Can I predict the fate of my manuscript (from information other than a decision letter)? On this site we often get questions along the lines of:

I submitted my manuscript to a journal. X happened. Does this indicate that my manuscript is about to be rejected/accepted?

Here X is everything but a final decision letter, for example:

a specific sequence of statuses in the editorial management system,
the duration of a particular stage of the editorial process,
a request for a revision,
some editorial communication.

Is it generally possible to divine the fate of a manuscript from such events? If not, what are some relevant exceptions to consider?
This is half of a canonical Q&A acting as a dedicated duplicate target for a certain type of question whose answers often boil down to the same point. I don’t claim that all the specific questions are without value as they can provide specific insights. However, I think that addressing this problem on a more general level can be helpful as well.

Summary
There is no way of deducing the fate of your manuscript with reasonable certainty except a decision letter that says so. In particular, if your manuscript is certain to be rejected, there is no reason for the journal to spend further time on it instead of immediately telling you.
Main Argument
In the vast majority of cases, you can apply the following line of thought:
The point of almost the entire editorial process is to find out whether your manuscript shall be accepted by the journal (or whether it has the potential to be accepted after modifications).
If at any time the editors decide that your manuscript is or is not suitable, the process is over.
At this point, there is no reason to delay informing you about this decision.
In particular, after rejection has been decided, it would be a waste to spend any further resources on this manuscript, such as further reviews or editorial assessment¹.
Therefore if your manuscript has been accepted or rejected, you will get to know this immediately.
From another perspective, you can always ask yourself: If the fate of my manuscript were already certain, would the journal act as it does?
Revisions
Similar thoughts apply to requests for revision.
If the editors think a revision is impossible, they will not invite you to submit a revised version, as this revision would have to be assessed and thus waste resources if it already is clear that the manuscript cannot be accepted.
In fact, journals rather tend to phrase rejections overly strongly to avoid authors engaging in futile rebuttals, resubmissions, etc.
Journals have nothing to gain from hiding a negative assessment between the lines.
For example, if the editors think that acceptance of your manuscript is possible but requires a specific change, it would be foolish not to tell you this, lest you waste journal resources with a submission that does not make this specific change.
On the other hand, if the editors decided that they probably want your manuscript, it would be foolish to scare you away – though the editors may put a strong emphasis on changes they think are possible and necessary.
Exceptions and Similar
You have to judge yourself whether they apply to your case or the information benefits you:

The one thing that needs to happen between the decision and letting you know is the preparation of the decision letter, which particularly includes phrasing the rationale for a rejection or the conditions of a potential acceptance.
In many cases, this is a matter of minutes as it only requires the editor to combine a few canned sentences or the reviews already do a good job at explaining the problems of the manuscript or the changes needed.
But even if the editor spends effort on writing the decision letter, the best time to do this is right after the decision, as they are already focused on your manuscript.
For these reasons, the preparation of the decision letter is a very short stage, and moreover, most editorial systems do not inform you about it anyway.
Still, if you see this stage without any previous peer review, you can be rather certain that you are facing a desk reject.
However, it could also be that the editor wants you to perform certain changes to the manuscript before peer review.
Either way, once your manuscript entered this stage, you will get to know its fate very soon.

Certain events allow you a better estimate of your manuscript’s chances, but never a definite answer (for the aforementioned main argument):
For example, for some journals, making it to peer review is a major hurdle, and if your manuscript passed it, the chances of your manuscript considerably increase.
Similarly, if a manuscript goes from peer review to editorial decision and then back to peer review, this suggests that the reviewers have conflicting opinions about your manuscript, which may be good or bad news, depending on your a priori expectation of acceptance.
Also, there can be other reasons for a return to peer review, such as one of the reviews containing no valuable information at all, or all reviewers stating that they cannot evaluate a crucial part of the manuscript.

The editors or reviewers intentionally delay your manuscript, e.g., because of a grudge against you.
This is hopefully very rare, but even if this happens, you will usually only get to suspect this a posteriori, if at all.
If you suspected this a priori, you probably should not have submitted to that journal in the first place (or vetoed that editor).

¹ If those reviews have a potential of swaying the decision, it was not a decision in the sense of this answer.


Is it okay to ask advisor how I am doing with my research? I have some idea of how well I'm doing with my research in PhD, but maybe it differs from what my advisor thinks. Is it okay to ask (e.g. at the end of a meeting) how well I'm doing with my research? Can I say "Oh, by the way, how am I doing with my research?"

Yes, this is a fine question to ask, although I might phrase is slightly differently:

  "How happy are you with the progress that I am making?"

which makes it a little more open-ended and focuses the question more on process and progress.


Would it be ethical for a computer science PhD student to hire an assistant (programmer)? I was wondering if it would be ethical for a PhD student in the field of Computer Science to hire a programmer in an specific domain; so that he could focus more on the algorithmic or mathematical part of the thesis. Would that be something ethical to do? Should the PhD student include this assistant as a co-author in the articles?

I don't think it is inherently unethical to do this.  If all relevant parties know about it and you scrupulously acknowledge this other person's work, then I see no specific problem.

Whether it is advisable is a different question...and one you should certainly ask your advisor.  I have to say that it does not sound like such a good idea to me.  Your thesis work is for you to do...almost by definition.  It is perfectly fine to get help from others on your thesis, and some people are better programmers than others (even in CS, I imagine), so getting some pointers from a friend is actually a good idea.  But paying someone to do a part of your thesis work just doesn't sound good to me.  Either the programming is an important part of your thesis or it isn't.  If it is, you should do it yourself.  If it isn't, maybe you don't need to do it at all, or don't need to do it to the degree that an outside professional would.

There is also the issue of the impression this subcontracting would make on others.  Perhaps the cultural norms in your field are very different from mine (again: ask your advisor), but I would have a rather negative impression of a PhD student who did this: they don't seem to be very committed to their own work.

Added: To be clear, I am interpreting the question as meaning that the doctoral student himself is doing the hiring: i.e., that this is his idea and he is using his own funds.  (If his university is giving him funding and simply asking him to pick someone to work with, then even asking the question "Is it ethical?" becomes less plausible.)

In terms of suspecting that this is not a good idea, I hope I was clear that this is my personal opinion, with experience from a field (mathematics) which is rather closely related to CS but is not necessarily identical.  As I said, the OP should consult their advisor about this.  However, for what it's worth I find it hard to believe that the reaction will be "Sure, spend your money."  While not unethical on the OP's part, it seems, shall we say, suboptimal if both advisor and student feel that this is the best way to proceed.


Attribution of diagrams made with Creative Commons software If I want to use diagrams I created using GeoGebra in a dissertation or paper, how do I properly credit/give attribution? The terms of service say:

  We grant you permission to use the Website Content under the terms of the Creative Commons Attribution-Non-Commercial-ShareAlike licence (version 3.0 or later), the current text of which can be found via this link. Attribution (as required by that Creative Commons license) should take the form of (at least) a mention of our name, an appropriate copyright notice and a link to our website located at https://www.geogebra.org.

  Use of existing "authored" materials published on our website are similarly subject to attribution, to include the name of the author(s) and link or hyperlink to the material itself. For example, "Created with GeoGebra, by [name of author of material]".

It would seem tedious and distracting to write "Created using GeoGebra (www.geogebra.org) under CC-BY-NC-SA-3.0" in every figure caption. Would it be acceptable to include a note on the List of Figures page, either mentioning the specific figures or just "some figures were created using..."? Or the Acknowledgements page?

You just add yourself as the source (Like - 'Source: Self elaborated with X software using data from...') in the citation and then in the methods you mention which software you used.


Who is eligible to apply for instructor or assistant professor positions? I am a math PhD student in my last year, and I've been on mathjobs.org looking for jobs.

I see a lot of jobs for instructor positions, or jobs titled "assistant professor", where the main work load seems to be teaching undergraduates and no research.

It seems that the main qualifications are a PhD. I am confused on what kind of applicant is qualified to apply. It seems that I am qualified enough to apply, assuming I receive my PhD by the time the job starts, but I am worried I am being naive. I do realize that someone that has already had an instructing position, or "assistant professor" position previously, or experience as a postdoc, would look better than a fresh PhD.

Are these jobs typically given to PhD's that have been through a few postdocs, or do PhDs straight out of grad school have a fair enough chance at getting the job?

To be blunt, am I wasting my time applying for these positions?

No, you are not wasting your time.  For assistant professorships at colleges with little or no research component, you should feel free to apply in your last year of a PhD program.

  I do realize that someone that has already had an instructing position, or "assistant professor" position previously, or experience as a postdoc, would look better than a fresh PhD.

In my experience that is not necessarily the case.  In my PhD program, probably more graduates go on to this type of job than any other career trajectory.  Many of our graduates do get tenure track jobs straight out of graduate school.  Getting such jobs later after doing a temporary position is still possible, but it seems to me that the chance goes down.  Even top twenty liberal arts colleges still hire many assistant professors straight out of grad school.  Obviously they could select candidates with postdoctoral / visiting faculty experience.  They often choose not to.  I would go so far as to say that in many teaching jobs, postdoctoral experience could be viewed as a bit of a mismatch.

(An old friend of mine has written an article about the pleasures of being a visiting faculty member.  To a certain degree it contradicts what I said above.  But I think he is more looking on the bright side of taking multiple visiting positions than suggesting that they are necessary.)

Three more comments:

You should know that an "instructor" position is typically very different from an "assistant professor" position.  Suffice it to say that if you want an assistant professor position, you probably do not want an instructor position.  In many math departments, there are recently hired instructors with PhDs teaching alongside of instructors without PhDs who have had the job for a longer period of time.  This is not saying good things about the current job market.  In my opinion, having a PhD makes you overqualified (and certainly, underpaid) for most instructorships, but of course it's up to you to decide on what's worth your while.
Rather than further academic training, what you want to have in order to get these jobs are a strong teaching record and excellent teaching abilities in an interview / model classroom situation.  Many PhD programs nowadays provide opportunities for their students to display these credentials.  If you are looking for a primarily teaching job post-PhD, I hope you have been doing everything in your power to acquire these credentials during your graduate career: in many cases, this provides the best opportunity to do so.  (If you are not sure where you want to go on the teaching/research perspective, I hope that you have erred on the side of acquiring more of these credentials than you will necessarily need.)
When it comes to individual departments, Nate Eldredge made a good suggestion: you can look through CVs of recent (and less recent) hires to see what their credentials are.  However, a small department may have a small sample size.  Nowadays many (most?) people on the academic job market apply to on the order of a hundred jobs; necessarily this includes many jobs for whom the goodness of fit is unknown to them.  Not applying to jobs because you are worried that you might not be competitive does not seem like a good strategy when so many other strong candidates are applying for everything in sight.  You don't have to stuff envelopes anymore (like I did when I was applying for jobs less than ten years ago!), so the differential amount of work in applying to some positions that you fear might be a stretch but don't know is small.  When in doubt, apply.  I say this as someone who reads through hundreds of applications a year.  If we're not interested, then we're not interested, but it's no problem.


Follow-up email after faculty position interview I followed up and was told that "we are still navigating the university's recruitment process, so still need several weeks to provide update". Could anyone explain what does it mean? Does it imply any positive or negative results?

The email does not imply anything.

The hiring committee/chair really can't say much to applicants during the process other than "we are still working on it." I emailed a few while I was going through the process and they all sent back generic responses.

However, if you email them to let them know you have other offers, that is when you would expect a different response. Every school that I emailed in this situation was very forward with information (e.g., "We are making a decision on March 15th and will call you that day." or even "Here is an unofficial offer. The paperwork is processing for the real thing, give it a week."). Good luck!


Do I need to send two official copies of toefl/gre scores to a US school? I'm applying two programs in different departments in one university simultaneously. One department has a department code and the other has not. Do I need to send two official copies of toefl/gre scores to the university?

Send the e-mail directly to the university asking for the related problem/confusion.
Every university is ready to help with these type of queries.
Send one email to admission director, or call their admission office. You will get the best clarification directly from the source because admission director will be the person reviewing your application!


Why is my published article seemingly not indexed by Google or Google Scholar? I am a Masters student, in the Faculty of Science in Canada. I have a question to ask regarding literature review. I am doing a bit of studying to find protocols for my experiment (where I hope to conjugate a certain linker to a nucleic acid). I tried looking for papers with different keyword searches on Google Scholar, as well as the WebOfScience.
There could be different possibilities here - either there are no papers that have been published, or the Search Spider was not able to find the papers (which is a False Result).
I therefore tried looking for a paper which we had published 4-5 years back in Journal of Chemical and Pharmaceutical Research. It does not show up in the search results, probably because it does not have enough citations (you can try by searching this paper on Google standard search, and on Google Scholar: Potential inhibitors against acetylcholinesterase and glutathione S-transferase associated with Alzheimer's disease).
Doesn't this give false hope to certain researchers, that the work they are currently doing is novel; or make it difficult for other researchers who are trying to find a protocol to adopt?
Hoping to get some insight from the community.

Although you asked a generic question, the answer is very particular to your own particular article. Most likely, @HoboSci, got the correct answer: you published in a journal of questionable ethical editorial policy that Google Scholar refuses to index. That is, "Journal of Chemical and Pharmaceutical Research" is probably such a journal (see https://bradleymonk.com/Beall%27s_List_of_Questionable_Journals).

I looked up the issue where your own article is published: JOCPR Volume 6 Issue 3: http://www.jocpr.com/archive/jocpr-volume-6-issue-3-year-2014.html. I searched Google Scholar for your article "Potential inhibitors against acetylcholinesterase and glutathione S-transferase associated with alzheimer's disease". I also searched for a couple other articles in that same special issue and none of them showed up in Google Scholar.

Unfortunately, I don't think there's anything you can do about it because once you've published in a journal like that, you can't republish the same article anywhere else. So,the lesson is to only publish your work in reputable journals, or else your published work might become almost invisible on the Web. :-(


What are the possible grants/stipends/scholarships that are available in the Republic of Austria? Yesterday I was offered to join Central European University (now situated in Vienna, Austria). The dream came true, and I was invited to get a MPA degree.
CEU Admissions Committee gave me a very generous tuition discount (more than 70%), but I still cannot afford this. It's too expensive for me and my home country - >3000 euro. I could afford this offer in case of selling all my properties. Obviously, I will not do it.
What are the possible ways to find additional financial support? What scholarships or grants options are available for Austria? What are the most suitable and reliable ways of receiving a funding for the non-EU resident?

Austria has an official agency for International students, called the OeAD, which, in turn, offers a database of possible funding sources for academic purposes at https://grants.at
Grants.at allows for a granular search. You can select your nationality, state that you are an incoming student, and choose the option of funding of a full study programme.
Here is an example screenshot if you are from Russia:

Good luck (and congratulations on getting accepted at the CEU)!


Software to create repositories of students' software projects I want to be able to store the software projects my students submit so I can catch plagiarism. Some students copy work from previous years and it would be really helpful if I could find a way to store all projects so I could compare.

My university currently uses moodle but I can't find a way to create a project repository to detect plagiarism. (We do have the JPlag detection system but that only works for projects submitted under one particular group (assignment)).

Any ideas?

I and my university have used MOSS (Measure of Software Similarity) by Stanford (theory.stanford.edu/~aiken/moss) - I'm not sure of its effectiveness to detect slight modifications, but it seems to be the standard of most university CS programs.


Locating old Russian literature in the US There are quite a few old Russian papers and books I've been trying to track down for a few months without success. (I have some listed here.) Many old Russian journals and books are in US libraries, and I think I'm aware of all or nearly all of the resources my library has available to me. If the journal is not available in the local library or online, I'll look on WorldCat, and use my library's interlibrary loan service if I can find an entry on WorldCat. Basically, if it exists on WorldCat, the interlibrary loan service is likely to obtain the paper, and if not, I'm usually out of luck. Overall my success rate is probably only about 50%.

Herein lies the problem. Very few Russian libraries participate in WorldCat, and in my experience libraries outside of the US are less likely to provide scans. Basically everything I have been able to locate this way existed in the US, and there are many Russian journals which never seem to have made the trip to the US. Or if they did make the trip, they exist only in the Library of Congress, which requires you to visit in person. (Not such a huge issue for me, as I have family in the DC area, but this could be prohibitive for others.)

Are there any resources in particular for Russian papers that I should be aware of?

The previous question titled "What do you do when you find yourselves with an unreadable/inaccessible paper?" is related to this, but I'm aware of everything mentioned there and/or what is mentioned there is not applicable, and am looking for something more specific to locating Russian papers in the US.

(I'm looking for engineering and physics papers primarily for experimental data and models to use in my own research. In general, these papers are quite old such that the authors are inaccessible, though in most cases the journals are still active.)

If it is a paper you are after, and the journal is still in existence, try contacting the editor of the journal, and asking for a copy of the paper.

Depending on the age of the material you are trying to access, it is quite possible that the original authors are retired, dead, or otherwise hard to contact. If the journal continues, however, the editor(s) of the journal will have an interest in helping you obtain the information you require, with a view to having their journal cited.

I had this exact problem with a few old (~40 years) papers published in Russian journals to which I didn't have access. I contacted the editor directly, and was rewarded with photocopies of the papers I needed.


Can Design & Implementation sections be combined in a project report? I'm writing a postrgraduate project report on a system I've built. It is not designed with the user in mind, it is a backend system to a simple web application.

I'm struggling to separate the Design chapter from the Implementation chapter in my report, as I didn't so much design the system as build it as I went, changing how it was built depending on issues I encountered during implementation.

Is it possible to add all design and implementation information under one chapter, as they are fairly intertwined, or is it necessary to separate them?

Edit

I have solved my problem; the Design chapter is the idea and outline you had in the beginning of what you would like to create, with the various components you think you'll use, and the Implementation chapter includes all the issues that cropped up along the way, creating the need to change the original design.

Thanks for all your input!

It seems you were given an assignment to design and build a system and then write a report to document your work. However, you decided not to do that assignment and instead you decided to build a system skipping the design step.

I would expect the person marking your report would see it as you did not complete the task as assigned. As JeffE's comment implies, there is a reason why you were given a task that included designing first then building.

I think you should ask your lecturer if what you have done is acceptable or if you must restart your assignment.


Can a co-author cut the whole paper? Once upon a time... A paper was submitted to a journal with the consent and knowledge of all co-authors. During the revision process, one of the co-authors (X) demanded co-authorship in the articles of other co-authors (Y and Z). This request was denied, as X did not meet the requirements of co-authorship in those papers. As an answer, X refused to allow the article to go forward, until one of the co-authors (N) being excluded. X explained this decision by questioning the contribution of N to the research. What might be a diplomatic and professional solution, if N and X are both valid co-authors? Can X cut the whole paper?
All characters and other entities appearing in this question are fictitious. Any resemblance to real persons or other real-life entities is purely coincidental.

Generally speaking, you can't publish something without the consent of all authors, so yes, it can happen.

This person is behaving badly. Perhaps there is a common authority you can appeal to so that the bad behavior stops. Even a threat to appeal to higher authority might make a difference.

It might be necessary, actually, to abandon the paper if you can't find a solution.

But don't work with this person in the future. If it is a PI/advisor, then you have a different issue, of course, as such people have power that can overwhelm justice. But, to the maximum extent possible, ignore the opinions of this person who is trying to optimize their own record at the expense of others.

But if it is a PI/advisor doing this, say so, and I can supplement this response.


Does applying for a Masters at a school when also applying for a PhD look bad? I want to go to graduate school for a PhD, but as a safety I'm also considering applying to master programs in the same or related field, if my undergraduate credentials are not strong enough for top programs. Would applying to the masters program where I am also applying for a PhD send the wrong message to the school though, that I'm not sure if I want to do this for a full PhD or not? Or do they understand that people apply to masters program as a back up for if someone's PhD applications don't go well?

Applying for multiple programs is common and unlikely to reflect badly upon  you. Applications committees for different programs are usually made up of different members and it is highly unlikely that they will even know that you applied to both programs. The only time it might be revealed is when it goes to the administrators who send out the letters, and frankly they could care less.

Something to note, which affects both this issue and your overall considerations of a program, is that schools usually look for different things in a PhD program vs. an MA, and that affects how they conduct their admissions. At many school, MAs are not just less-capable versions of PhD students, they are completely different type of student.

Terminal MA programs are usually unfunded, and include people who are less likely to conduct independent research. Some MA students will go on to a PhD program, but probably not at the institution where they get the MA. For this reason, MA programs at many schools are called 'cash cows' and admissions to those programs are less of a priority for the full faculty, with a lot of the sorting done by administration, focused on funding potential, and stricter considerations about things like GREs, etc.

PhD programs are research training to become academics, or at least independent researchers, and most PhDs are fully funded. Since the university is investing in you, and the faculty will be stuck with you in person for 5-10 years, and reputationally forever, the faculty care a great deal about this. Considerations like the ability to pay, and even strict measures of capacity like test scores, take a secondary role to creativity in the field, goodness of fit, and so on.

Simply put, in many schools you have to impress two different sets of people to get admitted, with overlapping but different priorities. There are idiosyncratic reasons why you may be admitted to one program and not the other, and sometimes it might even be that you get into a PhD and not an MA. (On balance, however, admissions to an MA program is more likely than a PhD, simply due to the volume of admissions.)


Should all recommendation letters be research- or teaching-related? I am applying for junior faculty positions at research universities.  Most job postings request three references (either just names and contact details, or actual letters of recommendation), and I've already secured these from the three full professors who can best attest, in different aspects, to my research and teaching skills.  One of these professors was my thesis advisor, and the other two are faculty at other universities with whom I have worked closely.

A few job postings ask for five references.  Now, I could approach two further senior academics who could also vouch for my research and teaching abilities, though there's no one I have worked with nearly as closely or as recently as my three top references.  I have no doubt that they could supply positive references, and while their names alone might carry some weight, they wouldn't be able to write about me in as much detail.

On the other hand, I do have some notable collaborations with professors on work other than research and teaching—namely, on outreach and knowledge transfer activities.  That is, we have cooperated on projects aimed at disseminating scientific knowledge and research results (not necessarily our own) to the general public and/or industry.  Would getting a reference from one of these professors be of benefit for a faculty application?  Or would most selection committees be looking exclusively for research and teaching references?

I see relatively little value in having additional letters that all speak to the same topics. If you think that the existing letter writers already cover your research in positive enough light that your research credentials are unquestioned, then having additional letters cover other areas is certainly a plus as it shows you breadth as a professional.

It would probably help if the other letters could at least very briefly mention the topic of research so as to not look like you're scraping the bottom of the barrel in coming up with more letters. This could be done by these letters containing statements of a form like this:

  I have known Dr. Psychonaut for several years and have in particular observed her greatly grow in her research since I first met her. I have also seen her give a number of marvelously executed talks on her research. That said, I know that several of my colleagues are already writing letters that address her research credentials in great detail; I will therefore rather focus on a separate area in which I have collaborated with Dr. Psychonaut -- namely, knowledge transfer -- and for which I know that my opinion is unique.

What I'm trying to say is that the letter should be written in a way to make clear that the letter writer could be talking about your research, but consciously chooses not to because they have this other thing they know and only they can talk about. This avoids the impression that there are only three people who can comment on your research and teaching, and that you needed to go out of your way to find a fourth and fifth letter writer.


Access to student records/grades Is it common practice within colleges/universities to allow all faculty within a division access to all student records within that same division?  (i.e., all Health Science faculty having access to all Health Science student records)
Wouldn't this violate FERPA?

Reading FERPA, this clause states that it is appropriate given certain circumstances.

  However, FERPA allows schools to disclose those records, without consent, to the following parties or under the following conditions (34 CFR § 99.31):

School officials with legitimate educational interest;
Specified officials for audit or evaluation purposes;
Appropriate parties in connection with financial aid to a student;
Organizations conducting certain studies for or on behalf of the school;

These would be closest to those that matched what you asked.

So if, for example, your HS faculty wanted to average everyone's GPA individually, he could potentially do that, as long as he doesn't post all the names in public.


What if I may not have research experience for math PhD application? I am a master student of some engineering (other than EE/CS) in a decent US institution who will apply for a PhD in mathematics in Fall 2014 (possibly in PDE / applied analysis, but not sure). I finished with three A's and five A+'s in eight upper-undergrad / grad math courses, along with four more to come this fall. Since my intention for a math PhD came pretty late, I am only able to look for supervisor this semester. The sad thing, as expected, is that all three potential supervisors declined my request softly. My previous engineering research experiences are mostly experimental, with little to do with math.

So I have roughly one full semester left, and my questions are:

Is it possible to gain any sort of research experience in this semester without a supervisor?
If not, then how can I show my research potential by other ways?
Will the three LORs solely from course lecturers be convincing, even if the lecturers are well-known, and I did pretty well in their courses?
In addition, is abstract algebra a must or at least very important in math PhD application? Since I have to make a choice between Algebra II and Dynamical systems, and I don't have Algebra I.

Thank you for your responses and criticisms.

Firstly, I should mention that I am a 3rd year math PhD student at Brown. So I have a hint of knowledge, but not as much as a professor who has been to more institutions, and certainly not as much as someone who has been  on an admissions committee.

Firstly, many starting PhD mathematicians have no real research experience. The reason is simply that research mathematics is so far from most undergraduate mathematics. This is also why doing research is so hard without a supervisor (for that matter, it's hard with a supervisor). Many candidates have done REUs, which look generically good but often don't usually result in a publication or anything.

What I recommend to you is that you:

Identify what you're interested in and pursue it. You say you maybe like applied analysis or PDE. Maybe see what some people are doing, read some of their stuff, backtrack if you need to. In this sense, you can just do research without waiting for someone else's permission. I'd like to mention that there is a polymath project you might be interested in, Polymath 7 on the Hot Spots Conjecture (here is a link to the most recent progress page). It's slowed down, but they've done some interesting things and the polymaths are generally good about leaving a clean trail of breadcrumbs.
Ask about showing research potential and getting letters of reference. Instead of worrying about what's the absolute best thing, I think you should worry about doing the best that you can do. You've tried to set up some research with professors and that fell through. You haven't done math research before, and you're probably not going to get far in the next 4 months. In particular, it's unlikely that you're going to come up with a result great enough to inspire someone you haven't worked with to write you a letter of reference. This is all to say that you should get your letters of reference from those best able to recommend you. If these are lecturers, then so be it. But I hope that you've been attentive, proactive, and inspired in those classes. For that matter, if you're inspired, you might be able to ask your dynamical systems professor for an interesting project - approachable projects exist. It might not be new research, but at least it would be something you, and others, could talk about. As a final note, you should talk to your math professors and ask them for advice - I suspect that at least one of them will be able to say something, and they're more familiar with your situation.
Have you done any research in your 'some engineering?' Conceivably, a great letter of reference could come from your advisor/a great teacher/I don't know these details. You should talk to them about this, and get their advice.
Determine what schools you're interested in applying to (apply to many), and their requirements. Brown's Applied Math department does not require algebra. But they do (essentially if not officially) require the math GRE, which does require algebra (though for less than 1/4 of the test). On the other hand, Brown's Pure Math department (the one I'm in) has a severe algebra requirement. Interestingly, PDE is done in both, though in different directions. Many schools require algebra, or require it in the sense that they will have qualifying exams and one of those is in algebra. My undergrad, which I'd say has an applied bent, had quals in algebra and both real and complex analysis. So you could consider taking algebra if you needed to or wanted to, based on looking into what universities you want to apply.

However, algebra II without algebra I sounds incredibly perilous, especially as the fall semester is upon us already, or is about to be. Perhaps possible with a lot of pre-work. If you are going to attempt to hop into algebra II, I recommend getting a copy of Dummit and Foote's algebra book (clear exposition at a low level).

Finally, plan on taking the math subject GRE. It's only offered 3 times each year, and you've missed the summer one. You should take it both times this fall, and those signups might already be occurring.


Choice between different PhD Positions I would like to ask you about the correct behaviour when applying at different universities for different PhD positions.
Currently, I won two PhD positions and a second shortlist for a third one. The third one is the one I really want, but the interview will be held on campus and due to coronavirus pandemic it has been postponed after the mid of August. I have strong academic and personal reasons to go for the third one, but of course I am not sure that I will win it. Now I have to decide between the two I already have. I would feel guilty to tell yes to one of them and later on withdraw the offer.
What is the acceptable time to change your mind? Should someone follow his personal motivations or be ethical?
Thank you,
Joy.

Is there a deadline by which you must accept the two offers you currently have? If so, send a polite email to those institutions explaining the situation and asking for an extension on the deadline until you hear back from the third. I expect they will be amenable to your request, given the circumstances.
If you accept one of the current offers without waiting for the outcome of the third, I don't think you will be very happy. You must pursue the position you want the most and feel is the best fit for you. Your PhD will be much more productive and enjoyable that way.


The exam time was less than the students expected Some time ago, a course I visited had final exams, and the time announced to the students in advance (several weeks earlier via email by the instructor) was 3 hours. Rather shortly after the students began to write (about 20 minutes), it was announced as a clarification that the room was booked for 3 hours, while the test itself would only take 2 hours.

I did not take part in this exam (I took the second one, which had similar conditions), but I'm sure the students were quite surprised. The exam itself was of average difficulty, had it been 3 hours, but very tough in only 2. This was reflected in the results: 90% failed, instead of the usual 30-50%, and the best grade was only a "B-".

I'm interested if this sort of thing is less unusual than I would think, or if there is a protocol how to deal with it as a student?

I would hope this is unusual because it's not very nice to the students.  Students deserve to know in advance how much time will be given for the exam. And in my experience, they usually do know this quite far in advance.

It doesn't make sense to me that the figure mentioned in
the instructor's e-mail would refer to how long the room was booked (which is not something that the students would care about) rather than how much time would be given for the exam.

Another thing that doesn't make sense to me is why, when the instructor realized that the students thought they would have three hours for the exam, he didn't just keep quiet and let them have the three hours.

However, I don't know what you mean by a "protocol how to deal with it." You could certainly let the instructor know that you are unhappy about this aspect of the exam.  But is there something that you think the instructor should do at this point to improve the situation?

Also, what does it mean to say that 90% of the students failed the exam?  It's not necessarily a bad thing if 90% of the students got a numerical score below 60% on the exam, but it would be a very bad thing if 90% of the students got an 'F' grade in the course.


How to address Phd dissertation committee members in email? I am in the process of notifying my PhD dissertation committee (already formed)on the proposal exam. I would like to send an email to all of them and now I am confused as to how to address them. Should I address them as committee members or Professors ABC, PQR, XYZ or Sirs, etc. What would be the best option to address them:

Dear Committee members
Dear Committee
Dear Professors ABC, PQR, XYZ
Respected Sirs
Sirs
Dear All

At my place, they are called SRC (Student Research Committee) members, so that makes the acronym more usable. I always started my emails by writing:

  Respected SRC members,

The SRC members part additionally makes the context clear (in addition to the subject of the mail). I prefer Respected to Dear, and while that may (or may not) be culture specific, it never hurts to shower respects on these people, unless of course, they explicitly ask you not to do that.

Additionally, I deliberately avoided Professors. Even though these committee members could generically be addressed as professors, one of my SRC members was technically still not a Professor, but an Associate Professor. While the distinction might be a bit over-strict in this context, I preferred being technically correct too. (That might be a nerdy, personal choice.)

Hope that helps :)


Why do many recent open access “mega-journals” only cover biological sciences? In recent years, there has been a number of quality peer-reviewed open access journals launched. Some of them are what I would call “mega-journals”, such as PLOS|One and the newly-launched PeerJ. However, most of those mega-journals which boast broad scope focus in fact only on medicine, biology and health sciences (e.g., PeerJ’s Aims and Scope). Why is that so?

Are there other such open access journals with high-quality, focussing on other topics (Physical Sciences, the Mathematical Sciences, the Social Sciences, or the Humanities)? If not, what is the specificity of biology and related sciences?

I think one of the major issues here has been the existence of arXiv in all its various incarnations. Since there was already a major open-source distribution network—even if it eschewed important parts of the publishing process like peer review—it made the need for a PLOS|One-like journal much smaller.

A secondary issue is that many of the journals in the mathematics and physics communities have fairly liberal policies on the use of open-source repositories to distribute papers; for instance, the American Institute of Physics and American Physical Society allow publication within their journals, while still allowing authors the right to "self-publish" using their own version of the materials. Similarly, the American Chemical Society, while having slightly more restrictive policies than AIP or APS, still effectively allow open access after one year of "exclusive" access.

So, ultimately, I think the emergence of PLOS|One and similar efforts is an attempt to move more in the direction that already exists in the various physical sciences communities.

Edited to add: One additional issue that may explain the state of activities are some of the recent decisions by the NIH to require that manuscripts published with NIH financing (thereby including the majority of biomedical research in the US) had to be made publicly accessible within six months of publication. This is a development that has not been matched by the NSF and other major funding agencies, nor is it a rule in most of the European Union, as far as I can tell (although I believe the UK is haltingly starting to move in that direction).

As a result, there is a strong impetus for open-access in biology and biomedical science that is not matched by the other fields (which might not have nearly as much money and therefore would not have the clout of the NIH).


Organized or co-organized? I organized a couple of workshops, as in I was the correspondent person, and I designed the workshop, invited others to co-organize with me, was the lead editor to proceedings etc. But I feel awkward when I say "I organized", as eventually there was a board of organizers.
Should I say "I organized" or "co-organized"? Is there a right way to do this? Is it vain to say I organized? On the other hand, if I am invited to take part in the organizing board, I say "I co-organized" and mostly I also indicate in which board, which responsibilities/tasks/roles I have taken on in an attempt to make it clear that I wasn't the lead organizer.

There are other, more specific, possibilities. "I led the organization of ...", or something similar. "I was the lead organizer and editor of...". On the other side, "I aided in the organization of...".
Don't make it a title, but a description, unless the organization requires titles.


Getting work experience recognised as a master's degree? Note: I'm asking for an older relative with close to 30 years of relevant experience in electrical engineering. He has a bachelor's degree. We both live in Canada.

Due to how his employer's criterion work, having a master's degree would help greatly for getting a promotion. He has published 2 articles in IEEE and 3 patents. He also works closely with the R&D department and has developed a new technology (on which the papers were based).

Is it possible to use relevant experience and publications to get a master's degree? Possibly an accelerated program that would not take two years?

From an academic point of view, no.  Work experience is not counted as a substitute for formal study in academia.

Academics consider the award of degrees for work experience to be fraudulent.  Some employers will accept these degrees for promotion purposes.


What if clinical leadership refuses to protect research time? I'm a physician-scientist currently on year 4 of a K23 (early career grant for physician scientists in the US), recently awarded first R01 (multi-year major research grant for biomedical science in the US) with 20% effort.  Problem is that despite the 'protected' time from these awards, my division/section chief refuses to commit, and as the only non-full time clinician in the section I seem to to be the first one asked to cover the clinical scut work (calls, service, etc.).  My division chief specifically said, "No one really holds to the protected time", so it doesn't matter if I get three more grants, it's not clear they'll ever actually protect my time.

It seems like the only option (other than leave) is to sacrifice myself by reporting to NIH, in which case I'd probably just lose the grants.  Has anyone ever successfully managed this situation without leaving?  Anyway brought in ombudsman, or other independent institutional resources?

Obviously, I'm posting this anonymously...

Take a look at the rules governing the ombudsperson before you go there. Good rules will ensure confidentiality and that the ombudsperson won't take any action unless you say so. That will allow you to freely discuss your problem. If your institution offers an ombudsperson with good rules, then talking to an ombudsperson would actually be very useful in your case. I would not start with the idea of taking action, but just as exploring what is possible.

Also don't take this personal. The leadership has to make sure that all tasks are performed with the resources at hand: if you do less, somebody else has to do more. If your grant compensated your department for that in full, then that should not be a problem. Though even then, if the departments resources are stretched already, then the leadership will still be faced with impossible choices. It should not be the case, and solving those impossible problems when they happen is not your problem, but understanding it can help not to take those choices personal. If your grant contains no or only partial compensation, then the "protection" from the granting agency is very cheap: basically the granting agency is not spending its own resources but your department's resources. Your department can be forgiven for saying that that is not going to work.


Allegations of harassment by a faculty member and reporting? This issue is about a university in a 3rd world country.

I friend of mine (I will call her "Z") is a faculty member at a reputable university. During one of her sittings with an undergrad student ("A"), she learned that another faculty member ("T") is sending "A" some inappropriate text msgs and emails. "A" also mentions that she has heard similar stuff from another student "B" about "T". "A" offers to show some texts to "Z" to which "Z" refuses. But "Z" does tell "A" that office of student affairs handles such matters to which "A" says that she is aware of that office but does not want to report. "A" just wants to graduate ASAP and thinks that "T" might damage her as he is quite powerful within school administration. Therefore no action.

I am convinced that, given "A" is not the only student who is being harassed, "T" will misuse his position and will continue his inappropriate behavior. And I am also convinced that office of student affairs will take action if notified. I guess that my friend "Z" does not want to be a whistle blower although she thinks that "A" is being truthful.

I think that keeping quiet will only make things bad for other vulnerable students. Please mind that for a female going to university in that country is a privilege. And "T" is not on the university's radar. So I am thinking of dropping an anonymous email to office of student affairs. Is it ok to do such a thing? I mean I have not even an iota of business with that university, "A", or "T".

So my question is:

Is it ok for a person, who has nothing to do with any of characters in the story, to drop an email asking administration to take a look into these allegations?

Note:
I understand that accusing anyone wrongly has serious consequences, both professionally and personally. But at the same time if these allegations are true and are left unnoticed, students and the university will be at the receiving end.

As Allure points out, opinions on this matter will vary, so let me note some points that I think are important here, and also offer an opinion that is slightly to the contrary of some other answers.  (For brevity, these points are framed as an answer to the person you are talking about who is the academic dealing with these students.)

Academics have a duty of care to students: Students at university are adults, but they mostly are still young and inexperienced.  In my humble opinion, academics should generally err on the side of pushing for assistance in cases like these, even if the students are reluctant.  Students are generally young adults who may be intimidated by the positions and standing of older adults who have attained academic success and institutional power.  Having another academic push the matter forward may be helpful in overcoming this disparity.
Harassers thrive on the "I won't make a fuss" mentality: Without making any assumption about whether or not harassment has actually occurred in this case, it is worth noting that cases of harassment tend to be done over and over again by a small number of individuals, and tend to proliferate because each person who is being harassed thinks it is only them, and they don't want to make a fuss and risk retribution by a powerful person.  In cases where a victim of harassment reports the conduct, it is not unusual for this to precipitate an avalanche of other allegations against the same harasser.  Recent events in Hollywood (e.g., Harvey Weinstein) testify to this fact, as do many other cases of sexual harassment.
Merely referring an allegation is not "accusatory": Reporting an allegation for it to be investigated need not presume the truth of the allegation, and need not be "accusatory".  That is the point of an investigation - to get to the truth from a starting point of it being unknown.  It is perfectly legitimate to report allegations you have heard on to the administration, while taking no position on whether they are true or false, but still asking the university to consider whatever investigation into the matter is warranted by the allegations.  There is no contradiction between wanting to bring this matter to the attention of the administration, and also wanting to avoid a false accusation.  Just make sure that if you do send an email to the administration, you write it in a neutral way that does not presume that misconduct has occurred.
In the end, evidence will be required: While it is legitimate to report hearsay allegations for the purpose of bringing a matter to the attention of the administration, you should bear in mind that your hearsay is not evidence.  Unless one of the affected students is willing to speak to the university administration about this, the university will probably be very limited in its ability to investigate the matter.  That is perfectly legitimate - after all, people should not be subject to negative proceeding against them without evidence, and hearsay evidence is weak evidence.
With this in mind, the contribution you can make here is to bring the allegation to the attention of the administration, leading to contact with the students, and giving them an opportunity to report this matter formally.  By acting as the initial referrer of the allegation, you can also show your students that actions are louder than words - you are willing to get involves, so maybe that will make them more willing.  Still, at the end of the day it will depend on them.  In my view even this step might be a good idea, even if the students ultimately decide not to proceed.  I don't agree with the recommendation to do nothing.
Have the courage to put your name to the referral: Think carefully about whether it is appropriate to report this anonymously.  If it is justifiable to refer the matter to the university administration, and if you frame your email in a fair way that does not presume misconduct, then you ought to have the courage to put your name to it, and stand by your own actions.  Reports of harassment are generally treated in confidence (at least up to the point where the accused is able to face the accusations), and this is an opportunity to set an example for your students and show that you are willing to act on your own principles.  If a grown-up academic can't show the backbone to make a report about a colleague, without hiding behind anonymity, why should younger students show the courage that is absent in their elders?

Anyway, that is my two-cents.  I'm sure there will be plenty of others with contrary opinions.  Hopefully others will also give their views, as it would be worth getting some contrary ideas on this matter before making your decision.


How to avoid and address a lack of gender diversity in grant proposals? I just got reviews back on a grant proposal.
On the whole the reviews were positive, but one reviewer criticised us because the five PIs are all male.
The proposed project arises naturally out of a couple of strands of work that we’ve been doing recently. The PIs are the people who’ve been involved in that work, plus the CTO of an industry partner. We’re in a niche area of applied math, and neither of the institutions involved have female staff eligible for the grant scheme working in the area of our proposal.
I support efforts to fix gender imbalances in academia, and I would have preferred a mixed-gender team. However, I’m not sure what I could have done for this project. The options seem to be:

Propose a fundamentally different piece of work with different participants. However, this would likely not be of interest to the industry partner, which is central to the viability of the proposal. Our original idea would then presumably not get developed.

Expand the proposal to bring in female colleague(s) at another institution. However, the funding scheme essentially only provides the salary for one postdoc, so the benefits for PIs at additional institutions are limited. The obvious candidates are all a long-haul flight away, so day-to-day engagement would be challenging. I’m uncomfortable asking people to do work on my proposal when I can’t offer them much in exchange.

Ask someone to put their name on the proposal “for show”. Clearly offensive and counterproductive.

Does anyone have any advice on how to best reconcile diversity considerations with practical realities in these circumstances?
My question is more about the general issue – and whether there is anything I should have done differently – than about how to respond to these particular reviews.

This is a hard and important problem.  There are a few things you can do to address it.
First, admit that there is a problem indicated by the demographics of your discipline.  Tell the funding agency that

neither of the institutions involved have female staff eligible for the grant scheme working in the area of our proposal.

Tell them briefly about your universities' plans for future diverse hiring.  Tell them that the grant applicants do not have control over the diversity of current staff (if this is true).
Explain how the project will contribute to gender inclusivity.  You said you plan to hire one postdoc.  How will you encourage gender minority scientists to apply for that postdoc?  How will your selection process prevent discrimination?  How will that postdoc receive professional development that will advance their career?
Will you be communicating about your project to the public, and will that be done in a way that reaches people of all genders?
It sounds like your project is applied.  Will the application benefit gender minorities?  Even if they get a minority of the benefit, it's still worth pointing out that your project does not exclusively benefit one gender.
Do not add a token applicant.  You are obligated to allocate the project funds efficiently.  Some people argue that tokenism has the opposite of the intended effect.


What is a good academic word for "verifiable by scientific data or experiments"? Is "empirical" a suitable word for that? What is a good academic word for verifiable by scientific data or experiments?
Is empirical data a suitable word for that?
P.S EDIT: my question is what is A single word for "derived through experimental data" (opposite to derived through observation)
I mean that word should explain that it can be precisely reproduced by others as well because it's experimental data.

Data are "derived" from observations. Alternatively said, observations become data when we record them. Otherwise, they remain as observations. By example, the only reason we know what Galileo observed during his observations of the moon is because he recorded his observations in pictures, making them data.
The next step in the chain is to "derive" a result. This involves analysis or interpretation.
In summary, the chain is

observation - (to written record) -> data

data - (through analysis or interpretation) -> result

The one word you seek is result.
When you want to further qualify the level of effort taken in making observations, you can use words such as focused, directed, or even scientific as opposed to random or undirected. The phrase "unscientific observations" is not necessarily a "good" way to express the opposite of scientific. So, data obtained from directed observations have perhaps a higher standard than data obtained from random observations.
Suppose instead that you need a qualifying metric that defines the trust that you have in a result that is obtained by the analysis of data from (scientific) experiments or observations. Consider these criteria:

verifiable - able to be found by others
certifiable - attestable
precise - reproducible
accurate - indistinguishable from truth
measurable - subject to quantification through observation
robust - impervious to unpredictable outcomes
empirical - derived through observation
first-principled - derived through reasoning

You may make variations. For example, a verifiable and robust result is one that others can readily find and that has no ambiguities. A robustly verifiable result is one where the method that one uses to find the result has no ambiguities.
A result obtained from experimental observations is essentially empirical by nature. First principled reasoning may be used to define the accuracy of the result. Replicate, certifiable experiments are needed to establish the degree of precision on the result.


Should I put my not-yet-submitted work on my web page? I am planning on submitting a paper to a journal.  Is it acceptable and advisable to upload it to my web page for public consumption, in the mean time?

I varies with fields and journals.

Some journals do allows posting preprints on one's webpage, or on a preprint server.

Some not, but they don't care. (And some academicians do put their papers on their websites, even if it is against rules.)

Some don't allow and do care, so putting the preprint on your webpage may disqualify you from publishing this work.

(If it fits your discipline, why not using http://arxiv.org/?)


Acknowledgement in papers I have helped a scientific(math) author to find a reference and I have corrected several errors in his paper. Should he acknowledges me when he publishes his paper? Will that affect my academic career positively or negatively? And if he doesn't acknowledge me what can I do?

should he acknowledges me when he publish his paper?

Acknowledgments are discretionary, so they needn't acknowledge you.

  Will that affect my academic career positively or negatively?

Any impact will likely be minimal.

  And if he doesn't acknowledge me what can I do?

You needn't do anything.


Should students who copy homework answers from somewhere else state how they obtained the answer? I'm an 3rd year undergraduate student, and this semester, I'm taking graduate course in one of my departments.

We have homeworks each week, and while doing the problems on those, I sometimes get stuck. In that case, sometimes I go to the instructor for some hints and discussions, and sometimes, if I really haven't made any progress in that question for long time, I search the answer onthe web (for example math.SE), and write that answer if it satisfies me.

In those latter cases, I put some notes/a disclaimer on the top of the question stating that "I've done these and these, but couldn't solve it, so I looked at the answer from the xxx website".

However, is this something that we indeed expected to do, or am I just making myself sometimes look like "incapable of solving even an elementary question" in the eyes of my instructor ?

Edit:
My question is about the general norm in academia, not whether it is considered cheating or not.

It is good to be honest in all that you do. You should, of course, ask your professor whether your "researches" are proper or not. I would treat asking someone on math.se for a solution to your exercise as improper, for example.

The reason for that is that you don't learn the necessary lessons by reading a solution that you do by creating it. So it is mostly an educational issue, not an ethical one. But your instructor will give you the most useful advice.

The professor hasn't asked you to solve a problem because he/she needs the solution. The question has been asked because solving the question will advance your  education and finding a solution will be much less effective at that.

Education is about changing how your brain works. In mathematics, especially, you need to do your own work in order to cause the brain to reorganize itself to make advancement possible.

Asking the instructor for help is better in this regard than asking someone else, say on math.SE. The reason is that the instructor can give you a hint that will help you advance, rather than a solution that won't. It may even be useful for  your instructor to know that you are struggling with some ideas. You may get advice that gets you past the block. Math.SE is very unlikely to do that. The answers you likely get there will be too helpful.

Becoming a mathematician is about changes in your brain, not about proofs printed on paper.


What can be done about a terrible galley proof of my accepted paper, which would be a lot of effort to correct? Recently my paper was accepted in one of the best computer science journals in Elsevier. In less than 12 hours, I received the galley proof of the paper. Initially, I was surprised at the speed of conversion of the paper into the final format, but when I saw the paper, it turned out to be in a terrible condition.
I wrote my paper with LaTeX; it appears to have been converted to Word, and the typesetting of all of my equations is ruined. The arrangement of figures, algorithms, and tables was OK in pre-print, in a one-column format; now, it has become a terrible mess.

What can I do now?

Email to the publishing editor to reconsider the final preparation of
the article?
Prepare the paper in a two-column format myself and resend it to the journal's office?
Ask the publisher to publish the paper typeset in LaTeX?

In such extreme case (which, by the way, are disturbingly frequent at larger, very expensive commercial publishers) I recommend sending an e-mail to the editor, including the proofs to show that you are not talking about a misplaced comma, and simultaneously answering the production that you do not allow them to proceed. Beware not to sign or click anything that might make them able to pretend you allowed them to send the paper into production (as it would be much more difficult to get things right then). Ideally (i.e. if you are not forced through a web platform) you would e-mail the production team with copy to the Editor in Chief or handling editor for the record, or the other way round.

I don't recommend trying to fix manually an absurd amount of problems in Galley proofs: 1. Many libraries put a lot of money to pay for this work, you and your institution should not pay with your time; 2. you are bound to miss some of the bad stuff, half your corrections might be ignored, and new problems could be added after galley proofs (I would not believe that if I had not seen it myself -- my first paper actually).

I don't recommend sending a new version and suggesting they start back from that. It is pretty unpredictable what they could imagine doing, and if they use the same process again it will not be pretty.

Any diligent Editor in chief, when receiving your e-mail, should reach out to the publisher's management to have things sorted out. Without management involvement, the production team will probably do what they are probably asked to by default: treat things quick and dirty.

Last, I hope you put your preprint on the arXiv. If you did, you can at least have this as a version of record (and Elsevier allows you to update it to a postprint, including referees' remarks). If you did not already put the preprint on the arXiv, then Elsevier's policies are too complicated for me to understand and remember.


How to write papers fast and efficiently? First, my question is not about how to write a good a paper, since there are already many guidelines on the internet, e.g. this one.

What often happens to me is: I designed algorithm, did all the experiments, and got good results. Now, I only need to write up the results to submit. But I just feel I can't do it, or at least not efficiently.

Although I have everything in my mind, I just stare at the screen and can't write anything. I just can't do it. And this leads to procrastination, which I hate so much.

Sometime, when I was doing the experiment, I thought I should write this way in the paper, and it should be very awesome. But when I actually wrote the first few sentences, they were just crap.

I thought I would start by describing the core algorithm first. But I didn't know how to present the idea, so I ended up polishing the introduction first, etc.

I'm not a new researcher; I'm already nearly one year into my post-doc, and have 6 papers published. It never took me less than a month to write just a 10-page paper, after several iterations, while some of my collaborators can write a paper in just a couple of days.

I thought it would be better with experience, but it didn't and I'm really frustrated with myself.

UPDATE

I think I'm suffering from the so-called ''blank page syndrome'' (or white page syndrome), but I'm not sure.

I'm not sure if it helps, but here are two ideas that work for me (sometimes).

Don't try to write the paper in its order. Instead, start from the technical parts. This is simple - it is just writing your algorithm. Now, once you try to write the algorithm (and abstract it from code into pseudo-code), you will get stuck because something is missing (notations? a neat observation? a cool idea that makes things clearer?); note these down. Then, expand on the things you wrote down. Another way to begin is with the "cold" facts: the numbers, the experiments - just write the details down in the most dry way...  (After the technical parts are written, move to writing the introduction and conclusion; by that time, you will have already broken your "writer's block", and the writing will flow much easier).

tl;dr start with the most simple (and technical) parts just to make the writing start.
Writing a paper is telling a story. You can't write it down? Try this - tell "the story of you paper" to someone else, say, a colleague or a family member. Do this twice or thrice, until you have a complete "story" in your head, and you gained some practice in telling it. Now, writing it down (just following the conversation you had with real people) may be way more simple.

Addendum: This is not a competition. Writing a paper well, takes about a month. Writing a good draft takes at least 2 weeks (of intense work!). Of course, some people can pull an all-nighter and come up with a paper. Don't pay attention to those, they are at the tail of the distribution.


Should I recommend accepting a manuscript with major revisions because of a strong topic, but quite poor content? I have been given my first manuscript to review for a journal. The topic is a very good one, it fills a research gap nicely and is an area that I specialise in. However, the execution of the paper is lacking. I am about halfway through making comments on it. The English is consistently poor in both spelling and grammar, and the structure is dire, which makes it hard to follow the main arguments. I am aware that bad English is no reason to reject a paper, but the English in this paper is very confused in many places, sometimes multiple times per paragraph, and it's a trial to follow.

I believe that the paper could only be salvageable after a rewrite, but by a third party. I don't believe the author's English is good enough to bring it up to standard. I do not care about being 'kind' to the author, but the topic is so good that I would love to see it go through, but I am torn between accepting it with majors or recommending rejection.  My PhD supervisor has advised me to recommend rejection, but I am still unsure which way to go. Should I recommend acceptance after major revisions in the hope that it will improve based on my [now extensive] advice or just recommend rejection?

Jeff Offutt has a very insightful scheme for calculating the final recommendation based on technical, presentation, and omission grounds (source):

The fields in the matrix correspond to different types of problems:

  Technical Problems
  Minor: Mistakes in background, related work;
  Moderate: Does not affect the key results;
  Major: Changes the key results;
  Critical: Negates the key results.

  Presentation Problems
  Minor: Typos, spelling, grammar;
  Moderate: Make understanding the paper harder  (organization, notation, repeated grammar);
  Major: Prevent understanding of part of the paper;
  Critical: Prevent understanding or evaluating a key result;

  Problems of Omission
  Minor: Omitted background, related work;
  Moderate: Not part of the key results;
  Major: Missing in the key results (proof or experiment,
  lack of control in experiment);
  Critical: Must be in the paper to evaluate the result
  (experimental study, etc) or not enough results.

The source also provides additional information and context.

Based on this scheme, I think the appropriate recommendation in your case would be a major revision.


Is a PhD (economically) still worth doing? I used to think that with every degree you get your salary goes up.
Universities produce more and more PhD's and i learned in economics 101 that once the supply is higher than the demand, the price (here salary) will drop.

Even if you get a little bump in salary, you have to take into account, that you are joining the workforce 3-4 years later and therefore "loose" those salaries.

From an economical standpoint : Is a PhD still worth doing ?

( I know, doing a PhD is not "just" about the money )

If you look at income alone, it's definitely not worth it - assuming you don't live in a country in which "Herr Doktor" is still highly regarded, and an almost must for high-end jobs in politics and business (like in Germany or Austria).

In industry, there are a few jobs (chip design for Intel or quantitative hedge funds come to mind; maybe in consulting it's a toss up; certainly there are others) where it might help. There are also jobs where it's required to have a PhD (some chemistry research, or such), or at least very beneficial. But outside these somewhat rare positions, HR will put you on a pile called "non-standard degree" which is largely ignored, and you rely on personal connections or quantitative recruiters to even get your foot in.

If you end up in academia as tenured faculty, you get a decent salary with a wide range (e.g., at the top end, Business School finance assistant professors lie around $200k at good schools, to a low end that's a fraction of that if the school or department is less wealthy, or the field less supported by industry). But if you're smart and driven enough to get there, you almost certainly could have long made partner at McKinsey by that time, where you won't go home with less than $1m.

I think the term "still" in your title is a bit off. I don't think this ever was different. You should write a Ph.D. as you're passionate about a field, look for independence, and genuinely love what you're working on. And you should be aware early, and accept, that this is not a choice made for the money.


How to write horizontally across the blackboard while keeping handwriting as horizontal as possible? Does anyone have tips on good ways of writing horizontally across the blackboard?

I notice whenever I write across the blackboard, the line will have a slightly downward slope of 15 degrees and it is quite visible from afar. It sort of looks like the bottom left half blackboard of this picture.

Does anyone have any tips of writing across the board as horizontally as possible? My board is about 10 meters wide divided in two halves.

Writing works different on different heights, so train writing at different heights. For me it is easiest to write horizontally if the baseline is about the height of my  mouth. Writing at the height of my stomach or my chest is almost impossible and I need much more care and it takes much longer. If you have to write at that heights, you could also squat down, but be aware that the things you write down there may be too low for some people in the audience.
If you can move the blackboard up and down, move the blackboard such that the line you write is on your favorite height.
Do not stand still and stretch your arm more and more, but move your whole body along as you write.
Related to the previous point: Use short lines. Two halves at a ten meter blackboard still make five meter long lines. Depending on the size of your writing, this may still be too long.
Try to get good chalk. I prefer chalk that slides over the board more easily. (The people over at mathoverflow have something to say about this, see here and here).
Try to adjust your font such that it helps you to stay on the line. Writing cursive for text (not equations) may work, but I think cursive needs more care on the blackboard.
If you practice, try to find a blackboard that has lines, a grid or crosses that help you stay in line.


Make my Professor a gift I just received my diploma from my university. I'm very happy and my results aren't that bad either. Now, as the result is already known, I would like to thank my professor and my supervisor for their support.

Would it be acceptable, if I make them a gift to express my thankfulness?
I was thinking of a bottle of a good liquor for both of them.

The safest way to express your gratitude is to (hand)write a thank-you-card. In all likelihood that will be appreciated just as much as a gift, and is guaranteed not to cause any trouble.


"Computers & Security" journal latex template? The following links explains the "Guide for Authors" for the "Computers & Security" journal:

https://www.elsevier.com/journals/computers-and-security/0167-4048/guide-for-authors

However, I cannot find a latex template for this journal. Does it mean that I can write the paper in any template format ?

Here is an example of a paper that is published in Computers & Security" journal. However, I need a latex template:

Example Paper in PDF

Following the various links of the Guide for Authors one arrives at the LaTeX Instructions page of Elsevier, which recommends the usage of the class elsarticle.


How to grade students' lab worksheets to prepare them for a final lab exam? I am a physics lab TA and I was recently informed that my engineering students will receive a lab final at the end of the semester worth 50 percent of their grade. The final exam is not personally created by me, but is decided amongst all of the lab TA's teaching the same course in the same semester. The meeting amongst the TA's will occur next week, however I am attempting to prepare for whatever will come, for better or worse for my students. I want my engineering students to succeed, and I want to give them all of my resources to give them the preparation to pass the final exam. I assume that I will not be allowed to tell my students what the lab final will be, or what types of questions will be asked. My students are required to complete 9 weekly lab worksheets corresponding to their specific lab of the week. All sum total of all lab worksheets are worth the other 50 percent of the lab grade.

One issue I am currently weighing in my head is how to grade the lab worksheets. Should I go easy on the grading to soften the blow of the final exam, or should I grade harshly to force them to correct every mistake they make in prepration for the final exam?

While I don't TA physics, but Geology, our labs tend to have the same structure. Luckily the labs are small enough that I can get to know the groups ect, So I can determine how hard they are working on the labs ect, so I generally grade 70% effort and 30% correctness. The difference is though, that you are teaching engineering majors, where I tend to teach non geology or STEM majors. Getting something in the lab 100% correct for my students isn't as important and following the scientific process, but, for a class of engineers, I would have higher expectations since the content they are learning is helpful for their careers later. IE, they should have a vested interest beyond the grade.

My experience with the Lab exams is that the students either do very well or very poorly. I would be somewhat lax on the labs, especially on first time mistakes. But there isn't much you can do if they aren't working hard and aren't completing the labs correctly and they will likely fail the test if thats the case anyway.


How do I find a journal's type (e.g. SCI, EI)? I'm filling out a form with information about my publications, and one of the fields is "Type of Journal." I'm not sure what this means, except that SCI and EI are possible values. I'm guessing the former refers to Science Citation Index, but I can't find what EI is. It seems this is something they are expecting me to know so I can only assume it is common knowledge among academics.

What are the possible types for a journal (if a comprehensive list exists), and most importantly, for any given journal how do I find its type?

I have set up a webpage (click here) which provides links to the list of journals that are SCI, SCIE, ISI and EI and also let you check the impact factor of a journal. You can follow the links on that page to find out if a given journal is EI, SCI, SCIE, etc. Hope that it helps!


Should I try to avoid being the single author of my patent/paper? I invented something as part of my job in R&D, and I plan to patent it and get clearance from my company for publication in an academic conference. All the key novel ideas are mine, and I implemented them all and ran all the experiments.

However, I just don't feel comfortable about putting down my name as the sole inventor and author. When I see single-author papers, they always make me wonder if the author is dishonest and/or bad at working with others.

But no matter how much I look at my paper, I just don't see any noteworthy contribution to it from any of my co-workers. We were working on the same problem, but each taking a different approach.

Hence, the solution I've come up with is to put a co-worker's name on my paper and ask (force?) him to make some contribution to it, like helping with the literature citations and/or experiments.

But even then, I'm pretty sure he won't contribute much and I'll still end up doing all the work.

Do I really need to go out of my way to avoid being a single author? :(

As the proud author of many papers with all sorts of numbers of authors, anywhere from just myself to dozens of co-authors, I see no reason to avoid being a single author.

In evaluating a researcher, I would only have concern with their ability to collaborate if they show a preponderance of single-author papers.  If somebody has a mix of single-author and multi-author papers, then my reaction will instead be more positive, because it shows they are both capable of collaboration and also capable of initiating truly independent work.

So: go for it on your single authorship (and/or inventorship)!  Just make certain that your co-workers agree with you that they should not be authors/inventors, or else you may have an entirely different type of problem on your hands.


How can I (and should I) approach a teacher with a difficult attitude in lessons? She's not exactly a terrible teacher, but she doesn't relate to students well, and the way she teaches in class discourages us from participating. For example, when asking someone to translate a sentence, after someone spoke out and tried to translate, she interrupted the student saying words to the effect of "No, that's wrong, you've forgot about this." Obviously a valid point, but her tone and the way she cut across was rude, and when she asked the next question, none of us really wanted to give an answer. I could find other examples, but I don't think it's relevant: the point is, the way she teaches - not the content itself - is problematic because it creates a bad environment in class.

The first question is: is it a bad idea to approach her directly to talk about it? Should I bring it up with the department office, or the department head, instead? I figured it would be better to talk to her in person, rather than flag it up with the department, as it's not technically their business, and maybe it could get her into trouble. But I'd appreciate advice on this all the same.

The second question is: if I do talk to her about her teaching style, what's the best way to go about it? I was considering visiting during her office hours with 2 or 3 other students, and trying to explain why we're having issues with her teaching style. Again, if you think there's a better way, or would strongly advise against this, please let me know.

I disagree that you should instantly resort to official channels. As an adult, in any environment, when you disagree with someone, or someone's methods or attitude, it is only fair to first allow the person you take exception with to know what they might be doing which upsets or discourages others.

As your teacher keeps asking questions, she is clearly interested in an interactive class, and probably wonders why feedback dies down. If you tell her courteously during office hours that some are intimidated by the way she formulates her corrections, she quite possibly appreciates that you let her know. Tell her to give feedback with a smile, to thank people for chiming in, and to maybe help the person when answering by letting them discover their error themselves ("You said X; but in this context, what about Y?" or such). If she doesn't change anything after meeting her, or it is clear she resents you for bringing this up, you can always escalate up the ladder.

Concern is mentioned that this could lead to retaliation after you politely make constructive suggestions.
As said above, I doubt that; and if she would retaliate, this is against all sort of regulations. This would endanger her standing at the university. You can never exclude the possibility, but if you don't stand up for yourself, and your classmates, now, when will you learn to? You will face similar disagreements throughout your career, and want to be prepared for it.

This applies particularly when your teacher is still working on tenure. Those many years are fairly brutal even under good circumstances. There is no need to have her summoned to her department head for something she isn't even aware of,


Should I obtain permission for publishing a vector drawing based on a published photo? I have drawn a schematic image of a museum object for use in my forthcoming paper. The object itself is over 1000 years old, and my vector drawing is based on a photograph published in an exhibition catalogue some 30 years ago (where the photograph is credited to the museum holding the piece). I will of course give credits to the image source in the caption ("Drawn by the author based on the photograph published in Smith 1985, 88 fig. 88" or "Drawn by the author based on the photograph published in ABC 1985, 88 fig. 88 (@ Museum XYZ)"). However, I would like to ask if I should also obtain a permission for publishing my drawing, as I would do if I republish the photograph itself. Or does the fact that I have drawn the image myself free me from that obligation?

My question is thematically close to the two earlier topics on Academia SE ( How do I give credit to some image I included in my paper? and Recreating images from a source ), however these earlier questions concerned primarily with credits, and my question with getting a permission. Besides in these earlier questions the image sources were drawing, and mine concerns with a photograph as an image source.

What is your original motivation to create that drawing? Escape reproduction rights? Or else?

The usual practice with museums and objects that are not involved in copyright any more because they are too old, is that you don't pay for the picture of the image if you take the picture of the image yourself. You pay if you use the image that the institution provides.

My guess is that publishing your drawing is not like 'republishing the photograph itself' because your drawing makes an original contribution that goes far beyond reproducing like for like the original photograph.

Agreed with commentators about approaching the institution out of common courtesy, if nothing else.


Why did I receive a negative response from a professor when emailing about course content and prerequisites of a course I am considering taking? I wrote the following email to a professor (I've removed any personal or specific details):

Dear Prof. Last name,
Hope this email finds you well.
I am Name, an undergraduate in the mathematics department.
I write to enquire about Course code - Course name being offered in fall semester. What can I expect from the course content and what are the prerequisites? Would it be along the lines of Name of a Book?
One sentence describing previous courses I've taken
Looking forward to hearing from you soon. Thanks for your time!
Best,
Name
Department
Institution

The subject line was:

About Course Name next Fall Semester

I thought this email is perfectly fine, and it's how I generally write to professors. To my shock and surprise, I got the following response:

I am sure very soon you will be writing many more official emails, so you must know how to address them appropriately. You may see course content on the department webpage.Initials

Could someone help me figure out (i) how to respond to this, and (ii) what went wrong so I can avoid it in future emails (to any professor in general)? Thus far, no professor has pointed out so explicitly that something is wrong with the language of my email - so I'm in a state of great confusion right now.

Additional details:

I haven't interacted with this professor before, so this was my first email to them.
It seems I was at fault for not checking the course content on the department webpage before writing this email. However, that page has not been updated in years and I just wanted to make sure the content is still the same. Lastly, I think this wouldn't have made them feel that I addressed them inappropriately - since that has more to do with email etiquette than the content of the email.

Follow-up question:
I'm thinking of apologizing and explicitly asking how I can improve my email's language: "Thank you for your reply, and sorry for the seemingly inappropriate language of my email. I would be grateful if you could kindly pinpoint what part of the email was inappropriately written, so I can be more careful in all future communication."
Would this be a good idea? I read somewhere on this very site that it's never impolite to ask how to be polite.

There is nothing inappropriate (that anyone can see here) in the way that you've written your email. The response from the professor suggests that they're some combination of (a) incredibly time-constrained, (b) sloppy and unclear in how they communicate, and (c) a jerk.

It's possible (as user2768 suggests) that the essential "offense" in their eyes was to ask about things available in the online site. If so, then their first sentence was a sloppy and mostly mindless piece of aggression that doesn't really mean what it says.

The curtness, snarkiness, and level of aggression communicates that they don't like interacting with students by email, do not want to spend time on it, and want such querents to go away and not bother them.

Given the above, writing them again and asking for more time to be spent on even smaller minutiae -- like revisiting what they meant in a hastily-written throwaway email, and to spend even more time parsing the grammar of the original student email that they've already expressed contempt for handling -- is only likely to make things worse.

I suggest that you accept this line of inquiry as not useful and likely to produce only further confusion and frustration on both sides. Do not email them again on this matter. If you must email them again in the future, on some different matter, make it as brief as you possibly can (shorter than your original email), and try to pose a question that can be given a very short, clear-cut answer.
I'll say that the only thing the professor really got right there was in accurately predicting your next instinct would be that, "very soon you will be writing many more official emails", and to be aggravated-in-advance by that prognostication. Resist the temptation to fully prove them right!
Also, consider asking around if this professor is good to interact with (maybe people you know or a ratings website). If their course is not required, then you may be getting a signal that they're just not a good professor.


Should I submit a major revision if it seems that AE has the intent to reject? A few months ago, I submitted a paper to the top journal in my field. I just received a major revision decision. There was an enormous amount of comments from the four reviewers on many different aspects but all of them specifically doubt if the proposed system advances the state of the art or if it is useful among other things. In reality, It is a novel and interesting idea/concept but it does not make the numbers (performance) better as the reviewers suggested.

The associate editor said that they will consider publication only if they received convincing responses but the wording indicates they doubt that I will be able to do. I could attempt to address the comments but I feel like my chances are close to zero given the number of comments and the tone of the AE.

As our group recently submitted another paper that was rejected by the same AE, I feel like the AE did not just outright reject this one because they just rejected the one before. Hence, a major revision.

I understand that the consensus in the community in the case of revisions is that the AE sees value in the paper but that does seem to be the case here from my understanding.

My question: with the information above, would it be a good idea to skip the major revision and submit to another Journal? My concern here is time as it will likely take three more months to get a high likely reject.

Also, how likely is it for papers to get rejected after major revisions?

Your call, of course. Either would be a step forward. But consider how much the revision will actually improve the paper. If a lot, then it is to your advantage to just do it, no matter where you submit. All suggestions should be, at least, considered for revision, as usual.

And a new submission will take its own time, of course. And a "top journal in the field" is probably worth some effort and even time.

As for the last question, each paper is different and each editor is different. A general answer does you little good. It is your paper that you care about.


CVs: How should I include papers that have been accepted as abstract submissions to a journal, but still need to go through manuscript review? To be specific, I've submitted an extended abstract to a special issue of an education journal (I'm a graduate student in STEM). Based on the reviews of that abstract, we've been asked to submit a manuscript in a few months.

This is certainly "acceptance" of some sort, but I'm wary of overstating this on my CV as there's still a chance they could reject in the manuscript review. However, as this paper is super relevant to an award nomination I need to submit my CV for, I'd really like to have it on there somehow.

How can I best note this on my CV?

(While this question and this question are close to my situation, they're referring more to paper manuscripts that have been accepted with some contingency.)

In my opinion, you should try to to be as candid as possible and simply state exactly what the state of the paper is. In this case, you could for example write, "extended abstract accepted - awaiting full manuscript submission" or something similar to that.


How can you determine whether a journal is indexed in ISI or SCI? What are the main difference between SCI and ISI Journals?
How  can you determine whether a a journal is indexed in SCI or ISI?

International Scientific Indexing (ISI) has a list on their website. The same is valid for the Science Citation Index (SCI). You can search for journals by title.


Are there universities/institutions which offers free (or almost) recognized degrees through online coursework? I heard that using online resources, some of the top universities like MIT (Micromasters) and Harvard are offering free online courses and specializations.
 I wonder if there are institutions that offer graduate and post-graduate degrees totally free of charge(or almost).

As someone who has delivered both free and paid-for online university courses over the past ten years, with a reasonable grasp of the market in the English-speaking world, I'm fairly sure the answer is no.

At the moment the free short courses have a very different business model to a full degree offering - they either (i) rely on huge volumes with (optional) payment for certification or (ii) are essentially marketing tools, working as "tasters" for the real deal. It's hard to see how to run a full degree (with the necessary staffing, accreditation etc) for free. You might wait a long time to find one!

Alternatively, travel to Europe where real on-ground courses are cheap in many countries even for non-Europeans. If you enrol this year in Finland, the Finnish government is happy to cover your fees, but act quick, as fees come in in 2017!