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Why do researchers in areas requiring minimal resources apply for grants?
I heard that many researchers spend a lot of their time (maybe even a half) writing the grants. I understand the researchers that need to purchase some equipment or fund their PhD students, although does not the department fund PhD students anyway?
But what about pure mathematicians and researchers who need a pencil and paper, a personal computer. Do these apply for grants, what for?

does not the department fund PhD students anyway? — Every department is different, but to close approximation: NO.

@JeffE: The poster appears to be a mathematician; math departments do follow a rather different funding paradigm than most other STEM disciplines.

@aeismail: Fair point, but the answer may still be no.  Some math departments (including the one where my wife got her PhD) admit more PhD students than they can support with TAships.

Also in many math departments the TAship only lasts during the 2 terms, the supervisor needs to cover the summer research period.

I am a theoretical computer scientists in a top-10 US computer science department.  To first order approximation, the only reason I apply for grants is to fund PhD students.

My research does not require PhD students, but it's part of my job as a university professor to advise them, I enjoy working with them, and I am considerably more productive when I work with them.
Students in my department that are not funded by research grants or fellowships are funded instead by teaching assistantships.  Being a TA requires a significant time investment, decreasing the time that these students can devote to research.  Being a TA can be incredibly valuable experience, especially for prospective academics, but the first-order criterion for judging the success of PhDs in computer science is the quality of their research output.
My department competes with peer departments — and I compete with researchers in those departments — to attract strong PhD students.  If we/I want to attract strong students, we have to make credible promises of future funding to do research, because that's what our peer departments do.  Prospective PhD students understand the previous point.
I work in a public university in a state with rather significant budget problems.  TAs are paid from state money, which is limited.  Thus, my department can only support a limited number of TAs.  So if I want the department to admit more than a small number of students into my research area, I have to demonstrate that we can fund a majority of those students through grants.
Students need funding to travel to conferences to present their research results, because they need to build a reputation in the research community.  I could pay for my own travel out of pocket if I really had to, but most PhD students don't have that luxury.

There are a few second-order concerns as well.

The day-to-day functioning of my department requires a steady stream of incoming research grants.  Grant overhead pays for a lot of basic infrastructure in my department, including the salaries of all the staff our business office, half of the salaries of most other administrative staff, support for non-instructional non-research computing resources like our graduate admissions database.  Grant overhead is also the source of startup packages for new faculty (for which we are again competing with our peers).
The only equipment I need is "pencil and paper"—or more accurately, a laptop with a stable LaTeX distribution and a drawing program, and basic internet access.  NSF no longer allows research funds to be used for general-purpose computing equipment, so I can't include that in my grant budgets anyway.  But my university returns a small fraction of overhead directly to PIs, and I can use that to buy new laptops, to pay for additional travel (by me, my students, or visitors), or even to help fund RAships.
Tenure and promotion decisions, and to a smaller extent raises, do depend in part on professors' proven ability to attract funding, especially in a department (and college) like mine where most faculty are extremely successful.
Oh right, I almost forgot.  I can pay myself an extra month or two of salary over the summer from my grants.  The university pays me for only 9 months of each year (although that pay is spread over 12 months), so each month of summer salary is actually more than 10% of my annual pay.

All these insights are even more helpful when your school is actually one of my I-will-apply-for schools. :) Thanks!

So you can't use grant money for basic equipment, but you can give it to the university, who immediately gives it back, and then you can use it for basic equipment?  Sweet.

@gerrit It's not as tricky as it sounds. The NSF (and NIH) don't like some equipment, especially computers, being purchased with direct funds - they view things like that as part of the infrastructure they're paying indirect funds for. Along with, you know, admin staff, keeping the lights on, etc. The university giving it back to you is just saying "Rather than us buying more file folders, why don't you spend some of your indirect on what you actually need".

Speaking as a pure mathematician, there are still plenty of reasons to apply for grants:

grants contain supplementary salary, the appeal of which should be obvious.  It also includes travel funding, so one can travel to conferences one otherwise couldn't get funded. (Also, the funding for conferences comes from grants).
generally the funding for graduate students is tied to teaching and comes from a fixed pot.  So having grant funding allows one's students to concentrate on research more.
there's an aspect of "keeping score."  It's generally hard for say a university administrator to judge the quality of a research program, so a grant is an outside stamp of quality.  If one might be interested in getting a different job, it's especially important.
pure mathematicians actually don't spend a huge amount of time applying for grants; they maybe average one every two years or so.  NSF grants last 3 years, with a few extra applications for conference or big group grants thrown in.

Generally speaking, the competitiveness for research money is a way to "ensure" that there is scrutiny of projects so that well founded studies get funded and less so may not. Like all systems there are flaws but the general principle is to extract the best proposals as seen by peers).
The funding for researchers through their departments varies substantially between systems and even between universities within any system. Some departments may fund PhD students, some may rely on external funding. Researchers need to go to conferences and publish papers (which may involve costs) so even if you only need paper and a pencil for the research itself, there are other activities that must be covered and the examples I gave are probably not covered by department finances. For most experimental research, costs for equipment, labs or field visits can be substantial.
In my system, partly due to credit crunch and a general interest in cutting costs everywhere, more and more must be covered, even office costs for performing the research and office costs for PhD students.


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Best strategy to learn programing for graduate research data analysis in biology
I'm actually asking this question on behalf of a sibling who's pursuing a PhD in Biology. While I'm a Mechanical Engineering student and am "computer-savvy" and experienced in learning programming languages from technical textbooks and internet forums, she is very inexperienced in programming in any form.
What textbooks would you recommend for the self-teaching of MATLAB and/or Excel for the purpose of data analysis? If she wanted a technical book, I could find one in five minutes. I'm looking for a book that can explain MATLAB to an inexperienced user with no programming background.
Also, if you learned MATLAB or a similar program with great success, what tips would you give for self teaching? Thanks!

Internet resources have been more accessible (physically and conceptually) than textbooks in my experience

I agree with @rch. I learned Matlab via online sources. There were a number of beginners booklets online already back then (~4 years ago), I imagine there's more now - it just takes some searching and picking the one best suited to the person.

If you happen to have bookmarked those resources when you used them, could you please post an answer linking to them? Online resources would work just fine as long as they cover MATLAB from the ground up. These are for a person with no programming experience.

In my experience, student blogs are good ways to follow along and get a SPECIFIC TASK done. Using this she can gain some familiarity with MATLAB. But regarding teaching the basics, MATLAB has a user manual for that, which doesn't assume programming knowledge iirc. Academics also make tutorials for students/new researchers (http://www.math.mtu.edu/~msgocken/intro/intro.html)

Another vote for sticking to open-source.  Matlab is pretty good at what it does, but I think the flexibility and handling that a language like Python introduces is valuable.  I am not in the field of Biology, but it seems like there is a relatively strong Python community (http://www.biotnet.org/sites/biotnet.org/files/documents/25/biopython_intro.pdf) (http://www.programmingforbiologists.org/why-python).  I used this site (http://www.pasteur.fr/formation/infobio/python/ch01.html) to help shape my own introductory lecture that I gave.

Is there any room for "don't"? Depending on your specific set of tasks, there are probably better (and cheaper) alternatives.

@pheidlauf, I'm sorry, I wish I could help you but I don't have the links anymore. And now that I'm living and breathing Matlab, I'm not sure that I could even judge what a good resource is for a beginner. But I would suggest looking for a resource that is close to something she knows well. Does she understand data analyses well? Then look for something that covers that. I started from something that covered digital signal processing, which I read about before.

I think Python would be much more suitable. Also, knowing some linux shell magic and maybe some Perl is very helpful for basic analysis and parsing.

@Bitwise did you really just recommend Perl to unexperienced programmers? I agree on Python, it can solve 99% of the problems she will likely encounter, if not 100%.

The best tool to learn depends on the actual job. For very basic data analysis, Excel has the lowest entry barrier, but the learning curve gets steep soon. Learning a full language will take some months, but will greatly expand the things she is capable of doing. Also, knowing programming in a field where everybody uses Excel can be a great advantage and unique feature for employment.
One important factor deciding which language is the environment she is in. Having people used to the tools and perks of a language can be very useful when learning from scratch. On the other hand, I'd only count "modern" options (some old professors are very fond of FORTRAN77 and IDL, but learning these is like learning to train dinosaurs).
She should consider not only her lab, but also ask at the Bioinformatics department, and take a look at other labs in the branch she is in. In my experience, for the most informatics side of the field, people use mostly Python, C++, and Java for some machine learning. I have encountered some MATLAB, but definitely not much.
One last note: I think in learning your first language you want the cleanest and less quirky possible. MATLAB in this respect is a mess of a language, with a crappy syntax and bad scalability. My personal choice would be Python, so here are some introductory materials:

Summer school on scientific programming and introduction to Python. All materials are posted.
The official tutorial. There is a lot of things that are not for useful for scientists, but it is very good introduction to the language.
Khan academy. They have everything. Very nice.
Coursera has a full assortment of courses. She will surely find something of interest there.

If it is just to analyze, do some stats, and plot data, there is no need to learn python or c++. It's true that Matlab is not  strictly speaking a programming language, but it has the advantage to have a large set of ready-made functions that are tested, debugged, and reasonably idiot-proof. It's far easier to learn than writing good quality c++ code.

@Jigg I definitely don't think C++ is a good entry language. But having been there, I do think that Python with the Scipy stack is easier to use and to understand than MATLAB, providing the same functionality.

MATLAB is fairly complete regarding data processing, but many things are hacky (nargin) or not neatly designed (parenthesis to call functions AND access elements, lack of namespaces, all modules loaded in the workspace).

It sounds like I need to check Scipy more in depth. For now I MEX stuff when I need more flexibility.

Learning Matlab (I prefer) or R will ultimately make you a more efficient researcher: not only do both languages allow you to do advanced mathematical data processes, but also make publication quality graphics. Excel requires much more work to get data visualization publication ready, in my experience.
While your friend is a biologist, and field where my impression is that R is more heavily used that matlab, if she really wants to learn matlab, this book is great:http://www.springer.com/earth+sciences+and+geography/book/978-3-642-12761-8
While it is designed for Earth Sciences, the tools are universal. Not only does it teach you how to use matlab, but, it goes over statistics and numerical methods as well in a very easy fashion. This book was used in one of my masters classes, and most of the people in the class barely had calculus 2.
My real suggestion is to explore R, as I think in general the world outside the physical sciences is moving towards using that.

In Bioinformatics, I'd say the main trend is Python, MATLAB being in the corner. R is perhaps more common in the Biology part.

If you happen to have bookmarked those resources when you used them, could you please post an answer linking to them?

A good online resource for MATLAB is found at the Introduction to Computing Resources page, put together by Andrew Török of the University of Houston. I linked to the main page as there are other resources listed in the contents menu which your sibling may find useful.

Also, if you learned MATLAB or a similar program with great success, what tips would you give for self teaching?

As with the self-teaching of other subjects, there is no good substitute for getting your "hands dirty" and playing around with what the tool has to offer. Start by learning the basics (as discussed in the online resource linked above), and progressively increase the complexity until you reach the desired level of understanding.

Edit — I'm including a few more online MATLAB resources that I know of:

UCLA MATLAB reference
Michigan Tech MATLAB help (also mentioned by @rch above in the comments)
Utah MATLAB help
GMU MATLAB page
Indiana MATLAB help

The book I used as an undergrad: Scientific Computing with MATLAB and Octave written by Alfio Quarteroni.
It's not a beginner's tutorial, but it gives you the mathematical theory behind some of the most used functions. I found it useful because it really helps to know what the functions actually do. It contains sample code as well.
One thing that biologist often need to do with Matlab is image processing. If it is the case, the book Digital Image Processing Using Matlab can be handy (lots of practical examples).
The second is most likely available in the library of your/her institution, the first is a bit more confidential but should at least be available through inter-library loan. Note that a good person to ask about books and resources is your librarian.
As a side note, an open-source alternative to Matlab is Octave, which has a good online community around it and shares a good deal of its syntax with Matlab.

(with full agreement with the people who says that online resources, including even youtube are nowadays better than textbooks)
If I were her, I first would learn statistics (that is relevant to her field). Is she an ecologist? A biochemist? Doing in silico bioinfo? They are pretty different fields.
Learning MATLAB without having any clear idea about mathematics (linear algebra, statistical tests etc) she wants to use, is pretty damn difficult. This is the typical "I just want to do ANOVA! just tell me where i should click?" problem. On the other hand when she is already able to write down basic equations to paper, and understand what letter is what, and have at least a vague idea of the mechanics, the MATLAb/octave part become pretty straightforward.
Two remarks:
- I wouldn't waste my time reading 400 pages books discussing everything from PDEs to symbolic calculations. Any 2-10 pages long tutorial from the net gives the same info, with often better pedagogical part.
- While Excel has many annoying features, it is very good to organize and save certain type of experimental data. You can put anything in it, figures, short notes, explanations for yourself, keep everything in one place and for printing one can use something else, gnuplot etc. Of course, it is subjective.

+1 for learning statistics relevant to the field. I would add that she should find out what software application is most suitable for what she wants to do. For example, in many uuniversities SPSS is used in life sciencies. And it is not clear from the OP's post whose idea it was to learn Matlab or Excel.

True. These are very different programs. Most probably there are already existing experiment notes, teaching materials, statistics tutorials, licenses in her new laboratory, that are tied to one or the other software.

Why do you assume the person doesn't know about statistics?

Since the OP not specific about the level, I assumed that she has an average biologist background. Also my personal experience is that people who have solid statistics training, can figure themselves out pretty fast how "ANOVA(..)" function works in Excel.

As said previously in the answers to the question, the textbooks do not usually work great for programming.
I am an Engineering Physics student working with Applied Mathematics and have been using and promoting MATLAB since I started. However, this summer I was out of my license and therefore turned to Anaconda.
I am going to go off on a spin and recommend Anaconda Scientific Python Distribution. Anaconda is based on Python which is a great language to start of on, if not the best. Not only is it free and open-source but can be used in so much more then MATLAB. They also explain why they give this out for free on their website.

We want to ensure that Python, NumPy, SciPy, Pandas, IPython, Matplotlib, Numba, Blaze, Bokeh, and other great Python data analysis tools can be used everywhere.
We want to make it easier for Python evangelists and teachers to promote the use of Python.
We want to give back to the Python community that we love being a part of.

From my experience so far, it has been more intutive to implement more complex tasks as well as being even a bit FASTER!!

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Submitted to a non Scopus-indexed journal, later found that University only accept Scopus journals. How can I submit to another journal?
I submitted a paper to Thomson Reuters ESCI Journal, and they are asking me to complete a registration and pay a fee of around $400 to publish the paper.
But later I found that my University gives preference to Scopus-Indexed journals. How can I cancel the previous submission (the paper has not been published), and how can I submit to another Scopus-Indexed journal?

Write to the editor and withdraw it? I don't see what the question is here.

In what way does the University give preference to Scopus journals? In evaluating researchers' productivity?

Voting to reopen. Thomson Reuters ESCI is not a sign of a predatory journal; calling it a duplicate is completely inappropriate.

If your paper is submitted but not accepted or published, it is still time to withdraw your submission. This is generally done by writing to the editor. I would recommend to do this as soon as possible to avoid wasting editors and reviewers time.
Now if the entire process is already over and you only have the APC to pay, it might be more difficult to withdraw but you can still try.
Once the paper is published you only option is retraction but I would not go that route just to please your institution's wishes.

@Roland, "not ethical" is rather too strong in my opinion. "Not polite", "not collegial", "not professional" might all be appropriate, but "ethics" involves a much higher standard that implies that OP is doing something that is considered morally wrong by most people in a community. I do not see that as the case. Yes, the journal would be justified to blacklist OP for wasting their time, but not because they lied or stole or cheated or something like that.

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Can I apply for a post-doc in theoretical physics without publications?
I am a theoretical physics PhD student from France. I have no papers after 5 years of my PhD. The problem I am working on has hit many road blocks and even my supervisor has no clue how to proceed. The results I have obtained are valid only for some aspects of my problem. So I could probably publish a paper, but if I do, it will not be a high impact factor journal.
My question is: can I apply for a post-doc without publishing any paper from my PhD?
I would like to apply in North America/Europe etc.

Of course you can apply.  I suppose you are really asking what your chances are.  It would be better to hear from a theoretical physicist, so I'll just make comments: in mathematics, it used to be extremely common for the PhD to get awarded prior to the first publication, and postdocs were awarded almost entirely on the strength of the recommendation letters (in confluence with an least reasonable research statement).  For instance I got my PhD in 2003, got a postdoc in 2003, got my first publication in 2005, and got tenure at a top 50 US research university in 2011....

....But I think times are changing.  In my experience, the distribution of graduating PhDs w/o publications is increasingly bimodal: either they have no interest in a research career (so are not applying for postdocs) or their program, their advisor and their thesis work is superior, and they are not going to divulge their superior works until they are suitably mature.  My guess is that physics, however theoretical, is at least a bit more publication-centric than math.  Anyway, if you truly are not satisfied with your results, maybe see if you can stay longer in your program.

Do you have preprints (for example, on the arXiv)? Like Pete L. Clark, I am also not a theoretical physicist, but I imagine your chances would be different between (1) having preprints but no formal publications, and (2) not having anything for people to read. I assume you have not written a thesis yet.

You could apply to a post-doc without a high-school degree -- an application only involves sending in the application package. No one is going to stop you from mailing it in.
That says nothing about whether or not you will get the post-doc, let alone if the secretary will just toss it in the recycling bin before it even gets seen by the faculty.
The real questions are:

What are the eligibility requirements of a post-doc?
How competitive is the post-doc?

For the first question, most post-docs require a PhD in hand or late-ABD status. Most do not require publications and if they do, they will state that clearly on the application page.
The second question is the real question. Post-docs are usually extremely competitive. In order to be a finalist, you have to be n+1 of whatever quality and quantity the faculty is looking for.
If your peer group has no publications (0) and you have 1 publication, you will stand out as the +1. Since it's not possible to have -1 publications, it's hard to stand out from a group  with 0 publications to your name. If your peers have 10 publications, you need to have either more in number or more in quality, or something else that your competitors don't have.
For example, some post-docs in some fields value other things than research publications. I occasionally read for post-docs in the humanities and there the quality of your dissertation and proposal is more important as most post-docs in those fields apparently have zero or near zero publications at the ABD stage.
And finally, there are some post-docs that just aren't very competitive -- either because of geography or topic or paucity of funding or other reasons.
I would also be remiss if I didn't mention the social/human factor. Many people get post-docs on the strength of their recommendation letters, as Pete Clark mentions. Strong recommendations attesting to your brilliance and to the problems you faced with your current project would go far in convincing a postdoc committee to take a chance with you. You could also try to ask your supervisor to use some of her/his social capital to try to persuade a colleague at another university to take you on.
Your mileage may vary.


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How can I avoid having a specific teacher?
I am mostly very happy with my teachers - they are almost all good or excellent at teaching, nice as people, and knowledgeable about their subjects. However, my chemistry teacher is a poor teacher, has behaved very unprofessionally in the past, and I suspect possibly does not know much about the subject.
The bottom line is that this teacher is, in my opinion, lacking in both subject matter knowledge as well as knowledge about how to behave with students. I want to study chemistry but I do not want to study with them. Changing schools is a tremendous challenge for me and because of my other teachers, I would strongly prefer to stay in my existing school.
Are there any options here to avoid this teacher in the future?
Edit: The issue was resolved, as the teacher failed to pass the exams they would have been teaching (teachers at my school have to do the exams every so often, presumably to check that they are competent), and I am very happy with the teachers I have instead.

I'm afraid questions about high school and undergraduate studies are not within the scope of this site.

@sweeneyrod, yours is a very good question.  Perhaps if you made the question more general (by editing out your age, for example), this question would be deemed more acceptable for this site.

@JoelReyesNoche I have massively edited the question to get to the core of the issue, which I believe is an issue at all levels of study. I hope we can re-open it.

Can you narrow down you question? Do you want to study chemistry or do you want to avoid her? Your middle part of the question does not go with your concluding question.

Please, can you add the level of your studies? I think it would be helpful as mechanics at high schools and universities are quite different. But in general, if the chemistry subject is mandatory and they are not many others how complain about the teacher I am afraid you cannot do much. After all, not all the people we encounter during our lives meet our expectations.

It's not clear to me what the question is here.  If several people teach the course, then take it from someone else.  At a university, this is generally easy; at a high school, it may require a special request, but you can at least try (it's often smoother to say you would like to take it from X, rather than you would like to avoid Y).  On the other hand, if this is the only chemistry teacher and you want to take chemistry, then you are stuck.  There might be other options (independent study, summer school, a course at a local college), but that depends on your specific circumstances.

@Earthling The question was more what do about the teacher, rather than how to avoid having them at a higher level of studies (sorry, I may have gone off on a tangent at the end of the question). Would that still be on topic for this site?

This question appears to be off-topic because it is about high school teachers.

@sweeneyrod "What to do about a teacher" is off-topic for this site because it is an administrative issue and not an academic issue.

I'd argue that this is on-topic, because the question can apply equally well to grad school courses in its current form.

I think there are two parts to answering this question. First, you should make sure that the teacher is incompetent and not merely unlikable. Second, if the teacher is incompetent, there are a number of options available to avoid studying with them.
With respect to the first point, it is important to note that a teacher can be unlikable, and perhaps even appear ignorant (to students), while still being great at his or her job: making sure you learn things. For example, group work and peer instruction are known to be effective teaching strategies. At the same time, they are also quite unpopular with students, and some students even take the view that the instructor is not doing their job when these strategies are applied (even though the outcome may be very good). Professionalism and teaching style are very personal traits, and I've not seen any evidence that they have strong impact on student learning outcomes. It sounds like maybe your personal dislike of the instructor is clouding your judgement about whether they could be an effective teacher. A teacher has only one job: making sure you learn things. If they can do that job effectively, then it shouldn't matter whether you like them or not.
Talk to students who have finished the course, and find out what they've learned. Often its only after such a class is complete that students realize they've learned a lot. If you know you'll get a lot out of the course, then you should probably take it even if you don't like the teacher.
On the second point, if the teacher really is incompetent, and former students are in strong agreement on this point (and they really don't seem to have learned anything about the subject), then you do have some other options:

Many schools will let you take online courses from other universities for credit. For a chemistry course with a lab, this may not work out, but otherwise this might be your best bet. You can shop around, find an instructor that you like, and still get credit for the course.
If the instructor is genuinely incompetent, you could speak with the school administration, and make a formal request for a different instructor. Often your request will be ignored, but I have seen this result in a new instructor being assigned once. Again, it is important that you make sure this is an instance of incompetence and not unlikeability. This is a serious step, and could have implications for the instructor's job (especially if they lack tenure).
You might be able to wait it out, and take the class with someone else. At the university undergraduate level, this can be the easiest solution, provided that the course is not a major prerequisite in your program. At the high school and grad school level, there may not be an alternative instructor in that subject area, so this may be infeasible.
Attend the class, but plan to use external resources to study. Consider forming a study group at the start of the semester, and meeting several times a week to talk about class material. Use online courses like those offered by MIT's Open Courseware, or any of the MOOC companies, to supplement the lecture material, and shop around online to find the best textbook at your level for this topic. You can make sure that you've learned the material well, even if your instructor is unable to help you learn it.

Thanks for the response, I have been wondering whether or not the teacher is actually incompetent, but I am fairly sure they are. Originally, I was asking for any advice if for if I went with option 2 - for instance, to write down any notable unprofessional or incompetent behaviour. Do you have advice about that?

Well, it ultimately depends on what you hope to do with that information. If your goal is to learn the course material (which it should be), then collecting that information is probably not going to help you. In the best case, you'll get a new instructor switched in after half the term, and if all you have to show for it is comments on unprofessional behaviour, that's not a winning outcome. Since you know that the instructor is incompetent in advance, a better solution is option 4, where you actually learn the material.


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Post Doc recommendation letters sent but no response
I have three letters of recommendation sent to a potential post doc employer but when I asked if my recommendation is completed, I did not receive any response from him and it has been a week. Before that, the post doc lab head told me that once he received my letters, he will arrange an on site interview for me. He was also quick to response to my email and showed great enthusiasm before sending out the letters to him.
Does that suggest something wrong with the letters that raise concern? Does that mean I'm out of the game or should I follow up with him? I may be impatient but as indicated in my previous question, my relationship with my advisor was not good and he had submitted a letter drafted by myself.
Very worry. Thank you for advice.
Update: Nevermind, just got interviewed and offered at other top ones.

Professors have a habit of forgetting to respond to emails. It's not rude to send a follow-up email at this point asking again.

In my experience, if application materials were sent directly to researchers it is a pleasant surprise if any response is received at all.


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What does "corresponding author" mean?
What is the Corresponding author about in the list of authors of a Journal or Conference paper? As fas as I read, it is the person who confirms results or whom actually is the intellectual mind of the idea behind the published work. Can it be more than 1 author in some cases then?


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What can cause the date of submission status to change without a change of status "under review" for Elsevier editorial systems?
I have a paper submitted to a journal of Elsevier.
From "Manuscript Submitted" to "with editor" took one day; then it was  "with editor" for five days, and then "under review". One and a half months later, the status of the paper was still "under review", but the date of status has changed.
What can cause the date in the submission system to change in the absence of a change in status?

Unfortunately it means nothing.

@StrongBad: Oh, maybe I did not make my intention clear enough.

possible duplicate of Question of under review -situation

@Kurt no I understood your question. The causes range all the way from something interesting happened with the progress of your manuscript to they rebooted the server.

@StrongBad: Ah I see; so spending time to guess is wasting time :)

@scaaahu: I do not see anywhere of this question making you vote to close :)

@scaaahu: Guess what? Just because something is insignificant to you does not necessarily mean that the thing is insignificant to others. Suggest you to think macroly.

I have nothing personally against you. The other question is a dup of this one, in my opinion. Both question have the situation "with editor" and then "under review" for a while. The only difference is that you name the publisher and the other one didn't which makes the other one more general than yours.

@scaaahu the questions seem different since in this question the status was recently updated (although not changed).

@StrongBad The OP of the other question commented that there was no time stamp of the status. To me, the spirit of the two are the same, like you said in the previous comment, it could be any reason.

I'd suggest you to write to the Elsevier support. Those status messages are quite opaque, and implementing a full "paper history" feature does not seem a daunting task. But if no one complains and submits bug reports, they will never have an incentive to change. If you know the editor or see him/her at a conference, you may consider pinging him/her about the issue, too.

One and a half months is not too long. If it stays like that for 6 months, then worry.

@Michael: Sorry, but my question is not about the length of time of being under review; it is about the changing of the date of status!

I know. And yet, from my experience (although not with Elsevier) it doesn't mean much. I doubt that your article was either accepted or rejected in five days (thus changing the status). It's probably a technical thing. If you're really nervous, just mail the editor or something, but take into consideration that an editor who gets mail like that feels like a parent with kids in the backseat asking "are we there yet?".

@Michael: Sorry, it must be the original statement of my question that confused you. I have edited it :)

I've had a similar experience with a Springer journal. As far as I can tell, whenever editor manages to find a reviewer, status changes to under review. This date change might have happened because he might have found the other reviewer(s) recently. Hope that helps. @Kurt

If you didn't sample the website too frequently, it's possible there was a status of 'with editor' for a day or two there. It can happen if the reviewers give back their reviews and the editor is still not satisfied (e.g. if there are two contradicting reviews, or if one declined). Since you sampled it, say, every few days, you just missed the status update and saw only the 'under review'.
I once had this 'with editor' and 'under review' back and forth for some time, not just once (it wasn't with Elsevier, though).

When a paper is assigned to a reviewer, the reviewer may decline or fail to review the paper.  In this case the editor will assign the paper to a new reviewer.  The status date will change at the day the new review was assigned, but the status will remain the same.

Thanks for your interest. But is the answer valid for my situation? I mean, would a reviewer decline to review a paper after one and a half month?

If it took that long, they probably just failed to submit a review.  We cannot be sure what happened in your situation without more information.

sometimes reviewers agree to review, but then fail to actually do so, as AnonymousPhysicist says. It's also possible that it has been sent to multiple potential reviewers, each about a week apart, and each of the first few declined to review, so it was sent on to another reveiwer. Or that it was sent to thr first batch of reviewers and the editor was slow to invite a new batch when the first declined. Or possibly, the date changed when the 1st review was submitted and you are still waiting on a 2nd or 3rd review.

There could me multiple reasions for the status date to change:

Reviewer comments are added to the database
The reviewer changes
Editor checks the database

See this question: http://www.editage.com/insights/why-does-the-status-date-of-a-submission-change-periodically-though-the-status-remains-unchanged

For that you need to know how the journal system works. When status is "with editor" it doesn't always implies that the paper is not send for reviews. Because in journals the configuration of online submission system is such that if at least 2 or 3 reviewers have accepted the review request only then status will change to "under review". Also when status is "under review" and status date is changing then it means the reviewers have submitted his/her report in the system (which have led to change in status date). When at least 2 or 3 reviewers reports (this count is configured by the journal) are not come till then status won't change. If they come then status may change to "with editor" or "under editor evaluation" or "required reviews completed". Under these status also the status date may change which implies remaining reviewer(s) have also submitted their reports.


text:
Is it appropriate for a prospective PhD student to contact phd students at a target school?
I am a prospective phd student. I wish to know if it is fine to contact the phd students of my target schools?
If answering this question requires more information, please feel free to state that.

It is absolutely fine to contact current PhD students of programs and departments that you are interested in. On an average, I get about 1 email of this sort everyday and I make my best effort to reply intelligently.
Keep in mind though that many PhD students will simply not reply to your email. Sometimes folks are inundated by too many emails and commitments to respond to any additional emails and sometimes people just have bad emailing tendencies in general.

Partially agreed. However, some people are just really bad with emails and communication be it for research or other extra curricular activities.

Could you please explain "reply intelligently" more?

Some prospective students have important questions of which the answers may not be easy to get. I try to respond in a comprehensive but concise and useful manner to said questions.

I definitely appreciate the quantitative "1 email of this sort everyday" ; I always want to know what the other party is dealing with when I contact them, and it's hard/impossible to predict this data accurately; much more reliable to get it empirically like this

We had great success when we extensively supported a PhD student who asked for a contact:
While doing my PhD we had a last year undergraduate student, who contacted my supervisor and asked if he can meet some of the PhD students. We decided to organize some shadowing for him, so he spent several days with me in the university.
I told him all I could think of in relation to my PhD experience, answered all his questions, and he did some real work - helped finding research publications in a specific area. At the end we asked him to write a short report about his shadowing experience - was it useful, pros and cons from his point of view, etc.
The experiment was so successful that the department decided to extend it and provide similar opportunities for other prospective PhD students.
So, by all means, do it - contact the supervisor or the PhD student. The worst thing that could happen is that they will say 'no'

Thanks very much for your rejoinder. I am a master-degree-candidate student in Asia, and I wish to apply to schools abroad.

I like what you're saying - but I almost stopped reading too early... could you add a "tl;dr" intro? Like "By all means.Do it - we had great success with..."

@VolkerSiegel A plea for brevity on a stackexchange site? Moreover one with a focus on academia? I think you grossly misunderstand this audience; perhaps you should explore twitter. #tldr

@VolkerSiegel, I am not quite sure what exactly you asked me to do. Please, feel free to edit my answer if it violates the site rules

Oh, the point is that the answer is good and verry convincing - but it somewhat hides the good part. The text is great, but to me it was ambiguous regarding whether it was a success or failure until end of the second paragraph. I was half expecting "Turned out we wasted lots of time..." or so. So starting with a statement of the positive outcome would change a lot. I'll try.

I have received tens of such e-mails so far in the first two years of the PhD program. 70% from India, 20% from other parts of Asia, 10% other.
Since I hate when people ignore my emails, or even reply unnecessarily late, I was trying at first to give some customized advice. After the first dozen of e-mails, I realized that I was being asked almost the same type of questions over and over, so I now simply reply with a template e-mails pointing to the main resources.
To answer your question, I would say it is totally fine but:

The more specific questions, the more likely you are to receive an interesting answer.
It is hard to be 100% frank with people we don't know. As a result, the answers you get are likely to be biased (typically "how good is the advisor?" kind of questions). As Pierre Beaumarchais said, where there is no freedom of blaming, there can be no genuine praise. The only solution is to know people personally or be referred by some common friend. Talking face-to-face can help reducing the bias.

I gather that in certain parts of the world (especially Asia), it is becoming a common practice to send out lots of emails like this.  It might be a good idea to try to figure out whether someone really has contacted you specifically before you spend any significant time composing a personalized reply.  As a faculty member, I often get "I'm very interested in your research and I'd like to work with you" emails.  They enclose a CV, which I read and see that their work is more than halfway to the next academic department.  This is a bit sad...

I really like your answer. I generally only respond to emails which have been crafted and ask intelligent questions well. Anything else is relegated to trash.

I am a PhD student in a really small department, and the only student in my particular research group. When we have students interviewing for a PhD in my group, I always spend some time with them answering questions about what it is like in the department and group, and what it is like working with my supervisor (very important!). I always give them my email address so they can ask me any other questions they may not have thought of at the time.
If anyone was to email me directly before applying, I would take time to answer their questions, but only if they genuinely seem interested in the specific PhD topic on offer. If it seemed like a really generic email that had been sent out to loads of people (obvious give away is if it isn't actually addressed to me!), then I wouldn't take time out of my busy schedule to respond.
In my research group, PhDs are offered based on a specific topic that we have got funding for. I know other big departments in the UK interview for PhD students generically and then they get to choose their topic from scratch, pick one from a list, or they are matched with a specific topic after their interview depending on their skills. I don't know how it works in other countries or other fields (I am in the climate/meteorology field).

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Internal PhD thesis reviewer pulled out a month before the thesis due date: Is this allowed? What to do next?
I have been a PhD student in an institute for the last 4 years and now my deadline to submit my thesis is in another 40 days. When I joined the institute, official papers were signed stating that Professor X will be my first reviewer and will grade my thesis. By regulation, the first reviewer has to belong to the same faculty, but he was not from our group, and we did not have much contact with each other.
Now that I am ready to submit my thesis, he decides to back out on reasons stating that I was not in touch with him (but I was never told by my supervisor or by him that I need to regularly contact him).
Does this happen and is this allowed since official University papers were signed 4 years ago saying he will be my first reviewer?

People can back out for whatever reason and it's not a matter of can or cannot. Once you learned that this person is going to be the reviewer, there should be a round of communication to settle the expectation, availability, and other specifications. Focus the energy on finding another reviewer, you don't want an unhappy reviewer who holds negative thought about you, even you could force the promised review to happen.

In the best of worlds, this is where your supervisor should come in and provide guidance and help. Hopefully your supervisor might have some ideas on how to either smooth it over with Prof X or how to connect you with Prof Y who can be your first reviewer.

Thank you all for your comments. Thankfully, my problems have been sorted out last evening and now I finally have an official supervisor who is ready to step in at the last minute.

One of my reviewers did it but was extremely rude about the whole process.  He didn't want to do it, but by rule, at our university, we needed an out-of-department reviewer.  I had actually taken a course from this professor, but the professor was still not very nice about it.

Such situations are not uncommon in academia.  I would caution you against trying to get this person back as a reviewer, even though you have signed papers from 4 years ago.  Simply respect that person's decision to back out, thank her or she for their time thus far, and invest your energies finding somebody that will serve as a reviewer so you can graduate.  Perhaps this sounds like rather odd advice.  Just put yourself in the shoes of a person who doesn't want to serve as a reviewer but is subsequently forced to do so.  You are at risk of getting a very unfavorable review, and the 40 days could become much longer.  You have plenty of time to get somebody on board, and you will certainly encounter situations in your future career that are far more egregious.

I do not know the specific regulations at OP's university, but in my view finding a substitute looks like a job for the advisor, not the student.

This happened to me, too: one of my committee members was suddenly unavailable for several months and unable/unwilling to work with me on scheduling my defense.
My process:

Took deep breaths and stopped panicking.
Reviewed the profiles of all eligible faculty members in the university
Picked a shortlist of 3 people in related fields that I wanted to meet
Asked my advisors for feedback (valuable - they knew who was a difficult committee member)
Emailed my top choice, Prof. S, to be on my committee.
Got a positive reception, met with Prof. S to discuss my work; they were friendly and mildly interested.
Scheduled the defense (tough, with five professors).
Sent my thesis out for reading, defended, and passed!

I believe this worked out well, and instead of a reluctant committee member, I got exposure to the leader of a significant program in my field. It still wasn't ideal, however, and I would've been in a bad position if Prof. S took issue with me, my other committee members, or my work.
You could also skip to step (3) and ask your advisors for advice - but I think it's worth taking control of an issue with so much potential influence on your career.

I'm glad your situation worked out well. That said, did you notice that this question was asked in 2014?

@EthanBolker Yes, but the problem isn't unique to the 2014 poster, and this question is general enough that it might attract future readers with the same problem.

@EthanBolker: StackOverflow actually has a "Necromancer" badge (for folks who answer questions 60+ days after they were asked and get five or more upvotes) to encourage new or higher-quality takes on previously-asked questions.


text:
How to explain things in the motivation section of a mathematical paper without proper definitions?
I want to start a chapter in my dissertation by motivating a mathematical operator by showing why it is interesting to look at it and what I can contribute to understand it better. However, I actually need to introduce some mathematical objects in order to correctly state everything.
I think it is a rather bad Idea to start first with a section of introducing the mathematical concepts (like measure theory) and then start the actual motivation. But if I do it opposite, then I am at a loss for words.
For example, in my motivation I would need to use a additive-finite measure space, a operator, the space of mu-integrable functions and a stochastic process.
How would you suggest to cope with such a situation?

As long as the terms are standard, you can probably safely use them without defining them in detail (especially in the introduction).

I know mathematicians don't like to hear that, but still: if you can't explain why it's interesting in natural language, you (probably) don't have a motivation (that appeals to non-experts) beyond curiosity . That's fair, but why pretend?

When I was a Ph.D. student working on my own dissertation, I went to the university writing center for help and had a revelatory experience.  The person working with me sat down with the first page of my introduction and effectively dissected it to identify the problems without understanding any of my technical jargon.  They did this by reading aloud as we discussed, substituting blank/nonsense words for every piece of jargon, e.g.:

Here we apply method X to determine whether adjective thingies can be made to wibble.

This type of substitution forces you to step back from the technical world that you have dedicated so much time and love to, and understand your narrative---or lack thereof.
In your motivation, you need to take a couple of steps back and ask: why does anybody care about additive-finite measure space ("frobs") and how it relates to the space of mu-integrable functions ("greebit-space") or a stochastic process ("wibbling").
You didn't pick these elements at random.  There must be some reason why you picked them and how they relate to the bigger community.  Are they intended to solve a puzzle that a lot of people care about?  Or a small piece of such a puzzle?  Do they unite two sets of concepts that people thought were different?  Will they help understand string theory or give better tools for interpreting MRI imaging?
You want to be able to write something like this:

People have wondered about how to better understand frobs ever since Richard Feynman first used them to pick the locks in Los Alamos.  Although X, Y, and Z attempts have been made, none of them got very far because they were all green-colored.  In this dissertation, I examine an alternate path, reducing the problem of frobs to the simpler system of greebit-space by means of an innovative application of wibbling.  These results bring us one step closer to solving the problem of frobs, and how they can be better used to quickly and cheaply pick locks.

Now, what I've written is pure gibberish, and your motivation will almost certainly be much longer.  The point, however, is this: your goal in a motivation section is to motivate by explaining that there is a problem that people care about and that you have an approach that gives at least a piece of the solution.  Explain it in a way that your jargon can just be placeholders in the reader's mind, and it will be fine to leave the complex definitions for later.

This is a concise and brilliant explanation of what an introductory chapter -- any introductory chapter -- should do.

When I encounter this problem, I write the introduction as if the readers knew the concepts that I mention, but I include a parenthetical comment or a footnote, after such a concept, along the lines of "This and other concepts used in the introduction will be defined in Section 2."

If you go deeply enough into measure theory and stochastic processes to actually write your dissertation about it, it is safe to assume that readers will be familiar with common concepts. So just assume that people understand what you write about. Do some handwaving if necessary ("we examine an interesting class of operators that are distinguished in that...").
Worry less about correctness than about telling a good story. After all, this is a motivational section. Don't include any definitions, or no more than one if it is utterly necessary. (And then, if you find that a definition is necessary in an introduction section, I'd argue that you probably need to revisit what you want to write in that section, until the definition is not necessary any more.)
Worry about correctness in the main body of your chapter.

In addition to other good points made in the other answers, I think too often people overlook the question of the actual, likely audience/readership for a piece of technical writing. For example, it is unlikely that anyone without at least a rudimentary knowledge of your general subject would look at your thesis at all, so you can safely use the standard, basic terminology to give an introduction and overview of a given chapter. That is, it is not useful to imagine that you are explaining "from scratch" to someone who's completely unacquainted with the topic under discussion, since the reality would be that they'd not instantly assimilate "definitions" in any case.
In other words, contrary to what we sometimes may imagine, there is a context in which we write, and that context is most often richer than we acknowledge. Thus, the work is not to re-establish the basic context, but to make larger points. That is, as in the other answers, I don't want to hear delicate (and possibly pointless) semantic distinctions about word-use, but, rather, about why you are doing what you're doing, etc.

Mathematicians have a tendency to train to hide away they tracks they used to take to get to their goal (apologies to Simon Singh). This means that motivation is the thing they have been trained not to give. As compensation, they give examples, ranging from trivial to realistic to absurd following the definitions.
This is the situation on the ground. The reason is that mathematical objects are often obtained by so many steps of abstraction of originally natural-world concepts that their real-world origin is often obscured or very difficult to intuit (think the - very compact - definition of topology).
Therefore, it is useful to the reader to "recreate" the bridge to reality (which is often possible) and explain which of reality's features are required and which ones are discarded. Measure theory is not so bad in that respect. Basically, you are talking about a kind of "volume". In "nice" spaces, such a vector spaces, you could consider n-forms as volumes (almost literally), but if the space gets nastier, without a concept of tangent spaces and the associated structure, you have to look at  which permits you to extend this concept to suitably selected subsets of your space. My favourite to asking the question what you miss if you have no measure is to respond with the Banach-Tarski paradox.
Now the game can also be played on a higher level if you talk to mathematicians who know already a lot of things. You now need to explain how your concepts will fit into what they already know. So, a group theorist may be motivated to look at semigroups by explaining which axioms you drop (and why). Or which phenomenon motivated your definition of semigroup (for instance attempting to model non-invertible operations).
In short: the point is to explain and to motivate what concepts and phenomena in "the universe of the reader" corresponds to properties discarded or generalised (abstractions) or newly studied phenomena in your universe.

It's a delicate balance. You say:

...in order to correctly state everything.

But why are you correctly stating everything if its just a motiational discussion? So you see you have a balancing act whereby you need to give up a little bit of space on the side of correctly stating everything in order to gain some space on the side of being able to flexibly discuss the concepts, ideas, history etc.
This is actually really hard and usually takes much more experience than it did to solve the research problem in the first place. So I think its common for e.g.  a graduating PhD student to have the technical knowledge to solve the problem but to find it difficult to articulate where the problem lies within a much bigger field of inquiry.
As you gain more experience you will know when and how to lie. And you will also know much better what counts as standard. When you've just spent years learning the basics of a research field you often feel like things need definitions that don't really. Other experienced mathematicians are probably more comfortable than you think with not fully understanding every detail/remembering every definition but kind of vaguely knowing what such and such an object X is and vaguely what it does and just more or less getting the idea until the later point at which you define everytihng.
To try to give one piece of practical advice: Look for ways to not tell too big a lie. Find places you can say that 'an object X is essentially an object Y together with a parameterization of its involutions' (or whatever) where object Y is something you a sure is more standard.
One example that comes to mind from my education is distributions. I heard both of the following vagueries:

Distributions are generalized functions.("OK right so I should think of them like functions")
Distributions are like the abstract dual to functions. You pair a distribution with a function to get a number.

This confused me when I was younger. But after some experience I guess you know the ways in which these are both true and you get that different contexts call for different lies.
The readers who don't know the stuff well will essentially have no choice but to just swallow the lies. Then you get worried about the readers who do know the stuff well. Because then when you tell a lie, they might get offended, like "gah this writer has oversimplified and left out the crucial essence of object X; how will anyone get the important content from watered down motivational discussion!?" So like I said, it's a balancing act.


text:
What to do when co-authors want to submit manuscript for publication and you think it still has problems?
I am a junior member on a research project. We have written a paper. I feel the work is not ready for publication and have issues. We have discussed the issues, and other members of the group including the lead author agree with me that there are issues. But the lead author who is more senior is too eager to get the results published to the extent that he is ready to mislead the reviewers/readers by exaggerating and misrepresenting the partial inconclusive results to get the paper accepted. I don't think I can convince him to allow more time for the project to reach a more satisfactory stage before publication. I am rather junior and have limited say on the project. I am new to the field of the project, and the senior author is established in the field and publishes several papers in top venues each year. Other members of the project are his students.
We don't have conclusive evidence for one of the central claims in the paper. It might turn out to be false under more experiments. The lead author, however, believes it is correct even though he agrees the evidence we have is not sufficient. He wants to publish the results and the idea as soon as possible, but accurately stating what we have and what we don't have will make the acceptance unlikely at this point. He is fine with getting the flawed results published and then continuing to work to fix the issues for the later publications.
I am not comfortable with my name appearing on the paper.
One option is to ask for the removal of my name as an author and to be mentioned in the acknowledgments. However, I have worked on the project for a considerable time and would like to get credit for my contributions, and I don't feel just being mentioned in the acknowledgments is good enough.
What would you do if you were in this situation?
How do you deal with major disagreements in writing a joint paper?
Would it be helpful if I post a different edited draft copy of the paper online where the claims are more accurate in my view?

"Issues" and "flawed" are not really synonyms. If there are issues matters can be published as long as the issues are discussed. Flawed is very serious so which is it?

Is there a deadline to meet?

The project will continue even after the publication of the paper. There is a deadline for submission but if we miss it or the paper gets rejected we can submit the paper to the next one.

As the lead author is eager to submit. It seems this year he has little to publish which justifies going with this partial solution. Specially if he is targeting a top venue (some people wants to be there every year regardless of their submission quality)

How do you deal with major disagreements in writing a joint paper? — Work them out like adults.  The paper cannot be submitted without the agreement of all coauthors.

I wanted to add a fourth possibility to @artalexan's nice answer that might be more diplomatic:

Make the paper technically correct with the results you have (even if preliminary) and submit to the current venue.

The major problem with submitting the paper is that it is dishonest, not that it is preliminary.
If the paper can be made technically correct and honest -- even if the results are preliminary -- it would be fine to at least submit it and let the reviewers judge if it is mature enough.
If you are a co-author, you should have the power to edit the misleading text. If the main author is stopping your efforts to do that, then ask to be removed from the paper.
Of course if the results themselves are incorrect (rather than preliminary) there may be no saving the paper.

On a side note, the attitude of the senior researcher in question towards publishing may be productive in the short term (getting some initial papers published quickly by misleading reviewers), but it is utterly counter-productive in the long run. Having a reputation for sloppy results/writing will seriously harm the trust that reviews/readers have in your paper ... and reputation is so important in research! I don't know your situation, but if the researcher shows no inclination to change their attitude, try to put distance between yourself and them.

Honest preliminary results (if exciting enough - if not, noone wants to publish an immature paper anyways) can often be published as short commuication. There, the preliminary nature of the results does not do any harm.

+1 for honesty, but is being removed from the paper enough if honesty is lacking? I'd rather refuse to remove myself and obstruct the publication until it's rectified than permit more dishonesty, especially from my colleagues. Their reputation can affect mine too, after all.

@NickStauner, I agree and I think the answer depends on the situation: I think there are gradations of dishonesty, from being slightly over-enthusiastic about results (i.e., overselling) to selective presentation of correct results to deliberate outright fabrication. If there has been deliberate fabrication, there's certainly a strong case to be made for escalating the matter ... but how best to do that also depends on the situation.

I see a few possible options for this.

You are talking with other co-authors of the paper then you all together talk to this lead author that what he does is going to affect not only his, but also your future in a very bad way.
You are making a rough estimation how quick you (and other authors) can fill all those gaps in this project. If it is let's say 15 days, you meet and make your exact suggestion. This concreteness will make the main author think twice.
Although you have done a lot of research, you should remove your name from this suspicious study (if you strongly believe that this study has serious drawbacks), because sooner or later it will become worthless.

I've seen some misleading papers written by popular names during my MSc studies. Yet, their popularity did not vanish in an observable amount of time. In research, we have many issues like this; and I believe it is not necessarily a bad thing. Sound articles would be cited by many, and they would definitely be helpful for new researchers and young students alike.
However, I have the following questions for you. Please consider them objectively.

Did you witness cherry-picking? Or any alteration/manipulation to the research results?
How inconclusive do you find the results? Please forget
    about the lead author, and give a number from 1 to 10 on your best
    knowledge.
Can you convince the lead to add a future studies section or
    a paragraph/sentence to your paper, to mention the issues you come up with
    about the experiment?
Can't you ask the leads approval to do more experiment? So that you
will have a fighting chance to make things right. If you are proven right, you may give the accurate results in the earliest revision.


text:
Because of past conflicts, I don't believe my advisor will write me a good LOR for postdoc positions. What should I do?
How essential is having my advisor's letter for post doc application?
I had a pretty bad relationship with my advisor for more than 4 years since I joined his lab and sometimes the relationship feels like slow inflammation that can easily flare up. We had very different opinion on how I want to approach my thesis and we argue very often on the experimental approach and the angle of attack. After that, he turned passive aggressive and completely hands-off. I noticed that he started slow to response to my email and given me very small amount time for meeting in comparison to other people in the lab. However, I proved to him that my approach was right and wrote the full paper myself and got published.
Recently, I got contact by a post doc employer who interested in my own work and request letter of recommendation. I asked my advisor for letter and he told me that I should write my own from which he can modify. I feel this is quite strange as he had wrote for all the other people in the lab, including a departing post doc who is currently interviewing for job. He told me he had done the same for other people but obviously he lied to me.
I further asked if he can provide me a copy of a completed version of the recommendation but he refused.
My question is should I still trust him to write my letter and is it essential? This post doc position is a great opportunity for me and either way I do is a big gamble.
Update: I decided to let my advisor wrote a letter for me and I think I may have made a big mistake. Since he wrote my letter, I asked the post doc lab head if my letter is completed and I no longer be able to hear back from him. Before that, he was quick to response to my email and showed great enthusiasm. As an insurance, I use one opportunity I have less desire to as bait to test the water and I still have one more shot at another position I really want.  Now, I'm thinking requesting open letter from advisor from now on for any future position or use letter service to check the letter.
Any suggestion? Thanks.
update: Great news! Got interviewed and offered at top ones! Thanks everyone!

Different parts of the world have quite different practices regarding letters of recommendation. In the US they are usually considered very important, in Europe not so much. Where are you located, and where is the institution to which you are applying?

According to me, it seems to be very common issues with a person to arrange LOR from your earlier supervisor with whom the student does not have a good relation for several issues. I faced the similar issue. But I somehow managed to have a LOR, which I think, it was not so much positive. However, always be in touch with you current Postdoc supervisor, and let him convinced by your work, not by your recommendation, your work should be able to recommend you at any sense.

@NateEldredge Recommendation letters in Europe are, unfortunately, considered much more important than in the US.

@TomDworzanski: Unfortunately, as the answers below suggest, not having a letter from your PhD advisor is also begging for disappointment.  It's quite possible that your best bet is to hope that your advisor can set aside personal issues and write a letter that reflects your abilities.

Actually, drafting your own letter of recommendation is not that unusual. It gives you the ability to emphasize points of interest to you.

@Ooker A [tag:conflict-of-interest] refers to when someone has an outside influence (like a financial interest, or personal relationship) affecting their professional responsibilities (e.g. a student being supervised by a family member). The tag doesn't seem to apply here.

@ff524 thanks for reminding me that. Should we have a generic conflict tag?

@Ooker Conflict is pretty well covered by the [tag:interpersonal-issues] tag. I don't think that's strictly relevant to this post, either, though (others may disagree). The question isn't about the past conflict with the advisor; it's asking what to do about recommendation letters now.

@ff524 Although the two top answers actually give the solution which aren't about the conflict, I would say that if we look at the atmosphere of the question and two other answers, it is the most relevant tag.

@GennaroTedesco What? Coming from somebody who worked his entire career so far in central Europe, this is completely wrong. Personal connections (yours, or your advisor's): yes, very important. Formal LoRs: nobody cares, generally assumed to be overhyped template text (which most LoRs of European professors indeed end up being).

@xLeitix Well, we have to convey that we have had different experiences then. It also depend on your particular field of interest, namely the fewer the general available positions the more important a recommendation letter.

"I asked my advisor for letter and he told me that I should write my own from which he can modify. I feel this is quite strange"   This is a common practice.

@JonCuster I find it interesting that "drafting" your own letter seems to be an acceptable and common practice, while "writing" your own letter is a big no-no (see also: http://academia.stackexchange.com/questions/16529/is-it-acceptable-to-write-a-reference-letter-for-yourself).

I said draft, not write. Giving someone a draft means (1) you are serious, (2) you know enough about the opportunity to want to emphasize certain things, and (3) you have skin in the game as well. Few things are as hard as staring at a blank sheet of paper wondering what to say that would help.

Once it became clear that you were not going to follow your advisor's advice on important issues, it might have been better to switch advisors to one you could work with. Instead, you continued, in effect, without an advisor. The limited meeting time, slow e-mail response, and requiring you to draft the LOR all suggest to me an attitude of "Why waste my time giving advice that won't be taken anyway?".
You cannot be sure he is lying about having other people draft their own LOR unless you have talked with every person for whom he has ever sent one. He may feel he knows some students well enough to write an LOR from scratch, but needs a draft for others.
The best you can do at this point is to write what you consider to be a reasonable LOR and give it to your non-advisor.

One thing that hasn't been addressed yet:

I further asked if he can provide me a copy of a completed version of the recommendation but he refused.

You seem to view this as a danger sign, but I would not.  Practices regarding letters of recommendation vary around the world (and you haven't said where you are), but at least for the US, the custom is that a letter is sent confidentially from the writer to the recipient, and the candidate (about whom the letter is written) never sees it.  The idea is that this makes it more possible for the writer to speak freely.
I'd expect your advisor to refuse such a request even if your relationship was great and he was writing you the awesomest letter ever.  It would be very unusual for him to agree to show you the letter, under any circumstances.  I don't think it was an appropriate request for you to have made.
Of course, it is possible that he is planning to write an unfavorable letter, but there is really no way to know without reading his mind.  To my mind, this particular fact (that he wouldn't show you the letter) isn't really evidence one way or the other.

That happened to me, but worse. My postdoc supervisor unilaterally rescinded my grant, I was never completely sure of why.
What I'm currently doing is to include my other advisors/professors and explicitly say that I had a disagreement with him, that he rescinded my grant, but I was cleared of any wrongdoing (the funding agency gave me a new fellowship a few months later) and that's why I didn't ask for a LOR.
My current supervisor was aware of the whole deal from the get-go and he was fine with it.
Be honest, be clear, do not hide anything.

Thanks, but what about graduate student applying for post doc? The post doc employer contacted me is from a quite prestigious lab.

This is a very good advice. Just be very honest about the situation. But please do not tell your future advisor things like "my advisor is a liar" because that will not be good for you.

+1, good advice. One more point: be factual. No emotional comments, just the facts. I have been on the receiving side of such a case and I appreciated the frank approach. There were other LORs (not that I cared much about them) but also recommendations from colleagues which helped to a certain extend to anticipate the character of the applicant. She ended up getting the job. Looking 15 years back it was a good decision.

@user10694 Doesn't really matter the specific position, the idea is exactly the same.

This is a very good advice. Especially when the OP published a paper as sole author (if i understand correctly), this will strongly support his case.

I think your attitude at this point has to be, "What I really need right now, and all I need right now, is a strong letter of recommendation. To heck with the past."
Your former adviser has actually made you a very good offer: write the letter yourself. Thus, do write a letter that focuses on what the project was about, what you believe you contributed, and what the results were -- including that the results were very meaningful and that your thesis led to a publication. Do mention which outlet the piece was published in. If you think it's relevant, you may also write something about how you think you developed as a researcher during the project. Focus on output and don't dwell on inputs, i.e., don't write something like "Mr. X worked long hours, including lots of weekends".
You have, of course, no control over how your ex-adviser may see fit to edit the letter once you hand it over to him. However, if you limit your letter to what's factually correct and essential to your potential future employer, I think there's an excellent chance that the ex-adviser may simply sign the letter and send it to whomever you say needs the letter. I see two reasons for being optimistic. First, don't underestimate the power of inertia: If the adviser wants to apply any edits (minor or major), he will have to do the extra work. Given that you described his eventual behavior (accurately or inaccurately) as passive aggressive, he may decide it's too much work on his part to edit the letter. Second, don't underestimate the desire of many established researchers to have successful advisees. If he were to write something unflattering about you, that may well be read as a sign of failure on his part. If he's at all rational, he'll want to avoid the risk of creating such an impression.

I think this is a good analysis. The advisor's reported actions are consistent with trying to minimize the time he spends on advising the OP. The minimum time handling of the LOR would be to ask the OP to draft it, and forward it unchanged if it is factual.

You are very unlikely to get a good post-doc position without a strong letter from your advisor.  If you don't provide a letter from your advisor, that looks like a huge red flag, and most people hiring are not going to consider your application.
If your relationship with your dissertation advisor was poor, that puts you in a lousy position.  However, having your advisor ask for a template letter to work from, while not ideal, is not necessarily terrible either.  It doesn't indicate the greatest investment on his part in your future success, but it doesn't mean that he won't write a strong letter either.  And I wouldn't assume that he hasn't done something similar with some of his other former students, either, even if you haven't heard about it.

I think I can't see through my advisor is because he lies. This impression is from my every day interaction with him for 4 years. He is always nice and friendly. He told you he can write stellar letter but he doesn't. This is very scary and turning me into paranoia.

By the way, I'm completely happy to write myself but the scary part is his final "modification", which cannot disclose to me.

Why would you want a letter of recommendation from a "lying" advisor? You are very quick to use the word "lie". As far as I can tell there is some blame on both sides, at least as far as human relationships are concerned.

As a general rule, this is untrue. At least, I'm the living counter-example. Stuff happens, as long as you are honest and stick to facts, isn't that much of a red flag. Most of the time, its nobody's fault...

Blaming others or yourself at this point is useless. I would do the following to go around the issue, by politely asking the following two groups of academics:

Your Examiners: During the viva, you will have a number of  examiners, these are one of the best people to ask about recommendation letter, as they know you by your final product (i.e., your thesis) and therefore they will go right to the point. Right in here, you could get at least your two recommendation letters; that is required for most postdoc jobs.
Other Professors In Your Group: Unless you have been a total social disaster in terms of communicating to the other academics in your research group, while you have been a Ph.D. student; you could ask a number of professors you know in your group. Ask them for a one on one meeting, explain your situation and kindly ask them for the recommendation letter. If you have been a bright student, believe me they have nothing to complain about and will give you a letter.

You are understandably nervous that something in the content and tone of the final submitted version would give away the strained relationship between you, and work against you in the application process.  It is impossible for me to say whether he would be able to write a nice letter without some subtleties of his feelings toward you and your work slipping through.  But I can say that it is damaging for you, psychologically, to experience this degree of anxiety and apprehension, and that a letter with subtle negativity, or a lukewarm tone, would harm your application.
You could try this:

Prof. So-and So, I know we've had our differences.  We're two strong
  characters with a passion for science, and we have different
  approaches.  Given the fact that things haven't always been smooth
  sailing between us, I wanted to ask if you are really comfortable
  writing a letter of recommendation for me, or if you think it would
  serve me better to try to find someone else.

You need to find some way of reading him, and getting a handle on what sort of letter he would send.
If in doubt, don't include him as a reference.  Do send the committee a brief explanation.  Keep Fábio's experience and happy ending clearly in your mind.


text:
What to do if I can't trust my advisor no more?
After so many incidents happen that my advisor trying to bad mouthing to my committee, sobstege my publication, secretly removing me from my PhD projects I feel I cannot trust my advisor anymore. Now, I feel everything he said was insincere and full of lie. My advisor always says positive thing but all end up negative. He is not consistent of what he said and what he actually does which disgust me. I don't want to let him handle my manuscript or assign me project because I always fear that he will do something underhanded. If I really grant a PhD from my advisor, I would be ashamed of such lineage. All I want now is live in bubble space undisturbed focusing on my own topics. I want to be myself as a phd student and one day as a professor. What should I do? Please help!

Switch advisors. There is really not much else you can do*.
*If the person does something truly unethical and you have definitive proof you can try to bring it up with someone who has more authority.

You say that that isn't an option, and it sounds like you're planning to stick it with this advisor until you get your PhD. Things to think about:

Do you think it's realistic to get a PhD at all with this advisor?
Are all of his grad students just as miserable, or just you? What are the successful students in his group doing?
Who are your letters of recommendation (you need 3, typically) going to be from when you apply for postdocs/jobs after you graduate?

Nuclear options (purely for completeness, I don't recommend them):

Apply to a PhD program somewhere else (you don't have to finish this one, you can apply while you're still in this one, actually, and only quit the program if you get accepted somewhere else).
Quit academia. (Warning: it's hard to get back in once you're out.)

I am not sure how you define "successful" (fellowship, publication, support)? I know there are people who were quite supported by my advisor because they know what my advisor like, and it's their way to get ahead. That's fine and that should be the norm but I'm not the norm.

Successful means publications (well, that depends on the field), research that is progressing in a clear direction, completion of milestones towards the degree. The advisor having successful students ultimately is measured by how good the jobs the students he graduated got are.
It sounds like he has students that are content to have him as an advisor.
It also sounds, from your other question and the comments there that you think that your advisor is incompetent, which means that you don't take him seriously.
This creates at least half the problem, because if you don't take him seriously, he won't take you seriously, which, among other things, includes telling his colleagues about how terrible you are, and not trusting you to write a manuscript for submission.
If you're staying in this PhD program with this advisor, you will make your own life a lot easier if you at least imagine that your advisor might not be incompetent.
When he gives you an idea for an approach, make an honest effort.
If it doesn't work, try to figure out why. If you figure out why, don't look happy about it: look concerned about it. If you have an idea that you think will work, propose it as a solution to this problem you just found. And by "propose" I mean actually ask him for what he thinks about it, and be interested in what he has to say.
This is what "taking him seriously" means. If you start doing that, he might start taking you seriously for a change.
Also try to have insightful research-related conversations with some other faculty (preferably the rest of your committee), maybe even have one or more of them meet with you and your advisor when you discuss research ideas (make sure to plan meetings so that everyone is in the loop, don't try to surprise anyone). Build those professional relationships for some good recommendations.

I am too late to switch but I hate where I'm now. If I really get a PhD from my advisor, I will hide my credential and get another one. Now I'm seriously considering getting another phd after this one.

"Too late" how? How would switching (and maybe losing a couple of years because you have to re-start the dissertation phase of your PhD with a new advisor) be any better for you than spending more time with this advisor and then spending four or more years at another PhD program?

I already talk to higher up and guess what they all sided with my advisor and think I'm ungrateful for his money. I don't want a dime to let my advisor control my thoughts or how I want to do my research because I 'm suppose to be trained to be an independent thinker not a thought follower.

My advisor have some connection so it's pretty hard to switch, most advisor don't want to get caught in line of fire. You know what I mean.

Hi trueality: I am not sure how you define "successful" (fellowship, publication, support)? I know there are people who were quite supported by my advisor because they know what my advisor like, and it's their way to get ahead. That's fine and that should be the norm but I'm not the norm.

@user10694 - Don't be silly about "lineages," "hiding credentials," and going after another PhD. Your doctorate bears the name of your school, not the name of your advisor. If you finish successfully, consider it a learning experience, and resolve to be a better advisor should you get a job as a faculty member sometime down the road.

When I read your question I must take into account that I am hearing one side of a dispute, so it is likely to be biased and incomplete. I don't know who is in the wrong but I can see a few pointers. Firstly you make very few specific complaints about what your advisor has done. You say he is trying to sabotage your publication and remove you from projects. It is the job of your advisor to decide when your publication is ready. He has much more experience of this than you do. He can see better than you what direction you need to go in.
No advisor takes on a student to sabotage them. An advisor can only have a limited number of students and they want them to succeed. You claim that things he says are insincere which means that he is saying positive things that you will not accept. It sounds like most of the anger is on your side. You even indicate that other students are getting along with him.
If there is a personality or culture clash between you and your supervisor it may be possible to talk to your department head about a change, but it is more likely that you are on a slippery slope towards failure and it would be better that you listen to your advisor who seems to be trying to help you. Put your ego aside and consider the possibility that your advisor who has been working in the field for many more years than you may know it better than you. If you still genuinely think that your ideas are better and you want more independence then you need to discuss this calmly with your advisor. He may agree to let you take that route but that is only likely if you are exceptionaly talented. If he doesn't he should explain why and you need to listen and find a compromise.
One last thing, your English grammar is not very good. I dont know if you are an English speaking native, studying in an English speaking country or writing papers in English, but if any of these are the case then you need to improve your English. It will have a bearing on your ability to communicate with people including your advisor.

No advisor takes on a student to sabotage them. I think that's probably true; however, I've known of cases where advisors didn't seem to have a very strong interest in seeing a student succeed after things got underway. Reasons vary.

Philip: Hello again.  You may want to click on the OP's user page and read some of the other questions: among other things your desire to see more specific complaints will certainly be fulfilled!  There is a general pattern of this OP's questions on this site: each of his questions documents an extremely distressing relationship with his advisor.  When you read any one or two questions you think "Wow, that's terrible.  I need to suggest that the OP (i) talk long and seriously with his advisor and/or (ii) find a new advisor."

But the OP almost never directly responds to these suggestions: instead the horror stories continue.  It gets frustrating after a while.  At this point I am not sure what more we can do to help.  Finally, I think it is overwhelmingly likely that the OP is not a native English speaker.  (Based on past experience I will guess that he comes from Asia.)  I had also assumed that he was doing a graduate program in Asia (or wherever he's from), but if he's not then you're quite right: a language barrier may be the ultimate culprit of many of his issues.  Thanks for pointing that out.

@PeteL.Clark I live in Taiwan and a native Chinese speaker. The OP's English does not look like Chinese English. I am not sure whether he is from Asia. Asians typically dare not complain about their advisors that much on English based network such as us.

@scaaahu: OK.  Maybe I should not have played "guess the OP's nationality".  It is quite clear to me that he is not a native English speaker, and thus if his graduate program is in (e.g.) the US then language issues may apply.