How common is it that publishers withdraw a paper due to incorrect conclusions? Today there has been significant news coverage (at least in the UK) that the BMJ are withdrawing statements from two papers on the possible harmful side effects of statins. Here are the Guardian and BBC articles on it.

This led me to wonder how common such issues are in academia in general. In this case it appears the authors made an incorrect conclusion from a study which was not picked up in peer review. I can think of lots of similar possible situations where proofs may turn out to be incorrect or other data may be wrong/not properly dealt with.

In particular I'm thinking about less popular/controversial subjects where such things are unlikely to make the general news. Is it standard practice to issue a retraction if things are incorrect? If anyone has any numerical data on this that would be ideal.

COPE (Committee on Publication Ethics) have recommendations for what circumstances should lead to retraction of papers. Retraction is considered a very severe action and is not generally done lightly. In a document from COPE on retraction guidelines you can see what they recommend.

Clearly that does not answer your question but the problem about being general in academia is that the effects of problems in written articles differ between fields. What is wrong is obviously wrong, but if the effects are risking lives  or is harmful in some other direct way will be more likely in some fields than in others. Hence retraction is probably far more likely in life sciences than in, say history or philosophy (feel free to disagree or add other better examples).


Ethics of using public and illegally obtained databases for academic purposes I'm on my senior year of college, and my professor and I have decided on an independent study where I will analyze and develop some method(s) for screening valid data sets for the 'selection' phase of data mining, where spam bots, dead accounts, and other irrelevant data sources are omitted from machine learning analysis.

The problem i'm running into is that I really want to use a data set that is from the real world, so I could truly discover something meaningful from the data that hasn't been discovered before.

My initial thought was to use the Ashley Madison hack dump from the summer of 2015, but I wanted to consider the ethical implications of using such sensitive data. Alternatively, I was thinking I could manipulate the data before analyzing it to provide some sense of anonymity to the victims of the hack (for instance, replacing all full emails with the first and last character of the name, as well as the @ and suffix).

My question is NOT whether you think these practices are ethical, but whether there has been some professional work done in the past anyone is aware of that can serve as a model for my current work.

For example, Facebook was caught manipulating the content of its users' Facebook feeds in order to measure the emotional reaction of the content on their future posts.

Relating to just the AshleyMaddison data, there is a plethora of articles on your exact question. I will summarize the main talking points and provide links at the end.

1. Can I download it?

The data is probably public-domain, but it depends on where you live. In some countries like the US, the data itself is publicly accessible and part of a wider conversation about personal rights to privacy, whilst in others like Canada, is has been explicitly decided that AshleyMaddison still holds the copyright and downloading the data is akin to acquiring stolen property (note, AM is owned by AvidLifeMedia, a Canadian company, and people have said that this decision was to offer some degree of protection to ALM, as hacked users cannot use the data dump as evidence in court). Other countries say that fundamentally nothing that can be downloaded can be stolen, so this doesn't even apply.

2. Can I share portions of the data with others?

If you are in a jurisdiction that allows you to download it, you can by default share it - and many (perfectly legal) sites exist for just that. You type your name or e-mail address in to see if you are part of the hack (or your spouse was). For better or for worse, there is no crime for making public-domain data easier to access.

3. Can I process the data and share summary statistics?

Oddly, unlike the above 2 issues, this is legal in every country which offers protection for journalists and researchers - including Canada. Many researchers, particularly those researching infidelity, have asked lawyers this question, and they all say the same thing - yes it's legal. In fact, top US lawyers have gone as far as to say that journalists are probably in the clear if they publish a list of names of celebrities who appear in the hack, for whatever little public good/interest there might be there.

Many articles also point out that there is a big difference between the legality of this, and the ethics of this. Both the law of the land and what is considered ethical behaviour changes over time, and they don't always have to be in sync. Some say that in using the data you are condoning and even encouraging the hack - which may lead to more hacking/data dumps in the future. Other's say that your research may be the only grain of good to come out of the whole debacle.

I will summarize by saying what I would personally do, which is use the data, get the outcomes, then way up the pros and cons of those outcomes with the example you will be setting for others in using this data. Legality is really not the issue here at all, because even if it is illegal, you are incredibly unlikely to find yourself going to court from either Ashley Madison or hacked users, as both parties would have a very poor case. Those aren't my words, those are the words of Jennifer Granick, a law professor at the Stanford Center for Internet and Society.

So if the real question here is the ethics, then this is something that is ultimately up to you to decide on. There may be all manner of real repercussions from your department - particularly if someone in the department turns up in the database... - but that's a very different question.

http://www.huffingtonpost.com/entry/ashley-madison-hack-creates-ethical-conundrum-for-researchers_us_55e4ac43e4b0b7a96339dfe9

http://www.al.com/news/index.ssf/2015/08/is_it_illegal_to_download_the.html

https://onlinejournalismblog.com/2015/07/20/ashley-madison-ethics-journalism-hacked-documents/

http://fortune.com/2015/08/19/ashley-madison-media/

Finally, there are many stories that people have posted online detailing their experience at the hands of the hack. Some say it wasn't really them, some say it was. Some are outraged, some are just numb. I would suggest reading one or two of the longer blog posts to really get a sense of what this data means to some people. It's more than just a resource. People have committed suicide due to the shame or discrimination they faced as a result - most notably people from the LGBT community - so it's really important to not shy away from that when deciding to proceed, or not, with your research.


Conference presentation of a weak paper to an expert audience. As a part of my research project, I am almost finished a first paper. I was proud of myself because of the contributions: I was able to take some ideas that has been used in the field for some years now, and I provided a unified point of view. However, as it turned out, some of those results had been already obtained before. Nevertheless, this results seems to be unknown yet in the community of the field.

A very important conference is coming up, in which the main leaders on the topic will be present. My supervisor wants me to give a talk about my results in this event. Given the fact that a few of these results had been already obtained (and of course, I am not taking credit for this), the paper with only my contributions (discarding what was done before) is not a strong paper. Although my supervisor thinks it is OK, I am afraid that giving this talk in front of these experts will result in them not taking me seriously as a researcher in the future. What are your thoughts on that?

Answer inspired by @Roland's comment.

First of all, have a little faith in yourself, your supervisor seems to believe your work is good enough and so should you.

Otherwise, if you really do have some doubts about the relevance of the paper you can stress the fact that these results seem to be unknown in the community.

Raise awareness on the fact that your project is interesting and that some work and results have already been made, yet seem to have passed under the radar of many.


Is my doctorate good enough? I received a doctorate from an online school Walden University. I have not had any luck finding a full time college teaching position. Should I pursue another Ph D from another reputable college? Can I use any of the coursework I already have to defray the expense?

There are many people who attend far more reputable institutions than Walden and accomplish significant amounts during their PhD program and still have problems finding meaningful teaching positions. It's unfortunate that you went through the entire program without realizing this.

Unfortunately, a lot of people think the process goes like:

Get PhD (in 3-4 years!)
Apply to a few great teaching jobs
Have to decide between multiple great offers

But the reality is often more like:

Get PhD... eventually
Apply to many jobs
Have a few interviews if you're lucky
Get rejected from most desirable positions
Decide to do a post-doc to get more teaching/research experience
Repeat while applying for post-doc positions

The academic job market is fairly saturated in many fields and so even if your degree was from an accredited and reputable institution, you may not have a simple case for getting a teaching job at a college. Particularly if your PhD experience did not lead to any teaching experience or publications.

I would recommend looking into local community colleges. It sounds like you did this online, which means you may have been working fulltime during your study - community colleges often have courses you can teach which you may be able to combine your academic study and work experience to be a desirable candidate.


How to gracefully leave a research lab (due to major change)? I'm a freshman electrical engineering student who has been working in a research lab for the past year. I decided a few months ago that I am going to change my major to computer science, and that I will be leaving the lab I'm still working at.

How can I gracefully leave this lab without burning bridges (I may want to use this job as a reference in the future)? Should I tell them I'm changing majors or will it be easier to not let them know that?

Nobody expects undergraduates to have their life plans all sorted out: if you tell the professor you are changing majors and planning to leave the lab, it shouldn't be all that shocking to them.

What you should do, however, is make sure that you leave things in good order.  Plan to complete your work for the current semester, and set up a plan with the professor and whoever else for how to leave things in a state where it will cause as little disruption in the work as possible.  This might be cleaning up your lab notebooks, or about finishing a certain set of experiments, or training another person who will take over your tasks.  The key is to have the discussion as early as possible, and make it clear that you take your responsibilities to the lab seriously, and want to act professionally in using your remaining time to wrap up and/or transition the work.


Is it ok to have paragraphs that have only one sentence in a formal paper? Or, is it a good practice?

I found most papers that I read are "block by block": they have paragraphs that are not so long, and not so short. Is it a convention? Should I mimic that?

The Wikipedia article on paragraph says a para could contain one or more sentences. The very purpose of grouping content into paragraphs is to organise similar thoughts into one unit. Too many small or one-sentence paragraphs will affect the cohesiveness of your content.

But a one-sentence para may be fine at the end of a section in a paper if it adequately summarises the content within. (Like this, perhaps!)


Can a PhD thesis in computer science have two major parts? Can a PhD thesis in computer science have two major parts? Lets assume the research goals are closely related, yet for the sake of better understanding and clarity, the thesis is divided into two parts e.g. parts A & B?

This is a question for your advisor. In general, what is acceptable in a thesis is what your advisor and committee will accept. If the division into parts makes everything clearer then all to the good. If the two parts complement one another, say theory and application, then it should be fine if the advisor agrees.

But also, what is a "Part" is also a function of the writing style. In CS, for example, one "part" might be new and necessary algorithms and another part might be how they are applied, or evaluated, or ...

But a thesis that tries to solve two different problems is likely less useful unless they are tightly bound. In such a case, focus on one "part" and save the rest as future work.


What is the timeline for UK postdoc applications in math? I (a graduate student in math at a US university) have heard a lot of advice about applying for postdocs in math at US universities. I've been told when applications for jobs and NSF are due, when you can expect hear back, and how long you have to make a decision.

What is the timeline for applications to UK universities for math postdocs?

The timeline varies from one place to another. Some Universities will compose a shortlist in a week after the deadline and call candidates in for an interview a couple of weeks later. Following the interview, the final decision can be made in a couple of days.

However, it is not uncommon for the shortlisting to take several months. For various reasons, the final decision after the interview can also take longer. I received my postdoc offer ~3 months after the interview date.


Do I have a chance at an academic career in North America or Europe? I have two masters, topped both of them, and published articles that have been widely cited, though they date before 2013. I am struggling with my PhD because of a lack of support from the faculty and funds. I have been too busy surviving after that. What can I do to maximize my chances of an academic career in Europe or North America? Is my age a crucial factor?

My answer to this question of yours Does the time taken to do a PhD affect post doctoral applications? does also apply here: There is a chance, yes. How high that chance is depends on many factors. Your age, your publications, etc. are some of them, but others are for example the quality of your work, the availability of the position you are looking for, the energy you put into applying (e.g. do you contact every last university in all of North America and Europe?), what you want as a "career"  - e.g. are you happy with a postdoc position that is not limited, or do you want to get to dean of the department before you hit 60 - etc.

So yes, there is a chance and yes, it is somewhat lowered by the points you gave. If you want to take it or not is your choice, no one else can make it for you.


Years of experience - how to count PhD and postdoc years I am a physicist specialized in developing algorithms for microscopy techniques and after a postdoc I am applying for data scientist / engineer positions at various startups. To estimate what would be a fair salary range, how should I consider my phd and postdoc years? My research work was related to data and image crunching, but the tools I used were more primitive than what is used in the industry.

Ok, let's see: First of all, Data Science is a relatively new field, Data Scientists are in high demand in many places, so estimations on salary are difficult to make, statistics found online are mostly not representative as there is not yet enough data.
Next, the fact that you have a PhD should count stronger than the mere years you spend on obtaining it.
And as a third point, the work experience always depends on what you did and what you plan on doing. Imagine you worked five years as a baker. While this is job experience, it might not be very relevant for a job (and salary) as a Data Scientist.
If you think that your years should count as experience, then make that clear, argue your case, show that you actually have experience. Salaries in the industry are usually not computed by a fixed formula taking your degree and years of experience as input but are up to negotiation (inside certain bounds), so if you can convince your future employer that what you did counts as experience towards the job you are applying for you can of course ask for a higher salary; if you yourself are not convinced then maybe you can't; but then again, having a PhD and the basic requirements to become a Data Scientist already means a rather high salary in many countries and areas.


How should a prof assign duty for a course with a discussion forum/board? I am (with a few fellow TAs) helping a prof with an online course in STEM that has a discussion forum/board. However, it seems to me that this wasn't really thought through and now we have reached a very difficult situation in the course.

The prof assigned these duties to us on top of all the regular duties during the non-covid years, e.g., grading and tutorials. However, answering questions is a very unregulated task, which can easily go over-time depending on the difficulty of the more or less spontaneous question we get from the students.
We have 2 TAs answering question each week. However, my fellow TAs don't really care about answering questions (maybe they think it is a waste of their time?) and the bystander effect rans rampant among the course staffs (all waiting for someone else to answer). The prof do not enforce the TAs to answer questions.
All of us have to follow every minute detail about the course because the question can come from anywhere. This puts an enormous amount of pressure on us as compared to non-covid years, where all technical course related questions are assigned to one designated TA. Now all of us have to be experts in everything.
The students are not well trained on how to ask questions, and many questions essentially boils down to "my computer is doing the wrong thing, help!"
Aside from that, the students also ask a wide range of questions. TAs essentially have became personal tutors, online IT technicians, mental health professionals (to answer general grade-related concerns from stressed-out students), and career counselors.

As of right now, the discussion forum has entirely been taken over by questions left unanswered (and students do not bother to mark which question that has already been resolved, so we may be wasting our efforts). Where did things go so wrong and what can we do (in the future)?

You ask "How should a professor assign duty ..." which is really an unanswerable question.  I think the real question is "How can the team of TAs handle this workload in a way that is fair and not overwhelming?"
As other people have said in the comments, I think you need to set some boundaries about amount of time, but also that you will not answer all individual questions. For example say there are multiple questions about problem 8. You do one answer for all of them. That's one reason not to rush in immediately, rather wait until you see what the pattern of questions are.
It's a little hard to address this without knowing the subject matter or the kinds of questions. Also in covid times it is important to be kind to and understanding of  students and the way that technology challenges are now a hundred times greater.  Further, problems that used to be solved in 2 minutes during a live class now take hours, both for you and them.
I know you are limited by what your supervisor will allow but I'd like to make some suggestions.   But before that I will also say that it is okay for you to set boundaries on when you will answer questions and response times. Don't be mean, but explain. For example, maybe a TA will come in at noon every day and try to answer questions, and another will come at 6.

First, discussion boards are not really a great way to do questions
and answers, and definitely not for expert answers (and the TAs are
the experts).  They can be great for peer to peer support and
that's what I'd suggest you encourage.  Can you ask your supervisor
if you could give extra credit (or even credit) for students who
answer questions?  Or even without that, can you encourage students
to jump in and help each other?  (I've found that my students can
often answer the technology questions really well, maybe they have
the same brand of phone or computer with the same OS which I don't
have.)

Second, notice on how Stack Exchange -- which is a set of sites
devoted to answering questions -- there are well defined rules
including obsessive refusal to answer duplicate questions.  Get
yourself and the students in the habit of searching for an existing
answer first. Teach them how to search effectively.
Also, write up a document "how to ask a good question" and revise it
as you get better at managing this. Put links to it everywhere.

Third, build up your documentation and knowledge base. You could
potentially use other features of your LMS for this (e.g. Blackboard
has so many ways of doing things that no one can use them all).  For
example, if the class is not using the wiki feature, start using
that. Or you could use Google docs. Or a lot of other things. You
could do FAQ but you can also start other things. Again, you can also
get the students contributing if it makes sense. Also if you are
answering questions that are strictly informational, post the
information prewritten (or less good, with well described links) at
the top of every page or in your signature. Try to do this in a way
that it can be used again next semester.

Fourth, teach students how to answer their own questions by showing
how to find information online or in their textbook or syllabus.
Many actually don't know how to use the index or table of contents of
the text books. Or, for example, "I searched with keywords x, y, z
and found this useful video."   This gets to asking good questions,
but also, don't just answer, do things like say read page 329 and
then come back with questions based on that.

Fifth, once you have figured out how to actively sort questions where
students are really having complicated problems from the rest,
consider going into a meeting 1:1 or with a small group.  It's much,
much easier to answer the questions that way because you go back and
forth in real time.  If you record (and everyone involved is
comfortable) you can also post the recording of the answer.

Sixth, provide structure (and you may have to experiment with what
works.  For example set up separate boards for questions about
technology, questions about due dates and other syllabus related
issues, and then questions about each topic or chapter and then you
can have others like "careers" and "random."

Seventh, have some prewritten templates so you can just fill in specific information.

I'm sure that there are lots of other things you can do too.


How do I deal with the overwhelming ambiguity of my project? I have a bachelor degree in applied mathematics and I'm currently doing a PhD in molecular genetics as a computational biologist. I started in my thesis lab in January and since then I've had serious problems understanding exactly what my supervisors expect me to do.

Here are a few of the underlying issues:

I've had to transition from a first principles based approach to problem solving to a top down, data-oriented worldview - something that has not come easily.
There are no upper-year students doing a project similar to mine that I can shadow while I learn the ropes.
My supervisors talk about my project and direction at a very high-level, so the details of what I should be doing or how I should be doing them are unclear.
I face a constant stream of discouragement, be it my peers succeeding while I don't, my supervisors just expecting me to 'figure it out' when it comes to the details, my unsupportive family, etc... and it's affecting my ability to work.
I did a number of very technical projects in my undergrad and I enjoyed them immensely. I have little love for my current project - likely a symptom of not succeeding.

How do I deal with this? Is it a normal part of the process to feel lost and hopeless - even this early on?

Most importantly: At what point should I cut my losses and drop out or switch departments?

Is it a normal part of the process to feel lost and hopeless - even this early on?

Yes, it is very normal. Particularly early on. There are many things you do not know or understand yet. I spent at least a year of my Ph.D. on projects that never amounted to anything (literally), and know there were many times I asked myself these same questions.

Now to the more practical question:

  How do I deal with this?

Based on my very similar Ph.D. experience, my best advice is to "own it". You need to convince yourself that you are doing the research that will go in your dissertation. It will take you personally making mistakes and learning from them. It will take you developing a workflow where you quickly prototype ideas so that the bad ones can be discarded without too much time lost. I would bet that although you feel like you are treading water, you are developing skills and insights that will be useful once you gain more traction.

For this to work, you may need to stop expecting your supervisors' directions. Instead, systematically "try stuff" on your own. Start by addressing some simple concrete question related to your project: try something naive and see why it breaks down. After you identify the flaws, think about and implement some naive modifications. Iterate on this process and document everything carefully. Use your supervisors as reviewers -- explain to them what you did and ask for feedback rather than direction. In my case, iterating this method led to solving a problem parallel to the one my supervisor had original posed, but in a more 'hot' area of research.

Finally, regarding this point:

  I face a constant stream of discouragement, be it my peers succeeding while I don't, my supervisors just expecting me to 'figure it out' when it comes to the details, my unsupportive family, etc... and it's affecting my ability to work.

I often felt deeply discouraged as well. First, comparing yourself to your peers is a recipe for frustration. Avoid this at all costs (easier said than done, I understand). Second, I found exercising, pursuing my hobbies, and meditating all helped curb the day-to-day frustration of the "treading water" feeling.  Talking to other grad students, particularly from different disciplines, also helped. I found this feeling is far more common than some of my peers would let on -- and being able to open up to those a bit removed from your specific project was always helpful.


From whom do I get references when my original advisor leaves academia? This is similar to a previously asked question, but deals specifically with addressing the problem on the CV. My adviser had a bit of a personal meltdown and left the department while I was finishing analysis of field data/writing up. His students were assigned the following year to a non-tenured professor.  This new professor was of little help to me my last year of writing up, sat on my dissertation with no comments for over 6 months and only produced comments after I went to the departmental chair. He did not think much of the type work I was doing and went so far as to say so during my defense. I will add here that I have a number of publications (>5) including single authored ones-which for my field is significant- as well as an excellent track record of funding and in presenting my research. I have a strong CV but have had no success thus far in securing a job. I once saw one of the letters he had written for me (it needed to be included in a single PDF so he had to send it to me) and it was terrible. It talked mostly about him and how he really did not know me well and with a few generic sounding "he will no doubt exceed" sentences that just sounded fake. Months later a colleague suggested that I find a different reference than my adviser (but was not clear as to why).

So, my question is this: since committees will no doubt look at my list of referees and wonder at my lack of an adviser-I have taken to including a short "note" in the "reference contact information" section explaining that 1) my original adviser left academia at the end of my time as a student and 2) that my new adviser was up for tenure the year I defended and very busy and was in a different field than mine, so instead "below are three people who are in a better position to judge me on my research, teaching, writing skills".

Is this providing too much information or is this instead ensuring that rather than questioning and then rejecting my application the committees will stop and think "oh okay, I can see why the applicant did not include their adviser"?

Your current advisor's letters are killing you.  Do not ask him for any more letters.  Do not list him as a reference in your CV.  Don't walk; run.

  I will add here that I have a number of publications (>5) including single authored ones-which for my field is significant- as well as an excellent track record of funding and in presenting my research.

In that case, you really should have no trouble finding enough other good references to overcome any concerns raised by not having a letter from either of your advisors.  Everyone reads advisor letters with a grain of salt anyway; strong letters from well-known senior researchers outside your home department have much bigger impact.

Of course, if anyone asks why your current advisor isn't writing you letters, you should answer honestly, but I think adding an explanatory note in advance is unnecessarily defensive.


How do I ask / inform my supervisor that I need to take a day off? I just recently got a job as a research assistant over the holiday (which will later turn into an unpaid independent study project). Before hiring me for the job, my supervisor asked me if I would be taking a week off for vacation during the holidays. I told him no. However, for Christmas, I recieved (as a gift) tickets for an afternoon weekday show of an expensive stage production. The show is about an hour and a half from where I live so I would need to take most of the day off. I will be informing my supervisor via email about this. How do I inform him/phrase the email?

XX,

I was just given a surprise gift -- tickets to a show in YY City.  It would be thrilling to go -- any chance you could spare me on Thursday?  Because of the distance, it would mean missing the whole day.  However, I'm free all day Saturday.  If you like, I could come in then to make up the time.

(however you like to sign your name)

Please feel free to adjust this as needed.  For example, you can make the tone less breezy and more formal if you want to.


What is the best way to explain unrelated work in a Masters application? I graduated in 2016 with degrees in Law and Arts, with Arts majors of International Relations and Criminology. Since then, I have been working as a corporate lawyer (specifically, insurance).

I have realised I don't want to do this long-term, and am applying for Masters degrees in the field of political science / international relations / public policy.

I have decent academics and plenty of relevant extra-curriculars from my undergraduate degree, but I am not sure how to best explain the last 3 years?

I am based in Australia and applying for coursework Masters programs in Europe and the US

It is unclear whether you are applying for a coursework Masters or a research Masters. If it is a research Masters, applying for a project that straddles across three disciplines seems unlikely (political science/international relations/public policy).

Coursework Masters tend to not have a high selection process as coursework Masters tend to be funded by the student compared to a research Masters.

So if it is a research Masters that you are applying for, then evidence of the ability to do research would tend to be the focus. If you have done an honour thesis during your law degree, that would be significant useful. If you have done extensive research and wrote long form analysis as part of your role as a corporate lawyer, then that would be relevant too. Some lawyers have written submissions or in-house publications, so that would be good evidence of your work.

Being able to show that you are able to engage with difficult political science and public policy issues would be useful as well.  You have done international relations in your undergrad but you may not be as convincing in the areas of political science and public policy especially at a research Masters level. Extra-curriculars would not be that convincing, unless it is extra-curriculars that has produced good work such as an editor of a student journal or publications that potential supervisors that are able to examine.


Advice on postgraduate study in experimental/theoretical physics for a 3rd year Mathematics student Firstly I hope this question is appropriate to ask here. I am a third year studying Mathematics at the University of Oxford, with plans to continue to 4th year to complete the masters course.

I have been considering many paths to take so far this year, I started off by looking into finance, this I found however incredibly unintellectuality stimulating. My passions have always been for Maths and Physics, this year I will be studying quantum theory, quantum computing, special relativity and fluid dynamics, which I will continue on into 4th year with the addition of general relativity, theoretical physics and other more general applied courses.

I'm very interested in applying for a PhD after 4th year, mainly because i've never been more fascinated by the subjects i'm currently learning, Quantum theory in particular is amazing and has really changed the way I look at the universe.

Unfortunately I'm only getting a mid 2.1, however it is from Oxford so I hope that this may carry some weight, but because of this I will be mainly focusing on applying to universities other than Oxford and Cambridge.

What I'm wondering is is there any point in following this dream? I'm extremely motivated but I feel not having a first might have ruined it for me. Can anyone recommend any strategies I can use to make myself more competitive?

Currently i'm planning on applying to universities for summer research assistant placements, paid/unpaid. I'm also reading the Feynman lectures to boost my background knowledge of physics, to help bridge the gap between physics courses and my mathematics course. Can anyone recommend any other books/ideas that could help me be able to apply for experimental physics? Also universities with departments that would be good to approach.

To sum up my long and laboured question, i'm extremely passionate about mathematical physics and the idea of stopping learning about it, and say going into a deskjob is sort of horrifying. Any advice anyone can give me I would greatly appreciate.

Don't go to graduate school in physics, at least immediately.  The best case scenario is a five year program, followed by three years of postdocs, and then THAT will be followed by five years of tenure review, and THEN you might have a chance at having a stable life.  All of this happens with a tremendous amount of competition.

Use that Oxford degree to find a job somewhere for a few years, and see if you still really want to do physics at the end of that.  If you must absolutely go to school, find a terminal masters program, and learn about research some.  If you don't know whether to prefer experiment or theory, you're going to have a horrible time picking a school that has a compatible advisor, and you want to be looking for compatible future advisors far more than you want to be looking for the Platonic "quality physics programs."  So, you'll be better suited to start a PhD program effectively (and getting a masters on the way doesn't really slow you down--you are better prepared to start research after that, and the first couple of years between your quals and really starting research is where grad students flounder most frequently).  Additionally, if you are in your current situation, this will enable you to rehabilitate your academic record.  Finally, if you do your two years and don't like physics, you can find something else to do.  As someone who has finished a doctorate, I strongly recommend against immediately entering a doctoral program straight out of college.

EDIT: Additionally, as you go through school, keep some sort of exit plan--sign up for those numerical projects and learn programming.  Take the sensor analysis class and learn how to align a laser.  Learn the basics of data analysis.  There are all sorts of skills that physicists have that are wanted not just in academia, but also in the private sector or government.  Make sure that you have the skills to go out and do something enjoyable, even if it is not academic physics.  Because the odds are really, REALLY against anyone making it in academic physics (and none of these things will hurt your physics career, to say the least).


Time allocation in conference presentations How much time should I expect to 'leave' at the end of a conference presentation for questions? This question suggests to allocate 2-3 minutes per slide, including front/back matter (like a question slide). Does this mean I should leave 2-3 minutes for every 15 minutes of presentation delivered? Is there a good 'rule of thumb' for this?

The only rule of thumb I'm familiar with is a bit like this, keeping in mind that some of the additional time may serve as buffer in case there are questions during the talk:

For talks of or less than 30 minutes total, include no less than 5 and no more than 10 minutes for questions.
For talks between 30 and 60 minutes, include no less than 10 and no more than 15 minutes for questions.

So that essentially means at least 5 minutes for each half hour (not too far off from your estimates).

For longer talks, there never seems to be enough time for questions, so I would suspect there isn't one rule for all situations.


What would I do if an editor didn't publish my manuscript? My paper was accepted to be published as a chapter in a SPRINGER book after it was presented at an IEEE-sponsored conference and gaining a high score form their peer-reviewers. The editor of the book series (also the chairman of the conference) invited me to submit an extended version of the paper (at least 30% of new ideas) so, I emailed the final manuscript but didn't get any feed-back until I figured out that the book is now available online but the title of my article doesn't appear in its table of contents! I asked the book editor about this issue but still haven't gotten an answer.

Based on your timeline, my guess is that your email didn't reach the editor. Perhaps it went into her spam folder, or he saw it and then forgot about it, etc. There's little chance this is malicious. After all, the editor has nothing to gain by holding your manuscript unpublished. Now that the book's been published, there's no chance of inserting your manuscript into it either.

You've already emailed the editor, which is all you can do. At least it'll make clear where the error was, and more optimistically, perhaps the editor will find somewhere else to publish your manuscript. It's all you can do, and next time, you can ask the editor for a confirmation of receipt if you don't hear back from her after a while.


Consequences of taking classes for someone else I am a low-income undergraduate student at a US university. Last semester, another student approached me and offered to pay me a lot of money if I take one class for him. Because of my family’s financial situation, I accepted this deal. Long story short, I have completely taken one class for him in Fall and one this Spring. I have also helped him with his exams and homework in his other classes.
It makes me incredibly angry that you can just buy your degree like this when you are rich. I would like to know what would happen to me if I report it to the university after I graduate or if there is anything else I can do about this situation without ruining my future.

I would like to know what would happen to me if I report it to the university after I graduate or if there is anything else I can do about this situation without ruining my future.

Both your own actions and the actions of this other student would certainly amount to serious academic misconduct.  It may also amount to some species of criminal fraud, such that it could also be a criminal offence.  If you would like to get reliable information on this, I suggest you go and see a lawyer in your jurisdiction.
In terms of what would happen to you if this became known, I would think that you would be found to have committed academic misconduct, and some substantial penalty would be imposed.  It is impossible to say what penalty would be imposed, but it could entail rescinding your degree.  On the other hand, your adverse financial circumstances might count as a mitigating factor, and so it is possible that a lesser penalty would be applied.
Whether this would "ruin your future" depends largely on your ability to change your future behaviour and bounce back from adversity.  I don't believe that a finding of academic misconduct ---or even a criminal conviction or loss of a degree--- is necessarily ruinous to one's future, but others may have a different view.

It makes me incredibly angry that you can just buy your degree like this when you are rich.

There is no valid cause for your anger.  You have facilitated precisely this behaviour.  Without the actions of people like you, it would not be possible for the rich to buy a degree.  We can be angry about it, but for the time being, you have lost the right to be so.
Perhaps when your own conduct is more remote, and you have had some years to reconsider this episode and lament your own participation in it, you will once again have standing to feel anger over the short-cuts taken by the rich.  For now, perhaps you should reserve some of that anger for people like yourself who defraud our educational institutions for money.


How should I cite products? This question is closely related to How should I cite a website URL? but more concrete.

I'm currently writing my master thesis. In the section "related work" I give an overview which also includes concrete products (normally software). Usually there is no academic paper published about this work and often there is only a product homepage, a git hub repository or a manual available.

How, if at all, should I cite this "products"? I thought about adding the URL just after the name of the product, adding it as a footnote, cite it as usual with a MISC BibTeX entry or not mentioning a URL at all (usually they are easy to find with Google). I'm a bit worried too blow up my bibliography to much.

I give a few examples to stay concrete, my thesis is about a pattern matching algorithm (well, very simplified) so I want to show tools that help programmers with writing regex:

The software RegexBuddy (http://www.regexbuddy.com)
The online tool RegExr (http://gskinner.com/RegExr/)
The Statically Checked Regex (a software artifact) in the Git Hub repository https://github.com/retronym/macrocosm
The function ctRegex in std.regex (http://dlang.org/phobos/std_regex.html)

Could you please also please also answer if it's OK to include a lot of citations (around 20) to mention this products although the text is only around one page, respective one sub chapter (in a work that is expected to have something around 100 pages).

According to the APA:

  Do not cite standard office software (e.g. Word, Excel) or programming
  languages. Provide references only for specialized software.

    Ludwig, T. (2002). PsychInquiry [computer software]. New York: Worth.`

  Software that is downloaded from a Web site should provide the
  software’s version and year when available.

    Hayes, B., Tesar, B., & Zuraw, K. (2003). OTSoft: Optimality Theory
    Software (Version 2.1) [Software]. Available from
    http://www.linguistics.ucla.edu/people/hayes/otsoft/

The IEEE style is almost identical. (I'd reproduce it here, but it's in a stupid flash file which doesn't support copy/paste.)

That being said, I notice that you cited software for parsing and understanding regular expressions. While there is no official rule that I know of for acknowledging software, it is typically only used for software crucial to the development efforts (i.e., an analysis tool). To bring a somewhat extreme example, while everyone uses some form of operating system (Windows, Mac OS, Linux), no one cites their operating system. Recall the purpose of citations; to enable others to understand your frame of reference and replicate your work. You should only cite tools that are specialized to your research that others would need to continue your research.

Additionally, I've seen many neuroscience papers where some software is listed but not cited (e.g., the Matlab reference here). This is typically done for tools developed outside of an academic environment. Here, Matlab is a non-academic commercial, but both SPM and Fieldtrip were developed using grant money, and both specify exactly how they should be cited in publications (e.g., Fieldtrip; I can't find SPM's now).


How to publish superseding results without creating enemies While working on a research paper with a coauthor, I found an unpublished paper in arXiv and discovered out that the technique we developed in our paper can be used to improve a result in the unpublished one. Specifically, we can design a superior algorithm to solve the same problem solved in the arXiv paper.
If we publish our results, then the author of that arXiv paper will have a hard time publishing his paper, since some journals will not consider his algorithm once a better one is available.
Of course, we cite the arXiv paper and there is no law against publishing improved results, but this may harm the author of the arXiv paper. Is there a way to publish the new result without creating enmity?

One potential option could be to combine the work and submit a joint paper. However, the papers do not "mix" very well since our paper is mainly about a different technique - the improved algorithm is only a usage example of it. Combining the papers will create a very large and inconsistent paper.

Another option is to wait until his paper is accepted for publication and only then publish our paper with the improved result. However, it seems unscientific to withhold results that we already know.

I disagree with the premise of your question. “Publishing superseding results” is basically the same as what’s known as “publishing”, since all papers build and improve on the existing literature in some way and push some older work slightly toward obsolescence or irrelevance. The extra twist in your situation that you are improving on unpublished work is of hardly any consequence and simply not worth worrying about, for the following reasons:

As others have said, the authors of the arxiv preprint still have precedence and will get credit for making their contribution at the time they did, before your subsequent improvement was discovered. Referees and journal editors should (and almost certainly will) take that into account, within reasonable limits.
In general, when you improve on earlier work you show that it is interesting and relevant enough for other people to follow up on. This is actually flattering to the authors of the earlier work, even if you imagine that it is unflattering (it’s also true that an improvement can sometimes portray earlier work in a slightly unflattering light, but my point is there would still be a separate flattering aspect that I think you are ignoring, and which in most cases will far outweigh any supposedly unflattering aspects).
The publication status of the earlier work is simply not your concern. It is up to individual researchers to submit their work for publication and otherwise promote it in a timely manner. If they fail to do so, they have only themselves to blame, and they should not expect others in the scientific community to delay their own follow up research, at the cost of hurting their own careers and slowing down scientific progress, out of pity or charity.

To summarize, I think the idea that you will make enemies by publishing honest work that you did in a STEM field, regardless of the specific circumstances, might make for a cute plot element in a satirical TV show or novel about academia, but is not a realistic thing to worry about in real life.


Should I contact professors directly if a visitor's office exists? I want to visit certain laboratories at Tokyo Institute of Technology (TITECH) when I go to Japan three weeks from now to get a feel for the research they do and if I would be a good Master's candidate for their labs.

My advisor has offered to contact the professors directly so as to give my request more visibility.
However, TITECH has a Center for Public Affairs and Communications.

I'd much rather contact the professors directly since I'm on a rather short notice and I feel as a less formal visit would accelerate things up.

Here's some other information that could be relevant:

I will finish my undergraduate degree in about two years.
I am NOT asking for any monetary compensation, theses visits are on my own vacation time and at my own expenses (unless that would be unusual?)
I'm mostly looking for simple tours of the labs, discuss their research a bit and talk about employment possibilities.

Would it be innapropriate to bypass the "official" process and contact professors directly?

I know people in Japan, have friends in Japan doing research, and traveled to Japan several times. One thing to remember: Obey the rules and hierarchy. Their system is based on respect for one another. Do not bypass a rule even though in your mind it sounds stupid/lame/waste of time.

So in your case, contact the center and wait for their response.


Choice between A13 Z and E13 for a post-doc position in Germany I received a post-doc offer in physics from a German University. The position has a fixed three-year term, which might be extended up to three more years. The original position description says that this is the A13 Z position, Akademischer Rat auf Zeit. It corresponds to a Beamter, or civil servant position. Since I am a foreigner, the inviting professor is asking, whether it would be OK for me to switch it to E13 instead (researcher), since my profile for the position in this case is not needed to be checked by the federal government and the documents would be prepared much faster and easier for the inviting University. The salary would then be increased, to match those of A13 (let's assume the same net amount).

What are disadvantages and benefits of E13 compared A13 if one ignores the difference in the salary scale?

Which one is considered better in a long term?

Some more information on the personal situation:

Let's assume I'd like to stay in Germany afterwards.
I'm going to marry before starting the position. My partner has two children from the previous marriage.
I am not a citizen of the EU or the Schengen group.

A E13 position may have a little shorter working hours per week, for eaxample in North Rhine-Westphalia you have to work 39 hrs 50 min/week as "Angestellter" (E13) and 41 hrs/week as Beamter (A13). At least until you are 55 years old, as the working hours for Beamte get gradually reduced as you grow older. But I guess this would not apply to a post-doc position as academic work groups usually do not record the time of their scientist (this means, they often work longer hours without recompensation).

As posted by Roland in his comment above, a Beamter has to get a private health care plan which can be expensive, depending on your age and health status, but as the state pays approximately half of your health care bills, the conditions Beamte get by the private health care companies are much more favourable in comparison to the ones offered to "regular" clients and in the end a Beamter has a higher net salary.

A Beamter has furthermore to pass a health test and perform a vow on the German Grundgesetz (constitution) and the German laws and is not allowed to go on strike. In case of permanent positions, the pensions for Beamte are significantly higher than the pensions for Angestellte. So if you are planning (or hoping) for a permanent position I think a position as Beamter might be more beneficial.

Your family status is also relevant for your salary as Beamter, this means, if you are married with children you will get a higher salary.


How do I politely ask a convenor to not publish my name on the conference website? I will be presenting a paper at a major conference in the Spring: this will be my academic debut!

The issue is that I have a permament teaching job (middle school) that does not permit time off to pursue academic pursuits: how ironic.  This conference entails an inter-continental trip and hence, three "sick days" off. Cough, cough.

My name is already up on the conference website for anyone to Google, i.e. my employer.

How do I politely ask the convenor of my session to hide my name or alter it in some form? Withrawal is not an option.

From both an ethical and a practical standpoint, you don't. The ethical reason should be obvious (and has been stated in comments); you are lying to your employer about leave, and asking the conference organisers to be complicit in this (presumably without their knowledge). If you want to take sick time when it's not permitted, that is your risk to take, don't ask others to shoulder that for you.

From a practical standpoint, you should really ask yourself if hiding your name in the conference proceedings is in your best interests (relative to the chances of your employer discovering via Google what you were up to). I will presume you are going to this conference to begin/advance/change to an academic career. Reputation is gold in academia, and by concealing your activity, you are actively hurting yourself and reducing the profile of your work. If you don't care about the profile of your work and your academic footprint, then why go to a conference? They are expensive, and there are much nicer things to do with your time on a transcontinental trip.


Which summer internship to take? I asked a similar question last year, but the stakes have changed slightly.

So, I have an offer from a top 5 program in Chemical engineering (my major). There are a couple of extremely accomplished professors in fluid mechanics here, which is what I want to study in grad school. However, I am not so interested in attending this school for graduate school because it does not send many people to academia post-graduation, despite being a top 5 program, mostly because it isn't a very big name school. Or at least I assume this is the reason.

The deadline to reply to this school is March 5th.

To complicate things, I am waiting on a reply from a much more prestigious university for a summer internship. While the school has a much better name, its ranking is slightly less (number 6 for chemical engineering). I think I have a very good chance of getting this internship (my PI went to grad school here and wrote a very strong letter, plus I have a good resume otherwise). However, I learned today that they will NOT be able to get a response back to me before March 5th.

I am much more interested in attending School 2 (slightly lower rank, better name), because they very frequently send people to academia, which is my long term goal.

School 1 (higher rank, worse name) was pretty firm in the March 5th date, so I don't think I can ask for an extension.

Financially, School 1 offered me a slightly better deal, I'd be netting about 2k more over 10 weeks. However, that isn't as important to me, since the experience is worth far more than the money.

I apologize for the long question, but any advice or guidance would be appreciated. Am I putting too much emphasis on the name and rank? I don't want to be greedy and put all of my eggs in School 2's basket, and be left with nothing if I end up not getting it after all.

Since these are both REUs, I do not think attending school 1's summer program will affect your chances of attending grad school and continuing in academia.  Most REUs are designed to give students an opportunity to see if they can conduct scientific research and / or enjoy it.  Depending on the university and the discipline, they may be considered 'recruiting' camps for people to attend that university's grad school program in your discipline.

Since you have a fairly strong inclination to working in academia, you do not need the experience other than to confirm your suspicions and to make you a better candidate when you apply to graduate schools.

As for what I would suggest --- ask when you think the earliest day / time you would be able to get a response from School 2 on acceptance or rejection, and then from there, try to see if you can eke out some more time on School 1's deadline so that you don't end up shooting yourself in the foot.

You may also be able to talk with your current PI and see if he can hear anything through some back channels as to whether or not you have a decent chance.

At the end of the day, it's up to you.  Consider all your options wisely.


What is the academic job market going to be like in September-November 2020? Is there any good reason to be optimistic? I have the impression that this may be the worst job market year in the past ten years.
Edit to be more specific: I am referring to hiring grad students, postdocs, and tenure-track assistant professors, primarily in the U.S., but in other countries as well. Have many universities instituted hiring freezes for this upcoming year?

At my US large state univ, there is a hiring freeze for this coming year. Yes, this did also happen c. 2008.
One difference is that in the US the trans-economic source of the problem is by no means resolved... and even when/if it is "resolved", I think the "new normal" is very hard to predict. So administrations are being, and I think will continue to be, very very cautious about commitments toward the future.
So, no, no reason to be optimistic, because we don't even see the end of the disaster yet. Sorry.


Message board for finding private grants I am a PhD student studying in the US and I am interested in finding research-grants relevant to the research area to which I have recently switched to, viz. computational geometry problems in robotics.

As of now, I don't want to apply for a grant, but I want to get an
overview for what kinds of problems do public and private research grants get offered to researchers in my field.

While googling I stumbled upon grants.gov on which different government agencies post funding opportunities relevant to their interests, and that this
database is searchable by keyword.

The NSF website is also very useful.  However
their grant solicitations like this one  seem quite open-ended
and are not more specific on what kinds of problems need to be solved, (but please correct me if I am wrong, I am still exploring this website! :-D )

QUESTION:

Are there similar "messaging-boards" where private companies, interested in funding university research for a relevant problem post their funding opportunities? If not, how do you efficiently find such grants ?

I am interested in this because I feel private companies will be more specific on what kinds of problems they encounter and would like to be solved.

In the US, students generally do not apply for grants (except for specific fellowships for graduate students - NSF, DoD, Hertz, and the like); it is the advisor's job to find funding for the student.

If you want to get a general sense of the funding picture in computational geometry, I suggest you look at recently funded proposals on nsf.gov (their abstracts should be publicly visible) and follow up directly (and with due preparation) with the principal investigator of the corresponding grant.

Your best bet is to attract the attention of a well-known researcher in the field, and, given the current academic pressures, they are very likely to have some funding for students.


How should I approach job materials for a lateral move entirely for two-body reasons? I am a tenure track assistant professor at a liberal arts college. I Iike my job quite a bit, but it is located in an impoverished, rural area. My partner works in the nearest large city, 2.5 hours away. I live there as well; the commute and the 2 nights a week I spend away from home are wearing on me.

This year there is a job at a very similar (on paper) instituion less than an hour from my house and accessible by public transportation. It is the same size, in the same region, serves a similar student population, and the departments are of similar size and composition. Adding a small amount of complication is the fact that my current institution is (slightly) higher ranked. I don't put much stock in such lists, but I could see it rasing eyebrows. If it matters, both institutions are top 30. At the very least, my current administration cares a lot about such things.

To be clear, I am unconcerned about my tenure case; I am an outlier in terms of grant funding and publications, I have solid teaching reviews, and my school has an 80% tenure rate. I also work in a field where transitioning to industry would nearly certainly lead to higher salaries; my field has abundant job opportunities in my city. I don't think getting denied tenure is likely, and if it happened, I would be ok with that.

My question is simply how do I pitch my application, particularly the cover letter? It is hard to come up with a compelling narrative for why I would leave my current job for this one aside from the simple fact that I would love to be closer to home and continue my work in a similar institution. I am not certain if addressing 2 body issues directly is a good idea. My partner is happily employed; they are not looking for work from this school.

Edited to add: I worry that by mentioning my personal issues, the committee will be disfavorably inclined, as @strongbad has indicated below. That is, they get hundreds of applications from qualified people, they do not care about my personal life. However, excluding that detail might make them think there is some difficulty that doesn't appear in my materials.

I would tell it like it is:  You have a two-body problem and a 2.5-hour commute that you need to solve.  As soon as you say those words, everyone will understand.


What does competitiveness of a journal mean? I was looking at metrics on Letpub for few journals. For competitiveness, few journals had "very difficult", few had "86%" while some other had "2%". What does the percentages represent? Is it similar to acceptance rate?

Example:
https://www.letpub.com/index.php?journalid=765&page=journalapp&view=detail

Based on the percentages, I would guess that "competitiveness" here means how many articles are accepted out of those that are submitted. Elsevier sees a much lower acceptance percentage, which makes sense, because the people who submit the worst papers that get desk rejected don't likely report what happened to the database. In the same way Elsevier reports a much shorter average review duration compared to the user-reported ones.


What would be a more academically acceptable name for a cluster of four courses? In higher education, we know what is a major or a minor.  What do we call it when there are only a cluster of courses, say 9-12 credit hours in the same discipline that is not part of a major like concentration or emphasis?  The intent is to make them available to non-majors to broaden their credentials. In some professional disciplines like education or social work, the name 'endorsement' may make sense.  In other areas, is there a name that is both intuitive and academically sound?

Such mini-programs are sometimes called certificates.

Certificate programs are sometimes meant to be completed stand-alone, often by students who are not enrolled in a degree program but are looking for continuing education in a particular area, e.g. to help with their career.  However, they can also be taken on top of a bachelor's or graduate degree. They often consist of just a few courses.

As an example, you can read about my own institution's Certificate in Music Technology, which consists of 12 credit hours.


Is an idea still 'novel' when already published in a blog post? Can I publish an idea as a paper if somebody else has published this idea in an online forum or a blog?
I believe it's useful to publish good ideas academically because posts on forums and blogs are usually of low quality and have a niche audience. I'm sure some journals will allow publication, even though I'll cite the blog posts. But suppose I want to submit to some high-tier journal like Nature. Will the blog post detract from the novelty of my work then?

Whether it is novel enough to be published is up to the editor of a journal.
But you are in danger of plagiarizing unless you are very careful about citing the  original idea. The idea isn't yours, but theirs. The "novelty" isn't yours, but theirs. The fact that you noticed that it was something new isn't the same as creating something new.
But even if you avoid plagiarism, you might be accused of scooping the originators if they have plans for more formal publication. I suspect that if they have a paper in preparation and complain to an editor you will be in for some problems.
The best way, I think, is to contact the original author(s) and ask them about publishing, offering to help and working out some details about authorship.


Advice needed--reaching out to a potential advisor I have applied to a Canadian university for a math PhD starting this fall. I was very keen on working with Prof. A and he in fact, had encouraged me to apply. Few days earlier, I reached out to him for an update on my application status and he replied saying sorry that his funds for this fall are already committed. However, he finished by saying that I may find another advisor to begin my graduate studies.

Now I know this does not mean that I am admitted. But can I reach out to other potential advisors now? As a matter of fact, I have been independently reading some new topics and been finding them much intriguing. Now there is a Prof. B who has similar interests and I like his profile too. Will it be worthwhile to write to him now? If yes, how should I broach this subject? Should I mention Prof. A? I don't want to look pushy, but at this time now, I really want an opportunity to start my graduate studies and Prof. B's interests are very similar to what I've been reading recently.

I am looking forward to your suggestions. Thanks in advance!

Of course you should contact him.  There is no harm in that.  But I wouldn’t mention professor A.  Write a simple and short email stating the you have already applied in the department and you are looking for a supervisor for your PhD. Then also mention that you have been reading papers on topic X and you find them interesting. And since his research interests are similar to what you want to do, would he be interested in serving as your supervisor?  And then end your email by asking him to review your application and contact you in case of any question or query.

Good luck!


Verbatim self-plagiarism in introductory sections I'm reviewing an article where the authors are kind of experts of a particular subject and published several similar studies in the field, some even in the same journal.

This apparently leads them to reuse part of their own content between articles, sometimes self-citing sometimes not.

E.g. there are a couple of paragraphs in the Introduction that are a copied almost verbatim from a study from the same authors (which they don't cite). They maybe changed some comma or a word here and there.

What's the best practice in peer-review about this scenario? Is this ethical? Can this be considered a reason for rejection?

It's mostly in introduction and material and methods sections and the study overall is novel enough, so I'd be inclined to suggest a self-citation. But I'm curious if there is a consensus about how to handle such cases.

There seems to be no risk of getting credit twice for the same work here, as the papers are fundamentally different. It is possible that more modifications to these paragraphs would make them better suited for their role in the new paper, in which case suggesting that the authors do so is appropriate for the referee. However, rewriting the paragraphs just for the sake of it seems like a pointless endeavour. As a referee, you should not suggest that the authors waste their time on this.


If I proposed my PhD this year (but have not defended) can I say that I graduated this year? I am in a PhD program, and all I need to do is defend.  There is still a little more work I need to do before this, but my degree is essentially finished. I have totally completed all other requirements (classes, qualifying exams, proposals, publications, etc).

In my field (engineering)  it is common to immediately begin applying for jobs after the proposal.  So, after many interviews, I was offered a job.  They want me to start ASAP.  I am thinking this will push my PhD defense back 1 to 1.5 years.

Anyways, on my resume, linkedin, etc I would rather say me PhD was 2009 - 2015 (6 years) than 2009 - 2016/2017.  (7-8 years).  Would it be acceptable to state that this year (2015) is my graduation year?  I feel I'm selling myself short is I state 2016 or 2017 as my graduation year.

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


Can I add a GitHub repository as an entry in Google Scholar? I published a paper, the code for which is uploaded in GitHub.
Is it possible to add the GitHub link as an entry in Google Scholar? If so, can the citations be monitored in the same way as regular publications?

The way with dealing with github repositories in a citable way is to draw a DOI from Zenodo. Zenodo allows you to create a tag or release in the github repository and make that citable.
I don't know specifically whether google scholar indexes that, but at least it is something you can put into a list of references.


Is it acceptable as referee to contact an author on a paper you review? I am reviewing the second revision of a paper and am getting tired of this incredibly slow process of me pointing something out that requires clarification just to hear back from those authors two or three months from now (at the earliest).

Do you think I would insult gravely the academic spirit and / or authors of that manuscript if I just e-mailed the corresponding author saying "Look I still don't understand X because of Y can you please explain?"?

Personally, I think that doing so would just be what science is about: a bunch of people interested in similar scientific topics talking to each other.

I am reviewing the second revision of a paper and am getting tired of this incredibly slow process of me pointing something out that requires clarification just to hear back from those authors two or three months from now (at the earliest).

You don't need to e-mail the authors directly to get the information you want.  The several month delay you are talking about is the time it takes to collect all the reviews, send them to the authors, and wait for a revised version of the paper.  However, in the journals I'm familiar with you could request clarification by asking the editor to send a short message to the authors now and relay the response to you.  Going through the editor might slow things down by a day or two, but not by months.

  Do you think I would insult gravely the academic spirit and / or authors of that manuscript if I just e-mailed the corresponding author saying "Look I still don't understand X because of Y can you please explain?"?

The phrasing of your question is hyperbolic, but yes, this is something that could be considered offensive or unethical.  Sending queries through the editor slows things down only slightly, while it avoids various difficulties:

Reviewers might bypass the editor on requests they would rather not call to the editor's attention (for example, suggesting that their papers be cited).  Along similar ethical lines, announcing to the authors that you are reviewing their paper might help you pressure them for favors elsewhere.  For example, it would be unethical to write "Dear X, I'm a reviewer for your recent submission to Y.  I'm having trouble understanding it, so I fear it might take a while to arrive at a decision, but it could help to know blah blah blah.  Can you supply any additional information?  Regards, Z  P.S. Have you reached a decision about participating in the joint project I proposed?"
It's important for the editor to be aware of all relevant information.  If several reviewers request clarification about something, then that is itself informative about the clarity of the manuscript, even if they all agree in the end that it is correct.  It's also valuable for the editor to see and judge the response itself (and not just to know whether it convinced the reviewer).

As Daniel Shub pointed out in the comments, you can always ask the editor whether it would be appropriate for you to contact the authors directly (it may depend on journal policy, customs in your field, or the editor's judgment of the particular situation).  If the answer is yes, then you are all set.  However, if the answer is no or you don't ask, then you should relay all communication through the editor, and I would expect that to be the usual answer.


Why do some universities not publish the list of persons who obtained a degree from their institution? Some universities do not publish the list of persons who obtained a degree from their institution. In order to verify whether an individual obtained a degree there, one needs to call them, for instance.

Example:

  Contact the Registrar's Office of the appropriate school to request degree certification or enrollment verification.

Why do some universities not publish the list of persons who obtained a degree from their institution? Among other advantages, this would allow to check claim of degrees more easily.

Scumbags like me could include that information when I  calculate a mortgage or credit card interest rate.

That's not a huge deal except I could implicitly include race in those calculations, because, for example, most people who go to a historically black college are black. And it'd be easy to hide behind a mathematical model by saying, "that's the model that reduces the sum of squared errors, not me breaking the law."

So universities shouldn't make that data easy for anyone to access.

(Disclosure: I wouldn't do this but I could easily see someone else doing it.)


Switching field from optics to atomic physics? I'm a fresh junior student doing some amo research. But my professor kept having me focus on the optics stuff. Although I learned plenty of skills, I'm also worried that this can negatively reduce my chance in applying to any real quantum optics/atomic physics labs? Since I had no real experience dealing with atoms, it might be harder to get accepted by those AMO groups? But I'm aimed to work in quantum physics.

The importance of a good understanding of optics cannot be understated in (experimental) atomic physics. I did my undergrad in condensed matter and had no difficulty getting a position in an AMO lab. What I would say is more important than direct experience with atoms is that you know your way around a lab, and I'd say your optics experience counts.


Travel grant for summer conference between PhD and first job? I am a PhD student in the US (mathematics) and I expect to graduate in May.

I got invited to speak in a European conference in June, which is in the awkward time between graduation and my first job (I expect to get a postdoc, and those start August or September). My current department has told me that they cannot fund me after I graduate.

The conference offers some support for young researchers, but it is very meager and I will be flying trans-continentally. I was wondering if there is an outside source that might fund single-conference travel grants for young mathematicians?

Here is a travel grant administered by the Association for Women in Mathematics: https://sites.google.com/site/awmmath/programs/travel-grants/mathematics-travel-grants

Here's one by the Society for Industrial and Applied Mathematics: http://www.siam.org/prizes/sponsored/postdoctravel.php (this requires affiliation with a US university; while your current graduate school and/or future postdoc employer might be unwilling to provide funding they are likely to be more flexible with `affiliation')

I've also heard rumors that a postdoc employer starting in August/September might be willing to support travel in the summer before the appointment starts, but this might just be wishful thinking on my part (but it can't hurt to ask?)


Should I accept review requests from dubious journals? I'm a graduate student with, so far, one published article in a peer-reviewed journal.  Since the article came out, I've been receiving increasing amounts of "academic e-mail spam" from people wanting me to attend their conferences, publish in their (usually pay-to-publish) journals or order research supplies from them.  (The latter kind tend to be the easiest to filter out — even though my field is biomathematics, it doesn't mean I have any use for frozen mouse embryos whatsoever.)

Some time ago, an e-mail turned up asking me to review a manuscript, conveniently attached to the message, for a pay-to-publish open access journal in a somewhat related field.  Googling for the name of the publisher, I found them described as e.g. "a borderline vanity press".

At the time, I wasn't really sure how to react.  On one hand, I could think of several reasons to just go ahead and review the manuscript:

The main complaint about the publisher seems to be that their peer review is insufficient — a claim supported by the fact that they seem to be picking random grad students as reviewers.  Still, given that they're at least making some effort at peer review, surely I should encourage them in that?  After all, if nobody agreed to review manuscripts for them, how could they ever improve their review process?
Declining to review the manuscript might deprive the authors — who, if the journal is indeed a "scam", are presumably the victims here — of useful feedback.  Surely they at least deserve that much return for their time, efforts and money?
Also, if the manuscript did get published in a scientific journal, no matter how dubious or marginal, it would enter the body of scientific knowledge, and might be used as a reference by others.  Given that, surely it is my duty as a scientist to try, given the opportunity, to do what I can to ensure that it is at least correct?

Still, despite these arguments, I initially found the idea of willingly responding to spam to be deeply unsettling at a fundamental, almost visceral level.  Also, I felt concerned that, by doing volunteer work for a possibly unethical publisher, I'd be supporting their business model and perhaps lending them an undeserved appearance of legitimacy.
In particular, given that the subject of the manuscript wasn't that close to my own field, I worried that it might have errors that I would not be capable of spotting, and that, even if I made this clear in my review, the publisher might still use the review to support the publication of a possibly flawed article.

(Edit: Just to be clear, I wasn't worried that they'd reveal the names of reviewers, just that, even if I was the only one who sent back a review, they might still use it to claim that "yes, the paper was peer reviewed.")

In the end, the decision was actually rather easy: after a cursory glance at the manuscript, it became clear that there was no way I could support its publication as written, especially given that large fragments of it were clearly plagiarized, and I wrote back to the journal stating as much.

However, if I ever receive a similar request again (and I assume I probably will, sooner or later), what do you think I should do with it?

You have no obligation to accept reviews from any journals.

In the long term, you should of course accept review tasks, since the review system is built on everyone doing their part in return for the reviews you get on your own papers. But if you think the journal is not serious, there is no need to waste your time on a review.

The problem will lie in identifying what is real and what is not. Apart from researching the journal yourself, as you have done, you should also ask more senior scientists of their opinion.

Edit: Following up on the request for additional input on whether reviewing for dubious journals could be harmful in some way:

I think the greatest risk is that you may provide legitimacy to a journal that is not legitimate. It may be harmful to you if the journal in some way represents, let's say, creationism, in that you may become associated with something you really do not support.

I do not see any clear problem for the authors whose paper you review. Their greatest problem, assuming they are common scientists, should be that they submitted it there in the first place.

Personally, I delete all e-mails with requests from journals I do not know of. I know the journals in my field, and the new serious journals that have sprung up have a firm basis in the community, so they are also "known". I do check on some of these unknown journals occasionally, out of curiosity, and I particularly check the sort of papers they publish and the editors of the journal. That usually tells me if the journal is of interest.

Some of these journals may be legitimate, but they end up being extremely narrow regionally in terms of the origin of their authors and editors, and thus probably also their readership. A new journal is a difficult thing to get accepted unless you start with a wide base in the community, so some of these journals may be very legitimate but still have to prove themselves somehow. The problem is how to distinguish good from bad, and that is truly not easy in many cases.


What are the risks of doing a PhD in a new department? I was recently admitted to a doctoral program to be part of their inaugural class for a new interdisciplinary science and engineering department. The program is located at a top-tier university in the United States and appears to be very well funded by the founding university.

The faculty that they have hired so far are all well established researchers in their respective fields. These faculty have also successfully brought the majority of their students and post-docs with them, so there should be no major loss of continuity as far as research is concerned.

My primary concerns are that:

the graduate curriculum itself is new
the program (outside of the reputation of the individual faculty/university itself) is currently not very well known. Will this look bad to prospective employers (both in industry and academic), or is the reputation of my faculty advisor more important?
professors may need to spend more time doing administrative activities for the new department

What other risks are associated with joining a new program, and are there any professional/academic advantages to doing so?

The risks are as you describe, although I suspect that the third item is not as serious (unless your advisor has a formal administrative role).

The pros are that you will have a lot more input into how the curriculum and the program is shaped. As a new department, people will try things, and not everything will work. There will be many opportunities to suggest improvements and how to do things differently.

If the parent university is well known, it's in their interest to make sure the new program succeeds, so you should also get some benefit from the level of attention paid by them. By bringing a number of faculty over, they've expressed "buy-in" to the new institute.


I've worked as a waitress. Should I indicate this in my PhD application? I've worked as a waitress. Should I indicate this in my PhD application? How will that affect my application?

That sort of employment is unnecessary to include and will be of no benefit if you do. I suggest only doing so if you need to account for a long gap. Even then, you should say why that was necessary to do. And, if you are in mathematics, as the "handle" implies, write about anything you did that was productive in that field.
It might even be better to describe it as "short term, non-academic employment" without describing its nature.
Most people will find this sort of employment irrelevant, and those that don't would be more likely to consider it a negative. You want your application to be positive-focused on how and why you expect to be a success in doctoral studies and thereafter.


If I abandon my PhD program, will it prevent me from continuing elsewhere? After some bad experiences in a master's program, I decided to become a PhD student in the same program. My plan was to finish a paper and leave as soon as possible, meanwhile earning the recommendations that my bad early experiences prevented. That's basically been the situation for a couple years now - longer than I ever expected. At this point, I'm finally finish my projects and I've presented at a couple conferences. I genuinely like the professor I'm working with now. However, I never intended to specialize in this research area; the idea of doing my PhD in this area is very disappointing to me. And (selfishly?), I very much want to move to a new institution.

At this point, I'm not sure what to do. My ideal situation would be to finish my current projects and move to a new institution to work in a field I was more excited about. However, I'm afraid that if I reveal my desires the professor I'm working with will try to sabotage me. I'm also concerned that leaving now will look strange on a graduate application: why admit a quitter? I'm also starting to feel a little old to be starting a new program.

I'd really like to just be done with all this, but the question I keep asking myself is, "Why get a PhD in something you're not interested in?" Maybe, though, there are good reasons.

I'd appreciate any advice you may have.

From what I could glean from this story, one thing is clear: you are confusing yourself a lot and your thinking is quite muddled possibly because of a few adverse experiences. Think on these lines:

What is the 'new' area to which you want to move to? Do you really love the challenges it poses?

If yes, find some nice professors to work with, mail them asking about positions. Forget about your age, the number of years it will take and a host of other details: if you are passionate, the passion will carry you through the doctorate.
If no, ask yourself if you are passionate about the one you are working on. From what you have written you do not seem to be so. Even your publications seem to carry this 'ulterior' motive of getting a better grad school. If you do not love your PhD, then you should seriously consider moving to the industry.

You have publications under your name, so it is unlikely that a professor can "sabotage" your application and more unlikely that he will. Get over the bad experiences with your first professors soon! Don't call yourself a "quitter", instead admit you have been working on a few research problems but do not want to work on them for a doctorate.


Is "I don't have enough funding" the most popular phrase used as hint for rejection From communicating with fellow peers, it seems that whenever a professor rejects a student for graduate entrance, he or she will say something along the line of "sorry there isn't enough funding" or "our funding cannot cover a spot for you this year...but feel free to apply again".

This phrase also work its way into graduate interview as well, where the prof would suddenly mention funding questions, and thinks out loud whether he will have enough funding this year to take you.

While all the students failed to get acceptance offer when something along the line of this phrase is uttered...I wonder if there is a pattern in academia (applying for post-doc position, or research) where rejections are treated as lack of funding issues.

It is likely an amalgam of the truth and a gentle let-down. It's a polite way to reject someone, in that it doesn't place the failure in the hands of the applicant. There's nothing you technically did wrong. Nothing you necessarily could have changed. It just didn't work out.

It's also very likely a truthful reason for not accepting a candidate. It's possible that, given a couple more graduate funding spots (getting lucky with a grant, or promised a few TA spots for their students, etc.) that they might accept an additional student, but when those don't work out,  there's nothing for it.


Is it okay that I don't meet my project supervisor until I can reach a certain subgoal of a long project? I am doing a project in my university under supervision of a professor. This project constitutes many subgoals. My supervisor told me to meet with him to discuss about the project. But I couldn't reach my weekly subgoal yet. Is it okay if I don't meet him until I reach my weekly subgoal?

It is useful to meet with your advisor on a regular basis, even if (especially if!) you haven't achieved everything you had hoped to since the last meeting.

Otherwise, you risk getting stuck in this "Avoidance Cycle":

(Source: PhD Comics)

Also, meeting with your advisor may be helpful because:

If you haven't achieved your goal because you are stuck on something, your advisor may have a suggestion to help you get un-stuck.
If the project is delayed because some part of it took longer than expected, your advisor may want to re-arrange or re-prioritize parts of it to adjust for the new time frame.
Having to report back on a regular basis motivates you to keep making regular, if incremental, progress.

But these are only possible if you keep your advisor informed of what's going on - whether the news is good or bad.


Are patents included in literature reviews? I'm writing a literature review on synthesis and biological activity of some organic compounds, and half the references I found on SciFinder are patents. Are patents typically included in literature reviews of this sort?
Thank you!

Everything is included in the literature search including patents. It depends on how deep you wish to search,  where you wish to stop and which range of years you would like to focus. Papers, reviews, patents, books, monographs, conference proceedings, handbooks, MS/PhD theses, technical reports, etc., are all part of a formal literature search.  You should not include unreliable sources like internet pages until and unless the author is known to be scientifically reliable. Wikipedia should also be the last resort...it is an excellent beginning for a topic search. A good reference list includes seminal papers (earliest ones) and the latest ones, emphasizing the recent ones.


Should I point out typos on students' important forms that I am signing? A prior student of mine is applying for a prestigious certificate in her field. She is asked to list relevant accomplishments. I was asked by the student to sign a this verification form since I am in a position to do just that: verify the accomplishments. Upon reading the accomplishments, I noticed a misspelled word. It's one of those words that is commonly misspelled, and I suspect this will limit her chances of being accepted.

Should I mention this to the student prior to signing my name? I am torn between wanting this student to succeed and having the student be self-reliant.

Additional info about this student: This student is only a "student" in that he was in a professional development course that I had a hand in teaching. He is actually a practicing K-12 teacher.

There was some discussion about the nature of the misspelling. The two words confused were colleague and college.

I suppose the term self-reliant was a poor choice by me in my original question. My question is more accurately stated as Should I point out the typos when the student was not directly asking for such feedback. It is not my intention to teach the student a lesson, as my question came across.

I would point out the error, especially if you have a reason to believe it will be taken into account in some nontrivial way.

I don't really understand why doing this goes against the student's "self-reliance".  I point out errors of this kind in papers that I am refereeing, for instance, and when people read my own papers or course notes or whatever, they sometimes point out my own typos including spelling errors.* I don't think that either I or these other adult academic professionals are failing to show self-reliance.

*: I do all my writing on a version of LaTeX with disabled spell-checking, so I have to spell my words correctly "the old-fashioned way".  Mistakes do sometimes creep in.  I could be setting things up better, but anyway the New York Times occasionally has spelling mistakes.


Can I put an IEEE accepted journal version on Arxiv without paying Open Access fee? I am targeting a IEEE publication which allows Traditional manuscript submission or Open Access (OA) manuscript submission. The OA fee is $2,045.
https://signalprocessingsociety.org/publications-resources/ieee-signal-processing-letters/information-authors-spl

1) If I decide not to pay the OA fee (ie, I go for Traditional manuscript submission), can I still put the accepted paper version on Arxiv?

2) If 1) is positive, what are the benefits of choosing the OA submission? What can't you do with the Traditional submission that you can with the OA one?

thanks!

Non-legal answer:

The journals (theoretically) are there to provide editorial services as well as manage peer-review.

As such, the final product, or "accepted paper version" as you put it, is a result of work of the original authors, as well as the editor and IEEE organization. These people own the copyright and so regulate the licensing. You can't just "put it on arXiv".

Legally speaking:

Consult your agreement with IEEE and potentially a copyright lawyer.

Here is what IEEE has to say, and a quote:

  Can an author post his manuscript on a preprint server such as TechRxiv or ArXiv?
  Yes. The IEEE recognizes that many authors share their unpublished manuscripts on public
  sites. Once manuscripts have been accepted for publication by IEEE, an author is required to
  post an IEEE copyright notice on his preprint. Upon publication, the author must replace the
  preprint with either 1) the full citation to the IEEE work with Digital Object Identifiers (DOI)
  or a link to the paper’s abstract in IEEE Xplore, or 2) the accepted version only (not the IEEEpublished version), including the IEEE copyright notice and full citation, with a link to the
  final, published paper in IEEE Xplore.


Has there ever been a successful copyright infringement suit against someone using a small amount of a protected work in an academic publication? I am familiar with what the US Code says about copyright and fair use, and am specifically interested in actual practice regarding academic publications which use small amount (under 10% of the original) of a protected work, without obtaining permission. Specifically, I would like to know if an infringement suit has ever been successful when the amount of copying has been under the prevailing "substantiality" threshhold, and the copying was in an academic publication. I'm not asking what might happen or whether I should ask permission. U.S. cases and non-U.S. cases would be relevant (to the extent that "fair use" concepts exist in other systems). Alternatively, if you know of a case where the copier prevailed specifically because the use was in an academic publication, that would be relevant.

One case in a similar direction is Sundeman v. The Seajay Society.  A researcher included quotations from an unpublished work in a presentation; this was upheld as fair use.  There's some discussion of the case and the outcome from the Columbia copyright office (have to scroll down a little bit).  There are some other related cases listed on the same page, e.g. involving fair use of copyrighted images in less academic publications.