How to tell what is 'widely accepted' or 'consensus' How can I find out what theories are 'widely accepted' in the scientific world at the moment? When I read about a theory, or read a paper, how can I tell what 'the scientific world' thinks of these?

Background:
When hearing about development or history of science, the phrase 'widely accepted' is quite popular. One of the common stories seems to be of some discovery which nobody wanted to believe when published, but a decade or a few later the scientific world came to accept it and it turned into consensus. Prime examples in history would be the heliocentric world view or the theory of evolution.
More recently, I have read 'The Selfish Gene' by Richard Dawkins. He takes every chance to provide evidence that the theory of group selection is unnecessary to explain evolution. The book was published in 1976, when group selection was apparently quite popular. In annotations of the current edition, he gives comments about how the scientific world has now more accepted that group selection is wrong. I asked a question about one of his claims which I did not fully understand (irrelevant here) on Biology.SE and - unexpectedly - promptly got answers by people claiming that group selection was presently very widely accepted.

Firstly, the "official" ways that researchers state their opinion is by stating it in either a publication or in a presentation at a conference. It is from here that we can gain any idea of what any researcher thinks about a given topic.1

That being said, the only way to know whether something is "widely accepted" is to be familiar with most of the current (academic) literature on a given topic. Only by really having read the publications of most of the preeminent researchers in a given field can you really get a sense of what the consensus is on that topic. This, of course, requires a lot of time and expertise (and, if you don't have access to a university library with journal subscriptions, money). It took me years as a graduate student to learn what was the consensus about certain topics within my own field.

Because of this, anyone can state anything and most people won't know the difference. The easiest way to really determine if it's true is to ask two or three recognized researchers if they agree with the statement of interest. You can do this via email, but they likely won't get back to you. You can ask grad students in their lab and the answer will be that much less reliable, but still close to the source. Beyond that, you'll just have to find experts you can trust and rely on them.

1 Obviously, researchers are people like anyone else, and will discuss their pet theories with friends and colleagues over email and in person; it's very hard to quantify these, and you only rarely see this sort of discourse being formally recognized. Occasionally a publication will cite "unpublished discourse", but that's a rare occasion.


Characterization of the lifespan of an academic paper Every paper has a life-span that could be measured by the time difference between the publication date and the date of the "last" citation (if one exists). Of course, it is not possible for one to predict when the last citation would be, since it is theoretically possible for a paper published 50 years ago with 0 citations till date to be cited by someone tomorrow.

But the basic idea is: given citation information till date, is there a way to characterize the life-span of an academic publication? Is this a concept that has been studied before?

Yes this has been studied before. One endpoint for what your looking for is the citation half-life.

Basically, this is a metric that calculates the median year age of articles citing a journal. This Science Magazine article discusses the topic further.


What constitutes an academic publication for people in the Creative Writing field? Based on my observation, Creative Writing degree programs seem to be heavily focused on learning a few timeless principles of storytelling followed by the production of a massive portfolio of stories (short stories, novels, poems, plays, etc.) demonstrating mastery of these principles.

Once someone has a degree in Creative Writing, or especially has become a professor of Creative Writing or aspires to be such, what sort of academic publications are expected or typical? My instinct would be to say that they simply write more (and hopefully better!) stories and publish them, but then that would imply that there is a difference between fiction intended for the academic community that is subject to rigorous peer review by fellow Creative Writing academics and fiction intended for a mass-market audience that is selected based on what the editor thinks will sell the most copies - does such a distinction actually exist? E.g. perhaps there is some writer today thinking "Hey, I think this story I wrote about wizards getting revenge on a king on Halloween is one of the best of its class in the past few hundred years, I'm going to submit it to the peer-reviewed Trans-Celtic Journal for the Advancement of Bardic Storytelling rather than Spooky Tales Quarterly. Tenure here I come!" Do separate peer-reviewed venues for publishing "academic-grade" creative writing not exist as such, and academics publish wherever they want (fanzines, pulp mags, blogs, Cosmo, wherever) and let their stories stand on their own?

Am I wrong on this? Do professors of Creative Writing actually concentrate on publishing research articles on the effectiveness of various writing techniques, tropes, themes, plot devices, etc. (e.g. "I did this study where half of my readers/subjects read my story [Appendix A] with the side love scene and half without, and the ones who read the story without it rated it higher [Graph B]. Conclusion: Don't include side love scenes.")? Do Creative Writing professors write literary analysis like Literature professors in the Liberal Arts?

There are plenty of scholarly essays that can be written about creative writing.

Here's a CV from one professor who teaches creative writing extensively. It lists, as well as books, short fiction, and poems she has published, a long series of scholarly essays that seem like your "literary analysis" category (titles like "Reed-Kellogg Diagramming and Vernacular Speech: ‘Telling It Slant’ in the Introductory Classroom", “Robert Penn Warren and Psychological Pastoralism,” “Agency in All the Kings’ Men: The Issue of Anne Stanton,”).

She also has a series of essays on writing which are probably what you're talking about with your "articles on the effectiveness of various writing techniques, tropes, themes, plot devices" such as “Don’t Be Afraid to Write Badly,” The American Scholar, January 2017 and “Writing ‘Bush,’” Fourth Genre, Summer 2011.

Here's another CV from an "Assistant Professor of Poetry & Creative Nonfiction" who has a section for "Selected Prose (Creative & Critical)" that includes what looks like both literary analysis and essays on the "effectiveness of various writing techniques" (Writers on Writing, “Why to Kill Your Paradise").

So yes, it seems that there are publications that take a scholarly attitude toward creative writing, and at least some professors of creative writing do publish in them.


How does one find "suitable referees" for publishing a paper in journal? In many journals, authors who have never published anything before are required to have two or more "referees" in order for the paper to be reviewed. Who are these referees, and how can one "find suitable ones"?

Also, how does one go about finding referees when one is not in academia (i.e. doing research as a hobby rather than a profession)?

From my experience, most journals do not require you to propose referees. It's more like the journal allows you to propose some names of potential referees. The referees are appointed by the editor and you as author will not know their names.

So the answer to "How does one go about finding referees when one is not in academia?" is

You don't have to.

just find a suitable journal that does not require that you suggest referees.

If you the journal system does not allow you to submit your paper without suggesting referees, either suggest authors that you cite or authors that cite the same papers you cite (using, e.g., Google scholar).


Seemingly-irrelevant papers, all with author in common, suggested by reviewer I recently received a decision letter calling for minor revisions prior to acceptance. One anonymous reviewer was extremely knowledgeable and provided many helpful suggestions to better explain and clarify my work which I have implemented. However, the other anonymous reviewer simply listed seven papers to include, suggesting I make a "theoretical comparation" and to "plesea [sic] compare them."

I noticed all seven papers listed had one author in common, and none of them are relevant to my work. Given that their review was two sentences with typos followed by a list of papers, I assume they spent little time on my manuscript and perhaps are trying to get their own papers cited.

How can I best politely reject these suggestions? May I address them all together? Could I email the editor with my concerns? Can I request another reviewer to assess my paper?

Think of the review process as a debate between you and the reviewers, with the editor as jury. You would like to convince the reviewers, but ultimately, you want to convince the editor. The editor has called in the reviewers as domain experts so will listen to what they have to say. But ultimately the editor makes up their own mind. It's just that the editor is most likely to give their go-ahead if you and the reviewers come to an agreement. But it's possible that the editor decides to publish even if a reviewer is not positive.

Also, consider that editors are basically the experts on the subject of "reviewers".

I would write three responses. The responses addressed to the reviewers are also passed through the editor (after all, the reviewers are anonymous).

One to the first reviewer, thanking them for their good advice and noting how you'll apply that. This helps to show to the editor that you're taking the review process seriously.
A second one to the second reviewer where you explain why you don't think those seven papers are relevant to your paper. Don't put any accusations here, just give your considered, good-faith view on the relevance of those seven papers.
A third note to the editor only, where you express concern that the second reviewer's review was rather short, that you don't really see the relevance of the papers, and that you noticed that they all have a common author. Ask for the editor's advice on how to proceed.

At that point the editor will probably take a second look at the rather poor quality review, and compare the author list of the proposed seven citations to the name of the reviewer. And advise you on how to proceed.


What should I write for "Research and Teaching Merits" when applying online for a PhD? Recently, I want to apply for a PhD position in a place which uses an online system to submit applications. The position is going be filled by either a PhD student or a Postdoc. There is a section in the application form titled "Research and teaching merits" with a mandatory field "Field of research". I wasn't sure what exactly I should write in this field so for now I left a '-' character there.

I searched on the internet but I couldn't find a clear answer about what I should write there. I also contacted the emails provided with the advertisement but there was no response.

What do you think I should write in this field of the application form?

AFAIK, the section Research and Teaching Merits ought to encompass accomplishments made as a researcher and as a teacher. This could include any distinguished teaching award you might have received in your teaching tenure. If there isn't a separate publication field, you may include your publication here.

As for the field named Field of research, this would mean your current domain within the main subject of research. For instance, in Computer Science, fields could be like Machine Learning, Computational Neurosciences, Wireless Sensor Networks, Data Security, etc. Likewise, there would be many specialization areas within Mathematics, Electronics, Instrumentation, Mechanics, and so on.


Computer Science Original Position Paper Questions I am submitting a research paper to a conference for the first time. I will be submitting an 'original position paper'. I believe this is what the paper should consist of:

50% background research (literature survey - summarizing the previous works/pointing out their drawbacks or areas not covered by them)
20% my new idea
30% implications of my idea and future work

Is this approach correct?

This depends on your discipline and on the conference in a fundamental way. If your advisor (or anyone you know) has submitted this kind of manuscript to this particular conference before, you should absolutely ask him/her for tips and suggestions.

You should also go to the conference's web site and look for their requirements for submission. Nearly all such organizations have a page or document that lists their requirements for submission. In the unlikely event that there is no such information at all, or in the more likely event that you still have questions after reading it carefully, look on that document or on the website for a submission contact person who will be able to answer your question(s).

Good luck!


Is there any formal format for statement of purpose? I'm about to submit my application for various PhD programs and I was wondering how should I format my statement of purpose.

Should it be addressed like a formal letter? Just contain my name and say 'Statement of Purpose'? Should I end it with something like 'Sincerely, ...' ?

When I applied to grad school I didn't give my SOP a title or address it to anyone in particular, or include any closing salutation.  Some schools required me to put my user id at the top, which I did.

(I was accepted to several places so I think the way I did it should be fine.)


Submitting two related manuscripts at the same time to two journals I have two ideas (manuscripts) that I am working on, both in the field of physics.

The first is theoretical, mathy and generalized. It is steered toward computer vision. Probably if finished, would be published in a multidisciplinary journal for physics and computer science.

The second is a mix between theoretical physics and experimental physics. It is steered toward astronomical physics only. It applies one of the results found in the first manuscript.

Is it ethical to submit these two papers separately? How can I cite the papers if they are both under peer review?

Note: The two manuscripts do not hold the same goal and do not have identical results. If I am going to put a percentage on how much 2# uses from 1#, I would put 20%. Further, if I would put a percentage on how much different 2# from 1#, I would put 90%.

Is it ethical to submit these two papers separately?

Typically, yes. Having a methods papers and one (or more) applications paper isn't at all uncommon.
It's sometimes appropriate to send them to the same journal (or same publisher), but that is more a matter of convenience than ethics. If you submit both to the same publisher, they might ask the same reviewer to referee both papers, for example. On the other hand, if one paper fits better with the scope of another journal, then sending it elsewhere is the appropriate choice. On the ethical side the only potential concern I see is that you might be perceived as "salami slicing", i.e. spreading a small amount of content into multiple papers, but if both papers are "meaty" enough then that shouldn't be an issue.

  How can I cite the papers if they are both under peer review?

In the fields you mention, it is standard practice to put preprints on the arXiv. The best approach for you would likely be to do exactly that before submission to the journals, and then cite the preprints as appropriate.


Postdoc Funding for an American looking to do a postdoc in europe (in Theoretical Computer Science) Hi I am doing a phd in theoretical computer science, and will be finishing this year and applying to postdocs for Fall 2016. I am an American, but for various reasons would like to study in Europe. Ideally the professors I am interested in would have postdoc funding available, but since that is often not the case, are there any grants/fellowships that cover postdoc salaries available for americans studying in europe? Are there other funding options I'm missing? Am I correct to assume that in europe like in America one gets postdoc funding from the professor (or from a grant), not from the department as a whole? As you can see, I know little about how funding works in Europe!

In case the answer to my question is country specific, the countries that I am most strongly considering so far are Germany and Switzerland.

Thanks for your help!

UK is definitely of the 'professor has funding' variety of post-docs. However, there are also Fellowships. This is funding intended for a researcher doing their own research and there are programs specifically for Early Career Researchers. For example, there are Fellowships available through the EU Horizon 2020 program, see http://ec.europa.eu/programmes/horizon2020/ (note - extremely competitive) and through the various discipline funding councils, I think computer science would be https://www.epsrc.ac.uk/ and the fellowship info is at https://www.epsrc.ac.uk/skills/fellows/overview/.

You can also try organisations such as Fullbright.

A couple of other points - you should be clear about what you expect. I see lots of comments here about postdocs being training positions. This has not been my experience, I have had little supervision and no training. If you want training, you would be best off to join a project that involves several people, or seek a Fellowship with a training component. Also, make sure you are on the email / forum lists for academic communities that interest you, this seems to be where a lot of post-docs are advertised.


What can I do to prevent ethnic conflicts in research groups? Many research groups are international. While I hope that academics are in general open-minded and tolerant, there might still be a potential for conflicts when researchers from different ethnic groups, which are hostile towards each other or are even at war, work together in the same group.

As a head of the research group, what measures can I take to prevent such conflicts from affecting the work of the group?

One of the advantages of being the head of a research group is that your position should give you a great opportunity to set the tone of the working environment for the group.

The first key to establishing a healthy research group is setting a good example. Try to be open about your views and encourage good interactions, and be careful not to implicitly support bad behavior by appearing to condone poor treatment or opposition to ideas based on who they come from rather than their merits. Your group will take cues from your behavior, which to some degree will implicitly define what is and isn't acceptable in your group.

Try to be proactive about including everyone.

Make sure your students and researchers are aware that one of the minimum requirements for participation in the group is that people treat each other with courtesy and respect. Unless it's a political science research group, politics and conflicts between ethnic groups should be tabled. It's understandable for people to have differences, but you should try to make it clear that your group is not the place to hash out wider conflicts.


What references must be acknowledged in a paper? This question came up from a discussion on meta.MSE.

My question is:

  Do we need to search MSE (or blogs, math forums, ...) to make sure someone hasn't already proven a result when writing a paper?

  What if we are already aware of a them (so no need for searching)?

  Is not citing such a post in these two cases considered plagiarism?

As I understand, the common practice is to check standard reviewed reputable publication venues (journals, conferences, maybe arXiv) and also with experts in the area to make sure a result is not already published nor a well-known folklore result. No one is going to search all over the internet and check every post that Google returns and citing other resources is very uncommon. I think checking MatheOverflow can be considered similar to the later (checking with experts) (also see this discussion on MO but that doesn't seem to apply to a site like MSE. I am not going to cite a discussion with some random person on the street (not a professional mathematician) who claimed to have a solution or an idea for a solution for a problem (which is not passed peer-review process and I might not want even want to spend time understanding or checking the correctness of the solution).

  What are the accepted practice for checking originality of a result?

  What is expected from authors regarding this before making a paper submission?

Some clarification since there seems to be a misinterpretation of the question about being academic honesty. The question is not about posts that

you are aware of,
contain a complete rigorousness solution (not just ideas), and
you are confident the solution is correct.

This is a question of academic honesty and due diligence.

If you did not arrive at the result yourself, but got it from someone else (either on SE or a homeless man on the street) then it is your responsibility to not claim credit for the result. Of course, in the case of the homeless man you can get away with claiming credit, and in most cases for SE, too. However, it is simply not honest.

If you arrived at the result by yourself, then as a research you should provide due diligence and check if the result is already known. This usually consists of checking the standard sources (i.e. published papers, books) and the communities which you are a part of. "Folklore" in mathematics is vast, and MO, math.SE, and cstheory are all becoming part of it. If you are aware that others arrived at a result before you then you should mention it in your paper (either with a full citation, if applicable, or with an acknowledgement).

However, just like you are not expected to search the back-log of every journal ever published, you don't have to scour the whole internet, either. If you want precedent of this: consider all the results that were published independently in the west and the soviet union during the Cold War. It would have been unreasonable of the scholars on both sides to be fully aware of the work of the others.


I submitted a paper to two journals, and the first published it, but I agreed to publish in the other; what can I do? I submitted my research paper in journal X on 7th July, 2014. Journal sent me one thanks email immediately. After that I waited for one month for any response from editor but nothing came from editor side.

Than I submitted my paper in other journal Y. My paper was accepted in that Journal and sent for review from editor side.

At 30 August, 2014 I received one acceptance email from the editor or journal X that my paper has accepted and I was asked to submit publication fee of 90$. But I could not reply this email due to busy schedule and I was also not interested to publish my paper in journal X. After that I could not receive any email or revision or anything from this journal X.

I continued to work with journal Y, modify paper according to reviewer comments, sign copyright agreement and now paper is in publication phase.

Yesterday, by chance I open my Google scholar account and find paper that was published in journal X to whom I was not interested and who was demanding 90$. When I checked the online paper, I was astonished that the journal published my paper in its July issue and date of publication was 1st July, even I send this paper on 7th July and journal X notify me about acceptance and fee payment on 30th August.

How its happened that Journal X published my paper without my consent and published it in back dates. Now what I should do because the same paper is in final publication phase in journal Y to whom I have signed copyright agreement also. Please guide me tell me any forum to raise voice against that journal X. Because I send many emails to editor of journal X but receiving no reply from editor side. Any penalty or any other thing which I can do.

The fault here is yours.

You should never have the same paper be submitted in two different journals at the same time. This is an absolute rule that protects both you as an author and the journal as the publisher from duplication of effort, as well as avoiding situations like this.

If you had wanted to stop the publication in journal X, then you should have sent them a letter clearly retracting your submission. This would have ended the process at journal X, and allowed you to submit the paper to journal Y with a clear conscience.

Now, however, since the paper has been published by journal X, you are stuck. If journal Y publishes your paper, you will have the same article published in two different journals, which is also a violation of ethical standards, and could lead to both copies being retracted by the publisher. So, unfortunately, you are stuck paying the fees to the journal X, and the work you've done to improve the paper with journal Y is now "lost" to the literature.

As has also been pointed out, journal X appears to be quite sketchy, and I would avoid any future contact or involvement with them. But for now, consider this a lesson learned for the future.


Difference between research gap and research question While writing a research proposal, I am confused about the difference between research gap and research question. What I understand is you can first identify the research gap and then move find research question in that gap. Is it correct?

Also, What are the central research question and sub-questions?

In short:

Research gap, I understand it as a field, subfield, mechanism, that has been under-researched and there is space for improvement.

For example, object detection using telepathy might be under-research, so there is a gap in the research of that specific field.

The research question seem to refer to a more specific hypothesis, which in cases, it can coincide with the gap. For example, can telepathy work to detect an object, or can telepathy work under these or those conditions. In my understanding the first could also be a gap, the latter is more of a question.

Then the main question could be, "can telepathy work", while the subquestions could be, "can telepathy work also while you sleepwalk", "can it work if you are drunk", "can it work if you are tired".

Just to avoid misunderstanding, I'm not from your field and I can only guess what you plan to work on. The maybe humorous answer does not intend to make fun of anything (I hope it's clear, otherwise I'm willing to retract it).


What do profs actually think when writing a letter of recommendation for an average student for grad school Grad school application starts now along with all the anxieties associated with it.

One of the question I ask myself and repeatedly get asked by my peers is that what would the profs think when the transcript and resume reveals that they are just an average student (i.e. 3.3 GPA, at minimum of grad school acceptance requirement).

Of course, the top factor here is that we are being evaluated by people who are exceptionally talented and likely the top students back in their days. And plus we may have built an amicable relationship over a long period, no one wants to appear like a useless person. Lastly, there may exist a significant time period between when an application is sent out to when the letter is received, during this time I find a lot of students will question whether the profs are still open writing the letter for them.

What if a professor doesn't like what he sees in the transcript, or feel that the resume does not reflect any exceptional talent, what would a prof usually do in this case?

If you want to go to graduate school and think you will be successful, you should apply. Let the admissions committee decide your package.

I've written plenty of recommendation letters for more "average" students and I suspect most other faculty have too.

The only time I turn down a recommendation letter is if the student really did poorly (e.g., sub-3.0 GPA) in my classes. Then I gently suggest students find another letter-writer. This has only happened once.

Plenty of average students go to grad school and most of them get Ph.D.s. The degree is not necessarily an indication of exceptional brilliance. There are brilliant Ph.D. recipients, and there are less stellar Ph.D. recipients. Instead, the Ph.D. indicates a number of factors, including the ability to do independent research, a great deal of learning and advancement beyond a master's or bachelor's degree, and a huge amount of perseverance.

So I will write a letter appropriate to the student. I will indicate the grade they received in my class, or the research work they did in my group (e.g., "top third" or "top half of the graduating majors").

In terms of writing the recommendation letter, I try to stress positive points, but I am also honest to the admissions committee.

On the other side, the admissions committee knows how to read recommendation letters. There are many graduate programs, and not all programs expect the truly top students. So they can translate your application package into an evaluation of how likely you are to succeed in their program.


Does posting a preprint to the arXiv reduce the chances to acceptance? Depending on the submission journal, there may be some explicit rules allowing or forbidding the posting of a preprint before the peer review process is complete. However, for those journals that don't forbid it, is there any evidence that doing so impacts negatively on the prospects for acceptance?

I'd say the answer will depend on the field. In maths it is hard to find new papers that were not posted to arxiv first. Disregarding or even disallowing such papers would spell death for a journal. Thus, regarding acceptance there are no pros and cons, it will simply not matter. Regarding all the other aspects, such as visibility, etc., publishing a preprint is an obvious choice, but that topic has been discussed extensively in previous questions.
I guess the same will hold true for physics and CS. It might be different in other fields where arxiv and similar sites are used less often, but it seems to me that there is a slow convergence towards extensive use of preprint repositories in all branches of science.


Switch to Physics from CS Career I've been considering a career change for awhile and recently discovered the Two-Slit Experiment, which, to put it frankly, blew my mind. I then started some hefty reading and investigation into all things Quantum (Bell, entanglement, QIT), which has led me here.

I have 20 years experience in IT working as a programmer, having graduated with a Bachelor in Computer Science back in the early 90s. As mentioned, I have been considering a career change for some time (having become quite burned out in this industry), and have found something that has piqued my interest more than anything else. I am not yet sure which area of "Quantum" I will be most drawn to, possibly Quantum Information Theory/Science.

I am aware that there is a significant amount of Maths and Physics pre-requisites involved. It seems likely, given that I have not done any Maths or Physics study probably since I was doing my CS undergrad, that I will need to start over with an undergrad in Science/Physics in order to get the fundamentals.

So my questions are:

What is the ideal path of education to get to QIT/QIS or QM?
Is the path to QIT/QIS also via the Physics route? Can I leverage my CS background?
Resources (books, online courses, etc) that would help with the transition from CS-type thinking to Physics/Maths-type thinking.
I'm considering Astrophysics as a minor (due to interest), but wondering whether it would be useful and complementary to Quantum Theory.

Apologies if this encompasses elements too broad or off-topic, I'm trying to get a better understanding on what is to come following this path. Thanks in advance.

Yes you can leverage.  At my university, these people work in the EECS department.  You could just apply to be a graduate student.
Study vector calculus and linear algebra.
Not really.  However, "big data" is quite popular in astro/astrophysics currently, so maybe you could get hired as a programmer.


How do you avoid favoritism and personal relationships from affecting grading? Universities do encourage close cooperation between students and faculty. However, how does one prevent close working or personal relationships from affecting grading, so that it can be carried out fairly and uniformly? Is there a method of avoiding "playing favorites" with students a faculty member has a "closer" relationship with than others?

I would suggest to design a rubric to assess the work of students. The design of a rubric is difficult and may require a lot of work for the teacher, but it will isolate the grading process from other factors. Here you can find a book about rubrics.

One of the advantages of using a rubric is that students can easily observe how their work is going to be evaluated. Another advantage is that teachers can easily apply the same criteria across all the work to be graded.


Can a professor ask you to get a medical clearance from your doctor My professor asked me to get a medical clearance from my dictor stating that I am free from my medical ailment. Can a professor do that?

Yes, the institution has a responsibility to all students and faculty in terms of infectious things and it is probably in the detail of the enrolment form you signed somewhere...

I have seen situations where students were told to not come to class and stay in their rooms until the Doctor cleared them - this was when europe had a "flu / respiratory " bug a while back...

Students are also sometimes required to provide proof of sickness, or death of a relative, when asking for repeat exams or assessments. Had one case where the student photocopied a medical certificate and changed the dates - got caught because the signature was identical on 5 certificates - size, position on the paper etc etc


Publishable with revisions I submitted a manuscript to a journal in the social sciences.  The response to the initial submission was "accepted with conditions".  The only feedback I received related to a few typos and grammatical errors.  I reviewed the entire paper for additional typos, made some minor edits to improve overall flow, and resubmitted the manuscript.  Four months later, I received a letter indicating that the manuscript "can be publishable with major revisions".  To me, this decision sounds like the manuscript is farther from being accepted for publication than it was after the initial "accepted with conditions".  Am I interpreting the journal's decision correctly?

The solution -- as in so many cases in life -- is to communicate. In this case, write to the editor in charge and ask what happened here and how they intend you to proceed. Like @Buffy mentions, it is likely that the second round of the paper went to different reviewers. This is not entirely uncommon, but awkward anyway -- the editor should have looked for substantive reviews the first time around already, rather than just go with the typo fixes. But it happens, among other reasons because a reviewer who promised a review just doesn't get it done, and the editor feels the need to go with what they have -- just to receive the missing review a week later.


Is it appropriate to ask the professor a trick question? I'm a CS student enrolled in a class about a certain programming language. Recently, I discovered a trick that is pretty useless in actual production code and doesn't seem to be known by many. The trick results in a program not outputting the expected result. The program is less than 5 lines long.

I am curious as to whether my professor would be able to uncover the solution and would like to ask him during his consultation time. My concern that I do not want the professor to think I am trying to be rude, disrespectful, or anything negative to him.

Would it be appropriate for me to go see my professor during his consultation hours and ask him why my program is not outputting the correct output?

Asking it as a "trick", where you pretend it is a real question and you don't  know the answer, could certainly be annoying depending on the professor's mood.  So don't try to be tricky.

  Hi Professor, if you have a few minutes, I came across an interesting puzzle that I thought you might appreciate.  I thought the answer was pretty surprising.  [if invited to continue:] Look at this program; can you guess what it would output?

You should make it clear that this is a "riddle" to which you already know the answer.  If the professor isn't interested in spending time thinking about it, he can always ask you to tell him the answer, or just say he is too busy right now.

Also, you know your professor better than we do; use your own judgment as to whether he is someone that would find this sort of thing interesting.

Some commenters have raised the question of whether this is an appropriate use of office hours at all.  My view is that it is, since it is at least somewhat related to the content of the course (same programming language).  It also has the potential to lead to a technical discussion in which you might learn something.  I personally would be happy to have this kind of conversation with a  student during my office hours.

Of course, it should be low priority. If there are other students waiting with questions that are directly about the course (homework, lecture, etc), then this is not a good time to ask your puzzle; go away and come back another time.

I am assuming that your honest goal in all this is simply to share something that you think the professor will find technically interesting, and/or to learn more about it yourself.  If your intention is actually to "test" the professor, or to impress him with your obscure technical knowledge, or make him think you are smart so that you get a better grade, then please don't; that would be rude and disrespectful, and professors tend to be pretty good at seeing through things like that.


Fired/project given to another postdoc during F32 fellowship I am in my third year of funding of an F32 NRSA postdoc fellowship (one month into my final year). My project is nearly complete and ready for publication, however, my sponsor/PI wanted another postdoc in the lab to conduct a few biochem assays for the project.

Over time, I have been cut out of my own project. My PI now feels that the paper is not near submission, and would like my project to be a "co-project" with this favored postdoc. My relationship with this mentor has started to deteriorate since that point. Favorite postdoc complains constantly about me to the PI, even though I remain positive and productive.

Recently at a meeting with PI and favorite postdoc, I was accused by the other postdoc of not properly analyzing a certain data set. In my defense I explained how I analyzed the data and why I employed the method I did. My mentor then cut me off and fired me from my position, citing that I had a bad attitude. I felt set up.

She asked me in a follow up email to give over all stocks, reagents, notebooks, and data files so the other postdoc can finish the project. I am to look for work, and I do not need to report to lab anymore.

What I don't understand is that this project is funded by an NIH fellowship in which I am the PI listed on the grant, can she give this project to someone else and take my three years of data away from me? Also, I had a year of salary/work coming to me, I was going to use this year to publish my work and apply for jobs but now I'm screwed. I was a free employee to the PI since my salary was covered, so I don't understand her actions. Any advice?

Generally speaking, it is VERY difficult to fire anyone in academia.  Speaking as a professor with a postdoc of my own, there are generally negotiated contracts between the university and the postdoc.  Faculty and the university can get in trouble if they violate the terms of that.  I highly suggest you talk to your HR person to see if they was all above board.  They will be able to tell you if any of the terms were violated.

Futher, NIH funding, like other pots of government funding, is a contract between the government organization and the institution, not the individual.  That being said, that is frequently overlooked for things like professors leaving one university to go to another and then taking their funding with them.  I would strongly suggest you get a copy of the exact contract between NIH and your institution.  There might be some language in there that can help you.


Is poor English grammar and writing style overlooked in otherwise strong math paper submissions? Is poor English grammar and writing style overlooked by peer reviewers and editors in otherwise strong math paper submissions?

Short answer: no

Longer answer: The purpose of the article is to communicate something. If poor grammar and style gets in the way of that goal, then that is something that needs to be addressed before the article can be published. If the paper is indeed strong, then that will typically mean you will get a "revise and resubmit" rather than an outright "reject".


Can I be admitted into graduate school in the US without undergrad degree (if I have master degree) I am considering getting a PhD or an MBA in the United States. I do not have a bachelor's degree, but I'm working on finishing a MSc in Computer Science from a UK university. By the time I'll be done with the degree, I will have more than ten years of experience in the IT sector in various positions and in various corporate environments (startups, corporate, government).

Do most universities in the US waive the undergraduate degree requirement if applicants have a UK master degree (without any undergraduate degree) from an accredited UK university?

The simply fact of the matter is that you have to ask each program you are interested in directly. Some schools have a specific bachelor degree requirement, some don't. Like all bureaucracies the costs of bending this rule can be quite large. Being an international student might actually make it easier since the offices that deal with international students have to do a lot of personalized evaluations anyway.  What all schools do have is a contact address for exactly these kinds of questions usually it can be done by e-mail now. So my best advice is to ask directly the people who make these decisions and not the "internet."

Once you learn whether or not there is a possibility of this plan working then you can worry about funding. The resident versus non-resident price difference only applies to public run universities but can be very significant. It does vary by which state the school is in does really matter. For example in North Carolina I know of a person who work for three years as a sheriff deputy (county-wide police officer) who was not granted in-state status at their universities.


What warrants acknowledgement or citation in a dissertation? I have just finished my dissertation and just have a question about acknowledgements and citation.
There was a line in a proof of a paper that I did not follow and someone told me what it meant.
Does that warrant citation or does it look silly citing such things? It wasn’t their own work, they explained where it came from.

Citing in this case is unnecessary. An acknowledgement would be gracious, but also not strictly necessary. My personal inclination would be to do it if their explanation led to some insight on my part.
But "Thanks to JDoe for their insights into Theorem 35 of Gauss", or whatever, is, as I say, gracious.
It is even less necessary if the person's job is to teach you stuff.


Is it appropriate to reply every time to a professor's "thank you" email? I want to know, since I am not a native English speaker, whether or not it is appropriate to reply to a thank-you email from a professor?

For example, if every time you get an email from a professor saying "Thanks," you reply "no problem" or "you are welcome."

Could it turn out to be annoying or offending if one replies to every "thank you"?

I realized sometimes misunderstanding may unnecessarily arise because of cultural differences. If one does not reply to a thank-you email from a professor, then would the professor be accordingly offended? On the other hand, if one constantly reply "you are welcome" or something like this, would he be instead considered prudish?

Email exchanges need to end at some point.
If the professor's email is a simple receipt of correspondence, then I don't think there's a need to reply. However, if the professor has initiated a larger email then a reply is probably appropriate. See these examples:

Thanks sent as a form of receipt:

  Student: Hi Professor Smith,
  I've run the analyses you have suggested (see attached),
  Cheers,
  Mike

Then the professor replies:

  Pofessor Smith: Thanks for that

In this case, I think there is no need for the student to reply "You're welcome".

It wouldn't be a big problem, but it would be mildly distracting for the professor. Email exchanges need to end. The professor's "thank you email" was already a confirmation email indicating receipt of your original message.

Thanks sent by professor as part of a larger email initiated by the professor

Imagine the professor sends you an email that provides detailed information that also includes a thank you.

  Professor Smith: Hi Mike, well done on your work in the lab the other day. You did a really good job of fixing that equipment. I really appreciate it.
  Cheers,
  Professor Smith

In that case it might be appropriate for the student to reply: "you're welcome".


How can you identify which are the strongest PhD programs in particular subfields? I'm an undergraduate student (United States) majoring in X, applying to PhD programs with a research focus in subfields Y and Z.

I conjecture that the best universities for Y and the best universities for Z are not necessarily the same, and I want to narrow down my PhD applications to universities that are known for one or both of these subfields.

None of the professors at my university's X department do much research in either Y or Z, and they seem to not have the greatest idea where I should apply - I usually get generic answers like Prestigious University U, which may or may not be what I'm looking for.

The other concern is that I've taken a few graduate classes regarding Y and Z, but in no way am I fluent in the fields, nor have I done direct research in these fields. As such, it would be difficult for me to attempt to read research papers about Y and Z to try to back out which universities produce the best work.

How might I go about finding the strongest programs in Y and Z?

Two suggestions:

Look at the research publications of faculty in your area of interest and then look for the most widely cited research in this area.  You can easily find such information using tools like Google Scholar.  Then find out where the authors of these widely cited papers are teaching.
Look at what happens to graduates from the different programs.  Many faculty have web pages that list their recent PhD students, some universities publish graduation programs that include lists of graduates, and there are sometimes other ways of identifying recent graduates of a particular Phd program.  If you can't find those people on the internet, that's a strong indication that they working in academic careers.  If you find them but they're teaching at community colleges and regional comprehensive universities, then that tells you a lot about how well the graduates have done in academic careers.


What images published in arXiv papers can I include in my education material? I am going to give a course at my company and I'm looking online for images that I can use in my education material.

Since many of the most interesting images suitable for this education exist in papers published on arXiv, how do I know which of the images found in arXiv papers I can use and which I can't? How do I know how these images are licenced?

I often see images published in arXiv papers that are later used in presentations given by other people and/or republished in other's research papers, sometimes without any credit given to the creators of the images and almost always without a link to any license (in fact I can't remember ever seeing such a link, but maybe I have just not paid attention). Under what circumstances is that okay?

A related question is, how does fair use come into all of this since we're talking about education material?

Contrary to the other answer, arXiv does not require that papers are posted under CC licences. The minimal (and normal) licence required is given here, and merely grants arXiv perpetual right to distribute the article. IANAL but I very much doubt this gives you any right to use individual figures.

You can find a (small) link to the licence for a particular preprint on the right-hand side of the abstract page in arXiv. You should see something like

If there is a CC licence you can use the image but probably need to attribute. Otherwise, I would contact the authors to ask for permission.


Where to publish a critical comment on an academic paper? Background

Last year, in October, an exceptionally weak paper was published in Nature. The publication of such a piece in a top journal was a clear violation of peer-review standards. Despite the title and publication in a reputable journal, this paper did not provide any evidence.

My attempts

I guess, I was the first to submit a Brief Communication Arising to Nature just a week after the initial publication. My comment was rejected two weeks later, and I published it in Publons system. I see that up until now there has been no clear statement in the peer-reviewed academic literature of the flawed nature of Dong et al paper.

The question

What is the best way to publish a critical comment on a paper published in top journal, if that journal rejected the comment?

I believe, it is very important to publish the critical comment in a peer-reviewed journal. However, usually journals are only willing to consider critical comments on the papers published in their pages.

Do you know what is the best way to publish a critical comment on a paper published in top journal if that journal rejected the comment?

In another top journal. But your comment "have take a form of an independent paper" as Alexey wrote.

Check those two examples from Computer Science field. First (1) from ICSE, Software Engineering community top venue, where Monperrus offers a critical review on others' paper. Second (2), Arapakis et al. challenge the results reported in Bandari et al.

In my opinion, you should go for a peer-reviewed paper, which is a very noble form of scientific debate.


Asking a journal for extended payment period I am in this situation where I have submitted an article to a journal and it is likely that, after the minor revision that they asked me to do, the paper will be accepted for publication (I hope so...). The situation that concerns me is that it is also likely that the email arrives in the middle of institutional vacation, (Clarification: I am a PhD student at the university, and the university pays the publication fee for the article), which means that my institution will not be able to pay at the time of the request. There is no personnel in the corresponding department.

To clarify the timings: I expect that the "acceptance" email will arrive in the middle of August, and my institution is on vacation for all of August. We are most likely not able to pay until September. In case that this email arrives during August, how can I convey, politely and gently that we cannot send the payment due to institutional vacation period? Also, I would like to highlight the importance of the publication of the paper in the journal. As it has one of the highest impact factors on the field of engineering, concretely on Internet of Things and it is the last merit milestone to finish my thesis.

I would write something like...

"Dear Ms. ,

Our institution  is on institutional vacation period during August. Unfortunately, we will not able to emit the payment before the date you request. The department in charge is on institutional vacation too. Publishing this article in  is of utmost importance for us given the  is a renowned journal in the field of the Internet of Things and my current situation as a PhD Student. We would like to ask you for a payment extension until September. Meanwhile, I will be pleased to apply any suggestion of the editor.

Yours sincerely,

 on behalf of the authors of the manuscript.
"

It is the first time I am doing something like this, and I would be glad if you can provide some help.

Usually there is a payment window of 30 or 60 days for example, so if it arrives  mid-August then paying in September is not an issue. Journals have dealt with university accounts departments before.

If you are the one stressed as you have to have it published to complete then you may need to be patient, but the payment itself should not be an issue.

For one paper, it took 4 months for the journal to get paid - several polite communications (and they were nice and helpful on both sides...) but all got sorted.


When applying for a postdoc, the contact person is not the professor I want to work with, what shall I do? My situation is that I want to work with Prof. A, but in the advertisement another professor (B) is the contact person. Now, I need write an email to send my CV and research statement to the contact person. What shall I write in the email? I will write in the email I want to work in the institution and my previous research activity very briefly (The institution does not want the cover letter, so the email will serve as my cover letter). Then the problem is: Shall I simply write "Dear Prof. B,..."? If so, I worry that Prof. B would think I want to work with him. But if not, I would write "Dear Prof. A", which sounds weird because the email is sent to Prof. B.

What shall I do in this situation?

It's simple: follow the instructions. If the contact email address is of prof. B, then you should address him in the greeting.

Do not make assumptions such as prof. B is recruiting postdoc for prof. A, or at least you should not bring this assumption to your conversation with prof. B, even if your assumption is correct. Many people may take it as disrespect.


Posting to ArXiv a longer version of a submitted journal paper I have written a paper (about 14 pages long) and submitted it to a journal.  The editors suggested I cut it down to a 5-page paper and resubmit.  I can do that, but will end up leaving a lot of material on the cutting room floor.  That material isn't strong enough to command a published article of its own, but I don't want it to be lost forever.  I am considering a couple of options:

Upload the original 14 page version of the paper to arXiv.
Try to piece together the scraps that were removed from the longer piece to make a ~9 page paper and upload that to arXiv.

Which of these seems like a more sensible / standard practice?

A secondary question is whether I should do this before I submit the 5-page version of the paper (and then include in that shorter version a reference to the arXiv version), or whether it would make more sense to wait until there is a decision on the 5-page version.

It's not extremely common, but you can find significantly extended versions of published papers out there on arXiv, authors' websites, and the like. And at least in my filed of research it doesn't seem like that big of a problem to post an extended version after publication if there is a merit and clear reason to do so instead of cramming everything in one place or writing a weak paper out of what is left out.

For example, this paper on arXiv is an extended version of a paper published in the IEEE Transactions on Information Theory and explicitly states when it was first submitted to the journal, when a revised version was submitted, and when the extended version was uploaded to arXiv (which was after submitting the revised version to the journal but before it got accepted for publication). There is a slightly updated version of the extended one on the personal webpage of one of the authors as well.

In any case, I think it's generally a good idea to respect the editor's opinion unless you have a strong reason not to follow their suggestion. But you may also want to ask the editor if the journal has online-only storage for supplementary materials to officially attach what they asked you to cut out and/or if the journal is ok with uploading the originally submitted, longer version to arXiv. If arXiv is common in your field, I highly doubt they say no to posting the longer manuscript online; if it's not allowed to post a preprint you submit to a journal, how on earth can we use arXiv as a preprint server anyway? What would they do if you had already posted the longer manuscript on arXiv before submission to the journal, for example?

My feeling is that as long as you don't abuse the system, it's ok to post an extended, fuller version online (with a clear note that it is an extended version of a shorter paper). So, for example, if the editor is not happy about a lengthy, marginal part which you think is helpful and of interest to some but perhaps not all readers, I don't see any reason not to upload your original manuscript to arXiv. You should check the journal's policy and the norm in your field first, though.


9 Years of PhD, bad supervision, no data. What should I do? I am a PhD student since 9 years. I am working on medical technology where I need intra-operative surgical data. When I joined, I was told that they will have collaboration with hospitals and other universities around the world so, I can have my experiments there.

After 4 years I got a chance to have my first experiment to acquire my first data with an artificial plastic bone and I presented my results on that data in a conference. After that my supervisor gave me some wrong data (someone else acquired that data for some other research) from a human patient to work on. Within a few months I told my supervisor that this data doesn't fit to my research topic. He forced me to work on it and modify the data so that it fits to my topic. It didn't work. He promised to have an animal experiment or cadaver experiment. But even after 3 years ( total 8 years from start) he didn't arrange any experiment for my research.

Then I forced and fought with him and finally I got chance for an animal experiment. That was also for limited data acquisition, for only one day. As this data was acquired by myself for my research topic, I got good results from it. I have written an article but now my supervisor is forcing me to include the old wrong data. I think he wants to get rid of the obvious accusation against him for wasting my time with the wrong data. He forces me to include the best result I got from that wrong data which I think is unethical and biased.

Even after 9 years he has not allowed my thesis proposal. Now he pressurises me to include that old part in my article and says if not, he won't allow to publish it and without publishing it he won't allow my thesis proposal which actually should have been passed in the first year of my PhD. So I have been waiting for 9 years to submit my thesis proposal too.

Besides, he never allowed me to visit other labs for internships. I had an international full fellowship from the European Union, which allowed me up to 12 months of internships in any EU country. But my supervisor never allowed me to visit any other country or other lab.

After 9 years I am still stuck in the same place, frustrated and psychologically stressed. I lost lots of money living abroad. For the last 3 years I have been living without any scholarship, only with my own money. I can't live with my family and can't bring my family to me as I don't have any money and I am in debt. Moreover, I have no thesis proposal submitted. It's a total ignorance to a PhD student, the poorest supervision. The university ruined my career and life by accepting me as PhD student but not providing the necessary resources for the research.

What can I do in this situation? Any suggestion?

Imho you are past the point of risking a bad relationship with this supervisor. Your case looks like terrible academic behaviour on their part bordering on psychological abuse. You need external advice on this situation, so you should contact the ombudsman or somebody with this role in your institution. Please note that this first step doesn't involve burning bridges with your supervisor and they don't need to know about it. Once you get their (hopefully useful) advice, you can analyze your options. Some of the possibilities could be:

the ombudsman/institution asking the supervisor what is their plan (sometimes a little official pressure is all that's needed to make things move forward)
a mediation with the current supervisor leading to a clear plan for you to achieve your PhD as soon as possible.
a change of supervisor.


What is the role of advisor in writing a PhD thesis? I am about to write my PhD thesis. The process is to first write the synopsis which will be read by examiners prior to agreeing to read the thesis. Now, I provided my advisor with copies of the synopsis and thesis a few months ago for review. But he was not able to read either the thesis or the synopsis. Since time for conduction of synopsis and subsequently thesis submission has arrived, he is now asking questions like "have you written the thesis", "if I will proceed with the formal procedure, make sure you submit on time".

I understand that during the course of PhD I have written many good papers, yet the situation leaves me wondering what is the role of supervisor in writing the final thesis document?

Note: To be honest, I have not written many theses' (my bachelor's thesis was the most ridiculous document I have written till date). My university is in India.

The general responsibilities and authority of the PhD supervisor will be quite different in different universities, especially in different countries. It may even be very different form one department to another.

I attended University of Toronto, Physics. In my case, my supervisor was very involved both formally and informally. He would visit my desk at least 2 times per week and ask how things were going. He would make helpful suggestions, ask useful questions that showed he understood, and would keep asking questions until he did. He was OK with me coming to his desk any time.

He suggested the topic. He gave useful hints on how to start. He answered a ton of my questions. He told me when it was time to write up some thing like a synopsis or submit some form. And he negotiated with the university to set dates for various exams, submission of various things, and who would be on my exam committee.

One of my profs described his experience at another university. His prof was a "big name in physics." He gave a talk at the department about his research. The BNIP was in the front row, asking useful and interesting questions, suggesting interesting ways the work could be applied to interesting questions, etc.

Then at the end of the talk the BNIP said to him "That was a very good presentation. Who is your PhD supervisor?" "... You are, Dr. BNIP."  "Oh! Oh! In that case, come by my office tomorrow and we'll set up your oral exam."

The thing to do is try to estimate if you are in fact getting what you need to complete your degree. As long as it's getting done then don't worry too much.

Check with other grad students what they are doing.

You might need to ask the support staff at your university if you are missing doing anything like submitting forms or things. They will know because they do the actual work most of the time. Your department head's secretary or the secretary of the head of grad studies. You should ask them if you are missing anything.


Changing Citation after acceptance of an article We submitted an article to a SCI journal 5 months ago. In the article there is a section which is based on a patent which we had submitted to our institute's internal  patent system. We cited the patent application in manuscript as under review patent. However, our institute has rejected our patent application so we converted patent application into an article and published into an international conference. Meanwhile, we received the acceptance letter for our SCI journal article.
As the cited patent application has been rejected and we already published a conference paper based on patent application. Now should we replace the patent application citation with the published conference paper? and do we need to report about this issue to editor?

You certainly should update the citation if it is still possible, so readers can follow up on your references without wasting time searching for an inexistent patent.

Contact the editor. Typically such minor changes can be done in the proof editing stage, but publishers are usually happiest to hear of such changes as soon as possible.

And congratulations on the acceptance of your paper!


Ask for reference letter for applying graduate school, professor agreed, but no more follow up I am currently preparing for the graduate school application. I was asking for reference letter from one of my Math professor who knows me well. I took classes with him for twice, went to his office hour frequently, and we were talking to each other for many different things other than the class/grades. He was very caring and helpful all the time. I asked him if he will be willing to write me a ref letter for graduate school programs, and after nearly 2 weeks, I got an reply said yes, he will be very willing to. But he reminded me that he is a very slow people and I will need to remind him at least two weeks before the deadline. After that, I sent him about some supplementary materials such as my CV/personal statements to help him write the ref letter and ask if he will need more information from me, I have been waited for more than two weeks, and I repeatedly sent reminder emails for three times, but I still got not reply from him. I went to his office, but because of the pandemic thing, he was not there. I am so nervous and concerned and not sure what sure I do next? I was calling the Math department secretary to ask her to send an email to remind him to check the email, but I also did not get any feedback from him yet. Does anyone have any suggestion for me??? I will be really appreciate for that! Also, if I got reply from him, should I politely ask him to give me his phone number in case I might not be able to contact him through email again. I am not sure if this is polite but if he cannot reponde me in time in particular when the deadline gets closer, that will be very awful :(

I suspect that he knows of your concern and will come through, though at the last minute. But "repeatedly sending reminders" is also "being a bit of a pest". Most people will forgive you for that, but not all.
But, he has other things to do and needs to think about what to write on your behalf.
Phoning him will just make it worse, interrupting his schedule.
So long as he knows of the deadline you should be fine. A message a few days before the deadline wouldn't hurt, mentioning your eagerness to know.
But replying to constant reminders just slows down the process, so they are often ignored. It is a mistake to make him less efficient than he could be. Relax for a bit. There is little incentive for him to rush it unless the deadline is immanent.


How to create HTML Slides with audio for online lectures? This follows on from a recent question about embedding audio in PDF slides. I don't like the thought of users needing to use a particular PDF viewer in order to hear the audio and I don't like the thought of needing proprietary software just to create the presentations. Thus, another option would be to create HTML slides. There are a range of HTML slide production approaches (e.g., S5, DZSlides, Slidy, Slideous).

Update:
I was thinking about  using pandoc to convert markdown into one of the slide formats. @Federico mentions the audio HTML tag. I assume that would be part of an overall solution. This presumably represents a basic answer, but I'd be keen to get some guidance about how this works on a practical level:

Are there any examples of implementing audio in HTML slides?
Are there any strategies for increasing the usability of consuming and activating the audio?
Are there any browser or operating system compatibility issues?

Thus, in a broad sense my question is

How can HTML slides be created in an effective and efficient way with embedded audio?

If I read correctly, in all those HTML slide systems you write the HTML file directly, it is not produced by some external tool. So I think you can simply put an audio tag in it. Or am I missing something?


What impresses more in a graduate school application for CS: an REU or an honors thesis? I'm a prospective applicant (or will be in the near future) for PhD programs in Computer Science.  I recently did an REU this past summer at a top-ranked CS school and am seriously considering graduate school, albeit after a break so I can be certain which particular area I may want to go into.

While I have my REU as some form of research experience, I'm wondering how much more I will need before I apply to graduate programs.  In my department, there's been a couple who have worked in labs for maybe a year or so (but so far, nothing like two or three years like I have heard at other places), and others in our Honors program are required to do an honors project with a professor at the end.  It's more or less rare that undergrads publish so much where I'm currently doing my undergrad.

While I have done the REU, I haven't gotten much further as far as doing research at my own school goes.  I tried working with a professor one semester during my senior year, but I wasn't able to get much done before I had to stop due to a busy semester next semester.  Generally speaking, is an REU more impressive to graduate admission committees over a senior thesis or doing research at your own institution?

I don't think that there is a definitive answer to the question as asked. It assumes "equal quality", which is unlikely to be easy to measure. Moreover, every reader of an application might favor one over the other, but in a different way from another reader.

So, I would suggest, treating them of equal "value" on the face. But what will be impressive to a reader is that the applicant has done "something" that required hard work and has high quality. You can achieve this either in developing a thesis or in an REU.

My advice would be to pick one that interests you and you are likely to work hard at, but also one for which you get some local support. An REU might be slightly favored on the latter idea (support) provided that the research is guided in some way. But even a thesis could be given support if the student meets regularly with a faculty member during development to get some feedback.

Do something hard. Do it well.


No PhD research group during my PhD. How do I handle it? I have been involved in my PhD now for about half a year but my setup is potentially more uncommon. It feels very independent because I havent got a research group I'm involved in at all. It's literally just me and two of my supervisors and I work in a completely separate building to both of them and I have absolutely no one to collaborate with or talk to about my research or ask for help. Is anyone else in this same or similar situation and if so/or do you have any advice on how I could improve my work situation because at the moment it feels very lonely and when I get stuck there is no one around to ask.

Besides the obvious answers (try to move closer to the place where your supervisors and their groups are and meet them more often) I suggest

try to find or initiate a seminar close to your interests.

This would provide a regular meeting point for you and your supervisors (besides meetings directly related to your PhD) and hopefully other people with interests similar to yours. Your supervisors may help to find a theme and spread the word (and probably take formal responsibility for the seminar) but you can and should offer to organize the schedule and the collection and circulation of abstracts.


Is it appropriate to contact a journal about grammatically erroneous editing? Recently, I submitted a paper to a maths journal (which is a decent journal with a solid editorial board). It was eventually accepted after making some revisions suggested by the referees, at which point I uploaded my final submission. This final submission was then edited by a copy editor at the journal; as well as the usual cosmetic changes in ensuring that my papered adhered to the cosmetic style of the journal, the copy editor also made several grammatical changes. I then was given an opportunity to read through this edited version and suggest any final corrections before my paper is uploaded to the journal's website.

This, of course, is all fairly standard practice. However, many of the grammatical changes made by the copy editor were incorrect. Of course, I noted this in my comments, so I hope these changes will be reverted before the paper is published.

  It is appropriate for me to take further action in notifying the journal (e.g. a member of the editorial board) that a copy editor is repeatedly introducing errors?

This of course seems a little petty. On the other hand, these same grammatical errors occur repeatedly throughout papers in this journal (at least in recent papers published online), and I'm sure that I'm not the only reader who finds these mistakes irritating.

In case anyone is curious about the errors, the most common mistake is that the copy editor repeatedly replaced with a comma my usage of a semicolon before an independent clause, especially such a clause in the imperative mood: an example would be something like "This can be proved via the method of Gauss, see [1]". Other such comma splices were introduced - all by replacing semicolons with commas.

Additional grammatical mistakes were introduced that were clearly incorrect: for example, I perhaps overuse the phrase "Note that", and this was pruned on a couple of occasions by the copy editor, but in more than one case, the rest of the sentence wasn't edited to ensure that it still made sense.

I can't give you a yes / no answer, but I can say what's likely to happen if you choose to complain.

If you choose to complain to the publisher: chances are they'll ask for some examples of poor copyediting and form their own opinion. If they agree with you, they might change the copyeditor (if it's outsourced) or provide him or her with the negative review and pointers (if it's an in-house employee). If they don't agree with you then probably nothing will happen other than giving you a vague "we are aware of the issue" response.

If you choose to complain to a member of the editorial board then:

It's possible the editor will say "this is none of my business, approach the publisher", or forward to the publisher "I received this complaint, what do you think" (in which case, see the second paragraph).
It's also possible (but in my opinion less likely) that the editor will take things seriously, in which case he or she will contact the publisher. Again, see second paragraph, except this time the publisher is also dealing with an unhappy editorial board member and so would be more inclined to make changes.

Finally if you choose to just make your corrections then your corrections get implemented and everyone just moves on to the next paper.

Having said all that, I gotta say, I don't see any difference between "This can be proved via the method of Gauss, see [1]" and "This can be proved via the method of Gauss; see [1]". Both simply say that the reader can find the proof in reference 1. It looks to me like an unnecessary correction, but it isn't per se wrong. I checked with another editor and he found both OK too. If you can confidently say that one of them is wrong, you have a level of English mastery that most other native speakers aren't even aware of.


Why do tenured professors still publish in pay-walled venues? I wonder why tenured professors still publish in pay-walled venues. I can understand that non-tenured professors are publication pressured, but once one gets tenured, why should one still place knowledge behind walls?

There are lots of reasons, but high among them are the prestige issues for their co-authors, especially their non-tenured, postdoc, and student co-authors. Everyone on the author list benefits from the typically higher prestige of the traditional (and paywalled) publishing venues.


My supervisor spells my name incorrectly I've discovered that every time my supervisor has cited any of the papers or technical documents I've written she/he would:

spell my name incorrectly or forget to add my name
spell the article/technical document title incorrectly

These are citation made in articles already published (!!) or at final stage (where she/he denied to make any effort to try to correct them). Althought this means she/he also loses citations of these articles she/he is doing mistakes only on my papers/technical documents, not with others.

I am obliged to add her/him in every paper as co-author, although she/he never engages in any discussion concerning any of the papers or phd. This is not someone that has a flock of PhD and MSc students under her/his wings, the number of students are really reduced.

How should I react to this? What should I do about it?

Mis-citing articles (and worse, removing authors) is one of those crimes that academics take very seriously (and no one else really understands). If you were a collaborator, then repeated behavior of this kind would get your advisor in trouble not just with you, but with editors at the journals, reviewers, and so on.

So you really should bring it up.

How do you go about doing it ? Because it's your advisor, you have to be a little more gentle: some options:

keeping it specific to each mis-cite: "I noticed you cited my work, but you omitted my name: can you please fix it". It sounds like you've been doing this already though.
the technical solution: "Here's a BibTeX file containing all my papers: you can use that for citing" - this works only if your advisor uses some kind of citation manager to cite papers.
the direct solution: "I noticed that in this, this and this paper, you omitted my name from the citation. I'd really appreciate it if you could contact the editors and submit a correction: I'd like to get credit for my work".

In other words, keep the discussion focused on outcomes and actions, rather than intent (because a) it's hard to argue intent, and b) you're in a position of weakness)


Is post-hoc hypothesis an issue? I was asked to serve as a reviewer in a peer-review process.  I remarked some issues and suggested a minor revision to the editor.  Now I received the revision back and generally think the authors did a good job revising the manuscript. The field is psychology.

There is one issue that I was not sure about. That is, the authors changed their hypotheses between drafts. This has something to do with the way they treated their data. In the first draft, the experiment provided data from two instruments (very similar instruments) and were analysed separately. Hypotheses were formulated separately for the two instruments.

Now, in the 2nd draft the instruments were combined and the data treated as coming from one instrument. Hypotheses were adapted to these new circumstances, but also were partly contradictory to previous hypotheses because then, the authors expected some differential results from the two instruments.

I am not sure how to judge this. Is this a big issue or just a minor thing?  Why is it an issue at all?  I have a feeling that this not too uncommon in my field (psychology), I mean to treat hypothesis testing somewhat lax.  I believe that in grad school I learned that hypotheses have to be stated before conducting the experiment and cannot change. But I was googling a little about this topic and did not find anything that would indicate that post-hoc hypotheses are a bad thing.

There is substantial divergence between fields and individuals to what extend twiddling with the original hypotheses post-hoc should be tolerated. Defensible positions range from "it's not a big deal if the experiment / write-up still makes sense with the new hypothesis" to "hypotheses shall never be changed". Only you can tell what your and your field's methodological stance on this is.

As Boris says, the main issue to avoid is "p-value hacking". That is, it should not be that the authors decide that whatever they find support in their data is redefined to have been their hypothesis all along - while exploratory research per se is not bad, it is distinctly different from hypothesis-driven research and should methodologically not be sold as such. You will need to evaluate whether this has happened for your manuscript. If the answer is "yes", this is certainly grounds for rejection.

However, from your explanation, it sounds to me like the authors did more of a technical refinement of their hypothesis, without changing the nature of it. If that is true, it sounds somewhat nit-picky to reject a paper on this grounds. I tend to be of the opinion that methodology should be considered a means to an end, not a strict rulebook that needs to be followed to the letter even if there appears to be no reason for some of its details in a specific case.


What is the use and importance of recommendation letters? In my country recommendation letters to enter the equivalent to an MBA or PHD are just a suggestion, not necessarily, and/or irrelevant. In some cases they are shunned because they are considered related to nepotism. The only time they are needed is when applying abroad.

The question is: Why are recommendation letters considered important (if they are) in your universities and how is that importance measured?

In some other places, such as the US, no one would likely view them as nepotism unless they came from a relative.

The purpose is to give the receiving institution an independent evaluation of the candidate from someone, such as a professor, who is in a position to know both the background and the likelihood of success of that person. Usually the recommender has some standing in the academic or professional community and who can be trusted to give an honest evaluation.

In many places, such as the US, they are all important, outweighing many other factors. It is unlikely you would be admitted to a program based only on letters, but very difficult without good and supporting letters. Don't neglect them if you are applying internationally.


Any shame in copying from a grant proposal body to create an abstract? I have to write an abstract for a grant proposal's cover page.
Is there any shame in strategically copying/pasting entire sentences from the body of the grant proposal and arranging them coherently to form the abstract?
On one hand, it feels funny to have (e.g.) the opening sentence be the same, and if the reviewers notice it, it might look unprofessional. On the other hand, if it's a well-written sentence, why should it matter if it were reused?

No, there is no shame in that.

  On one hand, it feels funny to have (e.g.) the opening sentence be the same, and if the reviewers notice it, it might look unprofessional.

I usually try to have the "opening sentence" be different, but that is really more a matter of personal preference than anything else. I don't find it "unprofessional" if I review grant proposals where the main proposal and the abstract start with the same sentence.


Can I invite my phd student to be a guest editor of a special Issue of a Journal I am guest editor as well? I am an Assistant Professor in the USA and I was invited to be a guest editor of a Special Issue for an international peer-reviewed Journal. I was asked to find 2 other guest editors. Can I invite my PhD student to be a guest editor? Are there any reasons not to do it? I thought it would look good on his CV. I will handle most of the papers, I will give him just 2-3 papers to handle so it won't take too much of his time. He has 2 papers published as first name on this topic.

As someone who served as guest editor already:
I don't see a problem in principle by inviting/recommending an additional person (including students) for this job. I guess I would ask the editorial team, as @Buffy suggested already.
I would not invite a student for other reasons though:
Usually this is a lot of work, which blocks students from working on their thesis or related studies. This depends of course if the student wants to do it as an investment in a later career.
Moreover, I think it would be good to have a few years of experience in publishing, which helps you to select reasonable reviewers. This will be different for other fields, but from my experience, there were almost never any perfect fits to reviewers. It was rather hard to identify, who may have expertise in some exotic areas to review a certain paper. Here a few years in the business definitely help. I assume this would be much harder for students - or it would all come back to you rather than taking work away from you.
Keep in mind, even if you give them just 2 or 3 papers, this can result in some serious work, if reviewers don't react or you don't have any good matches from the start, ...
Finally, the statement to "find two other guest editors" somewhat sounds like you would be working with a predatory journal. Without knowing the actual journal, this is how I would interpret this situation.


Academic writing: Referring again to the works of authors et al. Does date need to be included every time? If I were to refer to the work of X et al. [YYYY] several times within a paragraph does one need to write the date every time? It appears to disturb the flow of the writing and reads better without, however I'm unsure of the convention.

I've never taken notice either way when reading papers and cannot find an example. Perhaps it is bad form?

This is entirely dependent on the venue's style. It varies not only by field, but also by the particular journal or conference.

Ideally, your venue will have a published style guide.
Or at least a short document with explicit instructions.

Sometimes this will be in the citation style guide, other times you will need to look in the full guide.

Failing that, go digging through other papers published at same venue,
and see what they do.

Failing that, or if this isn't actually targeted at a standard venue (eg for a standalone book). Find a style guide, for your field. Either one used generally used in your field Eg the Chicago Manual of Style. Or choose on from a journal that you like.


Does citing reviewers' papers significantly increase the chance of the submitted paper to be accepted? A paper submitted to some peer-reviewed venue might cite some of the reviewer's papers.

Is there any research/study that looked whether citing reviewers' papers significantly increase the chance of a submitted paper to be accepted?

I am most interested in the field of computer science, and English-speaking venues.

I do not know whether citing the reviewer helps, but I know that the obsession with impact factors has lead journals to ask for citing articles which appeared in the same journal. I had two rejections for "not enough citations", and a friend had an article rejected because "the topic is not within the scope of this journal, which can be seen by the fact that none of the citations appeared in this journal".


What unusual/innovative methods are there to deal with late submissions of assessment? Some context: I was intrigued by a short discussion in another answer relating to dealing with late submissions of work by students, where Jeff suggested giving students a limited number of 12-hour "late tokens" that they can use at their discretion when submitting work late during a course.  The idea of this is to give each student a "budget" for lateness, so that mild sporadic lateness would be okay, but repeated or extreme lateness would break the budget.  This seems like a very clever idea to me.  Hence, the purpose of this question is to solicit information on any other unusual/innovative practices lecturers use to deal with late submissions of assessment in their courses.
Question: What kinds of unusual/innovative methods do lecturers use to deal with late submission of assessment?

In an effort to avoid whining and prolong the lives of grandmothers, I experimented with giving students a bank of "late days" which they could use to defer submission of homework.  In an effort to teach some time management, I made the students responsible for telling me that they intended to use late days before the due date of the assignment.
That did not work.  "I'm sorry my assignment was late, but...." turned into "I'm sorry I didn't tell you I was going to use late days, but..."


Using work from someone else's talk for oneself I work in physics.

Throughout my graduate career, I heard about people who have been known to see work done in a talk and subsequently catch up to that work and then-some, and attempt to publish first. I ignored this lore assuming it wasn't really true.

Now I am presenting at a conference where there will be someone (actually a big-wig) who has a reputation for this sort of maneuver, and I don't have a pre-print yet to post online.

Any recommendations about how to mitigate the potential for this to happen (besides being ready sooner obviously, I'm working very hard on this work). Thanks.

Give the impression that the preprint is almost ready so that big-wig sees no chance to be first.


Distributing your own papers in your thesis I published three papers during my PhD, I'm now writing my thesis.

I have written three chapters, each based around each paper, but re-written so as not to fall foul of self-plagiarism rules. However, I've still used ALL of the figures from the publication in the chapters.

My concern is not really with this aspect of my thesis, though please tell me if I've misunderstood.

Finally, in the appendix, as reference, I have included the PDF files of my published papers, exactly as they are from the journal website.

Am I allowed to do this?

If not, am I allowed to use my own copies of the paper (e.g. the versions submitted on the arXiv)?

I don't understand why you are repeating the same material twice in your thesis. Each of your three papers is re-cast in a separate chapter in your thesis, and then verbatim in an appendix.

You most likely have assigned your original copyright in your papers to the journal that published them.

I think adding the papers as an appendix is unnecessary, and may fall foul of the journal's copyright. The interested reader should be pointed to the journal article relating to each of the three chapters.

If you reproduce substantially the same figures as that which appears in the journal -- to whom you've presumably assigned the copyright in the figures -- then you will need to ask for a license to reproduce those figures.


What incentives do researchers have for applying for NSF grants? I do not understand NSF grants.

Does the researcher make any money from them?  I mean, if they spend 10 hours a week working on the project, are they compensated? Can they be compensated directly from NSF funds? Not to sound greedy, but let's say I'm a tenured professor who's perfectly capable of doing outstanding research on my own.  What incentive would I have to try to get a NSF grant, if it's just for my department to distribute to other people to work with me?  I want some money.

From a purely monetary standpoint, Principal Investigators benefit from grants in multiple ways: grants can be used to pay the PI's summer paychecks (faculty contracts usually mention that the salary is for 9 or rarely 10 months), grants can be used to travel to conferences, grants can be used to pay for hardware, including laptops, and so on.

Without grants, a faculty would have to pay for those things out of their own pocket (which, in the case of the summer paychecks, just means "do not get paid").

About the part of your question about the NSF "pitching in", here is a quote from the NSF Proposal & Award Policies & Procedures Guide (Part I, Chapter 1, E) :"Unaffiliated individuals in the US and US citizens rarely receive direct funding support from NSF".


How to have a fulfilling social life as an academic I will be a postdoc in the coming academic year. While I have not decided on where I will be in September, it seems likely that I will be a research postdoc at a decent research university.

An aspect of a life as a postdoc that I had never considered before is the following: what is your social life outside of academia like as a postdoc?

As a PhD student, I had a very tight group of friends; we were friends from day 1 in graduate school, and that friendship continued throughout. Our friendship strengthened by going through many difficult classes together, staying up all night finishing homework, and studying for quals together, not to mention talking about how much it blows to be a PhD student, and worrying about the job market.

I feel that I will not have this privilege as a postdoc. We are all there to do our jobs (i.e. research), and I do not see building the same kind of camaraderie amongst the newly-hired postdocs, for these reasons:

there are no excuses to spend a ton of time with one another (no homework, no quals to study for, etc.)
we will likely have different research areas, and possibly have nothing in common to talk about in terms of academics.
there are way fewer postdocs than there are graduate students. I would be lucky to have maybe three or four other postdocs hired with me by my department. Maybe we would get along, maybe we would not. I do not have the luxury of choosing the people that I like anymore.
at least some postdocs must have family. I have found that married people are less likely to yearn for a close friendship. This narrows down the possibilities for friends even more (not that I would discriminate against married people, but they often dissociate themselves from, say, a late-night out of fun).

I would love to hear from the people who hold (or held) research postdoc positions from PhD granting institutions. I feel that teaching postdocs would give different answers, as you would meet more often to discuss teaching.

The special thing for you coming out of (what seems) a pretty demanding grad school time is that being a postdoc is not so special at all. In most ways, being a postdoc is not unlike any other time-demanding job. You come to work in the morning, spend most of your day there, and, in the evening (whenever that is, time-wise), you will more often than not go back to your home and stay there to relax a bit. You bond with your co-workers, but usually more in an "acquaintance" than in a "friends-for-life" way.

Anyway, it seems to me that you are thinking that you can only hang out with people on your academic "level". This has never been my personal experience at all. In all my work places, grad students often hang out privately with the postdocs that they work with, and many of the younger faculty staff often join in for ad-hoc parties as well. I guess it is all a question of how you want to appear towards your junior work mates. There are people that see fit to construct an image of aloofness towards their students, and others like to mingle. Nothing wrong with either, of course, as long as your work relationship stays reasonably professional.


At what point do you decide to jump into research? Before diving into "real research", there are some students who prefer to learn bare minimum prerequisite courses/material and then start off reading survey papers and develop their skills.

There are others who prefer to go through courses from Introduction to Advanced to Independent Study before finally diving in.

The former would probably face problems of fundamentals while the latter spends too much time learning things which might not be completely useful.

At what point should one (Assume, if necessary, that I am talking about STEM) decide to dive into research while making sure that one is neither being too hasty nor slow?

Take for e.g. that a person wishes to code a software in Python which does engineering calculations. He would either read something like Intro to Python and then directly start coding or he could also read documentations of other Math libraries, similar libraries in C/Fortran, study coding efficiency and thumb rules and then start.

How do you prevent yourself from taking up too little or too much time to begin?

As aeismail says, there's no single answer. As with most things in life, it's hard to know when you're "ready" to do something. The best way is to jump in when you feel like you don't need to prep any more, and then be prepared to shore up weaknesses as you spot them.

Over time, you'll learn how to prepare yourself to embark on a new research topic: some people like to start solving a problem first, and then return to the literature when they get stuck. Some people like to read a few key papers to get a sense of the main open problems and techniques, and then go off and play.

The only important thing is that you do something, and not just wait on the sidelines for a mythical feeling of "readiness" to emerge. Be fearless, like a 2 year old who doesn't know enough to be afraid :)