"Retrofitting" sources There seems to be a sort of craze about having as many references as possible. Among the students at my university, it has become common practice to write a passage of text and later figure out if someone else has done something similar and attribute it to them, changing the original text if necessary.

Is this in any way, shape or form appropriate? It seems rather contradictory to me, since you are attributing your own work to other people, even if they came up with it first. The author did not have prior knowledge of this.

I suppose you could simply claim it as your own and note that someone else has come up with it, as well. Is this necessary? It is your own work, after all, even if somebody else came up with something remarkably similar.

Many problems have straight-forward solutions that you can easily come up with. I am asking this now, because I am writing my bachelor's thesis and have come up with some of those straight-forward solutions myself. I just now found, by chance, papers on exactly that subject and, reading them, realise just how similar our approaches are.

What would be the best way to handle situations like these?

Meta: I'm not happy with the title. If you can think of a better one, feel free to edit and remove this notice.

Among the students at my university, it has become common practice to write a passage of text and later figure out if someone else has done something similar and attribute it to them

Indeed, that seems to be a constant part of paper writing: A portion of what you have made up has been done by others the same way before. In my opinion, this is often because it is simply impossible to always know all details of previous work (that is by no means always "related" to your own work in its overall topic) by heart, and because it is often more straightforward to just do something oneself rather than dive into the literature that may or may not contain something vaguely similar.

Sometimes, it gets apparent even only afterwards that an aspect of one's work is non-obvious enough to be mentioned elsewhere.

In the end, it is simply a question of benefits vs. drawbacks:

Drawbacks

You do attribute your own work to someone else. Thereby, even though you may have spent some energy to develop or define something, you

falsely pretend to have relied on someone else's work
misrepresent the effort you may have invested for your work

Benefits

You secure yourself against claims of plagiarism. While you cannot possibly copy anything you do not know, the suspicion that you did actually know some previous work but failed to mention them can arise when certain of your ideas resemble those mentioned in other papers. As such, it is less cumbersome if you just pretend you are replicating someone else's work.
Usually, the statements subject to this phenomenon do not nearly seem complex enough to warrant the mention as a contribution. Hence, you do not lose much by not mentioning you were the actual source for a specific aspect of your work.
Citing in such situations strengthens your work. While the contribution of the cited aspects would be minor, showing that you build your actual contributions on top of proven practices makes your actual core contribution more convincing.

In particular, the last point is a major benefit compared to the drawback. This is reflected in your observation that some are

  changing the original text if necessary

Given that the original ideas are not a significant contribution that needs to be promoted, anyway, replacing them with a possibly better method that is truly taken from another source is fully reasonable and can help to further improve the overall document.

EDIT: To put this answer in relation to jakebeal's answer: I mainly interpreted the question to refer to the "third branch of possibilities":

They are writing down original text that they think is novel. Only later, they realize or find out others have done the same (possibly, in a completely different field or context, or with a completely different terminology, so finding the other work is likely a result of pure chance rather than an expected event).


Is it conventional to acknowledge someone who read a draft of paper but didn't suggest any improvements? Let us say you have a paper drafted up and asked someone to comment on it. If this someone replied to you with compliments but with no suggestions on possible improvements, is it academically conventional to mention this someone's name in the acknowledgement of the paper?

I intend to do that, verily. However, my concern is that I am not sure if doing this is appropriate, for doing this may be not fair to other people who made substantial suggestions and whose names are also listed in the acknowledgement.

Acknowledgements are mostly yours to do with as you please---in my experience in computer science, at least, there are few hard and fast rules.

For my own part, I typically keep my acknowledgements relatively spare, reserving them for people who made significant and meaningful contributions, but who did not rise to the level of authorship.  As such, I tend to not acknowledge anonymous reviewers, people who gave feedback that didn't result in large changes in the manuscript, etc.  You should feel free to be more liberal in your acknowledgements if you choose, however---the only real limitation is if either a) your manuscript may have length limitations or b) you do something that can be taken as silly (which can be OK for a thesis but generally not so much in a peer-reviewed manuscript).

It is pretty much always the case, however, that acknowledgements say what a person is being acknowledged for.  If you say that, then people will know how to calibrate the contribution.  If you have a hard time figuring out what to write, that may be a sign that the person didn't do enough to be acknowledged.


What do universities get from students with valuable research ideas? I recently stumbled upon an obscure economic theory. Currently, I'm trying to understand whether or not it makes sense. If it does, I intend to build a certain simulation of the economy (using some concepts of that theory). This software will allow to better understand the economy than existing approaches. Let's assume that everything went fine and I do have a simulator of the economy in my hands, plus (someone else's) theory which explains, why it works.

The next step would be to find a scientific institution (university), which could check my findings and officially confirm that they are scientific (look through the stuff I wrote, find logical errors, verify that this is not some hocus-pocus pseudoscience etc.). Thereafter it may be much easier to spread this knowledge. A little book published by a nobody (even if it contains breakthrough knowledge) won't be noticed and its wisdom won't be applied. When the same information has been verified by some prestigious university, it's a different game (there is more trust in these findings).

If I want the university to invest resources in such check (and do it better than many professors who don't even read the theses of the students they supervise), they must have some incentive. Let's rule out money (paid by me) as such incentive.

What do universities get from sound theories developed by people who study or cooperate with them?

In other words: Imagine, some of that university's professors looks through my writing, checks how the simulator works and comes to the conclusion that it, indeed, does what I promised. No fatal flaws are discovered in the work and they agree that this method is valuable (should be researched further).

How exactly does the university, its professors, and other people doing research and teaching there benefit from this discovery?

My answers:

Better rankings. If this discovery is truly valuable, it may increase the university's prestige and help them get more (or better) students, money from public and private sponsors etc.
The professor may publish a paper (together with me). If the findings are truly new, the paper may get cited and improve the professor's h index.
The university may get consulting contracts for applying my findings to client's problems.

Notes:

I need the answer to this question in order to determine whether or not I have a chance of "selling" the cooperation with me to a university. You can only sell something, if the buyer's (university's) benefits are greater than the costs.
I have very little academic background therefore the answers above may be wrong.

Your question is based on a few assumptions, some of which are loose or close to be false. I'd outline some of them:

Ideas are valuable to Universities.  No, they are not. Universities may be interested in hiring people who have ideas and are able to convert them into working implementations and/or academic publications, thus generating prestige for the University and attracting more grant money and more students. But if the University does not have people to get your idea onboard, your idea, however cool, is wasted on them.
Universities can check my findings and officially confirm that they are scientific. No, Universities don't do this. The only `official' routes to recognise the scientific contribution is to publish it in peer-reviewed journal or patent it. Both require much more effort on your side than just formulating an idea.
Professors look through my writing, checks how the simulator works and comes to the conclusion that it, indeed, does what I promised. Normally, professors would not spend time doing this unless they see a clear benefit in terms of publications and grants. This basically means that someone checking your work would expect to become a co-author of this work and share all the prestige (and potentially profit) generated. Think twice if that's what you want.


What motivates scientists to fabricate results in prestigious journal articles? As is well known, Dr. Obokata was accused and fired for fabricating her paper on STAP cells.

Report on STAP Cell Research Paper Investigation
http://www3.riken.jp/stap/e/c13document52.pdf

I wonder what her motivation was if that is the case.
If STAP cells do not exist, sooner or later her paper will be recognized as invalid by the science community.
However, someone said your scientific paper's being accepted by a prestigious journal would be prestigious enough if it would not be found as a fabrication.

Only if you're either really (really) stupid or desperate, or naive enough to think that you'll never be found out.

The person in question here seems to have been a serial offender. And I'd be very surprised if anyone who offends so blatantly has no previous history. Fraudsters always start out small and relatively inconspicuous, but confidence and brashness grows until they're caught.

Yes, fraudsters seem attracted by the prospect of fame – but I can't grok why you'd submit a fraudulent paper to Nature. Seriously!? Of course you'll be found out! But no, it's not worth it. Ever.


Unofficially switched PhD supervisor to one at a different institution. Can I get this officially acknowledged? My PhD (I have 1 year left in it) started out at institution A with supervisor A. For reasons not worth going into, I am now, in most practical senses, being supervised by supervisor B at institution B. It is the case, for example, that supervisor A asked if supervisor B could be the external examiner of my thesis, but supervisor B declined because they felt they were "much too close to the project".

I once asked to move my PhD entirely to institution B, but was told my funding was attached to institution A. This wasn't the end of the world; the arrangement we have is working pretty okish, and there's nothing acrimonious going on. So I am fine not changing anything practically

However: institution B is, frankly, much more prestigious than institution A. When I finish my PhD I'd like to be able to put institution B on my CV. I am thinking of doing some private tutoring after I get my PhD and the difference could genuinely be an extra 10% of my pay.

Can I get something official associating my PhD with institution B?

That is a question that only institution B can answer, but I doubt that they would be agreeable due to your formal link to A.

What you might be able to achieve is to have supervisor B included in some more or less official way in your process, though, as you say, he/she already declined.

So, supervisor B doesn't want to be your examiner, but perhaps, subject to supervisor A's sense of things, B could be a co-advisor and also sign your dissertation, giving titles and institution. A may even find it advantageous to have an association with B.

But that is largely a personality issue. I doubt that either institution would object.


How do US grad schools interpret international GPAs? I am an international student looking to apply for a PhD in mathematics in mainly the USA. My current university uses a 10 point scale for GPA but most of the universities I've seen, in the US seem to use a 4 point scale, and they rarely provide a conversion scale to convert a 10 point GPA to a 4 point one.
Some people suggest dividing my current GPA by 10/4=2.5 to get my 4 scale GPA but as my masters' GPA is 7.6/10 (not great, I know) this formula makes it 7.6/2.5= 3.04 and so just barely above the minimum required for the most places. And according to it, I can never get into a PhD program.

As disheartening as it is, IMO this does not seem to be a correct way to interpret an international GPA. After all, the universities abroad don't know how were the classes taught, their contents and how difficult/easy it was to get good grades is in different unis.

At my university, it is really difficult to get good grade. One can get one of the following grades, A, B, C, or a D and it is incredibly difficult to get an A, most of the times only one or two people would get it, and so slim chances of getting most of As. My transcripts are filled with mostly Bs, (and I know I worked really hard for them), a few As and Cs and unfortunately one D (worst decision ever to take that class, it's not related to what I want to study in grad school, the instructor gave one grade to each of the students who took the class). Also, my last two years of coursework was very heavy (at least for me), we'll have 5-6 courses (all math) each semester, and I struggled a lot with my time management throughout this. Combine it with some anxiety and overthinking issues, and you have a bad GPA as a result.

So, my questions are-

1) How do grad schools in the US interpret international GPAs?

2) Would it be okay to address the reasons for my low GPA in SOP)personal statement briefly, like in a line or two? If so, how should I subtly go about doing it? I don't want to make an excuse and of course, don't want to blame others.

3) Should I just give up on applying for PhDs then and focus more on the masters program, say in some Canadian universities?

(I should mention that in the name of 'research experience' I only have a bunch of reading projects/ independent studies and a Masters' thesis. My university didn't offer courses and a supervisor directly in my area of interest and so I don't have much background in it and that's why I don't feel confident to directly apply for a PhD elsewhere like in Europe or Canada)

1) How do grad schools in the US interpret international GPAs?

Exactly the same way we interpret domestic GPAs!  We rely on our previous experience with applicants from your institution and our (Google-enhanced) knowledge of the content and rigor of your degree program.  After all, there's no universal interpretation of grades even within a particular country.

And as others have already said, your GPA is only one component of your application, and not necessarily even the most important.

  2) Would it be okay to address the reasons for my low GPA in SOP)personal statement briefly, like in a line or two? If so, how should I subtly go about doing it? I don't want to make an excuse and of course, don't want to blame others.

You're assuming your GPA is low enough to require explaining, but that assumption is based on a naive numerical conversion, which really isn't appropriate.  Whether your grades are actually "low" is a good question for the people who will write you letters, who presumably have some experience with the type of PhD programs you're applying to.  (Otherwise, how would they know what they're recommending you for?)  In particular: Would your GPA prevent you from getting a PhD at your current institution?

However, I do think you need to explain your lack of formal research experience ("My university didn't offer courses and a supervisor directly in my area of interest"), both as justification for your current research record and as motivation for pursuing a PhD elsewhere.

  3) Should I just give up on applying for PhDs then and focus more on the masters program, say in some Canadian universities?

No!  Never throw away opportunities until you're sure you don't have them!  If you know you want a PhD, and you believe you are qualified for a PhD, and enough people are willing to write you strong recommendation letters for PhD programs, then you should apply to PhD programs!  But if you're still worried about your chances of admission, you should also apply to some masters programs as backup.


Highlighting PDFs in e-readers I am considering buying an e-reader and my friend lent me a Kobo to have a go (and buy if I liked it), but I found I could not highlight PDFs.  Clearly that is useless to me. I see Mendeley has a Kindle sync. Does anyone have experience with this?

I wonder if I am better off with a tablet despite the eyestrain.

I have the standard Kindle (the cheapest one) and it lets you highlight both pdfs and epubs.

However putting pdfs in your ebook can be quite annoying as the size of the page may not match the size of the ebook and it forces you to zoom and move constantly.

I've seen classmates being a bit more efficient than me (struggling with Kindle pdfs) with their iPads combined with both GoodNotes and Adonit Jot Pro.


How to take notes during lecture properly? I am struggling with note taking during lectures for a long time. I find that if I only listen to the lecture I am able to understand the concepts properly. But the downside is that I often forget some important details. On the other hand, when I concentrate on taking notes, often I just end up writing a lot of things without paying much attention to the concepts. I have been trying to improve my note taking skills by watching video lectures from OCW or YouTube. My lecture notes look more like lecture transcripts. I pause and rewind the video and end up writing a lot. I can't figure out how to improve. I would really appreciate if anyone could have any suggestion.
PS. I take notes with pen and paper and I haven't tried note taking on a computer.

I answered a similar question at CSEducators a few years ago.
I agree that taking notes with pencil/pen and paper is superior to doing it by typing into a laptop (see the reference). But to be truly effective you need to do more than just take the notes. I suggest that you re-read and annotate them as soon as possible after a lecture, adding questions as well as notes/corrections. The second pass will help firm up the ideas. This is best done immediately, but certainly within a few hours if classes are taken back to back.
Another trick is to capture, from the notes, the most important ideas given in the lecture. The instructor will possibly point them out, but most of us would go in to a lecture wanting to especially make one or two points. It is good if you capture them.
But a single pass over anything is unlikely to lead to deep learning. And utilizing the information (exercises) is even better for firming up the ideas.
As to taking transcripts of video lectures, the same can apply. When you finish such a video, re-read and annotate the notes, marking or extracting the key ideas and making sure you understand what is being presented.
For situations in which you have access to the lecturer, write out any questions you still have and try to ask them at the start of the next lecture, or using some other communication channel.

There is a joke that the "purpose" of a lecture is to get the teacher's notes into the student's notes without going through the mind of either. Don't let that become a reality.
I once took a "course" in which that was literally true. Two of us had an independent study with a professor who gave us the task of literally copying his written notes (no lectures) but gave no real opportunity for questions, exercises or feedback. It was among my worst educational experiences ever.

Also note that learning requires reinforcement. The review of the notes, with annotations, provides the start of that. See The Art of Changing the Brain by James E Zull for some of the science behind that. A search of this site for "Zull" will turn up some further mentions of these ideas.


How to submit a paper to Bulletin of Number Theory and Related Topics The journal Bulletin of Number Theory and Related Topics (Boletín de teoría de números y temas conexos) does not seem to have its own website, from where one can obtain article/paper submission details and instructions.  (I am interested in submitting a paper to this journal for possible publication.)

I did find the following search facility for the journal in the Hathi Trust Digital Library.  But then again, no mention is made as to the submission details/instructions that I require.

In Chapter 1 of the book New Visual Perspectives on Fibonacci Numbers (Introductory Remarks [by K T Atanassov]), the author mentions (in page 4) that "[he] sent some [of his results] to Professor Aldo Peretti, who published them in Bulletin of Number Theory and Related Topics".  (It appears that Professor Peretti is the Editor (?) of the said journal.)  However, when I try to Google for Professor Peretti's e-mail address, no helpful results are returned.  Additionally, I tried to search for Peretti's papers in the arXiv (if any), and found none, and therefore was unable to get hold of his e-mail address.

I am posting this question here in the hopes that someone with better Internet search skills can enlighten me.

You will need a time machine.  According to WorldCat and MathSciNet, it appears this journal ceased publication sometime around 1991 or 1992.


Should I review a Paper of NonSci journal I am researcher in computer science in India. Very recently I got an email stating that my work is great and they want me to review research papers.
I check about the journal. It is not SCI indexed journal (and it is a paid journal). Now I am not sure should I review a paper from such kind of journal. Will it be bad for my reputation?

They want your free labor. I doubt that there is a real person at the journal who thinks your work is great. I would say no, without even bothering to answer this spam request.
If they actually sent you a paper and it looked really interesting to you and worth your time, then you could consider saying yes.
Neither answer will affect your reputation in any significant way.


How independent is an assistant professor in Denmark? In Denmark, an assistant professor is at the same level as a postdoc in terms of their salary scale. I believe assistant professors in Denmark can do independent research and can apply for their own fundings, but do they also have an obligation to work on what their managers (more senior professors) tell them to do? If so, how should the priority be?

Most Professors in Denmark are Assistant or Associate Professors (AP) not full Professors (FP). Even if you are deemed competent to become an FP, you can only get that promotion if there is such a position available. Otherwise, you remain an AP. FPs have higher salaries than APs, and they often have an extra budget for their research. They have become FPs because their topic is of strategic importance to the Dept. From that also often follow extra funds.

Both as an AP and FP you can graduate PhDs. You can carry out independent research under the given economic limits. Very often, maybe always nowadays, you (FP or AP) are expected to seek your own funding. That's a kind of independence too; you decide what to apply for.

Hierarchies are flat in Denmark. We don't think about who are APs or FPs (or Technicians for that matter) in professional work. Well, that's the case where I go (Natural Science). I have heard stories from Health Science where this is not so, and the Professors behave like kings (or Gods). The general Danish population scoffs at such behaviour; I believe they are a dying race.


Politely ask a professor about my application status I have applied to PhD programs in engineering in the US. I have contacted a professor prior to applying and based on my resume he encouraged me to apply to his university. Now I want to politely ask him about the status of my application and also politely but implicitly ask him to review my application file and also maintain my contact with the professor.
The other thing is that I think that if I do not send this email, it may convey the massage that I have given up. I also want to mention that I have currently taken two other relevant courses to be more prepared before starting my program. Below I have prepared a sample email message.
I would be thankful for any help and suggestions.

Dear Professor ****,
First I want to thank you so much for your past encouragement regarding the next step in my academic development. I am very excited about having the opportunity to apply to the university of **** and having this honor to mention your name in my application form. I would be more than grateful if you could please let me know when I might hope to hear any response from **** regarding my application. I would also like to mention that I am taking the two **** and *** courses to be more prepared before starting my program.
Again, thank you very much for all your kind consideration.

I think that's too formal, you want to use a more informal communications channel such as email and just say "just wanted to ask if you know the status of my application" period.   That gives him the option of gracefully declining to answer.  You do not know what internal politics are going on in the program and what they are going to do with your application and there's really no way of forcing them to do anything.  All you really need to do is confirm that they got it.  Hopefully you are also aware that you should be looking at other programs and not setting your heart on just this one.

The other benefit of using an informal approach is that you can repeat it without appearing to be obnoxious.  Send him an email now, then keep doing it every couple weeks.  Sending a big old formal letter is kind of demanding a formal decision and response and puts them on the spot, and if you keep sending such letters then you come across as rigid and demanding.  Whereas an informal one-liner email isn't going to be perceived as demanding (it might be perceived as begging, but that's OK)


How does a research masters work? I always thought PhD as being the main post grad research path if you wanted to get funded and that Msc was the way to get yourself ready for a PhD. I recently became aware that not all master courses are taught and some are research based, so I am wondering whether it's normal to do a research Msc (as opposed to a taught one) and if so, are there any advantages to this over just going for a PhD?

Advantages of doing a research-based Masters (e.g an MRes) before the PhD:

learn research skills
explore your subject
refine your research question
get a big chunk of your literature review done in a structured setting
work out if taking a PhD is really for you - whether you've got the aptitude and the interest


Short-listed, but no interview invitation after three weeks - should I follow up? Applied for a faculty position and was notified three weeks ago that the Faculty Search Committee has placed my name on the short-list of applicants to be reviewed by all faculty in the department. I was also notified that if I am still interested in this position, I may be contacted within the next few weeks to be invited for an interview. However, three weeks have passed, I have not got any updated message. References were submitted by my referees at the time I submitted the application. Should I be more patient or just contact them by sending a follow-up email? Not sure what has happened. They lost interest to me or just act too slowly?

Congratulations on making the short list! There is no way to tell from the outside what the school is doing, but there is also little that you can do to change it at this point.

If the school's answer would change something for you in the short term - for example, if you have another job offer and want to know if the school is still considering you - then it would be very appropriate to send them an email.

If you are just emailing them to check on the status of your application, I would wait a few more weeks to see if you hear anything from them. This part of the application process is often a waiting game, unfortunately.  On the other hand, I think that a very polite, short message would not be likely to harm your application, particularly if you let them know that you are still very interested in their department.


Websites to publish for mathematics and statistics similar to arXiv.org? What are websites similar to arXiv where there's feedback that one can submit to for Mathematics and Statistics?

I don't know about statistics, but in mathematics it isn't common practice to post preprints to any website, which has any sort of feedback or commenting mechanism on the site itself. Such sites might exist, but they aren't in common use.


How will Phd guides treat students who are pursuing PHD under scholarships other than institute one? Okay. SO here is the thing.

I got national overseas scholarship from my government. The scholarship almost covers everything. My question is how will professors view those who are admitted under scholarships, other than institute scholarship?

I heard that PHD guides always prefer to spend more time with those who are admitted under institute scholarship, cause there is always a pressure from institution to professors about the scheduled time.

In my case, my scholarship covers stipend for 4 years and the pressure is on me to finish it in 4 years.  Will I be given the same importance by professors?

The answer is based on my experience as faculty at a UK university (engineering).

Officially: There is no discrimination between institute or externally funded PhD students (either from the UK or their home country). There are strict rules and a logging and management system that ensures all students get the same number of guaranteed supervision hours.

Reality: Our school management actually is biased to support more students with international scholarships. The reason is that they bring a lot of money into the school directly through the huge amount of fees their scholarship pays.

Other info: Supervisors (incl. myself) tend to bias towards stronger students in the long-term (no matter their scholarship). When a student generates a lot of results and writes many high-quality papers, then I am inclined to support the student more than the minimum required (review papers, have more meetings, work more closely, etc.).

The first 1-1.5 year I support weaker students slightly more than the “guaranteed” to give them a chance to catch up. If a student is weak after the first 1-1.5 year, then I tend to provide them with the minimum required supervision while spending more time with the stronger students.

The reasoning is that spending 100 hours extra with a strong student might lead to 3 strong journal publications while with a weak student 100 hours extra might lead to an average journal at best. Since my progression is heavily based on academic track record, it’s natural to bias towards the most beneficial use of my time. Note that these are extra hours in addition to the “guaranteed” by the regulations supervision.


Name writer by surname when citing Normally when writing technical reports, I just cite an article something like this:

  In the case of binary classifications, the softmax activation function
  is not efficient [1].

But if something is so crucial for a large part of the entire report, it feels like I should mention the surname of the author who contributed greatly in the area I'm writing about. So, should I do this? If so, how do I write that an entire section is based on a book (actually a PhD thesis) written by some person?

Would it be correct to write like this:

  Based on X [1], this section describes...,

where X is the surname of the author.

Or does it need to be written more clearly, like this:

  Based on the PhD thesis by X [1], ...

You can mention the name, and then reference the thesis.

I would write something like...

  Anderson [1] describes blah blah

Or something like that. But you don't have to mention the name so much as the concept or evidence, for example...

  Incentive salience explains a system of hedonic processing which draws  attention to rewarding stimuli based upon...etc [1]

*Incentive salience is theory developed by Robinson and Berridge, and is crucial to understanding hedonic processing. But I don't personally always refer to authors surnames in text. Appropriate citation to the references is more important. The writing style is up to you, but if you which to refer to a specific section you can add the page to the main text i.e.

  Chapter 4 of Morpheus's thesis found the Matrix to be all around us [1,
  p.15].

I wouldn't personally write like this, but it is acceptable for an undergraduate project, and as a comment on my answer mentioned, some people prefer reading the reference name.

Please see the linked pdf for some rules regarding referencing in the IEEE style. I also found this answer on the writers stack regarding IEEE referencing of thesis material, which could be of some use.

Robinson, T. E., & Berridge, K. C. (2008). The incentive sensitization theory of addiction: some current issues. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1507), 3137–3146. http://doi.org/10.1098/rstb.2008.0093


Acknowledging the discussion with someone in the paper but excluding this person as a reviewer: how to do this? While writing a paper I discussed its first draft with a certain colleague (he is from a different university, so it is not likely that he will be automatically ruled out as a reviewer as suggested in the Visoft's answer). He made a few helpful suggestions but by and large didn't like the paper: he would like the results to be compared with the ones one could obtain using his favorite method -- but this is a separate piece of hard work, and his favorite method is, to put it mildly, far from being universally recognized by the community of experts in the field.

I would like to acknowledge his helpful suggestions in the paper but at the same time I would like to rule him out as a possible reviewer (some journals give you an opportunity to let them know whom the paper should NOT be sent for review).

QUESTION: How should one word the acknowledgment of this colleague's helpful suggestions in the paper in a way compatible with excluding him as a possible reviewer, so that the editor who will handle the paper does not get confused by the whole situation and honors my request to exclude this person from the list of possible reviewers?

Also, which is the best way to state the reason for excluding this person from the list of reviewers (conflict of interests, or something else)?

Thanks in advance.

First of all, I assume that you do not mean "colleague" in the narrow sense of someone at your institution?  That would make a (nearly?) universally inappropriate choice of reviewer, right?

Regarding your question: I must admit that I don't have much direct experience with "suggested excluded reviewers".  I am almost never asked that question on papers I submit; I think I might have done so once: when I did it, the idea was to help out the editors by pointing to someone that they might have thought had a lot of directly relevant expertise but that I knew would not actually be so interested in reviewing the work in question.  The point is that I interpreted this as a (ever so slightly pathetic, I might add: I think this occurred at, by far, the lowest quality journal I have ever submitted to) request from the editors for me to help them out in finding a good person for the job, not excluding potential reviewers for "conflict of interest" reasons.

Because of this I am not totally clear on what constitutes a "conflict of interest" for a reviewer: in doing any referee work one volunteers to give one's professional opinion.  I don't have any "academic enemies", but moreover I once recommended for rejection a paper by one of my closest friends: and it was a very good paper; I just thought that it was not good enough for the journal to which it was submitted.  (Because I knew the person I also felt that he could get a better publication by working on it a little longer, and in fact that is what happened: about a year later he published a magnificent paper in a higher quality journal.)  Oh, back to you: is it clear that your colleague would actually be an inappropriate referee for the paper?  Were his opinions about doing the alternate method actually fully professional opinions, or is that just his more personal reaction to the paper, reading it in terms of his own interests?  Moreover, does his alternate perspective really lack validity in some sense?  If so, then wouldn't a good editor not choose him anyway?

To summarize the above: it is not clear to me that "X already read my paper, and he didn't like it so much" is a sufficient reason to exclude X as a potential referee.  You wonder what the language of exclusion should be, and I agree: you'll have to work a little harder to paint this as a conflict of interest: I'm not seeing that.

But okay, now a direct answer: well, they asked you if there's anyone you'd like to exclude, so it's really up to them to evaluate the reasons.  If you don't want this person to review your paper I would say so using exactly the reasons you've told us: then it is up to the editors to decide whether to grant your request.

Let me give one other piece of advice which may seem a little shady at first but which I claim is mostly practical:

  Consider not acknowledging your colleague in the first version of the paper you submit, knowing that you will put this acknowledgment back in the published version.

Concerning this, let me first say that you cannot do it if his contributions were beyond a certain point: it would then simply be academic dishonesty.  But many acknowledgments are subjective largesse: you have not just won an Academy Award, so you don't thank every single person that helped you.

Anyway, the reason why I recommend this if it is possible is to short-circuit the dopey editorial practice -- which I have seen happen several times -- that the editors send a paper to a certain reviewer because she is explicitly acknowledged.  What a frustratingly lazy practice this is.

The editors who ask the author's opinion on referees tend (in my direct experience) to be lazy types, who just might choose someone in the acknowledgments...and might do so thinking they are doing you a favor!  So the idea of delaying the acknowledgment to forestall a bad editorial choice seems ethically defensible to me.  Finally, if the editors are asking for the author's opinion perhaps they will also ask you for especially plausible referees?  If so you should think hard and suggest really good choices: i.e., the most qualified people, not necessarily the ones who would like your paper the best.

Added: After airing out my advice to unacknowledge your former collaborator X, I am having trouble standing by it.  Based on what you say there is a good chance that X actually would be the referee, and if he can then see that your paper has been modified according to his advice but that you have not mentioned him, then it is possible that he might be personally hurt by it and that this might come out in the referee report.  I think the "unacknowledgment" suggested above is only feasible if the version of the paper you're submitting does not bear any mark of X's helpful suggestions.  As I said, whether X is an appropriate referee for your paper really is up to the editors to decide.  You can help them out by giving them all the appropriate information.  Doing much more than that could be ethically problematic...

Added: Upon further reflection I can only clearly remember the practice of being asked to referee a paper in which I was acknowledged happening once.  I'm sorry for the inaccuracy.  However that one time was from a leading journal, and I made sure to ask whether the editor was aware that I had been acknowledged in the paper, and he was.


Why do others have these highly specialised research topics and I don't? I have some time now to think about what I want to write for my dissertation, but I just don’t know how to find an appropriate topic. I like what I do and I could do a lot.

Some people seem to have really interesting and specialized interests and topics for their dissertations. And although I am really into what I study, I just always feel like I haven’t got this amazing topic that hasn't been researched yet or that I could contribute something to. And I feel like I don't want to specialize just yet. I want to know more. But I already have a Masters. What went wrong there?

I basically feel like I have to make something up as it were, or even choose something at random (from within my general interests, of course). This being said, I will probably like it and do well. But is this just me? Does anyone ever feel like this? What would you do if you had all the time in the world (I do at the moment) to find a good research topic?

Professors usually love to find PhD students in search of topics, since they tend to have ideas that they hope someone will work on.  Even students who come with a defined idea often find advisors nudging them in a different direction than what they really wanted to do.

Talk to some professors that you think would be good people to work with as your PhD advisor, and see what thoughts they have on this.


Can novel findings be submitted rather than a novel methodology? Basically, my research was not into a particularly new methodology, but we have combined several existing methods to prove a result which has not been seen before under certain circumstances (rebalanced dataset, etc). Would this be an acceptable submission to a conference or journal, or should I go in a different direction and look for something unique?

For reference, this is in the field of machine learning / network security.

The point of a methodology is to be able to produce interesting and significant results. If you've managed to apply some combination of existing methodologies to discover something interesting and new, then that discovery is likely publishable.

What is not clear, however, is whether a community of researchers who are focused on making new methodologies will be interested. Thus, you might not be able to publish in the particular machine learning community that you are interested in. Instead, I would suggest:

Look for "applications" journals, conferences, or tracks associated with the machine learning community.  Many "tool" communities have these associated: for example, in the general AI world, the core conference AAAI is always co-located with the much smaller but still high-significance IAAI applications meeting.
Embrace the application community (it sounds like network security in this case), and publish your results there. They will be less interested in the methodologies and more in what you have done with them.


Is there any research on applying Agile/Extreme/Lean methods in academic research? I've been enjoying quite a lot of literature, all published within the last ten years, on how to handle projects, ideas, development, thinking, and so in with processes like Extreme, Agile, or Lean.  I have searched for similar literature on academic research and projects, but I couldn't find anything modern and relevant that links various parts of the research process, such as project management, hardware/software/experiment development, or refactoring of collaborative writing.

Are there any recent publications about applying these methods to academic research?

The paper Adapting Scrum to Managing a Research Group by Michael Hicks and Jeffrey S. Foster, describes the experiences of adapting Scrum to running a research group.

For those who don't know about Scrum, wikipedia has the following:

  Scrum is an iterative and incremental Agile software development
  framework for managing software projects and product or application
  development. Its focus is on "a flexible, holistic product development
  strategy where a development team works as a unit to reach a common
  goal" as opposed to a "traditional, sequential approach". Scrum
  enables the creation of self-organizing teams by encouraging
  co-location of all team members, and verbal communication among all
  team members and disciplines in the project.

  A key principle of Scrum is its recognition that during a project the
  customers can change their minds about what they want and need (often
  called requirements churn), and that unpredicted challenges cannot be
  easily addressed in a traditional predictive or planned manner. As
  such, Scrum adopts an empirical approach—accepting that the problem
  cannot be fully understood or defined, focusing instead on maximizing
  the team's ability to deliver quickly and respond to emerging
  requirements.

Scrum is built around the idea of a sprint, a short burst of activity. Again, from wikipedia:

  A sprint (or iteration) is the basic unit of development in Scrum. The
  sprint is a "timeboxed" effort; that is, it is restricted to a
  specific duration. The duration is fixed in advance for each
  sprint and is normally between one week and one month, although two
  weeks is typical.

  Each sprint is started by a planning meeting, where the tasks for the
  sprint are identified and an estimated commitment for the sprint goal
  is made, and ended by a sprint review-and-retrospective meeting,
  where the progress is reviewed and lessons for the next sprint are
  identified.

  Scrum emphasizes working product at the end of the Sprint that is
  really "done"; in the case of software, this means a system that is
  integrated, fully tested, end-user documented, and potentially
  shippable.

The emphasis is thus on highly dynamic, short cycles of work, and interaction between the team
members and the customer to get the right product delivered by rapidly ensuring that the development team is on target.

Now, returning to the paper: it  advocates 2 or 3 short meeting per week with the entire research group, rather than infrequent meetings between supervisors and PhD students. In these meetings goals, progress and achievements are reported on frequently. One outcome is that it helped quickly identify when a student was off-track, unmotivated or stuck.

I used the technique for my research group for a while. It was good for the various members to learn about what the others were doing, but as everyone was doing quite different things, in the end it didn't create any synergies I'd hoped for. Now that I am in a different institution and the new research group works on topics that are closer together, I think it could work, but we've decided to use a different approach to our research meetings.


Why don't some encyclopedias have references? Encyclopedia Britannica doesn't have references for its articles, even though some contain bibliographies for general reading at the end. This may be to save space and for a smoother reading experience, but isn't this against the grain of academic conduct, since we can't easily verify the articles' assertions or pursue primary sources? Why is this allowed and accepted?

Why is this allowed and accepted?

In short, because Encyclopædia Britannica is independently published and can make its own rules. If they want to publish an encyclopedia with no references, they're free to do so. And there's clearly demand for it, since it's one of the most popular and respected encyclopedias in the world.

Since an encyclopedia is a tertiary source, there would indeed be a great deal of merit in citing its assertions, a model used by other encyclopedias (like Wikipedia). But its general audience probably care little and the publishers don't see it as worth the effort of obtaining, formatting, and maintaining reference lists that very few readers will ever use.

Britannica makes a big deal of its contributors' impressive credentials, and expects you to trust their word as experts in their fields. Since the majority of the encyclopedia's content is likely to be uncontroversial common knowledge within the relevant field—and a great deal of the knowledge therein likely predates the formal system of publication and dissemination of research in an easily citeable format—they think that's enough.

If you disagree (which is an entirely reasonable stance), read a different encyclopedia, or start your own.


Article: Author information when occupation has changed I'm currently the main author of a paper. The work was performed when I was working at university X. However, I will start at a new university Y in one month, and the conference I'm presenting the work at is in two months. So, while presenting the paper I will be working at university Y (but the work was performed during my time at university X).

My question is the following, how would you present the author information:

A)

Both universities in the main information.

First name, Lastname (1, 2)

(1) University X
email@university_X.com

(2) University Y
email@university_Y.com

B)

Name and previous affiliation (where the work was completed) as the main information and the current affiliation in a footnote.

First name, Lastname
(Footnote: 'Currently working at University Y, email@university_Y.com')
University X
email@university_X.com

or C)

Name and current affiliation as the main information and the previous affiliation (where the work was completed) in a footnote.

First name, Lastname
(Footnote: 'Work completed at University X, email@university_X.com')
University Y,
email@university_Y.com

Or do you have any other suggestions?

This may be specific to journal, research area, whatnot. However, in a recent edition of Applied Physics Letters one finds in the author list:

The "2" corresponds to an institute in the affiliations list (other authors have other affiliations) where the author was at during the work.

The "a)" links to:

Followed by the new address for that person.

Other uses for footnotes include email addresses and apportioning credit.

This is how it was done some 25 years ago when I last changed institutions.


How do I describe my "academic profile" for graduate school application? I am filling McGill's Area of Research and Applicant Profile Form for admission to the Electrical Engineering M.Eng. program. I'm not sure how I should answer this:

"Academic Profile: Describe your academic profile, highlighting particular achievements and relevant scholarships or awards."

My scholarships and awards take up about 0.15 of the space provided, and I can't think of a particular achievement. Can I use this space to describe the projects I completed, the software I learned and particular skills I learned through coursework and special topics that were covered? I don't get to upload a CV for this application, and I was hoping I could mention these in this space. However I'm not sure if it would be appropriate.

Projects completed are more important than skills learned from coursework. Give preference to what distinguishes you from every other student. If you did an internship, mention that. If you worked on a project at a university department, mention that. If you did a Bachelor's Thesis, write about what you did there.

Saying something like "I learned about LTI systems in course X and I acquired MATLAB programming skills in course Y" will not distinguish you from every other Electrical Engineering student, so those statements should have the last priority.


Advice? One of my PhD supervisors is insisting on involvement with my article based off my Masters thesis. I'm a bioarchaeologist working on my PhD research in a field that incorporates biochemistry (stable isotope analysis) and bioarchaeology/anthropology. I have submitted my first peer-reviewed article based on my Masters thesis and am currently going through the revisions process. I casually mentioned this to my boss, who also happens to be one of my PhD supervisors, and he immediately asked to read the article and insisted that he wants to edit the stable isotope sections (he's a geochemist). I demurred, because the situation doesn't sit right with me, for several reasons:

First, he has absolutely nothing to do this article, as it is based on my Masters thesis research, which was done under a different supervisor and in a different country. Second, I'm not sure as to what his motives are. Does he simply want to help, or does he want co-authorship? I would rather not make him co-author, as, again, he has no business with my Masters research. Third, he's pushy. I have clearly stated that I am a bioarchaeologist/anthropologist who uses biochemical/geochemical methods (stable isotope analysis), not the other way around, yet he is still trying to push me towards geology. I also do not like this. But, because there is no other place in the country to do my research, I am here only for that reason.

Does anyone have some advice? Am I overreacting, or am I right in feeling that he's out of bounds?

Thanks!

The standard answer to all questions from graduate students applies here as well: Talk to your adviser. Have a frank conversation in which you bring up your concerns, have him explain to you why he wants to help, and then -- between reasonable adults -- come to a conclusion of the issue.

You can speculate all day long about his reasons and maybe he about yours. But grown-ups can have a professional conversation that resolves these issues to everyone's satisfaction.


What the benefits of summer school when working on masters degree? I have recently started my graduate studies and I am still new to some of it. I always worked in the summer during my undergrad, but I've heard that working in the summer while working on  a masters isn't what I am supposed to do. I can believe this, but I am confused. What are the benefits to taking a few classes in the summer? I don't need to retake anything because I failed or need the requirement, because I am just starting out. I need some advice on this.

The trouble with "what you're supposed to do" is that it often applies to some imaginary archetypal student or, worse, students of a very specific class and privilege. Not all students have the means to go without working, to help pay their own way through school. Academia is just starting to wake up to this fact, thanks to the consciousness raising of folks like Sarah Kendzior.

If you can find a part-job related to your field of study, then it's definitely OK for you to work over summer break. I was able to do this while in my MLS program.

If you are unable to find work related to your field of study--and if you aren't involved in student organizations or showing that you're otherwise productive in your "non-school" hours by starting to attend conferences, write papers, etc--then I could see it being a drawback to have a job in your "off" time.


What is the name for "section topics" printed in the margins In older publications of many languages, there are frequently printed text in the margins that detail the topic of a section of the text (see below on the left and right):
Excerpt from Magnum Oecumenicum Constantiense Concilium:

What is the name for these? I considered marginalia, but they are not handwritten.

Although many marginal notes are made by hand, the term marginalia is also often used for printed ones. There is even a book about "printed marginalia". A definition of marginalia given here states

The term "marginalia" generally refers to handwritten or printed text situated at the borders of the page.

Depending on the textual content, words like gloss, annotation or side note can also apply (although the latter also has a more metaphorical meaning).


Effective ways of organising one's time during a sabbatical I am about to take a sabbatical period of 6 months. I have planned it with a series of short visits to oversea colleagues (my department does not provide a lot of financial support), but most of my time will be spent in my home country.

The plan is:

to work/submit 4 major journal publications, and
to write a proposal for a local funding agency

This means that I will be mostly on my own, tinkering and pondering and less of a morning routine to go to work.

That scares me: having built a routine throughout all these years in academia, then suddenly spending a lot of time at home, or at the library, risk to become monotonous and ineffective.

What are effective ways of organising one's time during a sabbatical?

I work remotely as an academic editor and writer, and have done so for 5 years. The transition from full-time employment to part-time remote work was interesting. I tended to work all the time without leaving much room for self care. What we do in our jobs, we tend to do when our boundaries are relaxed.

I often have large blocks of free time. My productivity suffers (I have personal writing and creative projects) when I don't organize myself well. After years of fine tuning, I have a system that works well for me.

I discovered and addressed three issues:

I am effective for only about 5 hours a day. Anything more and the quality and efficiency of my work suffers; moreover, my physical and mental well-being declines. Accordingly, I work 2.5 hours (with a 5 min break) then take a large chunk of time to play; then I work 2.5 more hours (with a 5 minute break). I find that during play time, I often have creative insights.
Unless I schedule in fitness, fun, and socializing I am likely to waste my time with unhealthy (Netflix) activity. In your case, you might spend your whole time writing 4 articles! That is quite a hefty commitment and your sabbatical time likely should include time for pondering life's meaning and reading the stack of books that is piling up.
Get up when the sun rises and go to bed soon after it sets. I've done all combinations of working all night, playing all night and everything in between. I feel the best when I follow the sun. When I was in Orkney the nights were 4.5 hours long and it was enough sleep for me though I usually sleep 7-8 hours a night. I don't understand it, but there it is.

Although there are many options the productivity tool I found most effective is bullet journaling. It is simple and quick and there's no software involved (although you could buy some if you want to). I create a daily plan bar https://bulletjournal.com/blogs/bulletjournalist/daily-plan-bar

and I also have a weekly plan
https://bulletjournal.com/blogs/bulletjournalist/top-5-bujo-ideas-in-2016

And I never beat myself up for varying from the plan if something more enjoyable arises.

Have a great 6 months.


Can I send an email to the journal editorial board explaining a specific situation about the status of my paper? I submitted a paper to an Elsevier journal, and the status is "Submitted to Journal". That was a week and a half ago. I know it's not a long time, but I have an additional issue. I just need the article to be "under review" to defend my doctoral thesis. Can I send an email to the editorial board explaining this situation? Would it be wrong to do that?

Pragmatically speaking, you have nothing to lose! I don't think it's wrong, either, as your situation seems unusual. So the clear advice would be to send the email.

However, to maximize the chance that this is effective, I do think you should be clear that this is an extraordinary request. Don't expect or demand that they will be able to grant it, and be sure to thank them for taking the time to consider your email. If you are polite and to the point about what you need, I don't see how anyone could take it wrongly, but there could be some logistical, technical, or policy reason why changing the review status is not possible.


If wanting to read non-English references, then are there translators that work well for science papers? I've found interesting sounding reference written in Czech.
If wanting to read non-English references, then are there translators that work well for science papers?

Based on getting things like google translate to translate technical terms, I have to go with NO.
Works fine for simple language but technical language is a different game.
Even people who claim to be bi-lingual cannot translate technical information. I had this argument once and gave a lady who claimed she could translate anything a paper on stresses and buckling in 3 dimensions which proved she could not. :)
I have done some work translating a paper or two between 2 languages and it is challenging even for an engineer who understands the concepts to make sure what is stated is what is meant.


Approaching lab head about getting my name last on paper In my field, computational condensed-matter physics, the last author name in a paper is regarded as having a supervisory role. I know this is common to many fields but not all (notably, math).

I am a postdoc associated to a professor's group. By "associated" I mean that I have my own project and funding, on which I am officially and practically the PI. However, I am also carrying out supervisory work of a student in the professor's group, paid from a project on which the professor is the PI. Incidentally, I designed and wrote a large portion (circa 50%) of the proposal for that project, but I have no official attachment to it. Since the project kicked off, I have been redesigning the scope and methods of the project as we progressed through it, and the student is working basically on testing my ideas under my guidance. The professor knows about the main features of what we do but is not familiar with any of the details nor is proposing/contributing significantly to either science or supervision.

Everybody is more or less happy with the arrangement, since the professor sees progress, with minimal cost of his time and effort, on this research area of interest in which he can contribute little due to his lack of background on computational physics. I get some extra manpower to extend my ability to test some of my ideas, and the student gets supervised by someone who can provide expert guidance on the topic of this PhD thesis. The professor is easy going and everybody is in good terms with each other.

However, I am starting to apply for senior positions. In one of my applications, I was rejected mainly on the basis of being too junior, and a piece of critical feedback was on my lack of "last author papers". It had been agreed with the professor that I would be last author in some of the student's first authored papers (actually, he suggested that). However, in a recent manuscript draft where the student put my name last the professor corrected the author list and put his name last instead. This could be because he forgot about the agreement or (I suspect this one) he realized the paper was much more significant than originally expected and wanted to get some "extra" credit for it. This credit is needed for him to increase his chances at future funding in this research direction. However, I feel that this undermines my contribution and does not accurately reflect the role that each author had on the study, since I designed the project, proposed the ideas, did the actual supervision, and even contributed to getting the funding (and thus, the convention in my field dictates that my name should go last). Further to this, I desperately need to get this credit to just stay "afloat" in academia (whereas the professor "only" needs it to increase his funding pool).

I think it is only fair to work out a list of authors that more accurately and fairly reflects my contribution to our upcoming papers. However, I want to avoid falling off with this professor or introducing undue strain into our working relationship. How should I approach a request for my name to appear as last author in subsequent papers?


What is the best way of keeping track of academic readings and persons? I have started a brand new research from start of the year. I would like to know what are the easiest way of keeping track of the academic papers, journals and authors.

I use sites like Google Scholar, informatik.uni-trier.de for discovery of articles and following interesting conferences and people. I have used sites and tools like Mendeley and ResearchGate. I quite like the sites, but I am too reluctant to use them as for each of them I need to find everything by myself, create my own library to suit my interests.

I already got a warning by the stackexchange system saying The question you're asking appears subjective and is likely to be closed. but it would be great help if someone could explain some tools/software which do this?

Summarizing my questions:

How do you keep track of academic papers, authors effectively?
Are there any tools that can search/scrap the internet by some
keywords/name and keep track of them? [I know of
Google alerts, what
I seek is some kind of tool with a management interface]

Although you are aware of this already, I feel I need to state how satisfied I am with mostly using google scholar + a feed reader + a bibliography manager for this. Although it is not integrated, I don't currently feel any need to search for a better all in one platform.

I use google reader to subscribe to RSS feeds for online first and published articles for journals I am interested in (any reader which you can organize feeds into folders and search should be fine - I suspect many have better search capabilities that google reader). The vast majority of journals this is not much of a time suck to read all the titles and peruse abstracts I am interested in. The most prodiguous publications (e.g. Science/Nature) are only borderline annoying with 60+ posts a week, but even that is not that difficult to quickly navigate through.

I have a few fairly specific google scholar alerts (as well as general google alerts), so as to not get too much in my inbox. I basically have a few key words in articles specific to my research interest, and I have alerts for specific authors. I also have alerts to people who cite my articles.

I use CiteULike to manage my bibliography + personal database on my local machine to export various formats (e.g. bibtex or specific citation format). This has the added benefit that I can send articles directly from google reader to citeulike, but I suspect the same set-up could be crafted for other bibliography managers (Zotero, Mendeley) and possible other feed readers.

Basically in a nut-shell,

feed reader to stay up to date with newly published articles in journals I am interested in,
google scholar alerts for potentially related material that isn't in those journals, and
a bibliography manager to store articles to read later on.


Where to correct an inefficiency of algorithm in a published paper? I spotted a serious inefficiency in our algorithm, which was already published. Basically, we have an algorithm to encode a problem A into a formula X. But we later found that we can encode into a formula X', which is equisatisfiable, but with much less (up to thousand) of variables.

This change is very trivial in logic, if we need to correct the algorithm, we only need to change 1 line with one subscript. But it improve the performance drastically, up to 10 times in some instances.

If somebody build on our work, I don't want them to make the same mistake. If somebody want to compare with our work, I want them to compare with the improved algorithm, not the result we reported in the paper.

But the change is so trivial, how could I let everybody know?

The change only appears trivial to you now that you know about it.

Moreover, while the change may be simple, the validation of that change is not: I'm sure there's lots of experiments to run to verify your statement, and maybe some new analyses to be performed as well.

To me, this sounds like a fine opportunity for a followup.  If your paper was published in a conference, then the improved version can go into the "extended version" journal paper.  If your paper was already published in a journal, this is a good time to follow up with a short conference paper.  If you're in a field that doesn't like conferences, there will probably be journals that take "short papers" or "application notes" or some similar.

Bottom line: one way or another, there should be a good place to put this not-as-trivial-as-you-think piece of work.


Publishing without a pre-defined PhD topic? I tend to believe that starting with a well defined goal is an undeniable prerequisite for publishing a quality paper on a certain topic.

Alas, can a PhD revolve around a fuzzy subject, that offers the student a lot of freedom of choice regarding what problem to solve, as long as the problem is solved using the methods in that field of study?

More explicitly, is it possible to develop a quality research paper in an applied scientific field without fixing the goal beforehand?

Your question contains two related questions

"can a PhD revolve around a fuzzy subject... as long as the problem is solved using the methods in that field of study?"
Is it possible to write and publish a quality paper without a well-defined goal?

In research, almost by definition you do not know what you are going to find. (See the answers to this question.) If you did, it wouldn't be research! So it is definitely possible to have your PhD 'revolve around' a fuzzy subject. But when it comes to writing the actual paper, you will need a well-defined goal for the paper. The paper may not, and probably will not, cover the entire scope of your research. So although your research goal may be nebulous--at least in the beginning--when you are writing a paper to report the findings of said research, you should be able to very clearly articulate  the purpose of this specific paper.


Am I allowed to give a gift to a fellow student for helping me in a very direct way? Due to the COVID situation our lab course only allows one of two students in a partnership to run an experiment during a session while the other observes via Zoom. I can't make it to the next session so I asked my lab partner to go. It turns out that my lab partner is dropping the course and going to run the experiment anyway presumably just to help me out.
I just met the guy and that's such a kind gesture that I want to show him my gratitude by mailing him a gift card or something. My concern, however, is that this might be dangerously close to paying someone to do my schoolwork. Is it potentially against university policy to show my gratitude with a gift?
Edit: We're in the United States.

A low-value gift card doesn't adequately compensate the work, so there's no perception of paying someone to do [your] schoolwork. (I can't comment on whether it is against your university's policies, that's off-topic here anyhow.)


What should one do if they've discovered a "breakthrough" but lack academia credentials? Let's assume someone has a very thorough knowledge of a particular field of science but they have absolutely no formal education in this background.

This individual one day realizes a very novel approach to solving a somewhat complex problem.  After developing independent tests and coming up with rock-solid evidence that her method is groundbreaking, and consistently produces test results that would be impossible without a legitimate solution, what can she do with her research to both share the information with the world and retain some form of credit for the discovery?

In other words, how can one be both a hobbyist contributing to a field of scientific study and yet also retain the respect they deserve for their work if it is of great use and benefit?

To be clear, this isn't about having one's name appear in a Science Journal without the necessary credentials.  I think it's respectable to maintain certain sets of rules and standards for journalistic publications.  However, it also isn't fair for such a person to have to divulge this information to someone who is "qualified" and have them receive all or most of the credit for someone elses work, just because that other person hasn't earned a piece of paper.

How can hobbyist both share, and maintain, the recognition they deserve if they make a legitimate scientific breakthrough?

I see a few approaches you could take (or some combination):

Write up the idea as a white paper and submit to http://arxiv.org (or something similar). This gets the idea documented, public, timestamped, and allows people to easily cite it.
Reach out to researchers in the field to see if they would be willing to help you form a scientific paper based on your idea. Not all professors are scary!
Submit to the industry track of a research conference if you have an industry background (if not, then maybe a workshop). Some conferences elicit papers from industry that can get your idea out there, generate discussion, and allows you to get feedback. These tracks are often less competitive and very open to non-researchers. For example, Software Engineering In Practice at the International Conference on Software Engineering


At a conference, should I visit other people's posters during my poster session? Usually, conferences give you between 1-2 hours to present your poster. My dilemma is that sometimes I am interested in learning about other posters during that time period. But I also have to keep next to my poster in case a referee or a potential collaborator of the conference comes and wants to learn about my topic.

So my question is what should I do? Should I stay next to my poster and try to talk to the other poster attendees afterward or should I visit their poster and risk missing out on potential important visitors to my poster?

It depends on the venue. In a small room, you can easily wander around and get back to your poster quickly if you spot someone interested. In a huge conference hall, if you abandon your poster you may never know who visited it and when.

So, if you have a large venue, ask yourself, what is your priority: to get your work out and have a chance of presenting yourself, or to check out what others are doing. Both are valid options, and both are important. It's your call how to balance them.


Taking a course on Pass / No Pass Basis for Grad School For a PhD application: assuming a student has a good technical GPA (whatever that means from your point of view) and took some challenging technical classes and some grad courses; what would you think if he has taking some "challenging" courses for unrelated topics on Pass/Not Pass basis. My university lets me take one third of my whole units for P/NP basis. For example, as a math major, what if instead of taking easy humanity courses, I take hard humanity courses; but not for letter grade. How would this affect a grad school application?

I have been to Ph.D. admissions committees both as a grad student and as a faculty member. Generally speaking, if those courses are not very relevant to your major and your intended area of research, I wouldn't pay much attention to "Pass" grades (whereas low letter grades would probably stand out) We get plenty of domestic and foreign applicants with very diverse backgrounds and there are much more important things to look at in their application package.

I assume that the genesis of your position is that you want to be challenged in class, but not at the expense of risking a bad grade staining your otherwise impressive transcript in a subject that probably won't define your career. While this is certainly not the only approach, it seems sound thinking to me.

If they do affect your GPA in a negative way, however, I would consider a bit more carefully--perhaps not in a binary way, but in regards to how many courses to do this with.

By the way, remember that as a Ph.D. student you can also take courses outside your major you feel curious about. I certainly did that.


Do you let Google Scholar index popular science articles, conference abstracts, etc.? I enjoy that Google finds things I've written that I would never bother to link on my own web page, just because it's nice to have all my writing collected somewhere given I've made the effort.  But given that academics often assess each other from Google Scholar, I'm worried that my "year" index is getting cluttered and makes it look like no one cites my recent work.  Of course, some people allow Google to automatically list discovered works and have their indices full of articles that aren't even theirs, but that's obviously unimpressive.

If you are the kind of person that clicks "year" on Google Scholar to see what an academic does lately, and you were checking the Scholar page of someone you were thinking of hiring, funding, or working with, would you be put off by fluffy articles like book reviews, conference abstracts, and popular science mixed with good ones?

Personally, I think that it is important to let one's Google Scholar index all of one's work.

When I am assessing a colleague, I will often exclusively use their Google Scholar page, since every other search method I am currently aware of is either a) badly cluttered with not-their-work or b) tends to leave out significant "non-traditional" works such as white-papers, standards documents, workshops, and books.  I use both the "Cited By" and "Year" orderings, the first to see if they have made an impact and the second to see how active they currently are.

When I see a lot of recent publications, I do not expect them to be much cited, particularly given potentially long publication delays and the fact that most scientific work draws little citation, even if it is good.  Many publications, after all, are "bridging steps" that are important for building the foundations of high-impact publications but which may not be of interest outside of a very narrow group indeed.

What I would expect to see in a highly active researcher, then, is a couple of recent "hits" and a lot of recent publications with minimal citation.  If, in fact, I saw a person who seemed to only have "hits" in their Google Scholar record, then I would find it very curious and think they might be engaging in strategic non-publication.

Obviously, I apply these standards to myself as well.  Even if somebody can't be bothered to scroll down far enough to get to last year, they're at least likely to notice the recent citation statistics bar chart.  Bottom line: I think that it is a good tradeoff to risk giving a mis-impression those few excessively careless readers in favor of giving a better impression to the more careful ones who are likely to actually be interested in the full list.


What are the chances for a scholarship winner to be denied admission at Uni? If a student wins a scholarship (like the german DAAD scholarship, for example), does his chance for admission at an University to pursue a Masters degree increase?

Let's say he fulfilled all of the requirements for admission. On top of that, he won a scholarship that fully funds his studies. Would he be given advantage over other candidates that applied for the same MSc program?

It very much depends on the admissions system. If the system is based (almost) strictly on grades (the way the German system largely is determined), then having a scholarship doesn't help with admissions. This is also the case if there are minimal tuition and registration fees associated with admission.

In the US, though, funding is a much more important issue in admissions. Students with their own funding source definitely have an advantage over other students of comparable quality, since they cost less money, and thereby can be admitted when other students can't. However, a student who has a scholarship but might not be a good fit for the department might not be admitted.


Is having a specialised PhD topic a pitfall when applying to be a lecturer of STEM education, even with relevant practical experience? This is in a similar vein as What are the potential pitfalls of having a PhD, but where that was specifically targeted as entering industry, this is targeted at becoming a lecturer of STEM education (effectively a 'teacher-trainer').

Is having a specialised PhD topic a pitfall when applying to be a lecturer of STEM education?

To give an actual example*, I have completed a PhD in atmospheric physics (with a bit of programming thrown in) and 14 year high school teaching experience, I have applied to be a STEM Education lecturer - will that PhD be considered too specialised?

**note: this is just a real life example, not a self help question.*

Is having a specialised PhD topic a pitfall when applying to be a lecturer of STEM education? [with teaching and research duties]

I would not call it a "pitfall," per se, but rather you'll have to do some convincing that you're qualified to research in the field of education. I applied for a couple of similar positions (with somewhat similar experience and education as you, though with about half the number of years teaching high school), and the guidance I received was that I needed to demonstrate that I had a "research arc" (or research strategy) that was consistent with the research goals of the position. Having a good deal of teaching experience may have given me an edge as far as the teaching duties were concerned, but I only had one publication in the education pedagogy realm, and that (among other things, presumably) was not enough to make me competitive for the positions (i.e., I didn't get the jobs). In fact, it probably was the case that most applicants for such a position spent time teaching at the secondary level, and my experience there was a wash.

Bottom line: if you are asked to write a research statement, make sure it is highly targeted towards the position, and try to have a long-term approach to the research question or questions you discuss. Relating it back to your hard-science degree may be difficult, so leverage as much of the teaching experience you can to inform the statement.


What to do with a likely collaborator who is not answering mails? A few months ago, I contacted a person who conducted research in a topic that could easily be combined with my own work.
For this reason, I sent him an e-mail exposing my research and why it could be interesting to collaborate, taking into account his results.
He answered me and showing interest in the work (that is what I read between lines). Furthermore, he recommended me some literature.

When I read about half of the documentation, I sent him a mail with the insights I got and several of my publications, justifying my points.
He answered me again, discussing some points and glad to have my work pending to read.

I finished his readings and I sent back my impressions. He continued the discussion and excused himself because of not having read my papers.

After two months, I have no reply from him. What should be my next step towards the collaboration?

Presumably your prospective collaborator expects something more tangible than email discussions to come forward soon. So far, what you describe sounds fairly typical - material and ideas are exchanged, and papers are read (or not). However, at some point this needs to move into a more concrete direction than "discussions". That is, you are now in the phase where the pedal needs to hit the metal - somebody, presumably you, now needs to come forward with a concrete action plan or at least steps towards such an action plan.

Otherwise, if the discussions still remain on an abstract level even after multiple months and many emails being exchanged, I could understand that your collaborator fears that they may be wasting their time in this.

So the next step if you want to go forward with this would be to set up concrete next steps: arrange a planning call or even a visit, and then come up with concrete research methods and a methodology to address them. Particularly, be explicit about what you expect from the collaborator - the fact that they were not able to read your papers until now suggests they will be unable to contribute a lot of time, and it is better to clarify how they can contribute early rather than mid-way through the project.

I feel it is important to understand what the power and group dynamics are in such a collaboration. Why is everybody in the project? Who expects to get what out of it? Who is pushing / leading the project? Who has how much time to contribute, realistically?

These questions are all fairly different depending on whether you and your collaborator are students or senior academics. That is, if you as a student cold-mailed a senior professor the collaboration will ultimately have  different dynamics than if both of you are students, or both of you are similarly-senior academics.


Quotation/reference manager for print books What is an effective and efficient system for storing quotes and notes from print books to be retrieved later?

When we read books and articles in electronic format there are easy ways to mark quotes for future reference -- as discussed in the SE posts linked below. Although I read most articles on my computer or a tablet, I still prefer to read books in print format. I am looking for an efficient method for electronically storing quotes and notes from documents I am reading in print.

A brute-force method would be to read books with my computer at my side, and manually transcribe and tag all quotes I like from the book, electronically linked to the book's citation information. I'm hoping there's a better way -- this method might simply be too slow to be feasible.

There are good answers to related questions, but their discussion of quote-tagging and referencing is for electronic documents. The good SE posts out there cover:

i) Why one should use a reference manager: Should I use reference manager software?

ii) Using Sente or LaTeX+JabRef to store electronic quotes, or summaries/notes on books: Reference manager with note-taking/quote-storing capabilities

iii) using TextCite or Citavi for the same purposes: Searching for a quotation manager

A few notes before I make a suggestion: I don't usually volunteer answers unless I have a very clear, reliable workflow in mind. In this case, it's a bit more of a "workaround", and as such, it's not perfect. It's not going to work 100% of the time. But I do hope that it saves you a few minutes of typing here and there - it all adds up in the long run.

This is a modification of my workflow in undergrad, where I (regrettably) mostly just skimmed books without taking notes and had to track down quotes based on a very limited set of information.

It requires use of Chrome, a Google account, and a Doc designated for taking notes.

Here's how the workflow breaks down:

Search Google Scholar for your print material of choice.
Use the "search inside" function of Google Books to locate your particular quote. Usually just an uncommon word, phrase, or name will suffice. Be forewarned that the part of the book you're looking for will sometimes be withheld due to copyright.
If the book permits highlighting, you're good to go. Just copy the text you need. Unfortunately, it probably won't, so screen capture is your best workaround. I use Fireshot to take screenshots right within my browser without downloading them locally.
Take a screenshot using your preferred method of the paragraph or part of a paragraph that you need.
Now you have an image to work with. If you have the means, invest in an app that will do the OCR (optical character recognition) for you. That way, if you need to use the quote in your next paper, it's ready for you without having to type it all out yourself. Kami comes recommended and integrates with Google Drive, but I don't have any personal experience with it.
If you don't need OCR at the moment and just want to hold on to the quote for future reference, keep the image. You can opt to save it directly to Google Drive OR you can copy and paste it into a Google Doc from your browser.
Take notes, add context, jot down ideas, add more quotes, etc. directly in your Google Doc.

Optional

Use Paperpile to manage your citation information in Google Docs. I started using Paperpile while writing my Masters thesis and become rather enamored with it, despite never having used a reference manager before. Full disclosure: I now work for Paperpile as their Marketing & Community Manager.

From your Google Doc, you can add your own notes and context for the quote along with an in-text citation that links directly to your research library. Paperpile can pull the citation info directly from your Google Scholar search in Step 1. If you don't want to take notes in Google Docs, you can add them directly to the reference itself in the form of a note or attachment. And when you're ready to start writing your next paper, the reference is ready without any additional work on your part.


How do you and your lab use orcID? We have been asked by the powers that be to move away from Academia.edu and ResearchGate and adopt services like orcID.

https://orcid.org

The one big thing missing in orcID is that there’s nowhere to describe the lab or research team, all groups are on the faculty level only.

Do any of you have some creative work-around?

Having previously worked with ORCID and helped labs and groups add ORCID iDs to their workflows, I can share about how labs/research groups use ORCID:

As others have mentioned, ORCID iDs are to identify individuals -- they distinguish you from other researchers who may share your name. A lab or group should not obtain an ORCID iD for their singular "lab" identity as that violates the terms of use. (n.b. ORCID iDs created for what appear to be non-individuals are regularly reported to ORCID by members of the ORCID community. Check Twiter -- you'll see call outs.)

Every individual who creates an ORCID iD has an ORCID record -- a web page which lists things connected to their ORCID iD. These things can be added by the individual or by systems they grant permission to update their ORCID record, such as a journal with whom they publish or their employing institution.

Unlike Academia.edu and ResearchGate, ORCID does not allow you to store manuscripts, preprints, etc. You can however use preprint servers, zenodo, figshare, etc., connect your ORCID iD to your account in those systems, and then Crossref or DataCite will add your papers to your ORCID record.

Research labs or groups may have multiple ORCID goals:

Collecting the individual research members' ORCID iDs so the lab/group has them on record

Adding their lab/group affiliation to the research members' ORCID records -- so when the researcher submits a grant application or manuscript, the submission system will read their lab/group affiliation from the ORCID record

Using those iDs, regularly searching research information systems, such as Crossref, Dimensions, and Web of Science, for their members' works, grants, and more (only works when the members connect their ORCID iDs during submission or proofing)

Using those iDs, regularly accessing their ORCID records (programmatically) to learn of any new works, grants, research resources (facilities, labs, collections, etc.), memberships, etc. connected to their ORCID records

Physical labs with equipment, facilities, etc. used for research which have an access approval process may collect ORCID iDs during submission so they can record use of their facility as a "research resource" on researchers' ORCID records. More about this here.


PhD examiner disappeared, what I can do? I past my PhD viva with minor corrections in June. Both examiners were happy and promised to send lists of corrections the following week.

Unfortunately, only one did that (and confirmed I corrected all of his comments). The other examiner hasn't replied any emails from me and my advisor for two months until now.

This examiner is a really nice person, so I'm afraid something wrong might have happened to him. If this is the case, I will also be in a great trouble, because if I can't finish my PhD, I have to enrol again in September, i.e. next month.

I'm doing a postdoc in the US, doing enrolment again means I have to go back to my school in the UK to show my original passport and Visa etc.

My advisor told me I should not worry. But the September deadline is close, given 2 months without any responses.

My questions are:

What should I do now?
I also know prof A, who is the head of the group of this examiner. I talked to him twice in workshops, and connect with him on Facebook. It means he only knows that I'm a random student in that neighbour university. Should I ask him about my examiner?

In circumstances such as this, you should consult the faculty member or administrator in your department who is responsible for overseeing the thesis examination process for doctoral candidates.

Different departments have different ways of handling such non-responses. In some cases, they may simply say that the examiner has, through non-communication, implicitly accepted the thesis "as is." Other departments may unfortunately insist on having both examiners "sign off" on the final submission before it is accepted. My department, for instance, leans toward the first policy, in that it is the actual supervisor of the student who "accepts" the final submitted version of the thesis.

However, without talking specifically to people in your department, it is impossible to tell you what will happen here.


Will having a mediocre undergrad GPA ruin my chance getting into a PhD program I transferred from a four-year university into one of the UCs last year majoring in biological sciences. Unfortunately, my UC gpa is not as high as I wanted it to be. I used to have a 3.9 but can only get a 3.4 in UC. I am planning on applying for a biomedical PhD program this year as I am graduating next year but I am very worried about my gpa ruining my chance of getting in as PhD programs are highly competitive. I did okay on my major courses but I do have 2 B- in organic chemistry A and B, which I am really concerning about right now. With this kind of grade, will I stand a chance in the PhD application?

Mediocre grades don't help, of course, but a doctoral admissions committee will look at much more than your GPA. Many things are considered, especially the things people say about you in your letters of recommendation. Your statement of purpose, which is often required, can also be a big factor. You need to show that you are both highly qualified and a good candidate for success in the program.

So, yes, you have a chance, but the competition will also be fierce. If you want to continue in organic chemistry, or something that depends heavily on it, then you need to explain those grades, but, depending on the field you choose it might be a relatively small factor. But your record will be judged by humans, not an automaton, so many things can affect what happens.


Using figures from my thesis into publication post defence What concerns may arise if I copied figures from my approved thesis for submission of research article. This may happen to many during their final months in lab.
My thesis is submitted to the University. Shall I have copyright on my accepted thesis or my University will have? I am not sure if I need to reuse that content who will provide permission for doing so?

This is a quite common situation, so it will most likely be OK. The main points you will need to check are the following:

What copyright are you assigning your institution? The universities I have dealt with in the past all asked for a non-exclusive license, meaning you can publish all or portions of your thesis again if you want to. However, your institute's policies may differ; check your handbook or ask the administration.
Will your thesis count as a prior publication? This will depend on the venue you submit your paper to. In some places the thesis is even formally published (and has an ISBN assigned to it), which may increase the likelihood that the journal or conference will consider this work as already published. Check the venue's rules for submission and if necessary ask the editor before submitting your paper.


Is it a bad idea to mention informal PhD offers in a job application? I am about to get my master's degree and have published a few papers in highly reputable computer science journals. I have gotten an "informal offer" for a PhD position from a world-class university. An informal offer here means that a well-funded professor has e-mailed me, strongly encouraging me to apply and to make sure to mention his/her name in the application so it gets routed to him/her.

For various reasons, I'm leaning towards not pursuing a PhD so I'm currently working on my resume. I'm wondering if it's a bad idea to mention anything about this informal offer in the personal letter. The professor making the offer will not be the one writing my letters of recommendation. Verifying the claim would not be hard, but it's not really a tangible accomplishment. On the other hand, why shouldn't I highlight the fact that I could get into the best graduate program in the world if I wanted to?

tl;dr: No, you should not mention this "offer."

I wouldn't even call this an informal offer. An "informal offer" would be if you applied, and then were told by e.g. email or phone that you are admitted, and that the formal letter of admission will follow shortly. Encouragement to apply, no matter how strong, is not an offer of admission, and doesn't indicate that you would definitely get an offer of admission if you would have applied.

For example, you may sound great according to whatever information you sent to that professor, but your full application may reveal other things that lead the admissions committee to reject your application. Or maybe you really are that great and the professor has funding, but another, better, student applies that year and gets the offer instead of you.

Furthermore, individual professors have varying ability to actually influence the admissions process, depending on how graduate admissions actually works in that department.

Even for a "real" offer of admission, it wouldn't necessarily be a good idea to list it on a résumé. See for example this related question on listing fellowships that are offered, but which you decline. But being encouraged very strongly to apply to something is certainly not a CV-worthy accomplishment.