencing what a lot of graduate students go through—moving from being a big fish in a small pond to being a big fish among other big fish in what seems to be a vast, uncharted ocean. Feelings of frustration, confusion, and even bewilderment are normal. It's part of the adjustment process. The truth is that many of your classmates are likely going through the same difficulties.

The question to ask is not "Should you be in grad school?" The question to ask is "Do I want to be here?" If you do, then don't let imposter syndrome drag you down! Also, remember that research bears often little resemblance to classwork.

Now, on the other hand, if you've realized that you're not interested in doing a PhD anymore, then you'll be much better off figuring out what you'd like to do instead. There are a lot of career options for mathematicians, and wasting a bunch of years getting a PhD you're no longer interested in won't be of much use for you in the long run.


Is it ok to share a a client's dataset on github, along with my code?

My take, as someone who tends to use other people's data in extended analysis, and does enjoy having the most up-to-date version of an analysis/etc. up on GitHub:

  Should I ask each user if they want me to remove the datasets from
  their repository?

Yes. You should, fundamentally, be respectful of other people's data. Which includes things like "I'm about to put this on a website". While you haven't mentioned if your repositories are public or private, there's no guarantee that data stored in a private repo won't end up in the wild, one way or another.

  Should I remove all such datasets regardless? Why or Why not?

I don't know that I'd remove all the data sets that are already up there, but I would definitely ask for approval, and if you don't hear back, assume that the answer is "No".

  Is there something else I might be missing about this scenario?

Yep...

  These are mostly medical and health research projects.

You haven't said what kind of data, but beyond just whether or not your anonymization step is actually sufficient, is whether or not the agreements that generated this data - IRB approvals, informed consent documents, data use agreements, etc. actually allow it to be put online in this form. That is, by no means, a sure thing.


Invited paper: who has to be the first author?

If a person receives an invitation, the responsibility to deliver will be with that person. That does not necessarily mean that person will be first author although I suspect it will most frequently be the case. There are many posts on academia.se that deal with first authorships so I do not think I need to replicate many good answers here. Suffice it to say that you need to discuss the authorship with your advisor. Unfortunately, this should have been done early on because lack of an agreement on authorship ordering early on is what usually leads to conflicts in the end. I am not saying this applies in your case but the fact that you ask seems to go in that direction.

For authorship and contributorship discussions I can point you to two posts in Council of Science Editors and BMJ (formerly the British Medical Journal). There are many other sources but they provide the core ideas on author/contributorship. It is easy to agree with these ideas, more difficult to live by them, particularly in a student-advisor relationship.


How do I write a reference in my reference list which has various places of publication with different editorials?

You reference the one you actually read.


How can I keep up with all the important advances in fields related to mine?

There is no easy way:

First step would be to talk to your advisor.

Second step would be to look at recent issues of the main journals in your field.

Third step would be to attend some of the main conferences in your field, listen to the talks and talk to the people.

After that you make up your mind what your opinion the trending issues are, and repeat steps 1 and 2 (and maybe 3) to try to confirm that.


Can dissertation be included in publication part in CV

I think it is best to put your dissertation under its own heading "Dissertation". Even though this wastes a little space it makes the thesis easily identifiable. The value of a dissertation will diminish with time after the PhD so you can change its location later you want to conserve space. But, particularly in your early career many want to be able to clearly see what you wrote up for your thesis work.


How to prepare for first year university after college diploma?

It would be a good idea to Contact the professors of the courses.  Usually they are already assigned to the course before it is offered and something you can look up prior to the course starting.  They could give you a list of recommended reading/sites to visit or they may simply say you have nothing to worry about.

I too have switched between community colleges, public and private universities and I do understand your worry.  While the experience is subject to change based on the individual, I found there to be little I needed to do to change my study habits and achieve the desired grades between all 3 experiences.

Remember it is school where you LEARN.  You aren't expected to go in already being a calculus expert or a mad scientist.  These are the freshman/sophomore level courses where it is generally assumed little prior knowledge outside of the pre-req basics.  Of course some classes also go hard early to weed out students as well and force drop out.

The only other suggestion outside of contacting the school/teacher for materials
 is seeing if you have the text book for the classes listed already.  From my days in college, usually the online forum for the class had a home page that listed off basic syllabus info such as teacher name and course materials needed.
 If not you can always contact the school/call the uni book store to find out what the names of the books are for those specific classes.  You will generally be able to find text books on Amazon and will be significantly cheaper than the uni book store anyways.  Thumb through the chapters on your own leisure.  That way you can go through the book and write notes down on things that seem to be a struggle topic and do your own focused preparation.  Or you may go through all the books and see that you really were worrying for nothing!


Why might a paper published in a good journal no longer be available anywhere?

After forwarding my email to the director of the publishing company, he put the paper online, so it appears that this was an administrative issue. I thank everyone for their input and apologise for the noise.


How to deal with animosity between different "factions" in a certain field?

The same happened to me. I stayed friendly towards everybody and participated in both groups. I think it worked for me. It leaves all doors open. I think a key point is never agreeing with any bad-mouthing, ever. Sometimes this is socially difficult. I would play dumb and say "Oh" or "I understand", but never "You're right" or "Yes, totally".


Is TA-ing worth the opportunity cost (of having more time for research)?

Most people who TA don't have an option as it is what pays the bills and allows them to study. It is less valuable if you can pay your own way.

But it isn't entirely without value. I once held a full fellowship for study (multi year), but it still required that I spend one of those years doing the equivalent of a TA. The feeling was that it is valuable experience for any academic, even at an R1 university. And, FWIW, I actually made more progress after the fellowship ended and I was a "lowly" TA.

But not everyone winds up at an R1 and elsewhere, teaching is more highly valued. And a variety of skills on a CV is, IMO, an advantage, though others may disagree.

Additionally, having something to do other than your research is a useful way to let your mind rest and integrate ideas, which is a key part of learning. And a variety of experiences can be valuable in keeping yourself flexible for the future. And "more" research doesn't necessarily equate to "better" research.

Most doctoral students get along quite well having some duties, such as a TA position, in addition to their research.

But whether it is worth the opportunity cost or not is a completely personal thing. Maybe yes, maybe no. Think about your own needs and resources.


Stop someone Publishing a thesis without giving credits to original author

You can't reasonably stop someone else from trying to publish something.

You could however file your thesis right now (at ArXiV or a similar venue) to establish a time stamp. If then later your thesis is published under another name, you could ask the journal for a retraction. Be prepared to prove that you are not the one trying to get credit for your manager's work, though.

If you do not want to expose your current version of your thesis (and you do not want to demonstrate a lack of trust by publishing an unfinished version of your thesis), you could make a PDF that includes your name and publish its hash value in a way that it gets timestamped (there may be other services for this). This allows you to prove later that you had this PDF already at the said time of publishing the hash value.

Note that using your text verbatim without your permission is probably a violation of copyright. Again, you need to make sure that you can later prove that you are the author and you have the text already today to make legal actions possible.

I'm not touching on the topic of whether your suspicion is reasonable in this answer.


What are advantages/disadvantages of Habilitation over PostDoc in case of academic career?

PosDocs usually work on someone else's research programs. Often the program is an incremental or partial step in a larger research framework. Postdocs have some independence in choosing the methods for their research, but are largely supervised/trained by their PIs or mentors. Postdoctoral projects can be rather technical in nature. They usually result in a few journal publications. It is very likely that your colleague next door did or will do a few postdoctoral projects during their career.

Habilitation is a large piece of work focused on a large problem, performed completely independently by one person. It usually contains major theoretical breakthrough (e.g. a completely new methodology) and results in a number of journal publication and at least one major "manuscript" publication (e.g. book). It is not so likely that a random academic next door did a Habilitation (because in most countries PhD is a terminal degree and Hab. does not exist).

tl;dr: Postocs and Habilitation are completely different programs.


How can editors and reviewers detect data manipulation?

The image manipulations reported on Retraction Watch are most of the time naive collages of gel photographs or spectrograms. They get caught, among other things, because repeating patterns in the noise appear on closer inspection, or linear disruption of the noise are visible, see this.

For 1D data, the case you mention, there is the Benford's law and other statistical tests that can indicate potential manipulation of data. It usually relies on human beings preferring certain digits over others, even unconsciously, thus generating data that has a non-random variability.

Also, many journals ask for graphs to be submitted in vector format, which means you are actually sending the data points, and not just a rendered figure. Things like editing out a few data points to smooth a curve will be apparent.

Now, to the best of my knowledge publishers and, even less so, reviewers don't systematically screen for these things, they only do so if they have suspicions, because the scientific publishing process is based on good faith. But if the paper gets any sort of attention it will get caught by post publication review.

Don't fabricate/manipulate data. It's adding unwanted noise to an already noisy signal, it's dishonest towards your coworkers, the people who fund you, the publisher and the readership, and it will ruin your career.


Is it wrong to leave Ph.D program after MS?

It is often frowned upon to leave a PhD program after you receive an MS, if this is your intention from the start, because the program would have admitted someone else who wanted a PhD had they known. However, if you don't tell anyone that this is your intention, there is no way for the program to know; PhD students drop out all the time after getting a masters (it is usually assumed that this was not their original intention). But ...

You are lucky enough to have been accepted to a fully funded masters program! If you think it is a good program, you should go there. Fully funded masters programs are quite rare in most fields. Do the right thing and allow the person who really wants a PhD to enter the PhD program. The PhD program, most likely, has offered you funding assuming you actually want a PhD.

Now if you had not been accepted to this fully funded masters program you would have had a tougher ethical question. For people not accepted to such a program the options are to (1) doing something that is morally questionable (at best) and going to the PhD program, (2) getting a job and waiting a few years until that employer funds a masters degree or (3) paying the money for a masters degree and potentially going into debt. That is a much harder question to answer, my inclination on that one is to go for option (2) if at all possible. But the fact that you were accepted to this funded masters program makes doing the right thing a much easier decision than for most people in similar situations. Take advantage of it!

Response to edits made to the question: Note that you can still evaluate whether you want to go on to a PhD from your separate fully funded MS program. After your MS, you might even get into a better PhD program and have a better idea about what PhD program/advisor would be best for your research interests. The fact that you "may" want a PhD in the future is actually a good reason to take the fully funded MS program. The opportunity costs of delaying the PhD by 1-2 years, by doing a fully funded masters is much less than the opportunity cost in delaying an industry job. .


How to request an extension for submission to a conference?

The words you propose are reasonable, but unlikely to have much effect. Usually, you just plain cannot affect the deadlines of a significant conference. If it is a small conference, however, there is a good chance that you can get a one week extension, and even that they may give a blanket one week extension to everybody.


I'd send the .tex and .bib file, which seems by far the most logical thing to do, to both you and me at least. On explicit request I'll grudgingly provide the .bbl file.

This should make things easier for them, as you correctly suggest. It is easy and fast to convert a .bib to a .bbl, but the other way round is impossible.

If the journal has a workflow that can't handle .bib files, that seems their problem and not mine. They are the professional publishers who charge for the "added value" of the professional typesetting and printing service, right?


it is a good idea to use colors for citations in hard bound thesis(printed copy)

I agree, don't use colors for citations or any other text in print.

Besides being potentially distracting or harder to read, it's often more expensive to print.


Publishing Ethics: not listing Professor's name

Why not ask for his feedback and if he would like his name on it at the same time?

He has two responses:

Yes, I’ll give you feedback and would welcome my name on the paper.

Or: happy to provide feedback, but due to X, can’t put my name on the paper, thanks for asking though.

I have assumed that he won’t refuse to provide feedback. The first option may lead to a better paper.


The third route is the best option, because it does two things at once: it immediately tells the reader which book you're referring to, and the citation will provide information on the specific edition of the book you're working from.

If the book is well known, it doesn't hurt to make the reference explicit. If it isn't, then mentioning the title won't make a huge difference. And it's always a good idea to avoid stilted academic writing, so anything that allows you to avoid writing something like the first example is a good thing.


Software to make illustrative videos explaining a research topic

Not free or open-source, but my institution offers licenses to Camtasia Studio, which seems to be the best package out there for slidecasts/screencasts.

Educreations is a a comparatively much simpler - and cheaper - tool that allows you to create videos but doesn't play as well with slides.


What is expected when submitting to a conference

It is typical to just provide a title and abstract.  In my experience, they are usually submitted in plain text or TeX format, not even in pdf.  You are never asked to provide a paper, though for some conferences you may be asked for notes later.  Based on your question, I guess the organizers want you to submit a file that they will just link to on the webpage for an abstract, which could be a pdf or plain text.  If you're still uncertain about what to do, just ask the organizers what they prefer.


How valuable is a conference paper in Avionics and Aerospace Engineering?

There is 2 parts to this question:

(1) How valuable are conference papers to grad school admission?

The answer to that is field-dependent. In some fields, the value of conferences as means of publishing scientific content is perceived small. In others, primarily Computer Science, conferences are of major importance, hence papers in good conferences are perceived as very valuable for admission.

However, arguably, even in fields were conference papers count less, having published in and attending good conferences may make you stand out of the crowd in grad school admissions. Primarily, in these fields (e.g., physics), undergrads that have good journal papers to their name are very rare, so having been to a conference as an undergrad is already pretty good, even if it does not count for all that much in the grand scheme of things in the research field.

(2) Is it worth it given that conferences are very expensive?

I am of course generalising here, but as a rule of thumb, you should not have to pay for your own conference travels, as long as you have an accepted paper as an enrolled student. Most universities have stipends and travel grants that you can apply for, you can act as a student volunteer, or, most importantly, your university department covers your travel expenses.

Assuming that it is indeed not feasible for you to have your costs covered, you will need to take the decision yourself. Whether it's "worth it" depends not only on the value of a conference to the admission process, but also on how much >1000 USD are to you, personally. Clearly, the story is different if you are a foreign student living of a small stipend than if you come from an upper middle-class family in the US.


Postdoc application, different team, same institute

If you're interested in the new position, just go ahead and apply! If the two teams in question are working in closely related fields, the new position is presumably a good fit for your profile anyway. In that case you're unlikely to look like someone who just wants to work at that institute. If they're in rather different fields (maybe they fall on different ends of your spectrum of interests) make sure you really explain why you're interested in the cover letter.

In any case, what's the worst that can happen if you're viewed as only looking to get into institution X? You don't get the position there? Well, you're even less likely to get it if you don't apply for it...


One of the most revolutionary physics results of the last century is the Michelson-Morley experiment. The experimenters set out to measure something, but measured zero instead. It turned out that the basic assumption (Aether theory) was incorrect. That didn't jinx the experimenters in any way; instead their names have since become immortalized in undergraduate textbooks and one of them even went on to win a Nobel Prize.

Is it the supervisor's responsibility to verify these things before engaging a student? Maybe, but without knowing the details it's hard to say. In the case of aether theory for example, it's the experiment itself that's supposed to verify the assumption; in other cases, there's still a good chance there's something subtle that you're missing (or why would they engage you to study it?). This means the solution is to talk to your supervisor. See if you can convince him/her that the hypothesis is indeed incorrect, because a basic assumption is incorrect. If that's true, that's quite a result: it means both your supervisor and your supervisor's supervisor assumed something that seemed reasonable enough to engage a student to work on, and then later turned out to be incorrect. If the field at large also made the same assumption then even better.

As for getting into a PhD program, don't worry about it. Showing that a basic assumption is wrong is quite an achievement, and this should be reflected in your recommendation letters. It's possible the admissions committee will read your thesis and find out that you didn't discover anything revolutionary, but that's not a big deal: as illustrated above, proving that something doesn't work / doesn't exist is still a result.


My conference paper is not published in IEEE Xplore because we didn't fill the copyright form in time

The first author should have been checking their email.
They may be able to publish it during the next cycle, you will have to discuss it with them but by not replying to their email you did not give them many options.


Is it advisable to hand in a thesis by visiting my supervisor's house?

I wouldn't find it okay if someone would come to my house because of that. Work and personal life should be separate and it would be inappropriate to visit the supervisor there.

Does he not have an office? If nobody can tell you where to find him, then you should call him or write an email and ask for an appointment.


The structure of a multiple-study proposal/thesis/manuscript?

I had a similar situation. My thesis proposal included three different studies.

Obviously, you have a subject and both studies fall under that subject. This means you should have one introduction concerning this subject, one set of objectives and hypotheses. Personnally, it's in the method section that I would explain that I'm going to test those hypotheses using two research methods.

After that, it depends on your institution rules for thesis proposal. Just remember that your PhD is not about the experiment or studies you're doing. It's about answering a specific question, testing some hypotheses.The method you use is secondary (in my opinion).


What to reply a PhD supervisor who says my chances of getting selected in this scholarship program are not very high?

The professor is saying no. He is being polite about it, but he's saying he doesn't want you in his group. Arguing with him is not going to change that. (In fact it's more likely to solidify in his mind that you are a bad candidate, with poor social skills, who would be a poor fit in his program.)

Look for somewhere else to go.


Nature Genetics is a reputable journal that might publish papers in the category of "genomics," which itself is a subset of "omics." Broadly, omics encompasses the quantification and analysis of various biological components – for example, metabolomics uses LC-MS systems to quantify different metabolites (e.g. tacrolimus degradation products for therapeutic drug monitoring in kidney transplant patients). Genomics analyzes the genome, which includes all the genes we have.

OMICS Publishing Group is considered a predatory publisher due to an apparent lack of legitimacy in their peer-review process, excessive publishing fees, and fraudulent behaviors as described in Predatory Publishing – Experience
with OMICS International (Masic, MED ARCH. 2017). However, Genome Research is published by Cold Spring Harbor Lab Press, which is from a legitimate institution.

Searching for "genome research" "omics international" brings up OMICS' Journal of Genome, Human Genome Research Articles page, and Genome Research review page, so I don't think they have a journal called Genome Research.

Your mentor is asking you to review articles from genomics journals like Genomics, Cytogenetic and Genome Research, Genome, Nature Reviews Genetics, BMC Genomics, Journal of Human Genetics and others that you can easily find.

A final aside: Last November, the FTC won an initial court ruling against OMICS International for their deceptive practices. Do your due diligence as you complete your literature survey and stay vigilant against unethical and irresponsible publishers.

These topics are relevant to my home institution (University of Colorado): Jeff Beall was sued by OMICS for raising these allegations several years ago, and I just watched Eric Green (director of the NIH Human Genome Research Initiative) speak at my program's national conference last Sunday.


If you aren't allowed to make a correction then you can't and it is what it is. But since it was accepted, there should be no issue for the thesis or for your degree.

However, in the future, if you do a publication that needs to cite the thesis, you can make a correction there. I assume, of course, that the error doesn't call your main result in to question. In that case you would need to either ignore the past or give a rather extensive update to your thesis in a new paper.

People make mistakes. People correct mistakes. Science moves on and advances.

Your thesis probably won't be the last piece of work that you do.


How do we test in academia, if a research area is a money burning machine or non/pseudo-scientific?

This raises several difficult discussions. The TL,DR is: Don't worry.

First, one thing is to talk about reproducibility when studying physics or chemistry. If I can make electrons eject from a metal sheet by some method, so can you, as long as you "reproduce" my metal. In this case, both the matal, a source of light and some electron detection device should be accessible for another research group without much difficulty. And usually there is an underlying mathematical foundation that allows one to work around difficulties in the reproduction. I.e. if you don't have the same metal or the same light source, maybe you can figure out a different material and light frequency that works for what you get. Are you reproducing the my exact claims? No. Are we jointly validating (or attempting to falsify) the same general thesis? Yes.

If however, I'm trying to make a medicine study, and my sample is the whole population of New Zealand. How can you expect to reproduce my results? Will you test the same people again? Will you try to test the whole population of Equador or some other country? Or maybe a whole province in China? If you get discrepant results, will you claim my results are false?

If you like to think like a mathematician, Imagine I give you a black box that presents a different number every time you touch it. And I give someone else a black box that looks exactly the same. For some reason, both of you believe that the sequence of numbers they generate is very important, and you start conducting research on it. With enough research, you are going to conjecture and decide that it is impossible to falsify that both black boxes are embedded with a random number generator, but each one has been initialized with a different seed. You'll convince everyone of this thesis if you are both able to record all generated numbers, figure out the random number generator algorithm and the seed of each box.  To make things more complicated, imagine the generated numbers are actually feed to some kind of Infinite Impulse Response filter. And that the coefficients for each box are different, and also need to be discovered for the scientific truth of the box to be uncovered.

Now, try to imagine that while you are touching the box, recording numbers and researching its behavior, you also need to publish results.

First, raw data is hard to publish. You can put it on a public database these days, but it does not constitute an actual publication. Remember: publish or perish. Even if you do, your date is not the same os the other box. If a researcher on the other box publishes his data, that is widely different than yours, would you claim that he is reproducing his experiments?

Now, as part of scientific investigation, you will try to figure out facts about the numbers. Are they correlated? Is a moving average nearly constant over a wide enough window? Is there a trendline? But the numbers are random, so what if none of this properties are matching? Do you actually expect that reproducibility will be possible when studying such machines?

And see that there is indeed a well defined and deterministic behavior for this machine, but it depends on parameters that are unknown, and are not replicated in the different boxes as they're found. Yet, nobody knows this for sure as the search goes on. People might start to conjecture that the numbers are absolutely random, that they are affected by room temperature, time, weather, vibrations and so on. Some people will claim that there is absolutely no logic to these numbers, and that the boxes are completely different.

Given this scenario, try to answer your own question. One day, someone might be able to discover the algorithm, filter structure and a method to find the parameters and seed. This would mean that every box owner can reproduce the method, the results, and start forecasting the future outputs of the box. Until them, nobody has found the truth, and even incomplete parts of the discovery would be very hard to prove by themselves.

But so what? Should people not publish anything? Do we consider this box to be pseudo-science and not fund it? (To be clear, the hypothesis is that everyone is convinced those boxes are important, though if we actually performed this experiment, they wouldn't be).

But this enters another question: How do you measure return on investment on scientific research? And should some return be expected at all?

If PhD students pay nothing for the classes they're taking, equipment they're using and still receive some stipend. I'm pretty sure they have to deliver some result. Otherwise, we'd be talking about social welfare, not about research funding.

Notice that there are companies, trusts, funds and other profit oriented organizations that will promptly provide money for a high enough chance of return above the risk-free rate. Then again, I've rarely heard of this financial sponsoring within academic environments. There are cases were companies fund a few scholarships mostly to ensure that enough people will be trained on a certain field of knowledge, where "acquiring existing knowledge" is a goal different than that of "performing research", which is "developing novel knowledge".

People often justify that spin-offs or unprecedented applications justify research which initially is pure science (rather than applied science). Every time someone says this to me, I ask them if they've ever developed or at least read a business plan. Usual answer is "what is that?".

As far as I've been told, no university earns money with patents. Not even MIT, or Florida University (which I heard was the highest patent-earning university in the US).

There is the case where after 20 years of research, only a few more two are needed before a commercial product is developed with the technology. This a matter of science maturing into technologies, and while people love to tell stories of unexpected success, there is a survivor bias applied there, as nobody enjoys hearing about failures.

Then again, a few fiels do have expected sigma-levels, quoting this article:

  " For publication in Physical Review Letters, for instance, 5-sigma results are generally called 'observations' or 'discoveries,'" (...) 3-sigma results usually warrant calling the result "evidence" of a new particle, but scientists need more statistical certainty to include terms like "discovery" in a technical paper.

As you may see, this kind of requirement, which falls into the lines you've probably expected as an answer is specific to a journal. I doubt it is field-wide standardized.

So, if you are the editor of a well-respected journal, you can impose your classification system (what constitutes evidence vs. discovery). And you can choose to accept or reject papers based on how convincing the evidence with respect to how feasible it is to obtain evidence at all. But don't expect everyone too agree with you.

Also, note that there is this underlying belief that observations and/or physical phenomena have gaussian-distributed fluctuations. Which may or may not be the case for the boxes example. For arbitrary distributions, a bound on the probability of a value deviating so many times the standard deviation can be given by Chebyshev's Inequality, which provides a much more loose bound. Even 5 sigma for Chebyshev means only 96% chance. But hey... Where did sigma even came from? Did you estimate it? From the data? What is the certainty you have on estimating standard deviation?

Also, I've mentioned survivor bias, there is the obligatory mention of XKCD's Green Jelly Beans Discovery.

To make my point clear, I think a lot of research should focus developing methods, which in turn may find their validity by usage, or how often then can find information that resist falsification with available data and experiments. In turn, many methods create new kinds of questions, rather than answering previously conceived questions.

However, your question seems based on the mindset of answering laymen questions "with science", which I believe is problematic in itself.

For starters, science requires precise language, which laymen don't speak, laymen (and myself on my daily life) ask simple, but likely ambiguous questions whose answers they might not understand. If I ask: "Can every even integer greater than 2 be expressed as the sum of two primes?", I'm asking a simple question, but note that "prime" in this sense is a technical term. You have to study a bit before understanding it. And If someone asks me this question, I can randomly answer "yes" or "no". But that is is not "answering with science" (though, granted, I'm talking mathematics). Despite considerable effort, this question remains an open problem. So if it ever gets solved, I would expect years of training for the answer to be understood.

To give a contrasting example: If I ask "Is cabbage good or bad for my health?". How do you measure good and bad? Those are un-precise terms. And also, I've asked "for my health". So, we may simply not have tools to infer that whatever finding you had for a test sample is applicable to me. Even then, if you manage to "test goodness of cabbage" for a subject's "health", as long as there is a single discrepant result, you should not extend your answer to me. And notice: I want a "yes" or "no" answer. I don't want you asking me about my colesterol, allergies, blood type, hours of sleep, other eating habits, type of cabbage, weather and common diseases on my city. I may not even know how to answer these questions.

But, if you could isolate all these variables, run a DNA test on me, maybe you could identify certain diseases I'm less prone to develop if eating cabbage regularly. That is insightful, that is scientific. And it requires you to collect much more samples to determine all variables that need to be isolated. Notice that those variables are part of studies that may reach "inconclusive results" by some sigma-level metric. And this goes back to my argument, that data and methods need to be developed, even if no conclusion is in sight.

Finally, we have the problem with corrupted/falsified data/observations due to researcher's mistakes and or poor ethics. Honest mistakes are usually random and uncorrelated (though there are questions about common misconceptions in several fields spread out SE sites). They are the main reason some people argue there is a need to reproduce results.

But fake data of fake is a different problem. Deliberately fake data or results are no different than a deliberate false claim. However, is it really a relevant issue? A good journal should demand reproducibility means from its potential publishers, so fake data may at best waste the editor's money investigating false claims. Assuming that fake or irreproducible research does not find it's way to top journals, and if it does, it should be relevant enough to draw enough attention of people equipped to debunk it in a few years.

Do you actually trust sketchy journals and small conferences? Anymore than laymen news sources? And here is the laymen problem again. He reads news outlets. He expects them to translate complex "scientific discoveries" to his language. He doesn't even ask for the original sources and proper citations. He might as well believe a hoax shared on social media as much as he believes an actual scientist. But this a problem with basic education, not with science itself. Implementing scientific conclusions on daily life is also not a straightforward process. That is, there is a long way between researches finding out that "cabbage is good for health" and nutritionists actually start recommending cabbage for patients. There is a reason why one should prefer talking to a specialist despite the fact that information is widely accessible. There is a big gap between having information and knowing what to do with it.

But what if... These false claims become medical products? That is why more than scientific journals, we need regulation agencies. They are the guardians of whatever methods for reproducibility or further proof should be required before alleged discovers become accessible for a broader audience.

After all this discussion, has your question been answered? I'm guessing you think "no". But then again, aren't you trying to ask a scientific question with a laymen mindset here? Even if there was a methodology to assert a sigma-level required in each field before publishing conclusions, would it be reasonable to systematically reject publications based on this criterion? I'm inclined to say no.


Applying for a PhD group who has asked for my research interests

When someone asks, why are you interested in joining my research group, what are the usual points or aspects you talk about?

You have to read up on what the PI and the postdoc(s) and the students are doing and read some publications.  Then when you are asked that question, you can say what you found interesting or exciting about what is being done in that group.


How to interact with difficult supervisors after graduation?

Sounds like their issue is that they don't want to spend more time on your defense. They don't have an issue with talking to you in general. So just prepare your defense without asking for help from the supervisors which don't want to help. After you graduate, feel free to write back as you normally would. Just not about the defense.

Just as a remark, I don't get how your other supervisor wants to help you but your main supervisor doesn't want you to ask his help. Presumably the other guy is a free adult, and can make his own decisions. If he agrees to help you, why would your main supervisor object? It's not taking any of his time, and if your defense is better and makes you more likely to graduate, that's good for him too.


Doubts about an experimental PhD project

Do not spend several years of your life pursuing a PhD project that you aren't enthusiastic about. If you do not want to be an experimentalist, it won't do you much good. It will be a lot more difficult to overcome the challenges and setbacks you will face if you don't like your project. Moreover, it's harder to become "an expert in the field" if you're not highly motivated to do so.

However, that said, it is possible for people to move back and forth between computational and experimental work. It's perhaps somewhat more complicated now than it used to be, but it's still certainly doable. Unfortunately, it may take some additional convincing to show people that you want to be a modeler if you've only done experimental work.


How should I ask a potential advisor why they haven't published in the last 3 years?

Instead of a question that might be insulting, you should probably ask them what they've been working on for the past few years. You need to know that in any case and their answer might give you the reason that they haven't got anything out recently. There may be a lot of work in progress but not yet ready. That sort of thing can actually be an advantage to you and knowing what it is, certainly is.

But if their answer indicates not much research, then you might want to keep looking.

By the way, this is a topic for a sit down conversation, not just an email. The latter might work, but would require more work from the prof and so you might not get as complete an answer.


Wear a surgical mask and nitrile or latex gloves. Do not touch your face while working. Take frequent breaks to walk away from the pile.


Web of Science is terrible in coverage of many fields (not sure what yours is from the post), and if you're stuck with it, you're stuck with it.  Try to see if there's anywhere that you can also say, "and here are my important publications that WoS doesn't cover, and here are all of their many many citations..."


Is it inappropriate for a student to attend their mentor's dissertation defense?

It's fine. As you say, these are open to the public, and it's common for family members, department members, and friends to attend. Since you perhaps are not "firmly" in any of these categories, asking whether it's okay to attend is probably a good idea -- but you've already done this and been given the green light. Enjoy.


How to reduce negative consequence for the person I plagiarized my assignment from?

Whether your friend deserves a grade or not depends whether he was a willing accomplice or an innocent victim.  If he was a willing accomplice, then probably both of you failing the class is the best thing you can hope for (at least for most US universities, where there are consequences besides failing if the professor or TA chooses to report it).  If he was a victim (he did not share his project with you with the intent that you could just copy it), then he certainly merits a grade.

In any case, the proper thing to do is for you to arrange to meet the professor in person, explain the situation, and apologize.  If your friend was a knowing accomplice, both you and your friend should go together.  Then it is up to the professor.


Applying to religion affiliated universities: how to write Statement of contribution to mission

I think you should certainly apply, as long as you have no personal opposition to Catholic education writ large; the previous question you link is a great source if you are uncertain.

As to your question, for an example, I pulled the mission statement for Marquette University in Milwaukee, WI.

  Marquette University is a Catholic, Jesuit university dedicated to serving God by serving our students and contributing to the advancement of knowledge. Our mission, therefore, is the search for truth, the discovery and sharing of knowledge, the fostering of personal and professional excellence, the promotion of a life of faith, and the development of leadership expressed in service to others. All this we pursue for the greater glory of God and the common benefit of the human community.

Following this broad statement, they have four subsections on Excellence, Faith, Leadership, and Service. Of course the mission of your university may differ but I presume it will paint similar broad strokes.

I would write a statement that addresses the primarily non-Faith elements of the mission. Quoting again from Marquette, on Excellence they state:

  education must encompass the whole person: spiritual and moral as well as intellectual, the heart as well as the mind

Without aligning with their religious beliefs, you could certainly contribute to education encompassing the whole person, particularly in intellectual pursuits.

Most U.S. Catholic universities that I am familiar with belong to either the Jesuit or Franciscan orders, though there are others as well - it might be worth spending a bit of time researching the order of the university you are applying to. Painting in a very broad brush, Jesuits tend to value intellectual pursuits as valuable contributions to society, and lean quite a bit more liberal than official Church policy on social issues. Franciscans are particularly concerned with service to the poor, and as such their universities try hard to accommodate students with financial difficulties. Even if you disagree on the religious aspects, you can probably find something in the general mission of these orders you also support.


Should one cite a dictionary for every technical term?

It depends on your target audience. If they are familiar with that medical topic, then it's not necessary.

Even if they are not familiar, citing dictionary is an inconvenient way to do it because i) the readers need to stop reading and get that dictionary, ii) most people who are not familiar with medical terms probably would not have easy access to a medical dictionary. For this reason, I will recommend having a glossary list/table or providing minimal but sufficient in-text definition. The list/table method is better for mixed audience so that the more technically inclined can read on without any problem; the in-text definition method is more suitable for generally less technically inclined audience.

I don't think you need to refer down to the page number and have multiple citations when you cite them. Dictionary is built in a way that you can find the word without page number. And if you use a list/table, then a combination of superscript symbol and a blanket citation in the footnote is also a convenient to deal with it.

In any case, seek out other similar reports or talk to the editor on how to deal with your problem. They would reveal perhaps the most common or best practices.


How to /Should I include a disadvantaged youth in personal statement

If you prove how it has strengthened your character, then perhaps it would be a valuable statement to make.

If you do decide to put it in, then ensure you keep it short and matter-of-fact; otherwise it may seem like you are "milking" the situation for sympathy.


Can I apply to CS graduate programs and take a year off before actually enrolling?

As keshlam truly mentioned, you need to check the existence of any deferral plan for that program.

If your admitted position would be a course-based one (like MEng), the deferral possibility would be applicable, noticeably. But in the case of the research-based programs (like M.Sc., M.A.Sc., Ph.D. and so on), the deferral chance might not be high, because such positions are often defined based on the funding, provided by either industrial or governmental customers and would not be postponed, considerably. If so, you have to reconsider to apply.


Master’s program rejection with no reason. How to appeal?

Yes, that's totally normal. For example, my department typically gets 150-200 applications for the PhD program every spring, but we only accept ~20 students. That is a process that is exceedingly time consuming already as is. It is simply not reasonable to write up an explanation why the other 130-180 students were not accepted.

That's no different than for most job applications: The company you sent your application to will simply say "Sorry, we didn't choose you because we found someone who is better qualified", rather than giving you feedback where exactly they found your application lacking.

As for appeal -- I don't think any university has a process for this, but pretend for a moment that there were: What do you think would happen? The university made a determination that you were not as well qualified as someone else. You can appeal a decision if you think that a process was not followed, e.g., if your application had arrived in time but was rejected because the department (erroneously) claimed that it was late. But your question does not contain any indication that you have any evidence to this effect. On the other hand, you can't appeal a rejection because you weren't as well qualified as some other candidate -- your "appeal" in that case ought to be to get more experience and more education so that on your next try, you are better qualified.


Good examples for methods section in math or computer science

Since "none of the papers published by the journal provides [a methods section]," despite the journal's requirement for such a section, you needn't fulfil this requirement.* (It is perhaps a generic requirement that most of the publisher's journals demand, but isn't required by the journal you're submitting to.)

*You can confirm with the editor, to be absolutely sure.


Can I do experimental research after doing a computational PhD in Chemical Engineering?

Especially in chemical engineering, it is definitely possible for people to move back and forth between experimental and computational work, and even to combine the two in a single career (although this is much more difficult, obviously).

Both of my graduate co-advisors have made similar transitions during their careers—from a mainly computational focus to a primarily experimental focus. It is definitely feasible.

The main issue that you'd want to remember at the earlier stage of your career is that the further away you want to leap from your PhD research, the harder it is to find someone willing to sponsor you to do that. For instance, doing an experimental PhD related to the topic of your computational PhD should not be too difficult; moving from computational combustion to experimental biomedical engineering would be much more challenging.


Can reading book review substitute reading the whole book in a literature review?

I'd recommend you should at least read and understand the chapters pertaining to your research.

If you trust the other professor wrote a concise, but complete and truly impartial review (because "even some people from Stanford praise him"? Think again: does that sound like a valid scientific reasoning?), you certainly may decide at our own risk to cite only the review.

By academic standards, as soon as you just add something to the bibliography you didn't read, it's... an academic misdemeanor. And adding a reference to something you did not even browse is quite the opposite of "honoring the author".


Is there an implied requirement to include citations?

(this might strictly speaking be out of scope of this site, but I'll answer anyway as I think the question in general comes up quite often)

Generally, when one is asked to write a scientific paper of some sort in university, there is an explicit or implicit expectation that you will use references. Often, students think this is unnecessary because they feel they know already "everything", or at least enough, about the subject without searching through the literature.

This is usually a fallacy for a number of reasons:

Oftentimes, students check web pages like this one and learn that in a published research paper, a certain level of common ground can be expected and does usually not need to be referenced. However, what "can be expected" is clearly dependent on the type of paper you are writing, and a published research paper works differently than a term paper in a freshman course.
Further, there is an underlying misunderstanding of what one needs to reference. References are not only required for what you are learning from literature "right now", i.e., in the current class. The things you already know you probably did not research on your own, entirely independently. You learned them in a previous course, and (maybe long before that), there was a paper or textbook that introduced these concepts.
Keep in mind that any paper writing assignment in a course is foremost a learning experience. One of the goals is that you should learn to research additional material (hence the "This essay may require additional research outside of the text."), and to cite it correctly. Circumventing this learning goal by basically just writing down what you feel does not require citation usually does not make instructors happy.
Generally, writing (only) about your "own experience" is a bit of a fallacy in itself. You should understand that you are in that case basically generalizing from a sample size of 1 (you / your experience). Let's look at an example. Maybe you have, for instance, worked a bit as software engineer, and hence believe that you do not need to read the literature in order to write a paper about software engineering processes (I am making examples up here). However, in that case, you know exactly your own company processes, and know little about how everybody else is building software. This is where you would look over published papers for more rigorous studies.

All that being said, in the end Dave Clarke's comment is accurate: It would be worth asking your instructor.


Is it plagiarism if I copy somebody else's answer I already solved but misplaced?

Is it plagiarism if I copy somebody else's answer...

Yes. Without even reading anything else you wrote. This is exactly what the word "plagiarism" means.


Many departments don't have hard deadlines for the graduate school applications, but they might have some test requirements that you need to take for the school to finally accept your application (i.e., many public universities need a GRE score for all applicants).

In case the departments are fine with it, you can still apply and take the tests in the next month or so, although a lot of departments will start accepting PhD students soon (if they haven't started already).

The tests are usually a general test GRE, a subject test GRE, or the GMAT, but they may vary. Since you're from the UK you don't need the TOEFL english test.

I would suggest to email/call individual professors or departments and ask for more information.

In a lot of cases the graduate student assistants can give you a lot of answers directly since they handle most cases.

Usually departments have a faculty member in charge of the graduate student program. They are also good contacts.

When I applied for my PhD in the states I was still in school in Europe, so I went through a similar situation, although I was done with the standard tests by that December (eight years ago).


How should I help students establish career goals?

You do not mention if your research students are graduate or undergraduate students.

First consider the extent to which career services at your university may or may not be helpful for your students. For instance, it may be helpful for resume and cover letter writing or interview strategies. However, it is designed for the whole student body and many not be helpful in pointing students in a specific discipline into a career path. So, they may not value career services as a resource for learning about future careers.

Second, it may be that your students have a narrow definition of what types of jobs there are in your field or what type of work is involved with different types of jobs. Your students may be open to learning more, but are unsure what questions to ask or where to research job opportunities. This may also be why students are more likely to look into job opportunities later in their education, than early in their education. They know more later about the field.

One suggestion to improve the process is to organize a seminar that includes faculty in your department and local professionals in your field to talk about careers in your field. Students will find this more inspiring and can learn more. You can make this a regular event (annual, each semester) and rotate the panelists so that students can see a variety of job opportunities and perspectives. I've seen this done in several disciplines and students seem to appreciate it. Also, since the panelists are basically discussing their own experiences, there is minimal prep for the people who volunteer.


Should I use AP scores to exempt classes when trying to transfer?

You should maximize learning and not grades.  If you already took an AP course and actually learned the content, don't take a course that is the same as the AP course unless you are required to do so.
Repeating courses for an 'easy A' will waste lots of your time and potentially your money too.  And there's no guarantee the course won't turn out to be much harder than you expect.


How to cite earlier work, discovered only at the end, that claims similar results to a recently completed project?

In mathematics (maybe in other fields too), one would put at the end of the introduction a statement like "After obtaining the results in this paper, we learned of related work by X.  In particular, X obtained ...." Here the "..." would be a description like "a stronger form of our Theorem 7" or "a weaker form of our Theorem 7" or "a result related to our Theorem 7" or whatever it was that X actually got.

In computer science (maybe in other fields too), papers often have a separate section called "Related Work", and information of this sort would naturally go into that section.


review paper and authorship of ex supervisor

I would say that only citing him would be enough. My field is cognitive neuroscience, yours might have different rules. I was in the opposite situation, a figure from one of my papers was included in a review where my supervisor was one of the authors. When they described the figure they cited my paper. A citation is quite a nice thing to have, especially in a review.


In how many conferences should I serve as PC member?

There is no right answer here. It’s a function of the time you have available to do service duties, as well as the benefits to you of helping out. However, it is a significant time commitment, so it’s probably not necessary to do it more than a few times a year. But whether the right answer is one, two, three, or more is a question only you can answer.


How can one best seek out collaborators in obscure topics as a young researcher?

As mentioned by aparente001 in the comments, the best way to start collaborations as a beginning PhD student is through your supervisor.

Your supervisor is hopefully a well-established researcher who's made some decent contributions to the field. People working on close areas of research will likely know their name and what kind of things they work on, and consequently the sort of things their students are likely to be doing.

Your supervisor may bring up the idea of collaboration without you asking, or you could approach them with the idea you have and, if it has merit, they might suggest names of people working on similar areas whose work you could read up on and get in touch with.

In this day and age, it's easy to start a conversation through email, and your second point about corresponding with potential collaborators and asking questions about their work is a good approach, but make it clear who you are,  what you're working on and why you're interested in their work from the outset.

If you're serious about starting collaborations with people completely outside your network (or your supervisor's network), the best way to do it is face to face, at conferences, meetings or summer schools. The latter are particularly useful for PhD students, as the attendees are also going to be PhD students or post-docs, who will definitely have more time and incentive to start new collaborations than senior academics will.

Lastly, don't worry too much! People are aware that new PhDs are still finding their feet in academia, and as long as you are professional in your enquiries, I don't think you'll go far wrong. It's certainly not bed etiquette to want to work with different people and broaden your research horizons.


Thinking about leaving my PhD, thoughts?

It's good that you're thinking about this now, but unfortunately, only you know what you want with your life.

You've given a nice list of pros and cons of continuing to study. Let's summarize:

Work now

Longer work hours
Secure job
Better pay, or at least not worse than a future PhD graduate
Not exactly what you love doing

Keep studying

I love physics!
Nomadic lifestyle
No guarantee of job

One thing you didn't mention is whether you have a significant other. Nomadic lifestyles are bad if you intend to settle down, start a family, etc.

If you look at all this there's really only one thing that's in favour of "keep studying": your passion for physics. Is your passion for physics so great that you're willing to risk everything else for the chance to pursue an academic career? Unfortunately, only you will know the answer to this question.

Here're two things you can think of doing:

Keep studying, but emphasize picking up skills that are wanted in the industry in the event that you can't get an academic job. Look at the jobs available for physics graduates in your area, see what the requirements are, and make it a point to learn them during the PhD as a fallback plan.
Work for a few years, with the intention to go back to studying after having secured yourself financially.

Ultimately, only you can answer this question.


Editor refuses to handle my paper for “lack of expertise”

Unless you have strong reason to believe this is an important journal for your field, I would be extremely dubious about having anything to do with a journal with such a lack of organization.

Every reputable journal that I have dealt with has at least some sort of process for tracking and handling manuscripts, which includes the ability to transfer manuscripts to the editor best able to handle the manuscript. Thus, no manuscript would ever receive the sort of uninformative and unprofessional email that you report: either you'd be transferred to a more appropriate editor or you'd be clearly rejected.

The "dead end" email that you've received certainly leaves it open that you might email other editors at the journal to see if they will handle your manuscript. I am not, however, convinced that this would actually be a good idea for you to do, and would suggest shifting to a more reputable and professionally run journal.


In teaching evaluation, does the number of students a faculty teaches matter?

That depends a lot on local policy. Here (UTFSM, Chile), for load assesment, if a class is small (less than 10 finish it) it doesn't count (unless special circumstances apply, like the last few students taking a discontinued class), if it is very large it counts a bit more (or you might get more TAs or be relieved from other duties). For teaching evaluation, each class counts the same (the class averages are just averaged).


Where should the line be drawn regarding political statements in a scientific report?

This appears to have been under the instruction of President Trump, as news sites reported data on the EPA website was removed.

Speculation usually doesn't belong in a scientific paper. This is especially true when it does not further the scientific purpose of the paper.

The rest of the statement - about the document no longer being available at its original link, and a note regarding its availability on archive.org, is fine because it is not speculation and serves an academic purpose. However, you actually don't need to resort to archive.org, because the document is still available on the archived state.gov site.

Like whitehouse.gov, the entire State Department website is routinely archived at the end of each administration, and the new administration can put whatever they want on their new site. (For example, at the beginning of the Obama administration, they replaced the Bush-era State Department site on climate change with their own.) The state.gov material from the Obama administration is still available; you just have to replace "www.state.gov" in the URL with "2009-2017.state.gov".

(P.S. an archive of the EPA website immediately before the transition, created in response to numerous FOIA requests, is also available: https://19january2017snapshot.epa.gov/)


The vast majority of math Ph.D. programs in the US will require both the general and math subject GREs, so unless you specifically avoid those schools specifically, you probably will have to take them.  How schools use the GRE varies a bit, but for someone whose record isn't as strong, it can play a valuable role in reassuring schools, since it's the only thing they have which is uniform across schools and recommenders.

For schools that don't require them, they will likely assume that you have taken the subject GRE, and will assume that not sending in your score means it is really bad.  If your score is really bad (less than 30th percentile), then it's probably better to not send it in, but if it's not abysmal, then probably you should send in the scores.


I think this is usually done in the section where you list your degree:

2008-2012 University of Big City - BSc (Hons.) Difficult Subject (Class rank: 2 of 30)

or similar.


Ask opinion about situations in which researchers/non-researchers get involved in projects (externally) and the best way to avoid strange situations

Situation A is more or less common specially it comes to publications.

Generally in such situation,

Both the parties should have clear cut understanding of role of each other before starting working on the project.
Ethically, that researcher SHOULD knowledge you for your contribution in the project if she/he want's to get it published or submit to any grant agency.
If you have contributed sufficiently and you think you should be part of their publication, you can just express your opinion to professor and make it clear.
Do not 'assume' that they have kicked you out. There might be changes in their project direction and they might need some other set of skills.
Inform regarding this to your adviser. It is important to keep him/her in loop.

However also remember, sometimes whatever you have decided may not work out because experiments/analysis might need to get more help or reduce existing resources etc. Best thing to do in this case is talk to professor and see what is your role in this project. To avoid further such situations, always be clear about your role in project. Sometimes your role might change depending on direction or project or results you got. You should be flexible enough to handle such cases.

In the case of situation B, try to contact their organization/institute regarding this. See what is the purpose of that advertisement. As you had not provided them any details, they could have come up with similar thing by their own. See their website /publications if they had working on similar thing before. Be patient and contact them again regarding this.


How do I know if I am a competitive applicant for a top/second-tier grad school?

There is one thing that comes across clearly to me based only upon what you've written. I believe you are a very hard worker and you are willing to take risks. These two characteristics are very attractive to many people.

I think you need to concentrate on writing a succinct (but complete) résumé that showcases all of your accomplishments and evidence of positive character traits. To answer your main question, I already have a clear sense that you are definitely competitive. Your GPAs have shown an increase over time and you have a unique history. This means you also have a unique perspective on life.

If you spend money on anything, you'd probably get the most bang for your buck if you had a professional write your résumé. Then, you could make edits to that to suit your own personality. Get that done quickly and then start applying to lots of schools. Don't spend any more time worrying about whether or not you're competitive. You are. Stop worrying about making mistakes. This isn't life or death, it's simply grad school. Just make sure that spending money on grad school will actually amortize in a reasonable amount of time. I think it will definitely do so for you based on the avenue you are interested in pursuing.


Edit: Just noticed this was 3 years old. Hope the answer is useful to others.

I had a similar issue (though I finished my undergraduate at the same university(UK) I was given my PhD position.)

I had submitted a poster and was accepted at a conference. However, the conference was in September a month prior to my start as a PhD student and 2-3 months after I ceased to be a student. Technically as I was no longer a student at the university they had no responsibility to pay for me, but never forget if you are even a future PhD student they want you to do well.

Together with my future supervisor we contacted the person in charge of the budget for conferences and explained the situation, along with all the relevant costings for attendance.

It was accepted.

My answer to you is:

First you need to do your second question. In my field of Computer Science the websites offer "early bird" attendance rates, rates for students, and in some cases of large conferences offers on payment of accommodation etc if you fall into certain categories (for example if you want to volunteer to help). Once you know the true cost you can do the second point.
With your supervisor(they will know who is who) contact the budget holder for conference attendance at the University you are going to do your PhD at. As above, state what is going on, why it is important and how it will help with your future as a PhD student at that University.

Hope you get your workshop approved!


How to get three recommendation letters while I only worked with my supervisor?

These collaborators are exactly the persons who can evaluate your work, your person and so on really good and in the eyes of a hiring institute, are more objective, because they haven't been your supervisors. So, definitely write and ask them. Probably, they don't know about your future career and current projects, but, I guess, they want to talk to you again about this (via phone or skype) and then you can explain much better what do you want, what's your motivation is and so on.  I would also guess that one of them needs some help in formulating the LoR and then you assist with some bullet points (there are quite a few questions and answer here, for instance this  or that question with answers/comments).  So, go for it and good luck with it!


Why are some sources cited twice in a bibliography, once with DOI and once with arXiv?

I agree with Dave Clarke.  I think the primary purpose of a bibliography should be to offer the reader a way to read the cited material.  A version of the paper on the arXiv achieves this goal better than any other means I know.  However, it's also important that the cited material has been verified.  By citing the journal version of the paper, the author communicates that it has been.


Are academics allowed to own/be part of/found a private company (UK)?

I believe that this is university based. To make a long story short, the university usually owns some form of copyright on your intellectual work and passes it to you when you publish. If any of said copyright is used for commercial purposes then you need to make a deal with them on a case by case basis, though there are standardised contracts. University will have a office devoted to this. If the company is unrelated to your field/work than there's no need for such arrangements, but you still might want to double check with them.

This is my understanding having seen a colleague going through some of this (and eventually get told there was no need to make arrangements, essentially if is not something you devised or developed while working its ok)


To What Degree is Graduate School Acceptance Contingent on You Choosing a Specific Potential Adviser?

If you are accepted, then you are accepted. The prof is trying to "capture" you early, which is fine, but you don't have to agree to it. In the US you can generally choose a research advisor fairly late, especially if you come in with only a BA/BS degree.

There should be no problem at all if you don't want to work with them. But, it would be worth projecting a friendly and flexible face until you see more of the new program and get to meet a few people and (probably) take a few classes.

Your first goal will be to take enough advanced classes that you are successful in passing comprehensive exams. Then, you get more serious about research topics, and, for many, even research areas.

Note that in some other places, professors (PIs) actually hired their own graduate students. This is less common in the US and hardly ever in CS here. In the US, it is a department, not an individual, that accepts you, generally with the advice of a committee of faculty.

But if anything were contingent on anything else, then it would be explicitly spelled out. The prof is "reaching out" because you seem "interesting." Nothing more than that.


Supervisor wants me to support a diploma-thesis software tool after I graduated

I think you are being generous and, given what you say, should be able to step away from the project with a clear conscience.

If he needs the software he should be willing to find a way to pay for support, maybe not you, I think, but some support person.

I would see him if possible or send an email giving much of the information you've given here. The fact that you are doing very different things now and that support is disruptive to your main goals should be definitive.

But I agree that it is good to find a way to keep a good relationship with him if you can also achieve your main goal.