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How to avoid procrastination during the research phase of my PhD?
I just finished all of my coursework for my PhD program, and am entering the research phase of my degree with a topic already in mind.  I've already started the research, but I'm already finding that I end up procrastinating a lot of my time away.  When I was taking courses, I felt like i didn't have time to procrastinate because of the pace of the classes and I felt like I had to always keep up with the pace.  But now that I have no specific constraints, I feel like its harder to pace myself.
Of course, I know it's a bad habit to procrastinate and I should probably devote most of my waking hours to my research.  Sometimes, (especially when I get stuck) I find it's so easy to get distracted on the computer (websites, youtube, text messages, etc.).
What are some effective strategies to avoid procrastination during this research phase?  How do you stay on task, especially when you get stuck?

you are not alone :).

I think that taking micro brakes of 2-3 minutes can actually be beneficial and sort of restart your mind. But sometime I impulsively check the same site over and over again in a day just because I want to evade. I think it would be much better just to stand up and walk around. That helps me still think, you don't have to sit all the time.

I'm mostly impressed that your "research" phase is distinct from your "class" phase. I'm stuck doing all at once!

All PhDs procrastinate, just read PhD comics ;)

@PaulHiemstra "Abandon hope all [not to procrastinate] ye who enter [your PhD programme]"?

One simple solution I do is to get the hard copy of some papers + my notebook for sketches and go to a coffee shop without my laptop . Also, sometimes I reward myself by staying home and not going to school. Surprisingly, the latter can sometimes be very effective.

"I should probably devote most of my waking hours to my research" with this attitude there's no wonder you end up procrastinating. It can be more productive to instead limit your time spent each day doing research. Remember that doing research requires large amounts of focus; you simply will not be able to put out the required focus throughout a whole day.

I found this article really useful: http://www.mindtools.com/pages/article/newHTE_96.htm

spend 5 minutes daily to motivate yourself. Think how the world will be better after your paper published for eg you will gain recognition, your confidendence level will be high, people will respect you more etc.

I curse whoever installed Warcraft (the original!) and Doom on the Unix machines during my phd...

In retrospect, deleting my StackExchange account would have helped a lot in my case ;-)

One of my key productivity efforts through out has been to ALWAYS have side projects running. I can procrastinate from my legitimate research by doing odd-ball side project research, and through it all I eventually end up with a huge pile of finished work.

Have you read the book How to Write A Lot: A Practical Guide to Productive Academic Writing? It might help you out.

I did not know that PhD students have to finish some coursework when doing their PhDs. I used to think that PhD students need to keep doing many researches only until their papers have fulfilled the graduation criteria and then PhD's degrees are conferred on them. Now I understand it.

I write both weekly and daily 'to do' lists if I'm stuck in a procrastination routine. The weekly lists are more general, the daily ones as detailed as possible, with essentially everything I should do that day, however small it seems. It feels good to tick things off - it shows me that I made progress and gives me incentive to go on. Usually there's one or two things on the list that I really should not postpone for tomorrow, and many less important ones. I sometimes do the big stuff first, sometimes last, it really depends on my mood that day. I also allow myself to push the smaller things to the next day if I don't feel like doing them. That way I feel that I have some wiggle room, but it's constrained to the stuff that doesn't matter much anyway.
I also noticed that I tend to be more efficient when I have something planned at the end of the day, i.e. I know have to leave the office at five and stop working until tomorrow. This gives me a feeling of a small deadline, and deadlines are good at eliminating procrastination.
Finally, as someone mentioned already, nothing beats working with people. Having weekly meetings with my supervisor, where a decision is made on what I will achieve until the next meeting, tops it all.

+1 for to-do lists. For further reference I can recommend GTD-compliant personal planning software (I personally use Nirvana 2).

@user7116 I have got incredible amounts of stuff done in the hour before picking up my kid at daycare! It's magic...

I have found (and continue to find) two kinds of strategies that have some success in preventing me from procrastinating.
Silly, but scarily effective:

As silly as this might sound, implement a blocker like Leechblock or Chrome Nanny and block sites that you waste time on. I used to scoff at such things, but once I installed them, I found myself being forced to spend more time working.
Along the same lines, disable email alerts. Once I did this, I found that I could spend many hours working without getting distracted by random emails.

Less silly, and also less effective
Much of the procrastination when starting research in grad school comes from the lack of clear structure (as you indicate). So the trick is to create structure. For example, if you're working on one problem, and you've spent a little time generating a few ideas, write them down, and methodically start working through each of them one by one, going as deep as you need to go in order to test out an idea. When you're doing so, try to forget about the larger problem, the context, your Ph.D, your future career, and all other "big picture" matters.
More likely than not, the idea won't pan out (most don't!). In that case, move on to the next one.
The problem with early-stage research is that it doesn't look like you're making any progress, so it's easy to slow down and waste time. But if you can measure progress not in terms of "papers published", but in terms of "ideas tried", you'll get some sense of the amount of effort you've put in, and that can help motivate you to try more ideas, and so on. All these failed ideas are teaching you valuable things about your project, and they will eventually be useful because of what you've learnt.

one way of creating structure is by creating your own mini-deadlines. You'll be required to go through certain stages through certain points in time and you'll know when to rest and when to catch up.

I was going to write this awesome answer (+1), but was grading final exams instead of reading SE Academia.

@Fuhrmanator touché !!

Nanny for Google Chrome is excellent. Mine is configured to redirect to my todo list. This is easily one of the best answers I have read here. In fact, it's such a good answer that I am adding http://academia.stackexchange.com to Nanny for Google Chrome.

be careful with Productivity apps like Nanny though. Some sites that usually are a waste of time are actually some of the best tools for research, especially thinking of tools like "wikipedia" and "youtube"

Leechblocking StackExchange now.

Leechblock is your friend!

This fails completely if your time is wasted elsewhere, particularly real-life stuff - e.g. physical comics books or the TV.

IMHO to keep the pace, the most important thing is not to work alone.
First,  when I talk about my project on daily basis (which, sadly, it's not the case now), it naturally makes me working (as I don't want to make others wait, and it would be kind of awkward to say "I did nothing, because I was reading blogs").
Second, often getting stuck happens for a reason - and just 'working harder' does not help. Then it's important to have some other "seed", or a broader perspective, or just to learn that "it is not me who is stupid - this problem is hard for everyone".
But in case you cannot yourself from procrastinating (sometimes I know that it is not a day when I am good at thinking), try do some "white procrastination" - i.e. procrastinate from your duties, but in a way, which is constructive (e.g. learning a new programming language, reading papers in a different discipline, mastering your skills in something else, etc).
EDIT: In a longer run, it turned out that some of "white procrastinations" were more valuable than my "standard stuff". Remember, that not always you know in advance what will be fruitful in the future.

+1 "not work alone" - I did most of my best and most efficient late in the evening while my wife played World of Warcraft beside me.

I got a big boost in finishing my final projects for classes when my wife (then fiancee) sat next me and was available to talk about what I was doing. (She had some field experience with the issues that the project was about, which also helped.)

A strategy to try is to create/set a "work" environment in a specific location.

Remove as many distractions as possible from this location (e.g., if you can get away with no internet connection, do that, don't put any decorations or distracting electronics in the area unless they're specifically work related, etc.)
If you're going to put anything in that location, make it motivational to work.  One of my officemates put a background on his work desktop that said, "Don't be stupid.  Do your work."
Create a "work schedule" now that you don't have classes.  Set a time when you're due at "work" and a time you get to go home.  During your work hours, you go to your work environment/office/lab and you stay there until your work hours are over.

Having this separate location will put you in the mindset of working while you're at that location.  Setting a schedule for going to that location will force you to sit somewhere where it's hard to distract yourself and where you'll start to form a habit of being productive.

A work schedule is very important. +1

I mostly function by "work location" principle - I try really hard to do my work in my lab/office, and not do anything at home (in the room I relax and the room I sleep). Just having officemates helps as well, and I can control my procrastination to 3 times a day -- 10-15mins in the morning, after lunch, and around the afternoon break.

In addition to the other excellent answers, spending most of your waking hours on anything is not good in my opinion. The amount of hours you can really concentrate on research is probably around 8 (maybe even less). I think working 12 hours or more per day (6 days a week) on your research is not really effective. Working  these kinds of hours is going to lead to procrastination.
To be more effective (and less procrastinating) you could focus less time on research, but try and impose more structure and be more effective in those hours. This will make you feel more effective, and preserve a better balance between research and your private life. Especially with hard problems, you'll find that you don't need to spend more time researching, but some time runnng/reading/etc to clear your mind.

That's an excellent point. Because in principle you could be doing research all the time, it makes it harder in practice to focus. Designating "research time" and "non research time" makes it easier to do both.

I think people can do 12+ hours if their research has a lot of statistical programming. The first 8 hours can be intellectually intensive stuff (model building, maths, writing, reading literature, etc) and the last 4 hours can be statistical programming which doesn't require a well rested brain to do properly (assuming expertise in the language).

If the programming is really simple, I would agree. However, if the scripts become more complex, programming does really require a well rested brain.

Poor programming doesn't require a well-functioning brain. Good programming does. I wonder how much this attitude accounts for the vast amounts of terrible programming that I've seen in academia?

I am in the same situation as you are and tried several things to improve my situation in my PhD. I am sharing few ideas that work for me:

Time Slots: I use the concept of time slot or chunk of time (say 1 hour each) for a task where I will only focus or do that task or work. Single-entry-single-exit, no distractions allowed. I know, it's not easy not to get distracted, but I convince myself by reminding that I have other slots for other activities. Large slot of focused work helps me more than small chunks.
Most valuable task first: Doing the most valuable and productive task early in the day makes a lot of difference and it feels great. I observed that as the day progress, I also do better at other tasks.
Leverage on self: I have found few ways to make me act. Some of my favorite ways are: letting the person I hate most (and who would be most happy in my failures) know about my state;  being an example of such habits to my most loved ones (say kids)  etc
Change physiology and tone : I found the way I sit (posture) and the tone of voice with which I speak to myself has lot to do with procrastination. Changing the posture or position, and tone of my internal voice makes a difference. I just emulate a posture and tone when I had been most productive in my life.
Divide and conquer : I divide large task to manageable small tasks (of 1 hr or less). When I brainstorm, I list them  in reverse  order (with the goal/final result in mind). To get results, only taking actions will matter.

I dont quite understand the concept of "leverage on self"... Could you elaborate more?

To the many excellent answers, I will add:

"Just get started," which is a prerequisite to "Just do it." When a task seems too difficult at first, if you start trying to solve it, you often find it's a lot easier than you imagined.
Not all procrastination is bad. It can sometimes be good to delay important decisions until you have enough information. It can be good to work on the more pressing things, and put off the things that are less important.

+1 for just get started. Someone said something about chunks of time, often if you set this chunk to as little as 2 minutes it leads to hours of good work. Getting started is the hardest part.

Oh, you think you're in trouble now?  JUST WAIT TILL YOU ARE WRITING IT!  Or worse, doing revision #523...
My strategy was switching time zones.  I went to bed at 8pm, woke up at 2 or 3am, got a ton done while it was dark and everyone else was asleep.  You may think it hard to go to bed at 8pm - but that is just because you didn't wake up at 2am.  :)
There are a ton of other motivational hacks; like starting the day with an easy task (warm start) you could have done the night before.  And yes, email/internet off.
Take explicit time wasting breaks.  Try http://en.wikipedia.org/wiki/Pomodoro_Technique or whatever.  Mostly, be clear about when you are working and when you are having a break.
Mostly, though, I think you need to find your groove.  If you are bored now, maybe you need to reconsider your topic and find something that lights you up.
This book is pretty awesome (also, the cover lies), but the main point is you need to get at least a solid 15 (actually +1 hour) of time working on your topic a day.  The main idea is that consistent momentum gets you done - working on it one day a week will get you absolutely nowhere.
http://www.amazon.ca/Writing-Your-Dissertation-Fifteen-Minutes/dp/080504891X

Here is one thing that helps me:
Block out work time and allocate relaxation time for each day (relaxation does not mean sleep).  You cannot work 100% of the time, but you need to be vigilant about not engaging in leisure activity during a work time block.
Intersperse designated play time in between work times, but do not let the two types of time periods overlap and become blurred.  If you find an interesting website during working hours, bookmark it and come back to it during the next play time period.
Basically work during the work time, play during play time, and maintain consistent waking/sleeping patterns (try to go to bed on time).
Another thing I forgot to add was don't squander your prime time hours, whether it's by self-distraction or by others distracting you.
So for example if you get your best work done in the morning before noon, schedule all appointments and meetings in the afternoon.  Minimize breaks during your prime hours, since you probably don't need as many.  If you're an evening type of guy, then take care of events and social activities earlier in the day whenever possible.

I agree with most answers above. It IS important to create a working environment. I, for instance, simply can't work at my home computer without being distracted. Here are the simple techniques that worked for me:

set up a 'home office.' For me it was the simple fact of getting-out-of-my-comfort-zone that kept me going.
try working from a coffeeshop. Apparently, it was discovered that the ambient noise of 75 dc (approx. the pleasant buzz in a coffeeshop) is the best for productivity.
schedule the breaks. Breaks are as important for your productivity as the intensive work, so I found it most helpful to actually set an alarm clock for a 10 min break every 1.5 hrs.
keep a "success diary." Basically, it's a to-do list where you can tick the items you've completed. So, first, break down your workload into smaller tasks (for me it was smth like "write min 3000 word today," "finish that damn introduction already," and so on) and then tick them one by one. I guess, you can do it in an actual paper diary, but I used a task management app. It kept me on my toes.

Good luck!

Time accounting is a good way of making yourself aware of procrastination and consequently reducing it.
Here is how I do time accounting. I have an Excel document where

lines are for different activities (working on thesis, teaching, studying stuff that isn't directly related to my work, useful pauses (walking outside, eating lunch, etc.), and "fun time" (watching Youtube, chatting with colleagues, etc.)); the last couple of lines are sums of lines related to productive time and total time
columns are days of the month
sheets are months

Every day I register the time when I come to work and when I leave work.
I register everything I do at work up to a precision of 15 minutes. I do that approximately once every hour so that I do not forget when I did what. I put comments to cells in which I describe more precisely what I did (e.g. when working on thesis, did I read, write, program or what else).
In the progress of the day, I look at the bottom lines that sum my productive and total time to see the proportion of time I have spent productively. When the proportion drops, I try to work harder and take fewer breaks and especially spend less time unproductively. Sometimes when I have successful days I would leave early once my average amount of productive hours is reached. Sometimes I would stay at work longer to reach that average.
I have have monthly averages in the rightmost column. That helps see long-term trends in time use and assess whether I am heading in the right direction.
E.g. last Monday

I came to work at 08:05 and left at 17:20.

I spent

4 hours 15 minutes working directly on my thesis (there is more detailed information in the comment there),
1 hour discussing research with a colleague (which was not directly related to my thesis but still productive),
15 minutes printing things,
2 hours 30 minutes walking outside, having lunch, etc.
1 hour 15 minutes "fun time" (e.g. visiting Academia Stach Exchange)

That was a relatively OK day, but I know I could have cut on "fun time". Once I see figures above 1 hour in the line "fun time" I feel I need to control myself better. (Yes, this month I have been wasting too much time!)
My point is, just knowing how much time you waste and being forced to admit it multiple times per day may help.

first of all, you are not alone in this, as many other people already wrote. I have procrastinated to read your post and opened five other tabs. so this means, we procrastinate, even when we are utterly interested. procrastinating an exciting task resembles pleasure delaying. when i discovered this, it helped me a lot. try to take procrastination as a game you play with yourself. Devoting all waking hours to research is somehow not realistic and in my opinion not necessary. Having a long chat with a friend may seem like procrastination but you never know how your mind wants to unfurl: a friend of mine discovered the topic of her masters thesis during one of our chats. now she has a full grant.

The unpleasant feeling of procrastination comes from feeling you have to do something but not being able to do it. This creates a feedback that reduced your ability to do things. One trick to deal with this is to have smaller more specific goals. Finishing them creates a positive feeling that leads you to feel confident that you can do things. But there is the trap of feeling good about doing things but those things are not helping you in any way to move towards your bigger goals. So these small steps should move you towards your goal and as time passes they should become more challenging.
My second advice is that it is difficult for humans to hold themselves responsible. It is a mental conflict of interests and as it is known people are not good at handling conflicts of interest well. An external party who checks what you do and gives advice on your progress is much more effective. Someone who can regularly check your progress without a conflict of interest. Your supervisor is ideally supposed to be your mentor (like coaches in sports). In reality most supervisors are not up to this ideal. Most of them are either reactive in place of proactive or don't have the success of their student as primary goal (e.g view students as a means of publishing papers). Find someone you trust to care about your progress to keep you up to your plans. It is OK if you don't completed your plans sometimes as long as there has been good reasons for it.

If you are doing a PhD, I can recommend you to read the book "The clockwork muse". This book has good pieces of advice to progress in your writing and avoid procrastination.
It is true most of the things that other have written to you. It is not good thinking that you have to spend all your waking time studying because if you do not have time for yourself, you will find that your body will take it by itself.
So, work 6-8 hours per day (roughly 40 per week), it is good time. So, you can relax your body without feeling guilty.
I read all the comments and it is helping to me too. Thank you for writing about that.
Claudia

I use a tool to block certain applications (like Facebook and Twitter). Furthermore I set goals for myself and hold myself accountable (created a weekend project for that).
Monthly meetings with my supervisor help as well.

You should figure out the reason behind your procrastination and set up a time management to overcome it. You're an engineering student, you should engage yourself to an organization and create projects and portfolio, it'll would make you more productive and it'll help you gain network of friends and develop your skills. Find the motivation to do this and I’m sure it'll be easy for you to overcome procrastination.

Read Zen and the Art of Motorcycle Maintenance by Robert Pirsig. Read the whole thing. But pay particular attention to the discussion of gumption traps.
You will spend many hours reading the book. However, if you absorb its lessons, you will save many more hours in the future.
You must learn to understand your problem before you can hope to understand the solutions

Some explanation of the topics in the said books would be welcome. Especially since most academics have little time to go through entire books.

Yes. what's a "gumption trap" any way ?

Here is a concrete piece of advice I have heard recently, which has been surprisingly helpful:
Try to allocate 2 to 3 hours every day of unbroken time to devote to your most pressing task.
I like this advice because it simultaneously does a few things:

It keeps your expectations realistic. Like many graduate students, I have often find myself plagued with the thought that (as you put it) I should probably devote most of my waking hours to my research. This attitude is not only discouraging, it's completely unrealistic and actively harmful. Even very successful professors end up with so many meetings, emails, teaching duties, etc., that 2-3 hours of time to devote solely to their research can be rare, and is always very welcome.
It helps you prioritize.  Unwisely, I often start out the day with a list of 3-5 big, pressing things to do. Then I feel like a failure if I do not accomplish them all, or (just as likely) I manage to procrastinate and accomplish none of them, which fuels further discouragement and procrastination. Thinking of it in terms of 2-3 hours of unbroken time makes me realize I cannot do all of them at the outset, so I pick 1 or 2 things to get done, instead of 3-5.
It ensures a little bit of progress every day. Ensuring merely that one 2-3 hour task gets done is often enough to prevent a project from standing still. I would rather make a little bit of progress every day than spend a week procrastinating followed by some long late-night hours trying to catch up.

It is a hallmark of chronic procrastinators that we start out with vastly inflated expectations, followed by long periods of no work and short bursts of way too much work. We would get more done if we just set our expectation consistently at 2-3 hours per day.


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What kind of questions can I expect to see on a qualifying exam?
In mathematics, there are certain open questions which are the subject of current research (think of the newest papers in the top journals).  I have also heard that some graduate programs ask questions such as these on their qualifying exam.  How common is this practice?  What kinds of questions can I expect to see on a qualifying exam?  I know that a qualifying exam typically tests the knowledge gained in graduate school, but I'm not sure to what extent this knowledge is tested?  How "advanced" should I expect these questions to be?

I think you shouldn't believe everything you hear.  Mathematicians like to tell stories about posing various famous open problems to certain brilliant young students, the idea being that these students don't have the respect and fear for these problems that an adult mathematician would and that maybe, just maybe, they will innocently work on them and even solve them.  And it seems to be true that every once in a great while a student solves a serious open problem this way.  The vast majority of the time they don't, of course: a problem that the experts in the field want to solve but can't is not going to be accessible to a young student, however brilliant, 99.99% of the time.
So maybe every once in a while a faculty member decides to put a "ringer" problem on an exam.  What do you think is going to happen?  With probability very close to one, no one will solve the problem, and the writer will have to own up to the fact that the question was not an appropriate one and make sure the students were not in any way penalized by its appearance on the exam.  How many times have I seen this happen on exams I have taken, written, or otherwise encountered?  Zero.
In fact qualifying exams test a standard syllabus; they certainly do not test research level mathematics.  Every department does their exams at least a little differently (a very few departments, like Princeton, don't even have written qualifying exams!) so I don't think there's much point in preparing / worrying about quals until you enroll in a specific graduate program.
Conversely, when you arrive in a graduate program, you should start asking for information about the qualifying exams.  And you'll get it: most programs have posted syllabi for quals.  Many programs, including those I've personally been involved with, have years and years of old quals for you to page through.  Nowadays a lot of these are freely available online: in fact, please see Ohio State's webpage: not only do they do they have posted all of their own qualifying exams going back at least ten years, they helpfully post links to qualifying exams at almost 20 different departments.
Thus the way to study for and pass quals is to go through old quals learning the material and techniques that come up again and again until you can do most of the problems on a given qual in a reasonable amount of time.  It's not really any more mysterious or romantic than that...

+1 for "you shouldn't believe everything you hear". Universally correct (:

I suppose its more of an "urban legend" among mathematics graduate students rather than a realistic possibility.

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Why are PhDs without publications seen as questionable? Does this also apply to PhDs who don't secure external grants and/or fellowships?
I'm a 4th year PhD student in Experimental Psychology who should be graduating sometime in May 2024. I'm graduating from an R2 in a rural area of Michigan that recently suspended admissions for their Clinical Psychology PhD program (this is officially public and confirmed. If someone knows what university I'm talking about, you can see it on the webpage itself). My experience hasn't been ideal for a multitude of reasons but this recent news in particular really exemplified how my experience was bottom of the barrel.
Anyway, it's looking like I'm going to graduate from the program with my only author appearance as a last author on a still unpublished (it's been rejected twice) manuscript. Apparently, many who graduate from this program often have 0-1 publications. Students were also discouraged from pursuing external funding because it was seen as hypercompetitive to the point it was a waste of time (yes, faculty said that). The reason for this complacency was the generous internal funding given to the department, which has now officially come around to bite them via this Clinical Psychology PhD first year student admission suspension.
After I spoke to some colleagues, I've heard that someone who has a PhD and no publications is seen as questionable on the job market for both academic and non-academic positions. Why is that? Does this also apply when someone doesn't secure external funding as well? I have a fellowship from the state of Michigan for what that's worth in addition to a visiting appointment at a small liberal arts college (that isn't going well so far, sadly).
I could spend time discussing how I wasn't allowed to work on other projects as I did my doctoral candidacy qualifier project on my cover letter and my recent diagnoses with executive functioning symptoms, but I don't know how that would be seen either. Hopefully, this question is finally in line with moderator expectations at last. If not, mods can take this question down.

This is very field dependent. The publication process is too long in some fields for publication prior to graduation to be feasible.

Do you plan to continue in academia or work as a clinician? I would think (but don't know) that a publication would be less important as a clinician,

@mkennedy Neither. I'm in Experimental Psychology, not Clinical Psychology.

So many questions from students in Psychology in the last weeks here! I like

For the non-academic job market, you asked a question in the Workplace Stack forum, where you go the answer that no one cares what papers you published.

@user111388 I did see that but I still don't think it changes the premise of my question at all. I've heard a ton of mixed things from those within academia or ex-academics who've gone as far as telling me, "If you don't have publications then you don't have a Ph.D." Looks like I need to consult folks within my field now. I'm not sure who's replied to me and studied Psychology.

I didn't have any papers published when I successfully applied to my first postdoc at an internationally top-ranked university (see my own angsty SE post for all the gory details). I did end up getting most of my thesis out there during that contract, and I now hold a prestigious fellowship. I'm in the same field as you. So don't give up yet!

I am curious why (before I edited your question) you were typing PhD with a dot after the "Ph" but not after the "D"?

Not questionable. You’re in a competitive situation, that’s all.

A PhD is widely perceived as a sign that you're qualified to do research. Research generally leads to publications. It seems very unusual to graduate without publications, and casts doubt on the legitimacy of the program. What did you actually do in the course of your degree?
I've seen a program description that said that the student must publish at least one research article - and it must be a research article; review articles don't qualify - to meet the requirement to graduate.
Edit: about the presence or lack of publications in your CV when it comes to non-academic jobs, I am by no means an expert, but my impression is that although non-academics are not likely to care about your publications (unless they're in famous journals like Nature and Science that even they recognize), they would still like to see some publication. Any publication is better than none. No publication brings up questions like the above about what you did during your PhD. Notably this will remain the case even if it's common in your field for PhD students to graduate without any publications. If it comes to an interview, you might need to explain it.

My program does a qualifier project called the 800 Project that must be completed to enroll in dissertation proposal credit hours. The intent of this project was to have a publishable article. However, I only got a poster out of it! The reason is because my first Ph.D advisor left me (as well as the program) and didn't want to do a follow up study with me that would've let me take it from a poster to a full blown publication. That requirement you mentioned for most handbooks is not a thing in mine at all. As for what I did during the course of my degree, it's not a lot (see other comment).

My advisor wanted me to work 7-8 hours a day on nothing but that 800 Project. I also had massive health issues after that and still have dealt with over the course of the past 1.5 years. Long story short, I developed severe cognitive issues among other symptoms and have difficulty concentrating now. I have another conference I'm attending in 2024 but it's few and far between.

@zzmondo1 yeah, but then you wouldn't graduate. The requirements are there because they carry the weight of the university's reputation: by issuing you a degree, they effectively certify that you have met their requirements for a PhD. Illness, death, etc., might be mitigating factors, but they still don't change the fact that you've not met the requirements for a PhD.

I know of a high-school student who had terminal testicular cancer. He was sick enough that he couldn't go to school most days. The school named him a model student at the end of the year, but they did not promote him to next year's class, which is the responsible thing to do because he didn't pass the final exams and had not mastered the material.

I see. As a quick clarification, I am NOT required to have a publication to graduate with my Ph.D in this program. That anecdote does resonate with me as well, I appreciate you sharing that.

@Allure - It seems very unusual to graduate without publications, and casts doubt on the legitimacy of the program. - Are you specifically talking about Experimental Psychology?  In pure math, this is quite normal.

To support the comment of @Kimball, in pure math the dissertation committee decides for themselves whether the thesis is an acceptable thesis. Waiting another year for the paper to be submitted and refereed is quite often impractical. Yes, there is competitive pressure to get something published before graduation, but it is not at all unusual to not do so.

@LeeMosher while it is not so uncommon for students in math to graduate without a peer-reviewed paper at the time of their defence, this is usually explained by the extremely long delay between submission of the thesis and eventual publication.   My experience is that the results are at least publishable; whether or not the student and supervisor have enough stamina to see the process through is a different matter.

@ZeroTheHero Its also pretty normal in molecular biology to not have any publications at the time of graduation. Often because projects in mol biol are almost always bigger than a single person, and often take longer than the length of a PhD to complete. The words in our PhD criteria are "work that is judged to publishable, as a whole, or as a part".

@IanSudbery It's also phrased in my program as "work that's of publishable quality" as well. I have posters but that doesn't hold a candle to peer reviewed publications.

@Allure I thought I replied to you but I forgot. My program doesn't require any publications to graduate. I do want to publish my dissertation at some point, but I don't know how that will look since I will get it published after revisions most likely. If I'm inferring your comment correctly, the publication piece is an implicit expectation by others in the research end of things even if my handbook doesn't say I need one. I might need to start working on another project then but I think that I really, seriously need to re-evaluate what I can reasonably do in this program and after graduation.

My PhD program's standard was not published but publishable, which I think is a far more sensible standard. Published means you can get your PhD as long as you're willing to pay off a publisher and puts your degree on the clock of unreliable peer review timelines; publishable puts the authority in the hands of the thesis committee to judge the work themselves. I don't think this answer makes clear the connection between publishing and job search and I think has too much emphasis on the program over the individual relative to the other answers here.

One of the reason is that PhD thesis of a candidate is sent (by University/institute where the candidate belongs to) for review to the referees who are already familiar to the candidate's supervisor, most of the times. So the review can have a little favour/bias. But if one publish article in a standard journal, it means the article passed more authentic peer review procedure. This is the reason.

Gotcha. What about external funding (grants, fellowships)?

@zzmondo1, what is 'Gotcha'? Grants and fellowship have nothing much to do with peer review decision. I am myself a PhD student in mathematics and i also enjoy research funding but we must publish at least one article in journal to write a PhD thesis. Though this rule is relaxed recently, but I belong to the previous regulation which requires at least one publish article in journal.

@learner 'gotcha' = 'I got you' which here means 'understood'

@Kimball, ok, I learned a new word. Thanks

Your question is based on a false premise, but it’s a subtly different false premise from what other people here are saying. It’s not so much that “employers care about publications during your PhD” as you are saying or that “employers do not care about publications during your PhD” as others are saying in rebuttal. The more nuanced truth is that

employers want to hire job candidates who are impressive, and publications are one way in which a candidate can make themselves seem impressive.

The point is that there are many other ways to make yourself seem impressive and that will make you an attractive person to hire. Candidates come in all shapes and sizes and each one tells a unique story about what they have done and can do. (“Publications”, incidentally, also come in all shapes and sizes, and some will be worthless both in and outside of academia.)
If your CV has nothing to say about you other than that you got a PhD from a poorly regarded program, then you likely wont be attractive to employers, but it’s not because you don’t have publications, but rather because you haven’t revealed anything unique or distinctive about yourself that anyone is likely to be inpresssed by. Conversely, if you are an impressive person who did interesting things (within the PhD work and/or unrelated to it) but just happened not to publish anything, employers won’t care about the lack of publications per se.

I appreciate this answer. I'm seriously hoping my fellowship (even though it sponsors those who have potential to be future faculty) and full time instructor position at this SLAC (which is teaching me the hard way why people don't work full time during their Ph.D) can be distinct achievements for sure.

The premise of your question seems an overgeneralization to me. As far as I understand your comments on other answers, you're specifically looking for jobs outside academia. Academic postdoc employers care about publications (much less about pre-doc funding), because past pubs help them guesstimate which future output to expect from you. Non-academic employers try to estimate the output they can expect from you in their domain, for which papers may be largely irrelevant.
Try to think about how you're a good fit for the next job, rather than about metrics specific to your current one. Which skills is the employer looking for? What relevant achievements do you have? In my experience many employers outside academia don't even know the publication culture in a given field nor care. PhDs on the other hand tend to be aware of their technical skills (eg coding, data science), but much less of their more generic ones. Such generic skill often are deemed nothing special in the context of academia, but highly sought after elsewhere. Examples include skills in project management, supervision, presentation, budget responsibility or coordination of multi-team collaborations. All of these can be documented independently of pubs in an application.
Whatever you do, don't write applications in which you try to plant the idea that your current performance is a failure, but someone else or circumstances are to blame. If your institution has a career mentoring office I would highly recommend talking to them. If you can get hold of alumni who successfully applied for the types of jobs you're looking for, talk to them too.
Relevant experience and limitations: I'm in Exp Psych, have supervised PhDs successfully applying inside and outside academia, and seen many more doing so, because I'm based in a large department and network. However I'm based in Europe, so mileage may vary. Also, I haven't applied outside academia myself after graduating.

-1 Because papers are not irrelevant for future employers in the industry. If they are educated they know that the expected products from a PhD and postdoc are papers. If you didn't deliver any during 3/4 years then they know you are not productive. If I was hiring in the industry this would be a red flag for me.

@TheDoctor What about government? I'm looking into federal work at the moment. I'm in the US.

Sorry but I'm not familiar with the US culture with regards to governmental jobs.

@zzmondo1 There are a huge range of federal jobs. If you're looking at jobs that expect applicants to have a PhD, they're almost certainly going to care about publication record.

@BryanKrause The federal jobs I'm looking at right now don't require applicants to have a Ph.D. I probably should've put this in my original post (may edit it in but I don't know yet) but I'm looking at jobs that are normally Master's level since I think they suit my current skillset.

@zzmondo1: even for jobs that don't require a Ph.D., when you apply with a Ph.D. but no publications, if your interviewer knows how academia works, you need to have a good answer to the question of why that is so. After all, you just spent three years doing that Ph.D., and the typical outcome is a number of publications. Not having any is the equivalent of having worked three years in industry and not having a good answer to the question of "tell me about a successful project you were involved with", because publications, again, are how successful projects end in academia.

@StephanKolassa Between this and Bryan's answer of not mattering who is at fault (his comment was a reply to a downvoted post), I'm legit convinced that I'm going to end up unemployed post graduation for sure. I really feel like it was a mistake to not take a break last academic year when I otherwise should've done so (especially since I planned on not being alive at the end of this past summer) since my research project productivity was immensely poor when I had difficulties with concentration. Time wasn't exactly on my side at the same time though so I don't know anymore.

@zzmondo1 please seek counsel beyond this forum. Most institutions offer this. You just let us know you were suicidal earlier in the year and very much sound like you need help now. Given your background, you know that poor mental health can have a distorting effect on your perspective on the past and future. And I hope you know you matter far more than your situation.

@PBee My ideation was the case earlier this hear but thankfully it's not anymore. Lingering effects could have the distorting effect though (as you described) so I'm going to continue to seek counsel from my therapist.

Because you're competing against people who have published papers
It is rare for anyone to be the only candidate for any position. In order to get the position you need to convince the person/people making the decision first that you're worth calling for interview, and then that you're the best of the candidates that were considered worth calling for interview.
The decision to invite or not is made without knowing who you are or anything about your work. They're looking at your CV for things that make you better or worse than the other candidates. That you've not published anything is an easy way to put you to the bottom of that pile, and pick someone else instead. This is made worse because with recent PhD graduates there isn't usually much to distinguish them, once people who don't have any required skills/techniques are screened out, since pretty much all PhDs for a position will have a strong academic background prior to the PhD and probably in handful of similar subjects.
But the first sentence of the paragraph above is why it's not always the case that you must have published. If you haven't, then it is even more important than usual to look for work through a network of connections. People who aware of your work and skills already may pick you ahead of other options. And, of course, there are also a few people who can get lucky and land a position despite not having any publications.
I'll also add the usual disclaimer about different subject areas having different expectations. I'm told, for example, that it is rare for Pure Maths PhDs to have published by graduation.

For the non-academic job market, you are probably competing against people without a phd;-)

For most non-academic jobs, I doubt they care at all about publications. But there are jobs out there that demand a PhD and those presumably do.

I'm not in your field so I can't speak about not having publications. For my field (biomedical) and many other science fields I have friends in, it wasn't uncommon to have 0-1 at defense but have 1-2 under review and another 1-2 in the barrel waiting to go. All in all I got 6 out of my PhD but only 1 was published when I defended.
The lack of external funding and the attitude is somewhat normal if you're not on the coasts. An application was a requirement of my program but year after year and student after student you saw the same thing; great work great prelim data then some problems about the environment or mentor.

Aside from the replies about publications being a metric of productivity, I would add that your dissertation should be written in manuscript form. So it should be relatively straightforward for you to identify a relevant journal and publish a manuscript or two. It is incumbent on you as a graduate student to put in the work to make it happen.

My program actually requires that my dissertation should be in manuscript form so I have that base covered already. I need to format it with a Table of Contents later down the road once I submit it to the graduate school.

Good. You have 6 months before graduation. Take some time to find a journal that you can publish your work in. Once you find one (or two), examine their author guidelines for formatting details and then format a chapter of your dissertation using those guidelines. Once you are down you should have a a good draft that you can send to your advisor, committee and co-authors for review and editing. Depending on how much of your dissertation is done this should not take more than 2 weeks. You can have a publication or two under review by March.

I disagree with people when they say no publications equals not productive. My PI has been stuck on a paper for 4 years that keeps getting rejected of a student who graduated 4 years ago. There are 4 students/postdocs in the que for their papers to be worked on until it's my turn. I won't even dream about getting a paper in 5 years time. Sometimes it's not the student/postdocs fault.

Preprint servers help on that.

Nobody wants to hear excuses. Either you make your way and work around obstacles (look for collaborators outside your lab, talk to your advisor that you need the paper, he should be able to have multiple papers in the pipe), or you are going to fail in a job you are hired for, too.

A supervisor who doesn't ensure their PhD has at least one paper is a bad supervisor. You're right that it isn't always a reflection on the student, but unfortunately that doesn't mean it won't create a negative judgement towards the student.

Sometimes it doesn't matter whose fault it is. Lets say you're hiring someone to do heart surgery: do you want to hire the person who had a good supervisor and got a lot of great mentorship in heart surgery, or do you want to hire the person who had a lot of potential to be a surgeon but was assigned to a mentor that never let them enter the OR? It doesn't have to be that persons fault for someone comparing them to see who is a better fit for doing the job that they need done.

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text:
Pros and Cons of including less interesting results
For the problem I am trying to solve,
I considered 2 base algorithms and devised about 30 variations on each.
I then threw about 2 CPU-years and ran a number of simulations to see how they went.
When that completed I drew alot of graphs and came to some conclusions like:

Variations of the form X do almost exactly as well as the control
Variations of the Y family can be predicted to have unpredictable (and thus useless) results
The d[1,0*] variation is great under these conditions
The d[0*] variation is great under these other conditions

I took the last 2 and made a new algorithm and then tested that and found further useful results.
Now I am going to write my findings up into a paper.
I have 3 kind of results above:

Points 3,4 (and the subsequent improvements) are interesting and will be the main focus of the paper.
Points 1, 2, are kind of nonresults. They are failures, they did not produce anything useful.

For most it isn't even surprising that they didn't.
For others they are a approach by taken on a similar problem in a paper that inspired me to try and solve this related problem.

So should I comment at all about algorithm variations that were tested and found to not be good?
Why/why not?
Pros I can see:
This would help prevent others, not spend time trying them. I have read that it is a problem that in many disciplines (including this one) "negative results are not published".
Cons I can see:
Takes up space, may confuse reader as to which algorithm is the focus of the paper.
It feels abit weird that of the 2 CPU-years I spent testing these, and the considerable time I spent making the tests, I will only tell the rest of the world about 5% of my results.

You could omit the uninteresting 95% in the peer-review journal version, but include them as an appendix in the arxiv.org version of the paper. That way they're available but you're not forcing anyone to read them...

Or you could include them in the appendix in any version of the paper, if the journal does not have a space restriction.

@Wrzlprmft: That sounds good in theory.  In practice, all the journals I know evaluate the suitability of a paper in terms of (among other things) the total intellectual content divided by the number of pages.  Recently I got a paper rejected from a prestigious journal, and the referee pointed at about 20% of it as being "relatively straightforward" and used that as a strike against it.  A journal which really doesn't care if you make your paper 20 times as long and filled with less interesting results does not sound like a good journal to publish in.

Negative results are as interesting, in my opinion, as positive ones. They allow future researches to know what won't work, and prevent them wasting their time (unless they thing you did something wrong- in which case they will try it anyway :-). However, the main paper should probably focus on the positive part, since most researchers have enough to read already and will not care much about the negative results.
In biology at least, it is frequent to mention some negative result and then include "(not shown)". But nowadays with the facilities to add supplementary material there is no reason to not include some proof. I would suggest to include negative results as supplementary material and just mention them in the main manuscript.

Maybe I should have said "negative results can be as interesting...", so we don't dump any crazy experiment we did into the sup. materials.

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text:
What are the duties of the Chancellor
After asking this question,
I've realised I don't really have a good grasp on what exactly
the Chancellor does.
I know the Vice-Chancellor runs the university, but what does the Chancellor do?
I've been told it is something like:
If the Vice-Chancellor was the Prime-minister, then the the Chancellor would be the Queen.
Though that doesn't really say all that much.
Is it also similar to the corporate analogy of: the CEO and the Chairperson of the Board of Directors?

The analogy you postulated is a good one: the commonwealth Chancellor in such systems is pretty much a figurehead and PR person for the university, if he or she so chooses. He or she may or may not also run the executive council meetings; if not, such a duty devolves to the "pro-Chancellor."

Could you give a example of what kind of thing they might do as a PR person?
Is it like appearing in adverts, or writing to government offices or ...?


text:
What information to put in Bibliography for a Online Course
In preparation for my honours thesis, I recently completed a (free) Online Course on the broader field, presented by a world class expert.
I would like to (am ethically required to?) put this in my bibliography,
though I will not cite it directly, instead citing papers that it referred to.
What information should I put in my bibliography?
I'm not interested in the exact formatting, I'm using software to generate that.
I'm interested in what information I should put.

What category of material is it? It isn't a lecture as it contained 16 lectures and a bunch of assignments etc. Is it a Internet Document? A Unpublished Work?

Should the teaching assistants be listed as Co-authors? They wrote the assignments.

Should I not be putting it in the bibliography at all, but instead acknowledging it more informally?

Why not cite it directly?

This question was asking how (as well as if I should).

It should be appropriate to acknowledge the "head-start" you got from that course in the acknowledgements section of the thesis. It would be unusual to list a course in the bibliography unless there really was no more authoritative source available for some information or a method that you directly used.
The purpose of a bibliography is to cite the primary source of any information directly used in your work. If you use something from the online course worth citing, then you should cite it. However, it's unlikely the information in the course is new, so you should try to track down and cite the original source in a peer-reviewed article or textbook.

In what sense is the online course itself not a primary source? I don't see citing a MOOC as any different from citing a textbook.


text:
Using IEEE Citation style, how should I Cite a Figure, that was based on one in a text?
In a lecture I watched,
I found a very good diagram that explains a concept I am trying to explain.
I couldn't get hold of the original image, so I recreated it in Tikz -- with a few changes to make it perfect for what I am doing.
This lecture is not a primary source for the concept explained in the diagram -- it uses ideas from other papers I am citing. Though I do cite it a few times, where the ideas it explained were clearer than the base texts (as well as citing the base texts).
In the caption should I put:

... , then generating all the layers below. Right: A DNN initialized using the DBN [1].

Or

...  then generating all the layers below. Right: A DNN initialized using the DBN. This diagram based on one found in [1].

Or even -- since the caption is also drawing heavily on the lecture

...  then generating all the layers below. Right: A DNN initialized using the DBN[1]. This diagram based on one found in [1].

Where [1] is the index in my bibliography for the lecture.

Related: Creating a schematic figure based on an existing one

I am interested to know what the -1 was about. (Not too concerned though.)

The most common way folks in my neck of the woods handle this would be to say "... A DNN initialized using the DBN (adapted from [1])."


text:
If someone is a Canadian permanent resident, can they pay tuition fees at the domestic rate?
Every Canadian tertiary institution maintains different rates for domestic students and international students for the payment of tuition fees.
If someone has a Canadian PR (Permanent Residency), can he pay tuition fees at domestic rates? Or, is this facility offered only for full citizens?

I started as an international student, and got my PR while in school. The moment I got my PR I stopped paying the international fees. Of course, this could depend on the University

Yes, they are, at least in Ontario, Quebec, BC, Alberta, and Manitoba.
This covers 90% of the population of Canada, and I'm sure you could find the regulations for the other provinces and Yukon (there are no universities in NWT and Nunavut) if that's where your institution is with a quick search like I did.

Quebec  residents must also provide proof of residency in Quebec.

@ZeroTheHero Only if they want the Quebec rate, rather than the Canadian rate.

@PeterK. well I just learned something.  All I remember are the student protests from many (20?) years ago.

@PeterK. According to the page I linked, you have to provide proof of either.

@AzorAhai-him- Right: But the implication of the original comment was that Quebec residents have to provide residency in Quebec. That is not true, unless they want the Quebec rate. If they're happy paying double, then they only need to show that they're Canadian.

@PeterK. Oh, I suppose.

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text:
Is it okay to begin a chapter without an "introduction section"?
I'm writing my phd thesis. In some chapters I simply begin the chapter with one or maybe two (at most) paragraphs that mostly gives the outline, and then I begin the sectioning. That is, this paragraph has no section, the sections start right afterwards. I'm wondering if this is normal and acceptable or should I put it in a separate section?
This is how it looks in latex:
\chapter{System Modeling}

A paragraph giving the outline of this chapter.
Section ?? discusses this and that. ....

\section{Equation of Motion} %this is the first section of this chapter

Were you given style guide when you started your thesis? Did you ask your advisor this question?

In my University this is quite common to do, but like commented by @scaaahu I would ask first if there is a style guide.

there is unfortunately no style guide.

What did your advisor say? You do have an advisor, don't you?

Related question: Is it necessary that the the chapter introduction be made up of just one paragraph?

i don't think it is the same question. They ask about the introduction "chapter". Here I'm talking about an introduction "section" in a chapter

Please read the first line of the linked question In writing the introduction of a chapter and I did not say this question is a duplicate.

Figure out a style that fits the subject and both engages and respects the reader, rather than some fixed structure, and run with that. The best way to learn to write is to read and write. If you want to write like Wittgenstein, write like Wittgenstein. If you want to write like Kerouac, …, well don’t do that.

In general, sections should be organized to create a chapter just like subsections are organized to create a section and subsubsection should be organized to create a subsection.  In other words, the important unit is the largest one, and the smaller elements (sections, subsections, etc.) are used only the assist and guide the reader in their understanding of a large chunk of narrative.
As such, I would consider it the normal and preferred case to begin a chapter with prose, setting forth an introduction to the chapter before the first section heading.  In fact, a particularly short chapter might have no section headings at all, as it is a good rule of thumb to note use any textual subdivision until you need two of them (e.g., don't divide a chapter into one section, or a section into one subsection).


text:
How to present and refer to a paper that has been finished, and reviewed by almost all coauthors but not submitted?
I finished a paper with my Master's thesis advisor and some other colleagues in January of this year, but we have essentially been waiting on a professor from another university who contributed to the paper to review it and for some reason they seem to not have time to do so (3 pairs of eyes have already looked over the paper).
I am currently in the process of applying for a grant for a conference and I was wondering how to list the paper among the "publications and educational accomplishments" section. The paper is essentially ready for submission but has yet to be submitted.
My questions are:

Should I just list this as a "draft" or is there a better way to
refer to it to convey that we are just waiting on the approval of
one person but it is essentially finished?

Since everything is typed up and ready for submission, would it
be helpful to include the link to the finished document in the
application?

In cases like this recalcitrant co-advisor, I have sent emails like "Please send me any comments within two weeks, or we will assume you are OK with the contents of the paper." May help you get this out, good luck!

No, there's not really any way to list a paper as "It's done, except for one professor who won't get around to reading it."
Papers are usually listed as 1) published, 2) accepted, 3) in review, 4) in submission, and 5) in preparation.
Some people, including myself, find (4) in submission meaningless because the journal hasn't even accepted it for review. This paper is "in preparation," nothing else.
Yes, if you have permission to share the paper (e.g. it's already on *arXiv) then feel free to link that in your materials.

I mostly agree, but I think OP could add some phrase to say that we expect to submit it very soon, especially if it is their only item to list in that section.

It's not the only item to list. I have an REU paper, as well as a scholarship and research award but this is the most serious paper I have completed to date.

@toby544 Meh. What's "very soon"? Why does that matter? It just seems like CV-padding. Just list it as "in prep," that is a perfectly fine place to be.

OK. If it is the best or most serious, then I would add some phrase like I suggested. The link will be useful too.

@toby544 Feel free to post an answer as well.

I don't have much to say. Your answer and comments are good.


text:
Why and how commonly are scientists concerned about open peer review?
Some years ago I published an article in a Copernicus Open Access Journal. They have a peer review process called Interactive Public Peer Review, i.e. the pre-print and the reviews are open access. Additionally, everyone can submit a comment on the pre-print.
I liked this openness, although I didn't get any extra comments other than those of the reviewers.
Some days ago another scientist told me that several scientists have concerns about this openess. They don't like the idea that their work can be commented by everyone.
I would like to know why there are concerns and how many scientists have concerns about this sort of peer review process.
Are there any studies or surveys answering this question? Are there any reports about the effects of this sort of peer review process?

I suppose the main point of contention here is whether the commenters are really going to be "peers" or not. I'm imagining if some random subject gets politicized and "goes viral", for example.

Here's a very simple blog post on a neat trick in security: https://www.schneier.com/blog/archives/2006/01/countering_trus.html Now read the comments, and you'll see that despite the fact that the trick is relatively simple to understand, many people post that "it can't work", proving that they don't understand the technique at all. Now Schneier is a professional blogger and doesn't mind - and doesn't treat at as his job to correct all these misguided folk. But you can see why some people would be hesitant to expose their work to criticism from random people on the Internet.

This answer discusses a survey that indicates blind reviews are much preferred to open ones.  The main reason, from that answer, seems to be

Many people don't want to review non-anonymously.  I know many people on both sides of the fence on this issue.  Once concern is that authors are often sensitive to criticism and may harbor ill-feelings against a person who gives an unfavorable review (especially if the reviewers have not properly understood the paper).  Consequently, open reviewers may be biased (more so than blind reviewers) to colleagues they respect or want a good relationship with.

Fomite mentions a couple of other issues, but I see this as the main one (and it seems the survey does too).  Some other potential issues are

Certain "rivals" or "critics" can try to ruin your career by giving unfairly harsh reviews.
Some well-respect person could make a comment based on a cursory read of the paper that ends up heavily influencing the reviews, and maybe no one reads the paper carefully enough.

Thanks for the mentioned survey(summary), @Kimball. I discovered this article about the ACP publication process.

Scholarly communication and peer review, March 2015. Commissioned by Wellcome, this report by the Research Information Network examines the current status and possible future direction for the peer review of research papers. On pages 22-23 they provide a good summary of the critical aspects of post-peer-review and comments.

I don't know that there are any surveys looking at this, but some concerns I have, or have heard from peers, involve the following:

Open means open, which results in a way more expansive definition of "peer" than in other journals. This can range from the merely problematic (people outside your field ignoring field-specific convention) to crippling (mass commenting on controversial topic by trolls).
It's the antithesis of double blind peer review, which is also something that's being pushed fairly heavily. If you favor that approach, post-publication peer review is something of a problem.
Post-publication peer review is not fairly distributed. J. Random Student isn't necessarily going to get the same kind of comments as Professor Big Deal. It's possible they'll be different in volume, hostility, etc. Standard peer review, for better or worse, does ensure a set number of reviewers.

The Coperinucus peer review process ensures a set number (i.e. two) of reviewers picked as in any other peer review process. Comments from additional (random) people are only on top. Additionally, the commenting process is not as easy as commenting on any random blog, so mass commenting and trolls won't happen that easily.

@FuzzyLeapfrog Those are traits of a system - there are other open peer review systems that don't have the same properties.

Could you please privide some examples for (non-predatory) journals/publisher having a different (less quality controled) open peer review process.

@FuzzyLeapfrog PLOS Current Outbreaks, where commenting is literally as easy as commenting on any random blog, what with using WordPress as their publication engine.

Thanks, @Fomite! Would be great to know how much "trolling" PLoS observes. Sounds like an interesting project.


text:
As a reviewer, what steps can I take after paper is published despite major scientific and ethical concerns, with no explanation from editor?
I recently reviewed a manuscript for a journal I didn't know very well, but which was indexed on Pubmed and Scopus and seemed to be legitimate. In my review, I recommended rejection based on what I considered to be substantial flaws in methodology, data analysis, and interpretation. In addition, I had ethical concerns about the manuscript, including suspicions of self-plagiarism and possible copyright infringement. It seemed that the authors had inappropriately reused text, data, and figures from an article that they had previously published in another journal. I detailed all of these concerns in my report to the editor.
After an automated response from the editor acknowledging receipt of my review, I heard nothing from the journal for 3-4 months. Out of curiosity, I looked online and was surprised to find that the manuscript was already in print! In fact, it had been published less than 2 months after I submitted my review, and the published version is essentially identical to the draft version I reviewed.
I have since made multiple attempts to contact the editor, but have received no response. To be clear, I certainly understand that the editorial team may not agree with my review, but I have been quite disappointed to have received no response to address the scientific and ethical issues I raised. If nothing else, in my experience (and I realize this may be a niche-specific expectation) an editor for any reputable journal will keep reviewers apprised of the editorial progress of manuscripts they have reviewed.
Some readers have asked whether this is an online open-access journal with article processing charges, but instead it is a subscription-based journal. Thus, the journal and publisher are not eligible for inclusion on Beall's List (scholarlyoa.com).
Are there any other steps I can or should take? Anyhow, if I continue to be ignored by the editor, I am considering sharing this information with the editorial board of the journal that published the original paper (the one that I think may have been self-plagiarized).

One thing you can do is to copy your review comments on pubpeer.com

For what it's worth, even when reviewing for high quality journals (in mathematics), I've never been informed about the editor's decision.

@NateEldredge Whereas in theoretical computer science, I'm often informed of the editor's decision.  (At least, for journals; it seems normal not to inform the reviewers of the decision for conference papers.)

There may not be much you can do about the scientific issues.  A profoundly wrong paper should be retracted, and a correction should be issued for anything serious that's objectively wrong and correctable.  However, the problems you've identified (poor methodology and interpretation) may not definitively fall into these categories, depending on what exactly you mean.  There's no ethical reason why a journal can't have low standards or publish controversial papers.  The primary risk is that their reputation will suffer if they publish foolish papers.
It would indeed by unethical if they claim to be a peer-reviewed journal but aren't taking the review process seriously at all, and that sounds like what's going on here.  However, it would be difficult to prove based on an outsider's view of one case.  I imagine that if pressed, the editor would claim he/she evaluated the paper and your review and decided the paper was more credible.  It would be hard to prove that there was an ethical problem, rather than just poor scientific judgment on the part of the editor.
On the other hand, the allegations of copyright infringement and self-plagiarism are ethical issues that transcend journal standards or policies.  That might be a good place to begin, and perhaps more will come out during the investigation.
Here are some thoughts:

Your proposal to share this information with the editorial board of the previous journal sounds like a good idea.  I'd contact the publisher directly as well as the editorial board.
There may be an ethics committee in a relevant professional or learned society.  They could conduct an impartial investigation, which might lead to public censure or a retraction.
You could report these papers to the authors' funding agency, if any.
You could report these papers to the authors' employers.
You could publicize your experience on the web.

Among these possibilities, #1 and #2 seem most likely to make a difference regarding the journal, #3 and #4 might lead somewhere with the authors but wouldn't address the problematic nature of the journal, and #5 could be a valuable public service but is unlikely to change much by itself.

Given that the better journals have more submissions than they "have room for", the state described suggests that this is a for-profit "open access" journal, in the bad sense, so that they want to be able to claim "peer review", but also want to be able to publish as much as possible that's "been paid for".

I plan to move forward with suggestions #1 and #2 from Anonymous Mathematician. At this point I don't feel that my concern is with the authors themselves. It is quite possible that their only transgression was to produce lazy, poor-quality work that should have been filtered out by the review process.

@postdoc4J7: You're in the best position to know, of course, but if the manuscript has unacceptable overlap with a previous paper of the authors, they committed an ethical breach just by submitting it.  They don't get to push the boundaries of self-plagiarism and rely on the referee to tell them it's not okay.

@NateEldredge: to me the manuscript crossed that line, though I'd prefer for the judgment to be made by editors and publishers who have access to plagiarism detection software.

@postdoc4J7 The point of plagiarism detection software is to find the needle in the haystack that matches the new submission. Since you already have the needle, so to speak, there's no need for the software: it's just a judgement call whether the previous paper has been self-plagiarized.

@DavidRicherby: I disagree. I do not feel qualified to judge self-plagiarism conclusively, other than to bring possible cases to the attention of an experienced editor/publisher with access to objective metrics provided by detection software. Moreover, as a referee, I lack the power to discipline authors. I will turn over this issue to the original journal.

@postdoc4J7 My point is just that it's a judgement call, rather than something that software can do. My understanding is that the software just says, "Hey, this looks kinda similar to that" and then it's up to human beings to decide whether the similarity constitutes plagiarism. And, yes, it's not really a judgement call you can make, since you're just a referee and you've done all in your power. But the editors having plagiarism-detection software is somewhat moot at this stage.

"There may not be much you can do about the scientific issues." and "On the other hand, the allegations of copyright infringement and self-plagiarism are ethical issues that transcend journal standards or policies. That might be a good place to begin" summarize the current (rather dismal, IMHO) publication standards pretty well. Given that we are talking about the so called "self-plagiarism" (which is an oxymoron in any decent language) this reminds me of the phrase from one of the Chesterton novels: "you cannot indict him for his true crimes, so you'll have to prove that he stole some spoons"

This happens. A lot. You can continue to try to do the right thing, but it may end up earning you a reputation as a trouble maker which may come back to bite you in the back side.
I have said this before, and despite downvotes I will say it again: if an influential author gets rubbish published despite clear reviews pointing out the problems, you will often find that author and editor are beer buddies at "the conferences".


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Criteria of experience recognition for "TV-L 13" position
I know that the topic of stufe for "TV-L 13" contracts in German universities has been discussed several times, but I was not able to find the answer to my question. I am offered a post-doc position with salary level "TV-L 13". I have a 3 year PhD and 3.5 year research experience. However, the administration wants to put me on stufe 1. They argue that although my experience is relevant for the current position, the type of contracts that I had are not suitable. Is TVL experience really dependent on the type of contract rather than the actual tasks performed? Also if you managed to successfully argue for inclusion of you PhD as experience, how did you argue for that?
I understand that they base it on the following document (I used google translator so only roughly understand that point):

Liegen die im Weiteren erläuterten Merkmale vor, findet zwingend eine Anrechnung statt:
  Berufliche Erfahrungen setzen das Bestehen eines Arbeitsverhältnisses voraus (im Umfang von mind. 25 v.H. einer Vollbeschäftigung). Ausbildungszeiten, Volontariate, Praktika (mit Ausnahme eines Anerkennungspraktikums i.S. des Tarifvertrages), Stipendien, Werkverträge, freie Dienstvertrags- oder sonstige Vertragsverhältnisse können nicht als berufliche Erfahrungen angerechnet werden.
  Eine einschlägige Berufserfahrung liegt nur vor, wenn die frühere, prägende Tätigkeit im Wesentlichen unverändert fortgesetzt wird. Ausreichend kann auch eine gleiche oder gleichartige Tätigkeit sein, sofern sie in der Wertigkeit der jetzigen Eingruppierung entspricht. Maßgeblich ist das für die frühere Tätigkeit nötige Wissen und Können und die dort erworbenen Kenntnisse und Erfahrungen als prägende Elemente auch für die neue Tätigkeit. Beide Tätigkeiten (konkrete Aufgabenstellung) müssen nach Aufgabenzuschnitt und Niveau gleichartig sein.
  Liegen die vorgenannten Voraussetzungen vor, ist des Weiteren nach der "Herkunft" der beruflichen Vorerfahrung zu differenzieren - Zeiten bei anderen Arbeitgebern dürfen auf dieser Ebene grds. nur bis zur Stufe 3 (!) angerechnet werden. Die nicht zwingend anzurechnenden Zeiten können aber als förderliche Zeiten anerkannt werden, dazu s. u..
  Zu den vorgenannten Tatbestandsmerkmalen ist die Sonderregelung im Hochschulbereich zu beachten: Zeiten mit einschlägiger Berufserfahrung an Hochschulen oder außeruniversitären Forschungseinrichtungen werden bei Beschäftigten der Entgeltgruppen 13 bis 15 grundsätzlich anerkannt; bei Beschäftigten der Entgeltgruppen 9 bis 12 dann, wenn sie im Rahmen der Planung, Vorbereitung, Durchführung, Aus- und / oder Bewertung von wissenschaftlichen Vorhaben einen wesentlichen Beitrag leisten.

To make it more weird, I have previously worked for the same university on a short postdoc project and they don't want to recognize even that experience claiming that it was stipend based. All other positions were done outside of German system.

Can you specify what type of contract you had earlier? That's important for your particular situation, since TV-L experience indeed depends on the type of contract. A stipend won't count in any case because it's not an "Arbeitsverhältnis" (you were not an employee).

There were 4 contracts in total: employee (research fellow), employee (collaborative researcher), stipend and contract for service. PhD was scholarship based.

Be aware that this might actually be a university-wide cost-cutting gambit (i.e., backed by a directive from higher up to never hire above Stufe 1), which sounds likely if they don't even recognize their own contracts. In that case arguing with the administration will not be productive; only the person hiring you might(!) have some leverage. If you feel strongly about it, you could make your accepting the offer conditional on getting Stufe 2, and if they feel strongly enough about you, they could put pressure on the administration. (Not that I would recommend that.)

@Jakub when did you start and finish your PhD? You need real employment contracts and only experience from the start of your PhD really counts. Also, if you took 6 years for your PhD they'll just shorten that to 3 or 4 because you were slow for German standards.

@VonBeche I started my PhD in May 2012 and graduated in December 2015. However, prior to that I was working as a doctoral research fellow elsewhere as an employee. In addition, already during the latter part of my PhD I was employed at another institution. The problem is that they do not want to count neither my PhD experience nor any of these contracts.

Apparently my institute is quite generous going from the other comment thread, but counting the years of experience before starting a PhD is never an option. Also they default to limiting the years of foreign PhD experience to 3, the same as a nominal German PhD.

I would have no problem if they counted 3 years of my PhD experience. What I find harsh is that they basically do not want to acknowledge any of my experience, neither research not PhD. From the comments, I see that the policy is very university dependent, which unfortunately, will make it harder to negotiate.

Since universities are governed by state law, it matters which state this is in. In general, you should be hired at Stufe 2 if

you have been employed (i.e., not receiving a stipend or contracted to provide a specific service)
for at least a full year (this can be on multiple contracts, though)
in a similar capacity as the position for which you are to be hired (i.e., after your PhD at a German university, research institute, or comparable institution)
within 18 months (i.e., there should not have been a cumulated break of more than 18 months between these employments, including ineligible forms such as stipends and service contracts).

(If you have more than three years of eligible employment, you are entitled to Stufe 3, but that is usually hard to get.)
Things are a bit more complicated since there is a wider catalog of förderliche Zeiten ("beneficial time") which the university may recognize (but usually don't to save money, sometimes categorically as in Berlin). This includes the more prestigious stipends or scholarships such as DAAD or Humboldt fellowships. This is not something you can argue for, though, but the hiring person needs to apply for with the administration if they believe they have to offer it in order to attract a specific desirable candidate.

In my experience they count the years from the start of your PhD. This would mean that most postdocs are hired at Stufe 3. They sometimes Germanize the starting date though, starting your experience at defense date minus 3 years.

Thanks Christian for the information about förderliche Zeiten as I was not aware of it. The professor does agree with me, but it seems she does not know all the regulations. I will mention this to her as it might help with negotiations with administration.

@Christian is it always limited to the period after PhD? I thought that even PhD students can have "TV-L 13". I worked as a doctoral research fellow before starting PhD at another institution.

@Jakub You have to differentiate "einschlägig" (whose recognition is mandatory) and "förderlich" (whose is optional). The former covers only those work experiences which are basically identical to those required for the new job (and this is not directly related to the TV-L scale -- after all, you could have had an administrative E13 position). Arguably, the experience of a postdoc is very different from that of a PhD student. The years as a PhD student could be counted as "förderlich", but that is at the university's discretion, and different universities handle this differently.

In my case there is not that much difference between PhD and postdoc work that I am doing. The main reason is that I already had a decent amount of research experience when I formally started PhD. As a result during my PhD I was supporting less experienced PhD students and conducted most of my research independently in another country. That has been also acknowledged by my supervisor. Sadly, it is the same degree irrespective of how you obtain it, which means that it is the university's discretion whether they recognize it and by default they are not accepting it.


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Getting a reference from a PhD student
I am getting ready to apply to mathematics graduate programs this semester. As far as I know most school require 3 letters of reference. I've secured two letters but for my third letter I have a couple of options. I can simply ask another professor whose class I have done well in, but I am not confident in the strength of the letter. As for my other option, I have just finished a summer research program under the supervision of a grad student and I feel as if he has more helpful things to say. However, it seems like in general it is not the best idea to get references from people who do not have PhD's. I was wondering what the best course of action would be.

As a grad student, I would NEVER write a letter for graduate admission for a student I worked with. I have none of the qualifications that a professor (and thus an experienced academic letter writer has).  From Harvard's admission page "Letter writers should be faculty or others qualified to evaluate the applicant's potential for graduate study in mathematics. " It should be quite clear why grad students fail that qualification.

I wrote one just after I got my PhD for a friend. It worked. Our mutual supervisor was a bit shocked, however, that they were satisfied with a letter from me.

A very related question, asked from the PhD student side: Is it appropriate for a PhD student to write reference for a PhD applicant?

There are a couple of major dangers in asking a graduate student for a letter:

A typical grad student has never actually read a letter of recommendation and has very little idea of how they are written or what the standard of comparison is.  It's easy to completely misjudge the style or miscalibrate the letter, in which case a letter that's intended to be helpful can turn out to be useless, or even counterproductive.  No inexperienced letter writer should ever send a letter without first running it by a mentor, so you would need to make sure the grad student plans to do that.
Graduate students automatically write from a position of somewhat less credibility, just because they lack experience.  Someone with more experience can compare a student to past students whose later career trajectories are known, but grad students generally can't do that.

One possibility is for the grad student to write a letter jointly with his/her advisor.  That may or may not be feasible, but it's worth checking.

Indeed... Again, as in my other comment, and, apparently not so obviously to students, the point of these letters is not just to "say good things", or even "glowing" things, but to say good things and have considerable credibility in saying them.

If the PhD student is not someone I will not be my labmate but a leader of a volunteer organization, would he has the credibility to saying that? The letter doesn't say much about my research ability (of course), but written pretty well about my other abilities (teamwork, eager to learn, etc)

That won't help much with credibility, since it's a matter of sustained experience.  The problem is that a graduate student has typically not worked with many students and has not done so over a long enough time period to find out what actually became of them later.  So they've got a small sample size to compare with, and all they can do is guess about what this predicts for later success.

In contrast, jakebeal has an opposite thinking about "situations where the graduate student is the right person to recommend"

I don't recommend to ask a reference letter from another student. From my experience, the persons who will evaluate your application will most likely not trust a letter written by a student. In general, a referee is a professor, researcher or a person working in the industry. This person should have supervised you, collaborated with you or you should have taken their course.
So in your situation, you should ask the professor who is supervising the grad student instead of asking the grad student. Otherwise, you may always ask the other professor that you mentioned.

If I have never talked to his supervisor, how would this work out?

The professor is certainly aware that you have worked for his student, so you could talk to him and he should at least know that you exist, or if you don't feel comfortable with that, you can ask the grad student to talk to the professor for you.

Ok, I wasn't aware that this sort of ghost writing was an option. Thank you.

It is common for graduate students or postdocs to have a better grasp of the work that you've done on a project as generally they are the ones supervising and providing mentorship to research assistants/fellows. Generally, a lot of the text of the letter will be written by your direct supervisor (grad student or postdoc) who will provide this to the professor in charge of the lab, who will provide some additional comments and put it on their letterhead & sign it. Thus, you will need to ask both the grad student and the professor to combine forces on the letter. Sometimes the graduate student can facilitate this communication for you and sometimes you'll need to be more proactive. But this is extremely common and expected--the graduate student will provide concrete examples of your work & work ethic that the professor can then use.

Your answer applies to STE fields but not very well to mathematics: there is no lab, there are no research assistants, most undergraduates (even the best) do not do research during the academic year, and so forth.  In mathematics, undergraduates are expected to make contact with faculty sufficiently meaningful so that they can write strong letters for them, usually unassisted.


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How thoroughly do referees review papers submitted to theoretical computer science conferences?
Theoretical computer science conferences usually have a review period of about two months. Programming committee members have potentially dozens of papers to review, alongside their regular day jobs. How thoroughly are papers usually reviewed? What kind of heuristics are often employed to review papers faster? Does correctness of every proof get verified in detail, or do reviewers put some trust into the authors getting it right?

I just attended SoDA 2015, and although I didn't submit a paper, I believe that they only look at the abstracts. And if they want to know more about a paper, they will email the author asking for a full copy. How many papers are submitted and if they are reviewed as the full paper at all will depend on the conference.

There are lots of papers that fall in the category "even if all technical details are correct, this paper is not interesting enough for this conference". Helps a lot so that you can focus on the papers that should be accepted if they are correct.

This might be of interest to you: The NIPS experiment

It varies.  As a first year PhD student I was asked to review a theory paper, even though I had almost no background in the field.  The professor explicitly said I only had to read the first half of the paper, and I only had to tell him if it looked interesting and correct.
At the same time I'm sure many reviewers do a diligent job and don't outsource their reviewing to inexperienced graduate students.
Related: http://www.phdcomics.com/comics/archive.php?comicid=1760

If a PC member has dozens of papers to review, then either a) the conference is doing it wrong or b) the PC member is expected to outsource most of the reviewing work to external reviewers.  A good heuristic for not over-burdening the reviewers is to expect each reviewer to handle no more than 3-6 papers.  With those sort of numbers, it's entirely reasonable to expect that each paper will get reviewed in great detail.
In practice, however, a great degree of variability in the quality of reviewers.  Some reviewers will do a very thorough job---my theoretical papers often get back detailed comments from at least one reviewer that makes it clear that they worked through all of the math.  Everybody in academia also has "bad reviewer" stories about people who didn't take their job seriously.  For example, I recently saw a reviewer provide a review which, in its entirety, said, "Accept as talk." Good conferences with responsible program chairs try to mitigate these effects, but there's always a good deal of noise in the process.

If a PC member has dozens of papers to review, then the conference is doing it wrong. — Theory conferences use a different PC architecture than other areas of computer science.  For major theory conferences like STOC, FOCS, SODA, SOCG, etc., it is completely standard for each PC member to be assigned 30-40 papers.  PC members are strongly encouraged to solicit external reviews for their papers, but those external reviewers are not part of the PC.  It's not wrong; it's just different.

Also, theory conference PCs are kept small because PC members are forbidden from submitting to the conference, and because serving on the PC is a lot of work.  As a result, serving on the same PC more than once per decade is rare, and serving two years in a row is almost unheard of.

@JeffE This sounds like a difference in terminology then... what these conferences are calling a PC member, I have more typically seen called a PC chair, and the external reviewers are equivalent to what I typically know as the PC members.  I will update my answer accordingly...


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Do I have to translate primary and secondary sources into English for a dissertation?
I am writing a dissertation for my PhD in Romance Languages. I focus on Spanish literature and use primary sources all in Spanish and secondary sources in Spanish and English, but I am writing in English. Do I need to translate the Spanish quotes I use from my primary and secondary sources into English for my dissertation? I am using MLA style and I could not find a rule about this issue.

This might be of use: http://ask.metafilter.com/152553/MLA-style-citations-of-unofficial-translations

If it were me, I would err on the side of caution, cite the original language, and then footnote/glossary a translation.

This would seem to depend pretty heavily on the norms for your field, so why not ask your advisor?  I'm not in this field, but would seem to me that if you're writing a dissertation about Spanish literature, you'd presume your audience can read Spanish.  Indeed, the original Spanish might contain elements that would be lost in translation.

I wrote my dissertation about translation in Spanish, and I had to quote several non-Spanish speking authors (English, German, Catalan, French). I decided quoting in the original language and adding the translation in a footnote. When there was a published Spanish translation of the quote, I used it. But if not, I translate it myself.
However, it's a good idea to ask your supervisor if there is a style guide for this issues.

The general practice for translation in literary studies is that you translate if your audience does not know the language of the original, e.g. a Russian source on French literature. It may (depending) also be assumed that everybody reads French. But practices change over time, usually in the direction of increasing the need for translation. The best way to determine what the standard practice is in your field is to look at dissertations and academic articles in the field. I note that in some recent issues of Latin American Literary Review, articles in English are published with untranslated quotes in Spanish.


text:
How to evaluate an implementation Master's thesis in Evaluation chapter?
I am writing a Master's Thesis where I developed an application. The application was developed after the study of another similar application. My application does things differently but the principle is the same for both of the applications. Now I need to write an Evaluation chapter for my thesis.
So how do I evaluate my application in the Evaluation section? Is it by comparison or by mentioning my own results?

Speak to your prof, talk with your colleagues. Check out how other publications have handled a similar matter.

Since you mentioned that the application is similar to another previously developed application, your evaluation ideally should compare how yours stacks up to the one it is derived from. Mention what differences there are in terms of implementation, as well as what it does better, and also whatever pitfalls exist as opposed to the other application.
You want to show what you did and learned throughout the whole process, as well as what potential improvements you might make to the application in the future. Best of luck.