Resubmitting elsewhere without any key change when a paper is rejected

If the reviewers pointed out inaccurate citations, false or missing attributions, or statements in the paper that have been pointed out to be false or seriously faulty (and that you agree are false or seriously faulty), then it seems to me that you are ethically obligated to respond to these before resubmitting.

If the reviewers point out what they claim are deficiencies in your paper but these are subjective and/or you disagree -- e.g. poor writing or organization, insufficient motivation -- then it is up to you to decide whether to address these before you resubmit.  If you take them seriously enough, it is probably more efficient to do so, since the next reviewers could have the same issues.  In fact the next reviewers could be the same as the present reviewers, and if their serious critiques go unanswered, they are not likely to look more favorably on the new submission than the old one.

However, if the principal (or sole) cause of rejection was simply that the paper was not a good fit for the journal -- either by a mismatch of subject areas or simply by not being strong enough -- then it's plausible that this can be remedied by resubmitting immediately to a different journal.

When it comes to my own journal submissions, all of my rejections were said to be because the paper was not strong enough for the journal it was submitted to -- I imagine that the majority of rejections for sufficiently prestigious journals are for this reason -- sometimes accompanied by other commentary by the referees.  Probably more than half the time I have resubmitted without revision to a different journal.  This has worked relatively well for me: the papers usually get published after one or two more tries, and I have received absolutely no negative feedback about this.  In fact, most of the time the rejection letters I get explicitly mention resubmitting to another journal.  Sometimes they mention taking the referees' comments into account first.  When they don't, I read this to be a directive from the editor to resubmit without changes.


Final report rejected, institution asked to return funding and prosecute my supervisor

You are absolutely not responsible for returning any funding, certainly not at a moral level and almost surely not legally either.  You were engaged in research to the best of your ability; as you were not the person who obtained and was responsible for the funding, you are not responsible to the funder for any failures.

Moreover, I think it is pretty unlikely that the funding body will actually claw back any money from your former supervisor.  Unless there was genuine skullduggery and/or intent to misuse the funds, the worst that is likely to happen is that the supervisor will be required to resubmit a much better explanatory report.


As you already noticed, you do not need to decide for one or the other but have to make a trade-off. I would advice to make this trade-off strongly in favour of good writing, i.e., schedule your work such that you have sufficient time to write down your thesis (or similar) properly and to have it reviewed for intellegibility (likely by your supervisor) and react to this. The reasons for this are as follows:

Your work is wasted if nobody understands it. The people who reviewed your thesis usually include your supervisor, i.e., the person who is most familiar with and most interested in your work apart from you and the single person whom you really need to demonstrate the value of your work. If even they had no chance to appreciate it, what was your work good for?
Communicating your work is one of the most important skills of an academic and hence one of the most important skills to learn in your studies. Most academics spend a considerable amount of time by communicating their work to others and academic success crucially depends on it. For example, people only tend to cite your work if they understand it. as far as I can tell, this is no different when you intent to leave academia.

Thus, time invested in learning communicating your work, in particular time invested in writing a thesis properly, is certainly not wasted. From another point of view, communicating your work is one of the skills you should be able to demonstrate when writing and defending a thesis – it’s not just about your knowledge of your field and applying this knowledge.
There is a saying that goes along the lines of this (and which I fail to find properly phrased right now):

  You only really understood something if you can teach it to others.

While there are a few people whose didactical skills are exceptionally bad in comparison to their expertise, these are really the exception (and you should not strive to be one of them) and this saying is mostly true otherwise. There are two things to “learn” from it:

By trying to properly communicate your work, you take different points of view at your work and thus understand it. This may enable you to find ways to improve your work or to apply it and connections to existing work.

If you cannot communicate your work, this is usually seen as an indicator that you did not fully understand what you are doing and thus is likely to lower the opinion of others of your work, in particular of important people such as your supervisor.


Whether to exclude standard deviation in plot of outcomes of a series of experiments?

Don't do this.

Here is some random data with 21 experiments A-U, each one repeated 3 times. In both cases, the experimentwise means (indicated using red crosses) are identical, but the within-experiment standard deviations are very different (1.0 in the top graph and 0.2 in the bottom one). R code is below.

Just seeing the experimentwise means is very misleading. In the bottom case, the experiments seem to be pretty different, and you could start interpreting the differences between them. In the top case, it's rather obvious that the difference between experiments is dominated by the variance within experiments. Put differently: the proportion of variance explained by the experiments is very different between the two cases.

This is a crucial piece of information. Do not leave it out. Leaving the variability out does not "blur the results to the reader" - the variability may be more important than the means.

In particular, remember that most readers will only look at your graphics, and even if they do read the text, the main thing they will remember will be the graphic. If you only put the means there, readers will remember the means. They won't remember whether the standard deviations were large or small compared to the differences in means.

So: look for a way to visualize both means and variability. For starters, don't use bar plots. Use, for example, dotcharts as I did. With your small dataset, you can without problems plot all your data, plus means.

If you want to emphasize the means, you can do all kinds of things involving colors, shapes or sizes. For instance, I used smaller grey dots for the observations so the means (larger red crosses) stood out more. And I used vertical lines to indicate experiments, and these lines are a lighter shade of grey than the dots.

Note that the human brain is better at interpreting positions (as in a dot chart) than lengths (as in a barplot). Nor should you use so-called "dynamite plots", that is, bar plot with "whiskers" that indicate standard deviations (or standard errors of estimated means - one problem with dynamite plots is that it is not always indicated whether whiskers give SDs or SEMs, and these are very different things).

See here and here for more on dynamite plots. This earlier answer of mine gives a few more options for visualizing data.

R code:

experiments <- LETTERS[1:21]
set.seed(1); means <- runif(21)
obs <- list()
set.seed(1); obs[[1]] <- matrix(rnorm(63,0,1),ncol=3,byrow=FALSE)
set.seed(1); obs[[2]] <- matrix(rnorm(63,0,0.2),ncol=3,byrow=FALSE)

opar <- par(mfrow=c(2,1),mai=c(.8,.8,.1,.1))
    for ( ii in 1:2 ) {
        obs[[ii]] <- obs[[ii]]+means-rowMeans(obs[[ii]])
        plot(c(1,21),range(unlist(obs)),type="n",xlab="Experiment",ylab="Observation",xaxt="n")
        abline(v=1:21,col="lightgrey")
        points(rep(1:21,3),as.vector(obs[[ii]]),pch=19,col="darkgrey",cex=0.8)
        points(1:21,rowMeans(obs[[ii]]),pch="+",col="red",cex=1.5,font=2)
        axis(1,1:21,experiments)
    }
par(opar)


Is it ever advisable for graduate students to go on sabbatical for several months?

We encourage our graduate students to take internships for 3 months during summer (at Microsoft Redmond and MSR Cambridge). This is a bit like a sabbatical. In our experience, these are extremely valuable for the students and for fostering research collaborations. Usually one publication results for the student, but the experience and the contacts they gain cannot be measure in the regular units.

We do not allow our students to go on such 'sabbaticals' if they are not already performing well. The lucky students who do get to go need to act as ambassadors for our university. We do not use internships as a way of kick-stacking the research of a student-gone-astray.

Unless by sabbatical, you mean vacation, in which case, I've answered the wrong question. Students are entitled to 6 weeks vacation per year (not including Christmas). They may take it in one chunk if they wish. Whether we allow it depends on what project deadlines need to be met and so forth. Generally, we encourage them to split up their vacation into smaller chunks (1 week here, 2 weeks there).


Thesis in use, potential employer wants to see source code

This can be broken down into two issues:

(1) Can you show the new company your source code/can they ask to see it?

They have only asked to see it, not to use it. Maybe as a way to assess your skill, see if you fit their requirements etc. No problem in sharing this. You could even share a copy of your thesis. If they want to use the code, and say so, you can look into licensing options.

(2) Have you given away your right to share it?

No, because the absence of any written contract works both ways. It is part of your thesis, so it is still formally yours. Until and unless the target establishment tries to copyright it in some form, you have the right to share it.

An exception has been pointed out by David Z - there is a possibility that your advisor's 'tie-up' with the target establishment could constitute a work-for-hire agreement, and this may restrict your freedom to share. If such a case exists, either you or your advisor must be aware of the details and can find suitable redressal. If you were not made aware of this, ignore all concerns and share.

Do get your adviser's consent and guidance anyway, and also check your university policy on IP.


Accepted as PhD student, but my funding application was rejected. Now my prospective PhD advisor recommends that I should bail out. What should I do?

Probably write to that supervisor, asking that if you think you will be busy, then perhaps you can suggest any other colleague.
There can be many reasons which that guy must have shared with you. I am assuming a few instances.

First, as pointed out in the comment above, he may be thinking that
getting a self-funded Ph.D. is too over-burdening to you (which
frankly, it is, because unlike bachelors or Masters degrees, Ph.D. is not only
tough, there is no minimum time-limit per se)

Secondly, he may be leaving the university or department, or he may have other engagements that do not allow him to supervise you at the moment. In that case, your asking him to direct you to any other colleague of yours would make more sense.

But frankly, I personally think that one should do a PhD on any funded project. A self-funded Ph.D. journey often gets a bit bitter towards the end.


Has anyone failed coursework requirement and got terminated from PhD program?

Yes, it happens. And it has to be this way.

We've had students who do not do sufficiently well in the coursework, but do so well in other regards that they are allowed to continue on to their Phd: the research committee is there to weigh up the positive and negative signs, within the regulations set out for them. Occasionally, we have students who pass the coursework and then struggle with self-guided research. So now we have two gateways: the coursework, and then a year later an upgrade report and seminar, which is their formal transition from an MPhil programme to a DPhil programme.

A department may not get many opportunities to formally remove a failing student. This will vary by institution and discipline, but it can be the case that there are not many opportunities within the trajectory of a single PhD to terminate cleanly and indisputably.

We never like to do it. It's the worst thing we can do. Apart from the alternative, when the alternative is letting a candidate go forwards into a drawn-out and ultimately unsuccessful attempt at completing the PhD. This is exacerbated if they might make increasing demands on staff, and/or might become increasingly disruptive to other students.

If the supply of good potential candidates is greater than the number of available places; or there are financial penalties when students fail later rather than earlier in the process; then the imperative to filter out weak candidates becomes stronger.

Coursework, research proposals, upgrade seminars and upgrade reports, are some of the small selection of tools we have to help us identify weak candidates. Writing a PhD thesis is indeed completely different to doing coursework. And there are candidates that excel at coursework, but could not write a doctoral thesis; and maybe there are candidates where the reverse is true. Nevertheless, the coursework gives us an opportunity to assess a candidate's skills and domain knowledge.

So that's why a justifiable proposal is not in and of itself sufficient (even when it's a self-funded candidate). If successful coursework is specified as a requirement, then the regulation doesn't need to say what happens if a student fails the coursework: if any requirement isn't met, then the candidacy doesn't have a right to proceed - that's the essence of a requirement. There might be alternatives to some requirements: these should be in the regulations somewhere. Your supervisors, or the faculty's graduate tutor, or the university's graduate school, should be able to advise.


Why not asking about updates of search process

I think there are only two cases where you should follow-up with the search committee:

The time by which they said they would get back to you has passed.
You have another opportunity that requires a time-sensitive response.

A while ago I read some good advice (somewhere on this site) about how to deal with the waiting period after a tenure-track interview:

  As soon as you're done with the interview & visit, thank everyone who you've met, and then immediately move on with your life under the assumption that you did not get the job, i.e., search for the next opportunities, etc.


Is there an informal understanding at universities about PhD student funding?

I cannot speak for all US universities or all disciplines. That said, the graduate programs in the natural sciences that I have been involved with  do knowingly commit in legally binding fashion to provide five years of support with the caveat that this may come in the form of 20 hour per week TA appointments if no RA funds are available from the PI or the department.

Why would someone accept a lesser deal? If one has a better option, I see little reason to do so. If one does not, one might perhaps accept such an arrangement in order to receive a PhD education that, in many fields, vastly increases one's earning potential.


Academic Hiring Process and Practices for Junior Professors in Germany

As xLeitix mentioned in his answer, I do indeed hold such a position, and have also sat in on a search committee (as a non-voting "interested bystander").

  1) I notice that the application packages do not require inclusion of recommendation letters. In the US, the typical requirement is that the application package includes at least 3 letters. Will the schools require recommendation letters once selected for an interview or the job? Do letters or references play any significant role at all?

It could go either way, depending on the preferences of the chair of the committee. In my process, my references were asked for recommendations; for the committee I observed, they asked "neutral parties" who could comment on all of the finalists.

However, one thing is absolutely certain: your PhD advisor (or Doktorvater in German parlance) will never be asked to submit a letter of reference on your behalf.

  2) Selection: I know this should vary by case, but how many people do they tend to put on their short list?

Typically four to six people are put on the list of interviews, while two or three usually make the final "ranked" list to be asked if they are interested in the position.

  3) Interviews: I get a feeling that the interview process is brief and a lot less tiring than the American system (for a R1: Typically a 3-day campus visit, job talk, endless meetings with professors, deans, grad students, teaching demonstration, etc, etc). What do they focus on in Germany? (I am asking this as I was invited for an interview, but I was not even asked to do a job talk or teaching demonstration) Are there typically multiple rounds of interviews?

Typically, there is only a single interview, and it is indeed far briefer than a US-based job or faculty search interview. None of the interviews I've had have been longer than two hours in duration, including any teaching presentations.

The focus in such junior positions is almost always on research, with very limited emphasis on teaching. You should plan to talk about what you've already done, and what proposed work you'd want to start. You'd also want to give some thought as to how you would recruit students (always a challenge for junior faculty in Germany).

  4) Selection committee: That some European departments practically have a one-person decision making body came as a surprise when I first came to Europe. How is the case in Germany? How many people in the department are typically involved in the decision making process?

It's not a one-person decision making process, but it's also not a very large group, either. Typically, there will be between five to nine voting members of the selection committee, including the chair, other professors, and possibly students and equal opportunity staff from the university (who can refuse to give permission for the hiring process to go forward if viable underrepresented candidates were not given due consideration).

  5) Final decision: How fast do they move with their final decisions? For example, the job I am considering only has about a four-month gap between application deadline and position start date. This is significantly shorter than a typical US-Search where many schools begin examining applications a year before the position start date, and tells me that they should be moving fairly fast with the decision. Any inputs?

It took about six months after my interview to receive an "offer" from the university, which I found rather slow, but having had more experience with German academic bureaucracy, I no longer find that surprising. (I find the four-month timetable frankly overly aggressive, and would expect that the actual start date would be substantially later than their target date.) However, every university and faculty within a university has its own way of doing things, so what might take six months in one faculty might take two months in another.


PI published my work after I graduated without informing me (and with a different first author)

It is a difficult situation, and the course of action may depend on many things we do not know (e.g. the influence of the PI, your current situation and dependency from him – do you need letters of recommendation, or did you leave academia –, how much factual evidence you can provide for your part on the works, etc.).

Here are various approaches which seem possible, but any of them may be impractical or dangerous depending on the unknowns mentioned above.

Contact the PI to sort the situation out; it is better not to corner her, but to let her an honorable way out or probably nothing good will happen.
Contact the university or department to notify the misconduct. It might be better to only do that after contacting the PI, but it really depend on the history.
Contact an ethic committee if one exists in your field (e.g. an ethic committee for publications, including misattribution of authorship, has been set for maths by the EMS).
Contact the editor-in-chief of the journal the paper is published in, and notify her that you should be first author (providing evidence) and that you were not asked for permission to publish the work.

Be aware that any of the above move may turn out to be explosive; it is difficult to say more given the limited amount of information. So let me end with probably the most important advice:

Seek guidance by a senior researcher you know and can trust with your case. You will be able to discuss the specifics of your situation, and someone ready to back you up is of utmost importance in this kind of situation.


Can [edit: or should] a scientist's h-index decrease in the case highly cited publications are retracted?

The h-index is defined mathematically based on the number of publications and citations. So the only question is what data source you are using to calculate the h-index. If that source removes publications and citation counts upon retraction, the answer is yes, the h-index can decrease.

However, since this is source-based, you could even get occasional decreases due to other factors. Since many of these systems are automatic, you sometimes see incorrect publication associations and citation counts that can be later corrected, causing the h-index to decrease (I've seen this happening in Google Scholar).

I fail to see why this is interesting, though. Isn't this just like saying the number of publications and citations an author has can only increase, except in special circumstances such as retractions etc.?


Is is necessary to include computer code into thesis?

I had the exact same situation with the completion of my thesis.

The first thing I did was to consult with my supervisor - seek your supervisor's advice - particularly if they have supervised someone doing similar before.

What I ended up doing (in my successfully completed thesis) was to include pseudocode and explanations of that pseudocode in the context of the experimental data (and with any theoretical background also). I was advised and did put the .exe in a CD in the back of the thesis.

Additionally, I published papers about the program and made reference to them in the thesis.

Another option is to upload the code in an online code repository (e.g. GitHub), only if there is no issues with sharing the code.

(Note: where I am, research theses are peer-reviewed for assessment)


Is it common to cite conference papers in a PhD?

It has little to do with paper vs. thesis and everything to do with whether the person's field considers conference papers "real" publications.  If you read computer science Ph.D. dissertations, you will find them to be filled with conference paper citations.  In a field that disdains conferences, you will not.


Honestly, you should make no assumptions about what other people think, whatever we are talking about. People are just too very different.

I think that you should ask your professor, simply as that.

And good luck for you!


When should someone be a coauthor instead of being in the acknowledgements?

Usually, the key indicator for co-authorship is the contribution of creative content. Did the student have own ideas that improved the paper? Was the program/database he wrote just a technical thing, or did it contribute scientifically? These are some questions that can help make/understand the decision.

There is a fine line to walk sometimes. Especially between different subject areas, there can be discrepancies who gets to be co-author. Sometimes everybody is counted, sometimes only the first author and his advisor(s) without any students.


In what countries is it possible to enter a life science PhD program directly after a Bachelor's?

In general, applying for a Ph.D. program in life sciences with just a bachelor's degree is possible in at least some of the US universities (I do not know, however, to which extent this affects your chances at acceptance).

E.g. the Harvard medical school web site says "Minimal requirements include a bachelor’s degree and undergraduate preparation in the sciences."


Would I be disadvantaged in PhD admission if I took only few courses each semester during my Bachelors and Master’s?

During my undergrad I took 3 courses because: 1. I was working part time 2. My doctor recommended me to take a reduced course load. For my master’s program, I was working full time for my parents’ business. I didn’t mention this in my PhD application, which i think I should have. But it is too late now, the deadline has already passed.

Those sound like perfectly good reasons for a reduced study load to me, and yes, you probably should have at least mentioned your concurrent employment.  Since you were working concurrently with your studies, you might also consider adding that as a standard part of your CV (i.e., in the employment section), which would mean you would not need to make special mention of it in future applications.

Admissions for PhD programs are generally made based on assessments of the quality of applications by academics, and they have wide discretion over what they consider to be relevant.  Opinions on the relevance or non-relevance of a reduced study load will differ among different people, but I suspect that most academics will be interested in your mastery of the undergraduate material ---as reflected in your GPA and other relevant outputs--- than in how long it took you to attain this mastery.  There is no definitive answer as to whether this will affect your application, because it will be assessed by people, and people do all sorts of different things.

Achieving a 4.0 GPA while working concurrently in various jobs (and full-time during your Masters) is a crazy-good record, so you should definitely have mentioned your employment.  Even without that your academic record sounds very strong.  Nevertheless, if you are worried that you have an unexplained gap in your application, it might be worth sending an email to the admissions office giving them a short supplementary paragraph explaining that you undertook your studies at a reduced load because you were concurrently working at such-and-such hours.  (I would suggest you not mention your medical issues, since this would raise more questions than it answers, and your full-time work is already an adequate reason for a reduced study load.)  Ask them if they could please pass this supplementary information on the assessors of your application.  Even though the applications deadline has closed, you might find that they are willing to pass on a short supplementary paragraph; but keep it really short.


Can I copy text from a scientific paper onto my website without directly referencing?

You must quote copied text and cite it where it is quoted.

Citations at the end are vague and can be misleadingly general.  Specifically, it can give the impression that the cited works support all of the text on the page as a whole.  Specific citations are honest in that they clearly delimit what is being cited from the rest of the content of the page.


Are posters useful for experienced researchers?

I'm in the social and health sciences and do not know what field you are in, so this may be discipline specific. However, it is appropriate for advanced PhD students to give poster presentations. As a PhD student, you are considered a junior scholar (as you would also be considered as an pre-tenured assistant professor) and poster sessions are appropriate at this stage of your career. However, if publishing papers is more desirable than presentations in your field, it is advised that you spend more time working on getting your papers in print than presenting them at conferences. I know of academics who did not receive tenure, because they presented papers at a ton of conferences, but never submitted the papers for publication. Posters have great purposes, but may be less likely to turn into a paper.


Learning efficiency of sitting in first rows of the lecture hall

This article(The Effect of Seat Location on Exam Grades and Student Perceptions in an Introductory Biology Class By Steven Kalinowski and Mark L. Taper) examined the seat location during lectures and its effects on exams. It details the results of some prior studies and their own.
They assigned seating in the following way;

On the first day of class, we randomly divided students into groups of
three, and assigned each group to a row. Two groups were assigned per
row—except for the front row, which we left empty (because we believed
some students might be uncomfortable sitting in the very front). We
did not tell the class that we were studying the effect of seat
location on their learning

They used exam scores to measure student learning during lectures. Five exams were given to the class: four midterms and a final.
Their main finding was that there was no effect of seat location on exam scores
in the class.
They report that they obtained two noteworthy results.

First, we found no evidence that grades or student attitudes were
affected by seat location ...
Our second noteworthy result was that students who chose to sit in the
front of the lecture hall on the first class had significantly higher
GPAs than students in the back (P = 0.009, R2 = 0.18) (Figure 2). The
slope of the regression line was –0.10, indicating that, on average,
GPAs decreased by 0.1 point (on a 4-point scale) per row. This
represents a substantial difference in GPA between students in the
front and back (the regression line dropped from 3.9 in the front of
the lecture hall to 2.7 in the back).


Is it okay to address "Prof. X" as "Mr. X"?

This will depend on the norm within your country to some extent, but I'm inclined to say that at least in the US, calling a professor 'Mr.' is insulting, provided you are in an academic context.

My neighbors, many friends, and the cashier at the cafe know me as Mr. X. But on campus, I'm Dr. X...and you know I'm a professor. Using 'Mr.' seems strangely intentional in a way to diminish ones accomplishments.


I am not quite sure what you mean by "academic vocabulary". If you mean words which appear in your field, read papers in your field or, if their level is too specialized, books for students.

On the other hand, if you mean words like "paper", "rejection", "withdrawal", "paywalled journal" etc., you may want to start at Academia Stack Exchange: reading many questions and answers here gives you a good feeling what academia is about, what certain words mean (and how academics think).


What are the impacts of implementing a hot-desking model for grad student workspace?

I have seen hot-desking (or the equivalent) work well with undergraduate researchers. In the particular incarnations that I have seen it, however, it wasn't a large-scale formal hot-desking model like you're talking about, but rather a sort of "pool office" that was the shared space of a bunch of undergrads.
With the undergrad researchers, this worked well because the number of hours each student typically spent in the office was quite small, and they tended to work on projects for relatively short periods of time.

Graduate students are a different matter. They tend to be around for a much larger fraction of their time, and you want them to be in the office more and to develop professional networks and commitment to the group. Thus, I don't see the advantages of hot-desking for undergraduates translating well to established graduate students in most STEM environments.  Here is a report of a personal experience that seems to corroborate the problems.

That said, there are some environments where is seems like it could be appropriate, in which one does indeed expect an office space to be transient and sparsely used.  For example:

If students spent most of their time in lab, then their "home base" is their lab bench, and a hot-desking space for non-lab tasks could be workable.
Some graduate programs start with a year of "rotations" in which students work with a number of different groups before committing to one, and since rotation students are inherently transient, hot-desking might work for them as well.

This all seems to point to some potential metrics, along the lines of measuring how much time is spent working in the hot-desk space vs. how much of the tasks done in that space are being done elsewhere.  If students are elsewhere because they are doing different types of tasks, then it might be guessed to be succeeding; if they are doing the same sorts of tasks in coffee shops, libraries, etc., then it might instead be driving them away.


How can we justify basic research funding?

I split this answer into three sections by the type of source (peer-reviewed literature, Stack Exchange, and miscellaneous). Each source is followed by a quote and/or a short description.
I also included a summary of key takeaways at the end.
The Literature
Woods, N. N., Brooks, L. R. and Norman, G. R. (2005), The value of basic science in clinical diagnosis: creating coherence among signs and symptoms. Medical Education, 39: 107–112. doi:10.1111/j.1365-2929.2004.02036.x
This study investigated the relationship between basic science knowledge and skill in diagnosing relevant diseases. The researchers concluded the study by saying that:

[...] the study has shown that, in comparison with students who
learned conditional probabilities, students provided with a basic
science explanation for diagnostic categories were better able to
accurately diagnose cases after a delay.
A plausible explanation is
that the basic science information, because of its conceptual
coherence, was itself more memorable, and that it also provided a
means to reconstruct the features of individual disease categories
after the initial symptom lists had been forgotten.

Magne, F. (1993). Importance of basic research in applied phycology. Hydrobiologia, 260-261(1), 25-29. doi:10.1007/BF00048999
The section of the abstract below highlights what Magne views as the value of basic research in the applied study of algae (aka phycology).

It is noteworthy that [applied phycology] research can not avoid the
use of knowledge obtained by basic research; applied phycology is
especially indebted to basic research in adopting biotechnologies
which are typically coming from basic research.

Leander, C. A., & Whitton, J. (2010). Bling my research! A mock grant panel activity illustrating the importance of basic research. The American Biology Teacher, 72(5), 308+.
In a classroom activity, the researchers demonstrated the importance of basic research to first-year undergrads. In describing their methods, the researchers said:

First, show the class a photograph of a cancer cell
labeled "GFP." [...] Briefly
mention the leaps in understanding of cancer cell growth and cell
division that GFP has made possible. Introduce the students to [...] Osamu Shimomura, who [...] was hired to simply investigate why a dried jellyfish glowed
green when crushed. The resulting manuscript describing GFP gives no
hint to the future implications of this protein (Shimomura et al.,
1957), a discovery for which he would eventually share the Nobel Prize
in Chemistry in 2008.
Finally, [...] [m]ention the importance of sequencing in understanding
the evolution of HIV. [...] [I]ntroduce them to a profile of John Trela,
Alice Chien, and David Edgar, who discovered Taq polymerase during
basic research investigations. This discovery has earned billions of
dollars in royalties (Fore et al., 2006) yet was the unintentional
result of a basic research investigation into life at high
temperatures (Chien et al., 1976).

http://www.sjsu.edu/people/fred.prochaska/courses/ScWk170/s0/Basic-vs.-Applied-Research.pdf
Dr. George Smoot of the Lawrence Berkeley National Laboratory said:

People cannot foresee the future well enough to predict what's going
to develop from basic research. If we only did applied research, we
would still be making better spears.

Stack Exchange
Asked by biotech on Biology Stack Exchange: "Why is knowledge of bacterial pathogenesis important?"
Chris♦ wrote a brilliant answer in the link above. Below is an excerpt:

The contributions of basic research is the basis for applied research
and drug design. Without them, this wouldn't work. Besides that it is
also the curiosity of humans which drives science - without having any
particular application in mind. These often come much later.

An answer  relevant to this question on Academia Stack Exchange: "How can a researcher improve his contribution to society?"
User eykanal♦ said:

[T]ry to take to heart that basic research is directly useful to
society. Almost all modern pharmacology is based on decades of
fundamental biochemistry and biology research. Materials science is
based on years of basic chemistry and physics research. Basic math
research fuels advances in all types of engineering, from signal
processing to computational work to structural engineering.

In a comment, user Anonymous Mathematician responded:

I think it's important to frame things as eykanal suggests [...]
message should be "basic research is of great value to society in the
long run, and here are some other things I do that have shorter-term
impact", rather than "here are some things I do to make up for the
fact that my research sounds abstract and useless".

https://mathoverflow.net/questions/175847/how-does-one-justify-funding-for-mathematics-research
A sequence of compelling arguments in support of pure mathematics research can be found in the link above on Math Overflow.
Miscellaneous
http://www.icsu.org/publications/icsu-position-statements/value-scientific-research/the-value-of-basic-scientific-research-dec-2004
A statement by the International Council of Science said:

Whilst an exclusive focus on application may have some merit in the
short-term, there are several reasons why neglecting basic research is
seriously flawed in the longer-term:

Basic and applied science are a continuum. They are inter-dependent.
The integration of basic and applied research is crucial to
problem-solving, innovation and product development.

Skilled scientists with a good understanding of the basic theories and practice [are required for the] successful transfer of scientific
knowledge.

Excessive dependency on scientific progress in other countries is
rarely likely to lead to the resolution of local problems. Countries
need to be able to generate their own scientific knowledge and adapt
this to their own local context and needs.

The practice of science is increasingly international and the
research agenda is set by those who participate. A country with no
basic scientific research capacity effectively excludes itself from
having any real influence on the future directions of science.

A secondary source by the AAAS on an MIT report (the link to the primary source appears to be broken) states:

"Basic research is often misunderstood, because it often seems to have
no immediate payoff," the MIT report says. "Yet it was just such
federally funded research into the fundamental working of cells,
intensified beginning with the 'War on Cancer' in 1971, that led over
time to a growing arsenal of sophisticated new anticancer therapies —
19 new drugs approved by the U.S. Food and Drug Administration in the
past two years."
It adds, "Do we want similar progress on Alzheimer's, which already
affects five million Americans, more than any single form of cancer?
Then we should expand research in neurobiology, brain chemistry and
the science of aging."

A very similar question to this on Quora asked, "How do you explain the importance of basic/fundamental science to non-scientists?"
The most compelling answer to me by Marc Srour is quoted below:

I assume someone who needs to have the importance of fundamental
science explained to them doesn't care much for the "satisfying
curiosity and thirst for knowledge" aspect of science (which, to me
anyway, is the dominant one), so I jump straight to practicalities.
[...] [Y]ou can't predict the road
that science will take. Even if you try to only do applied sciences,
fundamental research will be needed to develop new tools and
methodologies, or else you'll just be running around in circles and
never getting any new developments.

In extension of Srour's attitude of doing basic research for basic research's sake, I'd like to quote an interpretation of the views of physicist Richard Feynman in a review by Chris Toumey of the University of South Carolina. Here, Toumey wrote:

The reason for [Feynman] doing science is to satisfy a curiosity about nature. [...] Too few people, he complained, understood "the emotions of awe,
wonder, delight and love which are evoked upon learning Nature's
ways…My lament is that a kind of intense beauty that I see given to me
by science, is seen by so few others" (24 October 1967).
In a 1959 television interview, [Feynman said]: "The reason that I do science…is…not the usual
motivation for helping human beings. The main motivation is the
curiosity and interest to find out about the world we're in" (pages
419-420). He easily conceded, of course, that scientists see the
consequences of their work, but he adamantly bracketed their
motivations from the applications of that work which the rest of the
world experiences.

SUMMARY
The following is a bulleted list of key takeaways from the sources above.

Basic science knowledge is linked to better clinical diagnostic skills (aka diagnosing diseases) (Woods et al., 2005).
The investigation of "why a dried jellyfish glowed green when crushed" led to the discovery of GFP (green fluorescent protein), which led to "leaps in understanding [cancer]." Furthermore, "a basic research investigation into life at high temperatures" led to advancements in DNA sequencing. This directly led to further understanding of "the evolution of HIV," earning "billions of dollars in royalties" (Leander & Whitton, 2010).
Basic research is a necessity if we want to meaningfully continue advancements in applied research, especially drug discovery (Chris♦, 2015).
As stated by Stack Exchange user eykanal♦ (2014), "Basic research is directly useful to society. Almost all modern pharmacology is based on decades of fundamental biochemistry and biology research. Materials science is based on years of basic chemistry and physics research. Basic math research fuels advances in all types of engineering."
According to the International Council of Science (2004), "Excessive dependency on scientific progress in other countries is rarely likely to lead to the resolution of local problems." Furthermore, "A country with no basic scientific research capacity effectively excludes itself from having any real influence on the future directions of science."
According to a 2015 MIT report, "Basic research is often misunderstood [...] because it often seems to have no immediate payoff." However, the report contends it has directly led to the development of 19 new anticancer drugs over the past two years.
The report further says, "Do we want similar progress on Alzheimer's, which already affects five million Americans, more than any single form of cancer? Then we should expand research in neurobiology, brain chemistry and the science of aging."
Basic research is beautiful. It's both intrinsically emotionally and intellectually stimulating; basic research for the sake of itself is rewarding unto itself.


How to get on my PhD supervisor's case without becoming a nuisance?

As confirmed in a comment, the "very senior" supervisor does have a secretary. I suggest explaining the problem, and the reasons for urgency, to the secretary and asking them for help.

The secretary can go to the supervisor's office without an appointment, and is likely to understand that some university paperwork really does have to be done on schedule. Ideally, the secretary will put together a packet with the partially completed report and any other relevant paperwork, such as previous evaluations, that the supervisor has.

I would concentrate on the progress evaluation, because that has to be done, and has already been deferred once.

As far as the travel is concerned, make sure the supervisor, or at least the secretary, understands that you need some notice, and will assume you are not traveling next month unless there is a definite decision that you are traveling.


Do Machine Learning and Vision Labs outside the USA hire non-student,non-postdoc Research Assistants?

Short answer to the question "is it possible?": yes, it is. E.g. in Germany, we can employ a person having some academic degree. The more important question is: What would you be willing to earn because at least in Germany, academic position usually are not the best paid ones.

If you just want to earn money and get experience, I would recommend a job in industry. If you really want to learn and develop yourself, and you don't have to earn much, look around in Europe. If you bring your own money (e.g. DAAD scholarship), you could start in my lab ;o).


What is the typical time between application and contact for a postdoc on Norway?

More than anything, the amount of time is determined by the number of applications. But in general, the hiring process in academia in Norway is much slower than what you're likely to experience elsewhere (at least outside of Scandinavia). To give you an example, I once applied for a postdoc in Norway. Only two people applied, but it still took six weeks before I heard back, and the interview was scheduled fifteen weeks after the application deadline. If you haven't heard anything by the end of June, your application was either unsuccessful, or they didn't manage to sift through the applications before the summer. By that time, I would e-mail the professor you've already been in touch with and ask.
For a postdoc position, I don't think you can count on being informed if your application was unsuccessful, but this might vary by university/department.


The precise extent of scholarly publishing is unknown, difficult to estimate, and the subject of some debate. That said, there is lots of evidence that Web of Knowledge and ScienceDirect are likely only the tip of the iceberg.

That is sort of the takeaway from an article I found in from Library Journal on Online Databases-Online Scholarly Journals: How Many? (Google WebCache because the LJ copy seems gone) by Carol Tenopir and published in February 2004.

Apparently, one of the best sources online is Ulrichsweb which is a serials tracking website that is part of ProQuest. I just did a search for "Academic / Scholarly" and "Journal" and came up with more than 107,000 different results.


What can I do if I want to publish my PhD thesis work as is, but my advisor wants months of additional work?

As usual, the first piece of advice I can offer is to talk to your graduate advisor to get his take. That said, it sounds like you're getting advice which will increase your chances of getting a paper accepted from people who have experience in the field.

Your theory that they're asking you to do work related to a "hidden agenda" seems a little far-fetched... when considering the extra analysis, writing it up, and publishing, you're looking probably 18 months into the future. Your committee is well aware of this. The likelihood of all that happening in any timeframe that would be beneficial to them is pretty darn small. Even more so, they have their own students who can work on their stuff. They wouldn't hang their hat on the chances that a graduate student who has already moved on will do some research that may or may not result in a publication. Long story short, I wouldn't worry too much about ulterior motives.


If a journal requires "Article Processing fee" does that make it a predatory journal?

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

To label a journal as predatory you need other (additional) criteria.


Relative pronoun 'who' or 'which' when referring to article by authors' names

This depends entirely on the subject of your subordinate (relative) clause.

If the authors are the subjects of the subordinate clause, use who. E.g.

  Many postmodernists reacted angrily to the stunt pulled by Sokal (1996), who they felt had acted unethically in an effort to discredit their field.

If the paper or text is the subject of the subordinate clause, use which. E.g.

  If you want to improve your mathematical writing, I recommend carefully examining Halmos (1974) which as a text manages the difficult feat of combining  scrupulous rigorous with broad accessibility.


What is the standard way to include math equations in a CS research paper?

If you can write in latex, you should write on it versus word. The latex is specially designed to work with technical documents with a lot of mathematical equations.

Also, you can write math equations in word using built-in equation editor of Microsoft word or MathType as a better alternative than built-in ones.
See this link for word equation for equation writing in Word with better configuration.

Technically the MathType produces equations with higher equality than Word built-in and I recommend it to use as a macro on Word.

About writing in Latex and then revert to Word, it wouldn't be recommended and will be reduced the quality of equations (due to reversion complexities and equation editors' of Word difficulties).


Can I take online courses to make up for poor past community college performance when applying to a four year college?

My advice would be to go to the website of the university you are thinking about enrolling in, find out who the course coordinator is, and email them about your situation.  Explain that you are willing to put in the effort to get your knowledge up to an acceptable level.  You may find that they can offer you a bridging course, or suggest having sessions with a personal tutor like you are planning.

I found myself as tutoring a mature-age student who was very much in a situation similar to what you described.  The course coordinator emailed the maths academics to see if anyone was interested in some private one-on-one tutoring, and I took up the offer.  Ultimately, the student opted to drop out due to the feeling of being overwhelmed with the content (and they were struggling greatly to understand basic high-school level concepts), but the fact is the university attempted give the student every possible chance of getting in. There is nothing to lose by trying.


Is it OK to include a personal (non-science related) statement in the final slide of a presentation

I think that writing on the presentation that you'll be looking forward to doing something is somewhat out of place.

In addition, it appears that you may be confusing two separate definitions of conclusion.

The first is the scientific conclusion, which you have defined. This is, as you've described, the takeaway message from scientific research, i.e.

  This research shows us that potatoes are actually tasty.

The second is a presentation's conclusion. This can be the scientific conclusion in a presentation about an actual study. However, you're referring to a proposal, which has no conclusion, or perhaps to a slide mentioning future possible research topics.

In this case, your conclusion should be a summary of what you've covered during your presentation, preferably onto one slide, i.e.

  Conclusion
   - This research will establish whether or not potatoes are tasty
   - Important to humanity as it helps determine whether or not further investment into discovery of potato recipes are practical
   - Funding this project will be cheap as potatoes are grown a lot already

Then, when you present your situation, you can mention I look forward to performing this research with your support. and it flows cleanly.

If I've interpreted anything incorrectly regarding your situation, OP, let me know.


Is it rude to ask an unaffiliated student to leave the PhD student office?

I will mention that while Nicole Hamilton's answer is fundamentally correct—this is an issue for your advisor, as well as the other PI's in charge of the office space, not you—there is one issue worth elaborating on.

In particular, it is an issue if someone who isn't part of the department is using the department's facilities, because of the liability issue if something were to happen. For those grounds, it would be especially helpful to mention that one of the people coming into the space is not actually authorized to be there at all.


Referencing specific files in source code in a dissertation

It's not uncommon in certain areas of CS to cite specific files. In your specific case, I would suggest that you include the git commit hash of the kernel.org sources in the citation, so that people can find the precise version your referring to.


It's spam: They gave you a free membership to rope you in, in hopes that you will pay for more memberships and/or publish with their journals. Don't fall for it. Just because this particular publisher isn't listed in one particular list
does not mean that they are acting respectfully and ethically.


Are open access papers read by a larger readership than paywalled papers?

This answers is not exactly what you ask for — you ask for readership, but most of the research has focused on citations. The two are, of course, related, and the answer seems to be a pretty clear yes. (In my field, it's practically the only way I find stuff from overseas, as many online repositories don't seem to have much international coverage except for a handful of big general journals but not the niche ones).

Gargouri, Yassine. “Self-Selected or Mandated, Open Access Increases Citation Impact for Higher Quality Research.” Public Library of Science ONE 5.10 (2010): n.p. Web.
This article indicates that citations are more common for open access articles, and that this is a result of higher availability and access (=likely readership) by researchers. [Link]
Lawrence, Steve. “Free online availability substantially increases a paper’s impact.” Nature 411 (2001): 521. Print.
This comes to the same conclusion — way back in 2001. The effect is found to be quite massive: “Averaging the percentage increase across 1,494 venues containing at least five offline and five online articles results in an average of 336% (median 158%) more citations to online computer-science articles compared with offline articles published in the same venue.” [Link]


Talks vs. poster presentations: Which is better for advertising your research and building research networks?

It depends on what you want to do. If you feel like at this point in your research it would be more beneficial to converse than to present, then I'd say that a poster session is the right venue for you. It's true that talks are considered a bit more prestigious than poster sessions, but you really should go with what you think will be more valuable for you, and for the conference attendees.

It's worth noting that you could always do a poster presentation this year, get the feedback that you covet, and then return next year to do a talk, and let everyone know how your research went over the subsequent year. That kind of progression is not a bad thing.

Also, if you are in the early stages of your research, it might not be ready for a talk. When I attend a conference talk, I'm expecting there to be some significant findings. Sure, talks might be more "prestigious," but, if there are some holes in your research, you could end up discrediting yourself. People aren't expecting the same level of maturity in the research during a poster session. So, as I said before, forget the prestige aspect, and choose what is more fitting based on your goals, and on what you have to share at this point in your research.


Are studies published in conference proceedings well-regarded in social sciences fields (e.g., psychology)?

I have worked at the intersection of psychology, educational sciences and computer sciences and there was always friction between the computer scientists who wanted to publish in conferences and the non-computer scientists who wanted to publish in journals. I think most psychologists who deal with computer scientists know about the conference culture, and most computer scientists that deal with psychologists know about the journal culture. That said, I believe, it is much easier for a computer scientist to get an idea about how competitive a journal is compared to a psychologist trying to understand how competitive a conference proceeding is.

If your plan is to stay in Psychology and you have the choice about conference or journal publications, then all things being equal, go with journal publications. If you want to go to the conference or you are getting pressure to publish in conference proceedings, then it is no big deal, although, there are even differences between conference proceedings and journals in computer science so you probably want to prove you can write/publish a full article.


To work in statistics for industry and research centers, is a masters sufficient or is there a major advantage to having a PhD?

Background: I have a math Ph.D. and am working as a statistician in industry.

I'll try to address both the general question you ask and your specific situation.

M.Sc. vs. Ph.D. in stats in general

This quote of yours is key:

  I do not believe PhDs would guarantee job security, higher wages, or happier careers.

And you are right about this. A Ph.D. won't guarantee any of these.

If you do a Ph.D., you will end up with a different qualification than with "only" an M.Sc. In doing a Ph.D., you will be spending multiple years thinking up new methods or algorithms. You will become an expert on an (admittedly small) topic, which you will know more about than your advisor. In contrast, in doing an M.Sc., you will learn a lot of different techniques and apply them, but you won't develop new ones. (Some M.Sc. students do just that - exceptions exist.)

What does that mean for your job prospects? If you are looking for a job as a "consulting statistician", "data analyst" or similar, an M.Sc. will usually be enough. Employers may balk at hiring a Ph.D. for such positions for multiple reasons:

Ph.D.s usually ask for higher salaries
Ph.D.s are older, possibly less flexible (families) than entry-level M.Sc.s
Ph.D.s may feel underchallenged and try to leave for more interesting work elsewhere
Ph.D.s may be specialized in one field - but an M.Sc.'s knowledge of multiple methods is more recent

So with a Ph.D., you would be applying for more "conceptual" positions, where you don't only apply your knowledge, but actively create new statistical methods to solve problems.

There are more jobs out there that require applying known methods than creating new ones.

You may be lucky and find a job opening that requires a Ph.D., or (even better) one that matches your Ph.D. research interest. (I wouldn't count on this last possibility - research is so specialized these days that it is rare to find a position in industry that closely matches what you did in your Ph.D. career.) If so, your Ph.D. pays off. If not, you may be in for a long search, or you may need to work for lower wages, and still need to convince an employers that he is better off hiring you than a new M.Sc. graduate - at the same wage. If this happens to you, you will definitely feel like the Ph.D. was a waste of time.

Overall, I would only recommend doing a Ph.D. if you are passionate about it, if you genuinely want to devote three to five years of your life to research. Don't do a Ph.D. for the career value if you plan on leaving academia. It likely will be a step backwards in terms of lifetime earnings or your career progression. (Around me, I see no correlation between having a Ph.D. and job security or higher wages - I can't judge the happiness of my colleagues' careers.)

Your specific situation

  I have a bit of family pressure to get a job and work to build income.
  ...

  It seems like an unwise choice to pursue a PhD and graduate at age
  35-36 without work experience and having to start earning income.

  ...

  ... On a personal note, I am quite disenchanted/burned out with higher
  education.

I see a lot of skepticism about doing a Ph.D., and much focus on your alternatives. I don't see anything indicating you would love to do research for research's sake. (Please don't misunderstand me: I'm not saying you are lazy. I am pointing out what your priorities seem to be, based on your question.) Compare this to my recommendation above.

It does not seem to me that doing a Ph.D. would be a wise move for you.

Nevertheless, we can't usefully help you a lot with your decision. I'd recommend you talk to people who know you and your specific situation.

This and this earlier answer of mine my be helpful.


Confusion on whom to get letter of recommendation from

If your ability in developing circuits for electrochemical studies sheds light on how good you would be designing circuits for mechatronics (and I suspect it does), definitely get a letter from them.
If all the professor can say that addresses your ability in mechatronics is "he was smart, diligent, and careful," then that's certainly better than no letter, but you might be better off with a letter from somebody closer to your field, even if you haven't worked directly with them.


What is a good ice-breaker question on the first day of the classes?

"Ice breakers" are not a good way to meet people in any context.  When you are meeting a new class of students, it's better to:

Let them know what they need to do to succeed
Tell them about the resources they have available
Tell them why the class is important
Assess their current ability
Actually teach


Citing draft papers found on academia.edu

In my experience, absolutely anything can be cited, but not everything should be cited. Papers uploaded to Academia can often be what's called post-print, i.e. they are the version that has been peer-reviewed, accepted by a journal but not copy-edited by the journal [this is the point where the article still belongs to the author, after copy-editing it is the property of the publisher]. In this case it would still technically be a draft, but quite a long way down the line.

Of course the paper can be cited, as long as there is enough evidence that the research is of good quality [if it's been accepted by a journal then it generally would be]. Things that should be cited are works like academic books, journal articles; whereas things like Wikipedia should not. Then there are grey areas such as drafts and online articles: basically if you know the researcher and field, and you trust the quality of the research, I see no reason not to cite it and include it in the bibliography.


Is more independent-study type work considered research? Or is it necessary to be actively helping a professor with their research program?

In my experience, it's best to be actively interacting with a professor. But in most cases it's unlikely you'll be actively assisting with their research programs (they have usually have graduate students/postdocs for that).

You could be given either a small project related to their funded work or possibly some crazy idea they're unwilling to let a grad student spend time on. Or anything in between.

  What do graduate admissions committees really consider "research", though?

If you can do any work that results in something published in a journal or conference, or even a poster, will be very valuable for graduate school admissions. It doesn't matter if that work is lab or computer-based. (Better yet if you can prove (with a publication/poster) that you can do both "wet" and "dry" lab work.)

  As an undergraduate sophomore, I'm really not in a position to do groundbreaking research. What's considered a good research experience for me?

When I was a junior I emailed every professor in the department. Two responded and I ended up doing "independent research credits" with one of them. It worked out really well.


Isn't it injustice on behalf of editor to assign article status as "under review" when actually it is not?

"Under review" may include the review of the editor or editors, so in this case it may be under review. It also may be (as Maarten commented) that the paper was sent out and the reviewers indicated that the paper was not suitable for that journal without comments.

A few years ago I had a terrible experience where a journal had a change in editors and management and they lost my paper. I had no idea and they would answer my emails about the paper, but never get back to me about why I couldn't get any information about my paper. This went on for about a year. Ultimately, it worked out, but remember that editors and reviewers are often volunteers, so some may not put their reviews as a priority in their schedule. This isn't fair to the authors, but it is the truth. I'm sorry you dealt with this frustrating situation, but I find that these things are a lesson learned and if anyone asks you about your thoughts on submitting to that exact journal, you know what to tell them.


Prerequisites for Master's Degree in Pure Mathematics (and eventually PhD)

Although I am doing a PhD in the field of Computer Science, I of course cannot give specific advise on what you should do about mathematics MSc, but here are some of my observations on the general case.

In the last two years, I have applied a lot of PhD programmes across Europe. I have been accepted to one recently. And that is probably one out of fifty if not more.

As far as I have observed, the priority is not a student with "a lot of knowledge", but a student "who can study hard on the given task." This observation is based on the profiles of accepted students instead of me (stalker alert).
Some of them have lower GPA, and almost none of them have publications. I think what they somehow proved that they can study harder and be more productive.

The interesting part that matches with your question is, both their theses and their stated area of interests were less related to the research area.
Surprisingly, someone who took his degree from mathematics was accepted to a research group that focuses primarily on application rather than theory.

If we switch from PhD to master's degree, I don't really believe having a relative background should have more weight than being a hard-worker (of course I am not talking about another discipline like psychology) in the process of decision.

If I were you, I would direct the exactly same question to a professor from the department you want to apply. Questions like

  How can I convince you that I am good enough to pursue a master's
  degree?

or

  Are there any specific criteria you are seeking such as having a
  relatively strong background on pure mathematics?

would do no harm. I think being deeply interested as a master applicant in a research topic puts you one or two steps further. Of course you somehow have to show that you are actually deeply interested (this is the hard part that I could not figure out how).

In short, do not over-try to "boost" your application and do not hesitate to contact one of the faculty members.


How professional it is to ask for rebate in conference registration fees?

It is unusual and it is likely that the organizers would see it as unprofessional, especially if such request is coming from the industry.

How valuable are these publication for your employer? You could try to speak with someone at a higher level and persuade them to pay the conference fees. Alternatively they can advise submitting the papers to another conference with fees they are willing to pay. Or if publishing benefits you more that the employer, you can perhaps cover the difference yourself.


Points to remember when having to write recommendation letter yourself

The ethics of the question is moot here; this practice is widespread, and the questioner is asking for a solution to his problem, not for an ethical reform of the international academic community.

The guidelines for such a letter would be identical to writing any other letter of recommendation. If you must write your own and have a professor sign off on it, read up on how to write a good letter of recommendation and follow any tips you may come across. You probably have little to no experience writing letters such as this one; there are many subtle nuances, both in what you say and in what you don't say. Take the time to write it correctly. If you find yourself completely stuck, ask someone else with experience to write it.

If you're having difficulty writing a letter about yourself, imagine you're writing about a colleague who has done all the things you have done. It may make the task easier.

Regarding trying to mimic the professor's style, if he asked you to write your own letter, then he likely asked all his other students to write their own letters. There will be no consistent style, and that will be a reality of this individual's letter. If the department/faculty member receiving the letter has received letters from this professor in the past, this likely will count against you, and you should consider that when asking this person for a recommendation.


What citation style is mainly used in political science?

Political Scientist here. @aeismail is correct - different journals use different citation styles, as do different academic publishers. The best way around this is to use a reference manager (such as Mendeley or Papers) to not only manage your academic articles, but cite directly into your publications. These software packages are capable of formatting your citations in whichever style necessary.

With that said, my experience is that, generally, APSR's citation style is broadly accepted, with minor variation.


You are confusing your CV with your SoP. Your CV details your past accomplishments. Papers and research reports of your experiences are listed there. Your SoP should be forward looking, not backward, so nothing in your list is really the right thing for the SoP. The "Purpose" in SoP is your goals for your education and beyond, including some idea of the area you want to work in.
Even something like "I want to study at MIT because..." is misplaced. Immaterial. Naming a professor may be necessary (some places) or not (other places).
But your past can be briefly mentioned in the SoP if it says why your background makes you a good candidate for success in your chosen field. "I want to explore F. B and E give be a good basis to begin that study..."
But you are wasting an opportunity if you just detail how A - E fit together.  If they support F directly, then say that and assume the reader understands the connections.

CV = your past accomplishments
LoR = great candidate, certainly a success
SoP = goals and plans, research and career directed

Then a reader can get a complete picture


Asked about bibliographic search skills for application

I would assume 'bibliographic search skills' means the ability to find appropriate literature 'from scratch' as @Tobias suggests. If that's the case, can I recommend a book that helped me with my literature searching, and can be read easily within a day:

Booth A, Papaioannou D & Sutton A (2012) Systematic Approaches to a Successful Literature Review. Sage Publications Limited.

It's written from a health science perspective, but I found it useful in the social science to identify search terms, databases, perform searches, and filter results.


This (lack of motivation) is common in graduate school.  Without delving into the way you personally like to work (whether you are intrinsically or extrinsically motivated, whether your advisor is involved or uninvolved, whether you are motivated by reward or punishment, etc.), it's difficult to give specific advice.

These are some general motivational strategies:

Get up and start something small.  Doesn't matter what it is.  As long as you are working on your project (even formatting your thesis), you are okay.  This is not to say you should be working on it all the time, just that even the small things are helpful.  Small tasks get you into the groove and ready to tackle larger problems.
Leave things unfinished from the day before.  If you reach the end of the day and are in the middle of a task, leave it, don't stay up to finish it.  This way you have to get up in the morning to keep doing what you were doing, rather than waking up and saying "I don't know where to start."

Finally, if you think you may be depressed (if you are constantly saying "I have no reason to get out of bed"), please talk to someone or see a doctor.  It gets better.


If I proposed my PhD this year (but have not defended) can I say that I graduated this year?

No, you can't state that 2015 is your graduation year. The year you graduate has a well-defined meaning -- it's the year the university confers your degree to you. Period. Writing that 2015 is your graduation year would be the same, ethically, as writing that 2013 is your graduation year just to make your resume look more impressive.
Your resume will, correctly, indicate that you're working at the same time as completing your degree, which should be impressive enough for anyone doing bookkeeping on your dates.


Can a predatory journal have a quite high Impact factor?

Yes it can.* That's because the two things are orthogonal. The asterisk is because you need to define "predatory", and different people often have different definitions. Still, most definitions are orthogonal to what an impact factor looks at.
The impact factor is calculated by a company called Clarivate. It depends on the number of citations articles published in the journal have received in the past two years, divided by the number of citable articles published. In other words, it depends only on the number of citations received. That means all other considerations that routinely show up when discussing predatory journals, such as the APCs they charge or who they have on the editorial board, are irrelevant.
So yes, it is possible. Caveat: if you believe that the distinguishing hallmark of predatory journals is accepting articles quickly with little or no peer review or quality control, then having an impact factor practically proves the journal isn't predatory. Journals with no quality control are not likely to be indexed by Clarivate in the first place.


The best answer may depend on what other questions are asked on the application form. These types of questions are usually used to assess whether you have a clear research line moving forward, but it is also helpful to know how you are going to break your research line into smaller goals. This is typical for grant applications -- high level research questions followed by measurable research activities.

So, if the 650 words gives you space, I would suggest providing both answers. The high-level research questions you want to answer and the first few research activities that will support this.

I wouldn't spend too much time talking about general service activities such as reviewing papers, but organizing a workshop to support those working in your research area would be worth mentioning, as this demonstrates broader impact.

After the edit:

As I suspected, the other questions are related to the first question you asked about. So, my overall advice doesn't change, but you can spread the answers across your questions as appropriate.

For instance, what you hope to achieve is related to the planned activities, but is looking for a broader answer - here is where you can talk about the expected impact of your work on the field.

In your dissertation or present research summary you can introduce some of the higher-level questions being answered, leaving more space to talk about specific activities in the response to that question.


Should academic CVs include reviewing, non-academic service, hobbies and languages?

An academic CV is not intended to describe you as a whole person, but rather to describe your qualifications and accomplishments as an academic.  The assumption is that of course you lead an ordinary human life (with hobbies, friends, family, religious beliefs or the lack thereof, etc.), but the people reading your CV are not trying to evaluate you as a human being and aren't interested in reading about the rest of your life.

Anything academic is fair game for an academic CV, including reviewing.  How much to emphasize it depends on how many more important things you have to list.

Language skills are relevant to academia because they can assist with research, teaching, and public communication.  You are right that this information could be used to discriminate, but I doubt this particular form of discrimination occurs often enough to be worth much worry.

Hobbies and non-academic service are generally not relevant (although there could be exceptions).  It's not necessary to discuss them at all, and nobody will assume you have no hobbies or service activities if you don't mention any.  It's OK to mention them in a very short section at the end of the CV if you feel it's important, but you should definitely not emphasize them.  There are at least two reasons for this:

It could come across as cluelessness, like you think they are an important factor in hiring/tenure decisions.  This certainly won't ruin your chances, but it could look silly.
It could be viewed as a defiant statement, along the lines of "I'm letting you know that my hobbies are particularly important to me and I intend to spend more time on them than you would like."  If your CV is great otherwise you might be able to get away with this, but it will work against you.  (I've seen this happen with graduate admissions, where someone devoted part of their personal statement to a favorite hobby and the committee worried that this hobby could be a distraction from research.)

Hiring committees do care about hiring reasonable colleagues who aren't going to be jerks, so human qualities are relevant (and not just academic accomplishments).  Interviews shed light on this issue, as do letters of recommendation, and the CV is not so relevant.

Note that academic evaluation criteria are entirely different from undergraduate admissions in the United States.  In that case, colleges are trying to assemble a self-contained community, and they really care about breadth, well-roundedness, leadership, personality, etc.  Showing something about yourself as a human being is absolutely crucial.  However, this is an anomaly of U.S. undergraduate admissions, and graduate admissions, faculty hiring, etc. are done completely differently.  [I know your question never mentioned this comparison, but I decided to mention it for completeness since it's a common cause of confusion.]


Literature search engine including citation count, year, and the conference presented at

As commented by Jon Custer, Web of Science has information about citations, conference and publication year in its database and shows it in the results of a search. You can even filter and sort by citations and publication year. Unfortunately, Web of Science is a commercial service and your institution needs to have an agreement with Clarivate Analytics (the provider of Web of Science) to grant you access to the database.


If my B.Sc.project contains source code, should I include it in an appendix?

Putting it into an appendix (maybe not in full but the core parts of it) seems the best solution. This is not only some sort of "proof of work" but gives examiners also an opportunity to assess whether the results generated by the code are indeed correct, so it helps with verifiability. This will be particularly important with code that generates numeric information, which you use to draw conclusions.

There are only very few cases where code should be put inline in the main body of the thesis, e.g. when you invented a new language or a new library and want to show how much easier / more readable / more concise / .. something can be formulated in your language / library and when this was indeed the main purpose of it.


Writing someone else's master's thesis: Unethical and illegal?

Think about it this way: Eventually one of those people for whom you write the thesis will be working for your stockbroker and influencing your investments, or working for your doctor or a hospital and influencing your medical care, or working for your government and influencing permits and regulations, or ...

Leaving aside the potential immediate consequences for your "principal" and yourself, you would be making the world a worse place for everyone.

Does that answer your question?


When presenting an idea to a professor: Be optimistic or realistic

Be realistic. A seasoned professor has (by necessity) developed a keen BS detector (required to wade through teaching, at very least). A (prospective) student who doesn't know how far they can realistically go will either turn out reckless (and dangerous to the project) or get frustrated when things don't work out, perhaps dropping all (and thus being dangerous to the project). As the professor in turn stands of falls with his successes (and "my PhD student failed me" is no excuse, really), it would make you a risk not worth taking.

Yes, it is nice to show that you know where success in the first step(s) could take you, but they might fail, or turn out unexpected results leading elsewhere.


I would say that you started rectifying the mistake by informing the coordinator. I would apologize sincerely and offer to to deliver the tutorial at another time. Mistakes happen and you are only a human and you were sick and that is understandable. Also, make sure not to miss any other tutorials in the future.


A paper review I've undertaken turning out to be harder than expected

Is it common for a reviewer to review only a part of the paper, and leave the rest of the paper to other reviewers?

I have done that on at least two occasions. Sometimes it is the only honest option.

  On the other hand: is it my duty, as a reviewer, to complete my review, regardless of how much time it takes?

Not really. It is commonly considered a duty of a career mathematician to contribute to peer review of mathematical works (at least) proportionally to their own publishing. Whether you achieve this by refereeing some really tough papers or a lot of simple ones is up to you.


My adviser keeps changing his mind about my papers. What should I do?

I experienced a bit of what you're describing near the end of my PhD. I got a lot of good advice from colleagues that had completed their doctorates. Here's how I dealt with it.

Remember that it's your PhD, and you are (mostly) in charge. At this point,  you should have a pretty good idea of what's really required for a PhD. (If not, skim more dissertations from similar research projects.)

There will always be more that could be done to further the research. There's always another technique you could try, another analysis to do. Your goal should be to do what's required to finish the PhD, no more. (Of course, you want to do quality work, but if you've made it this far, I doubt you'd settle for less.) You can always continue the research as a postdoc, or let someone else continue it. That's what the "future directions" section is for in your thesis.

Your advisors are focussed on the research itself, and the logical next steps, rather than on wrapping up your PhD. That doesn't mean they're bad people, or deliberately trying to frustrate you. They're just human.

Sit down and figure out what you think needs to be done before you are ready to finish the experiments, finalise your thesis, and defend it. Then meet with your advisors and get their feedback. If they suggest doing more experiments or analysis, beyond what you think is necessary, you might say something like "I agree that's a good future direction, but I think that could be done post-PhD." Your goal is not to convince them that X doesn't need to be done, it's to discuss whether X needs to be done before the PhD can be awarded. Negotiate things from that point-of-view, and I think you'll find it easier to reach agreement.


Are interdisciplinary STEM PhDs qualified to become professors?

Yes, interdisciplinary Ph.D.'s are qualified to end up in academia.  In fact, I think hiring interdisciplinary faculty is a quite a popular idea with university administrations, and so my feeling is that there has been a bit of a burst of interdisciplinary positions created.  If you do really excellent interdisciplinary research, I think you should have a very good chance of getting an academic job.

I think you do correctly note some disadvantages that come along with it: hiring and tenure decisions tend to be made within departments, and interdisciplinary work can sometimes look not especially deep from the perspective of either of the disciplines, or simply be difficult to see the importance of if you don't see both perspectives.  But if people really do come to see the connection, then it will be highly valued.


Well, there is only one thing that is for sure: Be consistent.

Other than that, it really depends. If no specific style is prescribed, ask yourself the question: Does the reader benefit from visually marking the foreign words? This shall be your decision point, and we can't know the answer without seeing the manuscript.

Second thing is, how shall these be marked; there are several options:

  We encoded the list of the National Classification of Occupations (Clasificación Nacional de Ocupaciones, CNO).

  We encoded the list of the National Classification of Occupations (ES: Clasificación Nacional de Ocupaciones, abbr. CNO).

  We encoded the list of the National Classification of Occupations (“Clasificación Nacional de Ocupaciones” or shortly “CNO” in Spanish).

...

Which one you choose is up to you. You probably don't need to specify the language if all your foreign terms come from a single language. And so on. The style is mostly up to your or the author's preferences, just remeber: Be consistent.


I am writing a paper, need some review. I want to send it to IEEE, without the name of my co-authors.

Short answer: Hell no!

Depending on the editorial policies of the venue you submit, they may or may not allow to add co-authors during the review process. Some may even accept you to add co-authors after acceptance of the paper.

However, note that in all cases, it is unethical not to have a correct/honest list of co-authors at time of the first submission. All persons who have made significant scientific (or “intellectual”) contributions to the work should be co-authors in the submitted version of the paper.

“Hiding” co-authors during the first submission, even if you intend to add them at a later point, is a clear ethical violation. It probably also violates the journal's (or conference's) policy, which typically stresses the importance of having an appropriate authors' list (and even sometimes provides criteria for authorship).

The reason that editors may allow you to add authors is for special cases. The main reason why it would be used is when, during revision of the work to address reviewers' comments, someone who wasn't a co-author of the initial manuscript has been brought onto the team. For example, if you asked someone to ran some extra analyses and his contribution warrants authorship of the revised manuscript.


Postdoc job inteview presentation - slide "livery" / logos and references?

Typically, in the departments and universities I'm familiar with, as a student you're also an employee of your current institution, benefiting from their space at the very least and participating in the local research culture. As such, it's appropriate to keep the branding on your job talk slides since it's not just some obligation to the university to credit them, but it grounds you in a context of the research at that university.

Additionally, it's appropriate to keep your acknowledgement slides if there are people to acknowledge. Many PhDs are done as part of a team, and so you shouldn't drop this credit from your slides. That being said, in a job talk, even a short, introductory one, you should concentrate on the parts that you did. You probably shouldn't spend the time reading off all the names and roles of the people who contributed.

Now, given that this talk is short and intended to only be about how you fit the role, it's not even clear to me that you should be treating this as a traditional job talk about your research. I would focus down on the posted criteria and carefully and thoughtfully address how you satisfy them. Presumably you're being given the opportunity later in the interview day to give a traditional academic job talk (i.e. an hour-long seminar), and that's the place where you can dive into your research, credit your team members, funding agency, etc.


How to handle a student who will not accept that he is wrong?

Should I just tell him to talk to the instructor, and that my job is just marking?

Yes.  There's no point in getting into an extended argument with this student.  The student thought his answers were correct and you explained why they were not correct.  Since you've denied the student's appeal of the grade, the next appropriate step is generally for the student to appeal to the instructor.

It's a good idea for you to warn the instructor that the student is likely to appeal the grade and to provide whatever information you can (such as a photocopy of the marked up exam question and any grading key that you used).


Definitions and proofs in extended abstract(mathematics)

Before you start writing, try to create a 5-minute elevator pitch talk about your paper. Imagine you're describing the results to your friend (or actually invite a friend) and talk through the main idea of the paper. Practice it several times and note which things you keep in, and which you decide to leave out. This will give you an idea of what to include in your extended abstract.

It is simply not possible to squeeze everything from 20 pages into a 4-pages without losing something, so stop trying. Inevitably you will have to omit some results, or simply name them without going into details. You will have to drop some technicalities (which can contain some useful ideas as well) and so on. The aim of the extended abstract is to communicate the core ideas, not fully elaborated proofs and  methods. The elevator pitch technique above helps you to tell what's central and what's not.


Applying to Graduate School with misdemeanor charge?

I probably would not worry about this at all.  Conviction of a misdemeanor (as opposed to a felony) would not disqualify you from any of the U.S. graduate programs that I have been familiar with.  Schools will not necessarily even ask about misdemeanor convictions on their applications, nor will they be running criminal record checks on their applicants.  It is, of course, possible that some faculty reading applications at some schools may be vociferously opposed to admitting anyone with any kind of criminal history.  However, most places simply will not care.


What are specific strategies to help someone who does not do well under pressure

Not sure about the specific department about which you speak and in reality most departments and supervisors vary according to organisational policy and personal/relational differences. Having said that however, my understanding of the Ph.D.process is very different from undergrad studies for both the student and supervisor.

Optimally [and again this depends on egos etc.] your supervisor will encourage a collegial/peer based relationship with you whilst providing support and guidance which will diminish over time as you become more independent, assured and gain ownership over your work. In this scenario being timed should not be a factor.

However, this implies a sense of responsibility in your actions leading to academic/professional independence - and at least the potential for this has to be apparent to your supervisor and peers from the beginning of your tenure. In this respect, I would suggest the following:-

Approach your supervisor and discuss the issue in a  solution oriented manner. When doing this try to avoid an attitude of 'well this is just the way I am so suck it up';
Seek out intervention programs at your organization that might assist; things like time management courses, project planning, communication skills and if applicable anxiety management/boosting your confidence therapy/courses.

By being proactive about this issue you are setting boundaries with your peers which can provide breathing space for you thus allowing you to relax into the process and hopefully fulfill your responsibilities with respect to deadlines/time frames and expected output.

**However!**By doing this it is incumbent upon you to take responsibility for the above, find ways to manage what ever it is that causes you to feel as you do and perform as expected. Having a good contingency plan for when things stuff up would also be a good idea. As is being able to re-calibrate if you fall off the wagon so to speak. As they say the best way to deal with a mistake is to learn the lesson and move on. Try not to get embedded in the problem.

And lastly... hopefully not but you may need to acquire some negotiation and/or conflict resolution skills .... sometimes we come up against people who simply don't/wont/cant understand your position and try to impose their regulations/values/modality onto you...

Avoid such people if you can;
Negotiate 'normal interactions' with them carefully and in a non-reactive manner;
Seek advice immediately if they impose.

Hope this helps :-)


Puzzled with "Paper not suitable for this journal" decision for applied mathematics paper

First, I am not familiar with the "Elsevier Journal Finder," but any automated tools like this should be regarded as search tools and not wholehearted recommendations.

Second, there are a few obvious reasons why your paper might not be considered on topic.

Your paper has too much mathematical content or is written in too mathematical of a style for the journal, despite having applications to a relevant topic.
Your specific findings or methods are considered too specialized/not of interest for (the target audience of) this journal.
Even if this paper was pretty similar to your previous paper, different editors may have somewhat different views on what papers are relevant.  This also means that the types of papers published by certain journals can change over time, as editors change.

Generally it's a good idea when you're journal shopping to do the following to check if your paper will be a good fit: 1) read the "scope & aims" section of the journal, 2) look at the list of editors to check for overlap in interest with your research (if you haven't heard of any of them, that's usually not a good sign), and 3) look at some papers the journal has recently put out to see if any are similar to yours.


I doubt that you have any need to move and disrupt your trajectory. If your research is truly on the cusp, then you can probably move seamlessly into field Y even with a degree in field X. People change fields fairly regularly, especially if the change isn't radical. All of my education was mathematics, but lack of job opportunities when I finished pushed me to computer science where I had a long career.

The only problem, I think, would be in finding your first position. You need to have some contacts in field Y, perhaps professors, who will be happy to support your entry into the field, regardless of your doctorate.

And there is great value in interdisciplinary work in any case. So, building a circle of collaboration with people in both fields would probably be an advantage to you in the long run.

Once you are employed in some permanent position (tenured or similar) your choice of research is pretty much up to you. No one will care, anymore, that your degree is in a related field.

Having a degree in field X needn't lock you in to working only in that field.


How many publications to list as "selected"?

I would certainly include them all (the seven). Even more than the seven top tier ones. If you were an old hand in academia with hundreds, then you select. A young starter-upper should include a much larger fraction of the published work.

Don't neglect that in CS, conferences are usually primary.

But seven seems too few if you have more than 20.


Is there a good site for holding online discussions of scientific papers?

Might I suggest http://scicomp.stackexchange.com ?

While the StackExchange system isn't the best - and indeed isn't designed - for "discussion", I've found that many "What did you think of this paper" type questions can be phrased in SE-compatible formats. CrossValidated has a semi-periodic "Journal Club" bit, and questions and musings about scientific papers come up a fair amount there.

I think if framed correctly, they might find a useful home here.

Generally though, I think the online discussion of scientific papers suffers from a few problems. Generally, the two I find the most problematic:

Lack of a clear community to talk about papers in. Essentially, the problem your question is looking for an answer to. I haven't found a really good general purpose one, though I would love to if I did find it. There's blogs and the like, but even the ones talking about peer-reviewed papers are somewhat one sided in terms of their communication, and not great for anything but transient chatter.
A hesitation to talk about that online. Among colleagues, it seems somewhat easier to summarize things like "Bad paper is bad", or slice apart someone's methodology. I'd be somewhat more hesitant to do that anywhere where my identity is both traceable and the conversation is saved for eternity (the internet).