text:
Is there an alternative to traditional exams?
It seems like the traditional exam model (two midterms at 30% and one final at 40% of the grade, closed book) is flawed. For instance:

Students are not allowed to access resources, whereas in reality they would
Students get only a few minutes per questions, whereas in reality they would get days
Students are not allowed to collaborate, whereas in reality they
would
Students cram for the exam the day before, and forget what they
learned after the course is over
Students focus on the exam to the detriment of learning the material
and understanding real-world applications
It is difficult to claim
that the exam score demonstrates mastery of the course material in
contexts other than an exam

But in practice, is it possible to improve on these flaws, without introducing major increases in workload for the instructor? Is there any system of evaluating student performance in an undergraduate course which is an improvement over a traditional exam approach?

One argument against some of those points is that exams are meant to test knowledge, not ability (the difference being I have no idea what Henry III did, but I can easily look that up--I'm being tested on whether or not I can personally tell you anything about Henry III, not my ability to type Henry III into Google).

@waiwai933: I assume you mean "mastery, not knowledge".

@BenCrowell It's not too rare for even upper division and graduate level courses to be graded on a similar rubric, where "knowledge" (as per waiwai933's example) is a (or often the most) significant factor.

"Students cram for the exam the day before, and forget what they learned after the course is over" - That's right, but the next time they need the knowledge, the re-learning process will be much quicker than the initial learning. Such is the nature of all learning, not just for exams.

That is way there are also assignments.

Collaboration poses an issue. What if there is only - student taking the course? Or students are only studying via distance? Actually the midterm exam is foreign to me. All subjects that I have enrolled in and also taught have had 2-3 assignments and 1 final exam.

Take-home exams that test the student's ability to apply the course material to a small set of real problems. The exam takes a few days, not a few hours. Students can access resources, students can study while the exam is in their possession. Just clearly limit collaboration among students (plagiarism). I have found this most effective for upper level classes, where students are generally honest and care about the course material.

On my uni, most courses were project driven group tasks that took all the semester (sometimes even two or three semesters) coupled with a few customized oral tests for each group regarding what your project was about in a informal, free form talk with the teacher where you had to explain what your project did and what was your part on it. Sure, it was CompSci stuff, but those courses stuck like glue with me. The format was way more intense and productive than the regular tests.

One alternative that's been gaining momentum in actual classroom use is standards-based grading (SBG): http://www.fwps.org/teaching/sbe/grading-system/
In SBG, the instructor establishes a list of milestones that students are expected to attain throughout the course. The students then can provide evidence of any sort -- within parameters set by the instructor -- that prove they have met the standard. Student evidence of attainment of a standard is marked on a scale usually from 0 to 4 (unacceptable, novice, progressing, acceptable, and mastery -- or something like this) and grades are assigned at the end of the semester based on how many of the milestones have been met at "Acceptable" level or above.
For example, in calculus, one standard might be "Take the derivative of a second-degree polynomial using the limit definition". A student might show that they know this by doing a problem on a standard timed test. But maybe they don't have it down as well as they should, and on the test their work is marked as a 2 out of 4 (progressing; maybe they got the definition right but did some of the resulting algebra wrong). This isn't the end of the story. Later in the course, the student can show evidence again that they've learned what they need to learn -- for example, they can schedule time in office hours to come work a problem or two to show you they've met the standard. Or maybe take a short quiz in class, or work a problem during unstructured group work time in class meetings, or whatever avenue the instructor allows.
The point of SBG is that we want to assess students based on what they know, and give them multiple ways to show that they know it. SBG can therefore be a superset of traditional timed testing -- students that do well in timed situations will do fine in SBG, but students who struggle with timed testing can have multiple chances to get their act together, and as long as they can prove they've mastered the material by the end of the course, that is what matters.
I don't personally practice SBG but I would like to. I'd suggest this blog post by my colleague Jon Hasenbank who is a big SBG proponent: http://profjonh.blogspot.com/2014/02/sbg-mia14.html

+1 This is the only answer so far that details an alternative to traditional exams, as requested in the question.

+1. This is what drives me to learn as a student. I couldn't care less about my measured worth based on a 1-2 hour test. What I accomplish is really important to me, and exams have never been an accurate measure of what I have personally accomplished. I feel that working toward a goal (completion of a project, demonstration of principles in practice, etc) are worth much more than answering questions on an exam. While exams are an "objective way to test performance," so are personal projects/(work in general) which demonstrate the obtained knowledge.

I think this answer needs some updates. ;) The last paragraph is severly outdated, after all.

Although exams have the flaws you described, there are also many positive aspects you have not discussed:

Exams are actually an objective way to test performance, in a "hard to copy" environment. Although one may disagree with what is actually being tested, objectivity is usually not questioned
They are fast. It takes 3-4 hours to test hundreds of students
They are universally used and most of the students are accustomed to them.
It is an excellent way to prepare students to perform under stress, a skill which is extremely useful in any work environment. All works / skills have some sort-of-testing (e.g. presentations, interviews). Even getting your driver's license requires testing. So, learning to do well in exams is a crucial real-life skill.

The only complementary (but not good enough for actually completely replacing exams) tool I can think of, is project assignments. Especially in CS, projects are a very effective tool to prepare students for real-work assignments. But they are not a good enough method on their own without some sort of personal written examination. They allow too much collaboration, copying and usually when done in teams, the good students do most of the work while others slack. While a professor might take measures to minimize this, it is impossible to avoid it 100%.
So, I do not think there is a universally better way to test students' performance than written exams. One may complement it with projects, assignments, oral examinations but in most of the cases, completely abandoning it is probably a mistake.

The objectivity can be questionable when the exam is not good, something that as a student I felt unfair many times.

@Davidmh Were the exams not objective, or did they not test the right skills? Most bad (written) exams fail in the second category, but I don't think that many exams are actually subjective in the sense of the word.

One example from QFT: "Question 1 (20%), apply this mildly obscure theorem to get a classical quantity in this situation. Question 2 (80%): express the solution to ex. 1 in terms of creation and destruction operators." You can say that it is objective (either you know how to apply that theorem or you don't), but you don't really get an objective feeling of the knowledge of the student. I guess it is mostly a matter of terminology.

Others are poorly worded. When I was asked "historical meaning and experimental evidence of Maxwell equations", I explained the most important experiments and landmarks, all the way to Einsten's tensor; it got a low grade because they were looking for "$\nabla \cdot \vec B = 0$ means there are no magnetic monopoles". Others were "the definition is correct, but you didn't give an example, as you should have implicitly understood from the question, half points". [But I am tending to rant here].

@David - I once took a college course called Tests & Measurements, an entire semester devoted to the art and science of constructing fair tests that accurately measure student comprehension of course objectives. It was one of the best (and most useful) courses I've taken in my life, and it addressed pitfalls such as the one you mention here. The course was designed for K-12 educators, but I think a lot of profs could have benefited from the material in that textbook. Your initial comment is on the mark: as a measurement tool, not all exams are equally accurate, and some can be outright bad.

@J.R. that sounds like a very interesting course. Is there published material? I must say that, as a student, I felt very good when I got a well done exam, regardless of my actual performance (a deserved failing is not as bitter).

@xLeitix Research shows that many are, in the following sense: For the same written answer, different raters will assign widely different marks.

This answer is mainly focused on defending the statu quo and does not seem to address the question.

@user11596 - It's worth pointing out that about 75% of this question is taking swipes at the status quo, so defending the status quo is not irrelevant, but pertinent to the matter as posed by the O.P. There's more to this question than the bottom-line question.

@J.R. I see how this preamble might rub people the wrong way and why many seem to feel the urge to object or to voice their disagreement by upvoting these extended comments but that's still not the question being asked.

@user11596 - Is there any system of evaluating student performance in an undergraduate course which is an improvement over a traditional exam approach? Ans: Yes, by complementing the exams with projects and assignments. Is it possible to improve on these flaws, without introducing major increases in workload for the instructor? Ans: No, I do not think there is a universally better way to test students' performance than written exams. How does this NOT answer the questions posed by the O.P.? (Or are you only looking at the question in the title?)

@J.R. As I said, it's mostly focused on defending the statu quo. There are a few relevant bits but they are not even as clearly stated as in your latest comment. I would simply need more of the relevant stuff and less irrelevant (and, to me, self-serving and unconvincing) commentary to consider this answer usefully addresses the question and upvote it. See for example the answer by Robert Talbert.

@David - The textbook we used in that course was Measurement and Evaluation in Teaching by Norman E. Gronlund. Each chapter is replete with examples and checklists, and there are suggestions for further reading at the end of each chapter. (If you don't mind buying used, I noticed you can get newer editions than my hard copy for a mere few bucks on Amazon.)

@user11596 - You also said this answer "does not seem to address the question" – I guess we'll have to disagree on that. Anyhow, methinks you have an axe to grind.

@J.R. Maybe I could have added an adverb in there, does it really make that much of a difference? I think I already gave a lot of feedback about what I think is missing, what's irrelevant and how a good answer could look like (which is what comments are supposed to be about). What's unclear about that?

Students are not allowed to access resources, whereas in reality they would

Not necessarily so. Instructors can allow "cheat sheets," or allow open book exams.

Students get only a few minutes per question, whereas in reality they would get days

Not necessarily true. My boss often asks me questions and expects me to give prompt answers. I don't always have the luxury of asking for a few days to research something. If we are in a high-stakes meeting with customers from out of town, my organization's effectiveness might well hinge on my ability to ask or answer intelligent questions on the fly.

Students are not allowed to collaborate, whereas in reality they would

True, but exams are designed to measure individual ability and performance, not someone's ability to contribute within a group, or accomplish some objective as a group.

Students cram for the exam the day before, and forget what they learned after the course is over; students also focus on the exam to the detriment of learning the material and understanding real-world applications

Perhaps so, but that's what we get when we test on the minutiae and the trivial, as opposed to testing on the synthesis of high-level concepts (more on that later).

It is difficult to claim that the exam score demonstrates mastery of the course material in contexts other than an exam

Maybe so, but it's not difficult to claim that, as a general rule, if students are given identical exams, students who score above the median probably understand course concepts better than those who scored below the median (with some possible exceptions, due to factors such as test anxiety, and perhaps even a little luck).

In short, you bring up some possible shortcomings with what you call "the traditional exam model," but you can address some of these simply by redefining your parameters. Instead of two closed-book exams that count toward 70% of the student's grade, give three open-book exams that count toward 50% of the student's grade. Make one of them a take-home exam, and you at least put a dent in the "few minutes per question" problem. By reducing the exam percentage from 70% to 50%, you have an extra 20% to play with, so assign a group project worth 20% of the grade, thereby addressing the collaboration problem you mention.
As for cramming and concentrating on the wrong things, that's what students will do if you structure an exam that requires them to commit a lot of petty knowledge to short-term memory. I try very hard to make my exam questions address higher-level concepts, rather than nitnoid facts. I ask them to explain these concepts, often by weighing in on hypothetical debates. (Sometimes these debates aren't even hypothetical; I'll find a online discussion thread where a debate is raging, then paste it into my exam and ask them to chime in). In other words, insofar as I can, I test on what I want them to remember five years from now. If I want them to solve a problem, but don't care if they've memorized a requisite formula (because they'll be able to look it up anyway), then I'll just include the formula in the exam. I often tell my students, "Anythihg you would need to memorize will be put in the exam itself. If it's something I have trouble remembering off the top of my head, I don't expect you to memorize it for the exam."

But in practice, is it possible to improve on these flaws, without introducing major increases in workload for the instructor?

Ah, now, there's the rub. If you followed my suggestions here, look what I've done! There are three exams to grade, not two. These exams don't have a lot of multiple choice questions, and then there's that new group project I mentioned (which needs to be drafted up, assigned, and graded).
It's hard to get something for nothing; most meaningful improvements are going to come with some cost.

The first point is important: allow students to bring material but ask harder questions, in particular not only knowledge-recitation questions. It's hard to succeed in exams that require independent thought by "cramming".

For the most part, this answer does not seem to address the question, instead focusing on unconvincing rationalizations.

@user11596 - I'll grant you that my answer here focuses more on the premise of the question than on the question itself. However, if the premise doesn't portray an entirely accurate story, I think there is some benefit in addressing that.

In courses that focus more on real world practical ability, assignments (like creating a project, software, etc) are a suitable alternative. It can be done during more time, using literature and, if preferred, in a small group.
A student still needs to defend an assignment (demonstrate it working and answer enough questions to be sure the work has not been copied from somewhere).


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Do contemporary publications cite more sources? Why?
When I read very old, classic papers in biology, I am struck by how few sources they cite. Watson and Crick, 1953 cites 6 sources. Luria and Delbrück, 1943 cites 9. Sanger, 1977 cites 14.
This is in contrast to contemporary papers, which often have a whole page, in very small type, listing the sources.
What is going on? Am I correct in concluding that over the past century, the number of sources referenced by each paper has increased? What does this mean? Is biology (and perhaps other sciences) simply maturing and becoming more collaborative? Has the availability of computers and the internet made it easier to find more sources? Are standards higher nowadays about grounding your work in literature? Is it just that stuffing your bibliography with copy/pasted sources has become fashionable?

'stuffing your bibliography with copy/pasted sources has become ------' dangerously easier! Tracking references in the library used to be a drag.

jakebeal has pointed at the more technical reasons for the increase of references. We should, however, not forget some of the more subtle, but perhaps also, more fundamental changes that has happened.
First, there is a gradual change in how science is communicated. Scientific papers have developed from letters that were read aloud in front of scientific societies and also published as personal letters. The scientific debate was more closely akin to debates between persons making observations. Obviously this was possible for the reason that there were very few involved in any one research question. So, in part the development seen is due to a development of publishing driven by changes in the form and volume of debate.
Second, research questions have become more complicated involving larger and larger groups of scientists with varying expertise. This increase in complexity also means references are no longer required to cover just a specific question but also information from adjacent or supporting fields.
Third, science is disseminated in smaller parts today that what was the case back in time. This is partly out of necessity related to the second point above. Additionally, and this is perhaps not the greatest aspect of developments, there is the pressure to publish due, mostly, to the fact that academic careers are measured in terms of number of publications and number of citations. The number of publications has thus increased for several reasons and hence also the number of somewhat relevant papers to cite. I will not get into bad behaviour such as self-citations here but it is clear that any system will have flaws and some people will make use of such flaws to benefit themselves.
So at least some of the change in number of publications is due to developments in the way we perform and communicate science and also changing pressure from the academic world on researchers to publish and be cited.

If science is disseminated in smaller parts, shouldn't this reduce the number of citations? Surely a tiny discovery would have less background work to reference than a large one?

Contemporary publications definitely cite more sources.  There are likely quite a number of different forces in play, and I think that you have touched on a number of them in your question.  In my experience and opinion, however, much of it can be derived from the basic purpose of citations: to acknowledge the context and foundations of a piece of work.  Over time the "density" of context has increased in at least the following ways:

The number of active researchers has massively and progressively increased over the past century.  This means that for any given area of interest, there are likely to be more people doing work that pertains to that area.
Frequency of publication has been increasing for a number of reasons, including the continually increasing ease of manuscript preparation and (more recently) the increasing use of publication metrics in evaluating researchers.
Improvements in information systems mean that it has become progressively easier to become aware of and obtain copies of the publications of others, such that there is less "excuse" for not citing a relevant publication.

Each of these increases the amount of information that can reasonably be considered relevant context and that a researcher is expected to be responsible for knowing about, and thus naturally the number of citations.

Because as time goes on, more and more research is performed, and knowledge is accumulated and published. Early on, the literature is not abundant. Also, it is easier to identify and locate relevant literature now.

I tend to motivate this mainly with two facts:

As science advances and topics become more complex, research papers become more specific, so that one may need to put together many "little" pieces in order to deduce and/or motivate new insights.
Thanks to the internet and more advanced channels of communication, it is nowadays easier to discover and exploit the work of other researchers

Luckily, we have the second point! Otherwise we would be lost ;-)
I like to think of this as a world-sized brain which keeps on growing, where every researcher plays the role of a single neuron, and the network between them makes it possible to expand our knowledge.

Although other answers have already mentioned this as one factor, I believe that the main driver for increased citations is simply the fact that it is much, much easier to rapidly and exhaustively search academic literature now than in the 1940s or 1950s.  (In economic parlance, the "search costs" have decreased.)  Academics who are operating now can easily use online search resources like JSTOR or Google Scholar to find papers on a topic of interest, and it is extremely simple to identify large numbers of related papers very rapidly.  In my experience, I can begin research on a topic where I have no previous knowledge of the literature, and within a few hours I can comfortably identify twenty or thirty relevant papers.
If one compares this to the difficulties of research through libraries in the 1940s and 1950s, the difference is quite staggering.  In those days, even finding one paper would have required travelling to the library (no sitting on your computer in the office for you!), searching printed index-cards, and finding physical copies of the paper in the stacks.  It could also require journals to be physically transported between libraries before being available to you.  Obscure works might be present in only a small number of libraries, and it would be difficult to be alerted to their existence at all.  While it is certainly true that there are other factors at play (e.g., the accumulation of more work over time), my suspicion is that most of this is down to diminished search costs.

Indeed, it is easy to forget what searching the literature was like.  I spent hours and days in the library when I was in graduate school, seeking all possible papers relevant to my work.  Twenty-five years later, I revisited one of the topics in my dissertation.  It took about five minutes on the internet to find several papers I had missed in my pre-internet search.

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What are the obligations of a principal investigator?
Obviously a Principal Investigator (PI) has many responsibilities toward his or her subordinates, including mentoring them, helping to direct their research, providing funding, and resolving difficulties.
But, in practice, it is often possible for a PI to avoid many of these responsibilities and "get away with it". By this I mean that failing to address these responsibilities has little effect on the PI's own career.
For example, it is often understood that a PI should have some input when PhD students are writing manuscripts. A PI with a large lab may have a policy of leaving students to fend for themselves in this regard. With some intelligent selection at the hiring stage, this PI may ensure that most of his or her students are already capable of writing papers with no assistance. The few that slip through will fail to have a productive PhD, but this will not directly impact the PIs career all that much.
Similarly, a PI may be unable to come up with good research ideas, but this can be compensated for by actively seeking out graduate students who do have good ideas. Since it is rare to explicitly state in science who had the idea for a project, the PIs CV will still look good thanks to the papers the students end up publishing.
However, an example of an obligation is applying for grants. If a PI is ineffective at securing grants, it is very unlikely that their career will not suffer. Students and junior lab personnel simply don't have the knowledge or experience needed to put together a good application, and while post-docs can secure their own funding, the majority of funds in a typical lab is brought in by the PI. If the PI decides to not bother himself with obtaining funding, the lab will become financially hamstrung, research will suffer, and even to a casual outside observer it will be obvious that the scientific output of the research group is appreciably constrained.
My question is, which responsibilities cannot be avoided by a PI without necessarily producing severe negative consequences? If after a cursory examination, a PI's career seems to be going well, which responsibilities can we be certain have not been neglected?

That's actually a pretty good summary of how things actually work in my experience. At least, this question could be like a mini-instruction manual for the people I have "worked for" in the past. I also think you have answered your own question for the most part. Are you asking what responsibilties in addition to grant-writing cannot be avoided? Well, teaching comes to mind. Also, "which responsibilities cannot be avoided by a PI cannot be avoided". You have some repetition in there.

I've never seen the phrase "obligate responsibility" before, nor does google seem to know if it. Did you invent it?

I'm also curious about your reason for asking this question. Of course, that is not something you need to specify.

@FaheemMitha Thanks for catching the grammar mistake. Since I am not myself a PI, I was wondering if anyone on here would point out something I hadn't thought of. "obligate responsibility" is not an actual widespread term as far as I know, by it I tried to describe responsibilities it is practically impossible for a PI to not fulfill.

@FaheemMitha As for my reason, mostly curiosity. Clearly, just because two people are both eminent professors with an impressive body of published research, doesn't preclude them from being very different in many ways (for instance, management style). But in what ways can we know that they must not be different (since we have the non-trivial information that they are successful scientists)? In other words, you could say I'm asking about common features which all successful PIs can be expected to have, by virtue of having been able to attain success.

I see. A more blunt way to put it is - if "two people are both eminent professors with an impressive body of published research" doesn't preclude one of them being a crook, and the other one being talented. :-) Anyway, it's a good question.

@FaheemMitha Maybe the OP meant 'obligatory' instead of 'obligate' ?

@xLeitix Perhaps. That does get some Google hits.

The word is "obligation". I've edited accordingly.

My question is, which responsibilities cannot be avoided by a PI without necessarily producing severe negative consequences? If after a cursory examination, a PI's career seems to be going well, which responsibilities can we be certain that they have not neglected?

In my (extensive) experience with large labs, the only responsibilities that a senior professor can never delegate are networking, certain types of review work (e.g., reviewing for well-respected grants) and certain committee / administration / board work. Basically everything else seems to be fair game.
I find it interesting that your prime example are grant proposals - in many groups in my field, writing grant proposals is mostly a postdoc responsibility, so that is certainly not a duty that is never delegated. However, that might be an european speciality.
I would say your question is actually standing on ill assumptions. You assume that successful profs. are distinguished from no successful ones via the things that they still do themselves. In practice, this is generally not correct. In my experience, most large labs work well because the prof. has a track record of acquiring good people to do things for her/him, not because (s)he does so much her/himself. Further, successful profs. are able to establish mutually beneficial relations with those good people. That is, if you want long-lasting success, you cannot expect e.g., your postdocs to just write grant proposals for you all day because you told them to. You need to find a model how it is actually in their best interest to do so. All successful profs. I know are supremely good at binding strong people to them via the power of mutual interests.
Now, all of this is not to say that a prof. has to delegate everything, or that any given professor even wants to. I know many successful professors that would never delegate some aspects of their job (for instance teaching), either because of a sense of responsibility or because they just honestly like doing certain things themselves. This is just to say that I have seen almost anything being delegated in different large groups.

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Who benefits from the anonymity of the peer review process?
I was reading an answer to another question, which says on the topic of a reviewer potentially contacting an author under a special set of circumstances

Some would say you should wait until it is public, so as not to break the anonymity of the reviewing process. Others think it is fine to reveal yourself and contact the author directly

My first thought was "The anonymity is there to protect the reviewer, so of course he can give up the protection and initiate contact". But then I realized that maybe there are other people whose interests might be hurt if this happens.
So, let's assume that the anonymous person (the reviewer, and in some cases also the author), always benefits from his own anonymity. Is there somebody else who is interested in the reviewer remaining anonymous?

possible duplicate of In single-blind peer-review, can you reveal your identity without the editor's consent?

I think this is a different question: "Who benefits from referee anonymity?", not "Can I, as a referee, reveal my identity?"

As JeffE said, I didn't intend to discuss whether the identity should or shouldn't be revealed. This is just the background of the question. I am asking exactly what I said in the title: assuming the anonymity is kept, who has benefit of this.

@JeffE If the question is considered different, is it fine to (almost) copy-paste an answer from the other question?

The readers and the editors can benefit.
I know this is a contended issue, and there are many different views.
But as you've asked specifically whether there's somebody else who is interested in the reviewer remaining anonymous, let's just look at that.
As a reader, I want the peer review to have been fair and thorough.
If the reviewer is able to review freely, without fear of comeback, then they can be much more frank. They can shoot down a bad paper, even if one of the authors or one of their colleagues could hold some kind of power over the reviewer, whether it be funding, future job applications, peer reviews with the roles switched, whatever. Anonymity may enable reviewers to be more frank, more honest, and more direct in their reviews. And that directness can be of benefit to the editors, too.
I'm not saying this is the way. I'm not saying this has to be the way. I'm discussing possibilities here.
It would be great to have some solid evidence on the pros and cons of anonymity. At the moment, there seems to be a great deal of discussion, but I don't see much science on the subject.

Since I do not see benefits this answer will in essence not answer your question. It is possible to imagine benefits but reality is what counts and that tells a different story in my experience.
So, from my experience as editor, author and reviewer, I have to say, I am not impressed by anonymity in this process. Anonymity has a tendency to free some people from much of their socially acceptable behaviour and the review process is not the place for anything other than objective criticism. I should also add that in my field reviewers are more often known than anonymous and the general trend is towards more openness.
When I receive reviews as an author, I find that i am far more likely to take suggestions seriously if the reviewer is known than when there is an anonymous reviewer. There are probably several reasons for this. If I know the reviewer (as a peer in the subject) I can better read between the lines and understand from where the comments come from. with an anonymous review you loose that possibility. If there is a name at the other end, it becomes more of a person than otherwise so I believe anonymity makes it easier to disregard from criticism or take it less seriously.
As an editor, I can see many anonymous reviews containing quite rude remarks. As an editor, you have the right, perhaps obligation, to convey what you perceive as being constructive information to the authors for their revision. If I get a rude review, I may not convey the entire review to the author, or more commonly, I will excuse for the poor behaviour of the reviewer and highlight the parts that the author should focus upon. So an editor has a moderating role in such cases. But, most bad (in one way or another) reviews come from anonymous reviewers. In some ways reviewers may of course feel awkward for providing a very negative review that they wish to remain anonymous.
So to try to look at the big picture, I would say that most reviewers do a good job but anonymity seems to bring out the worst in lots of cases and in ways that are not founded in what should be in a scientific review.

What sort of rude remarks do you see in reviews?  I've only seen this once as an editor (when the author turned out to be plagiarizing the referee's work), but maybe you're thinking of a lesser degree of rudeness than I am.

The only rude remarks about my work I've ever seen (in contrast to frustrating ones) all had the person's name attached.

@AnonymousMathematician I am sure you realize the impossibility of answering your question?

@PeterJansson: I don't mean to ask for specific quotations, but I'm curious about what sort of rudeness.  For example, are you talking about deliberate insults?  ("The author writes like an undergraduate.")  Sarcastic comments?  ("This paper fills a much-needed gap in the literature.")  Harsh, blunt judgments?  ("This paper is completely worthless.")  Mainly, I'm just surprised since rudeness in reviews isn't something that seems common to me, so I'm curious whether we have the same experience (and are just describing it differently) or different experiences.

I have met many rude people, both in anonymous circumstances (including a review so vitriolic the memory still stings even though the paper got published), and in person. I have worked with them, lived with them and loved them. And none of them was a sadist who liked torturing others when he thought he can get away with it. Rather, they were arrogant jerks who were convinced that they are right and their behavior is above reproach. And they did not shy from exhibiting it face-to-face. So, while I believe you that rudeness in reviews is a problem, I don't think it's enabled by anonymity.

"If I know the reviewer (as a peer in the subject) I can better read between the lines" - that is a valid point for some reviews. However, I would also consider it as a flaw of the respective reviews if there is such relevant information hidden between the lines (as that may mean editors and authors receive quite some different information from the same review).

"Anonymity has a tendency to free some people from much of their socially acceptable behaviour" -but the referees are not anonymous to the editors. Even without disclosing any detail, I would assume socially inacceptable behavior in a review would bear quite high a social cost.

I always thought the revised paper will benefit, in that objective comments will be taken into account based on what they say rather than who wrote them. My impression is that keeping reviewers anonymous serves to avoid a certain bias that would be present if certain referees were recognizable as much more senior than others.
When referees are known, a nonsensical suggestion by a well-known researcher might be applied out of the authors' respect for the "big name". Likewise, a well-justified comment by a junior researcher could be ignored due to the perceived irrelevance of the referee.
Along the same vein, I feel remarks that might come across as "rude" are easier to ignore that way: You can simply discard the respective statement without having to consider the ramifications about a fellow reeearcher's personality or their stance towards your work (which means, probably, overthinking things, anyway). Instead, as an author, you can fully tocus on the provided suggestions and weigh the indicated justifications.
In this sense, the effect of making referees anonymous towards authors mirrors the effect of making authors anonymous towards referees. In both cases, an intention is to avoid a bias based upon the writer's name.

The other answers and comments are completely reasonable, and/but, seriously, there is the obvious synthesis, which we all really know, namely, that human behavior has a certain range...
So, yes, ideally, it would even be better to have a double-blind system... or, wait, ideally, no one would behave prejudicially. :)
Ok, start over. So, assuming people might react prejudicially, the typical single-blind system only protects the reviewer/referee, not the author, from subsequent complaints. No, it does not protect authors from the many different possible prejudices of referees. Yes, it does allow referees to be bitchier than they'd be if they were in a public place. This conceivably has some purpose, but, also, it might just be venting.
And, then, there's the point that with substantial work, the coterie of competent referees is small, and that an observant author can infer the referee by use of language and other mathematical details. "We're not stupid". :)
At this point in my life, I think a not-at-all-blind system would work better. In particular, referees would be culpable for blocking competitors' work, or for gratuitously disparaging novices' work.
Next, we can ask why the traditional publishing houses control scholarly "publication" ...
... nevermind...

To be fair, I've been in situations where giving a negative review publicly would have been a serious issue: I was a doctoral student at the time, and the researcher was rather famous in his/her field. This means that a well-known scientist in my field would have been in a position to hold a grudge against a young(ish) student. The opportunities for abuse in this situation are endless.

@cody, I agree, there is potential for abuse, probably in any version of the game. Probably an editor should choose a referee whose "status" is close to, or above, the status of the author, whether blind or not.

@paulgarrett I just compared your answer here with that in the question linked in the OP. What caused your change of heart?

@sgf, I think it's not that I had a change of heart, but that there are two distinct questions. The other thing (linked-to) refers to a situation in which the default is single-blind, and the question is about stepping outside that. Here, the question is whether the assumption/context of single-blind is a good idea itself. So the other thing was about "failure modes" of single-blind.

The only one who benefits is the community, or, if you wish, the science itself. Blind review allows more fair reviews, the reviewers need not to fear getting revealed (in the ideal world).
I don't see how I as a reviewer benefit from it. When blind review is dropped, I start to make not-really-honest reviews because I don't want to be frowned at by my colleagues, no gain nor loss for me personally, it's loss for everybody. Unfortunately, the authors often think that the reviewers are responsible for the fact that the article is a crap, which causes all this. We aren't able to accept honest opinions.


text:
What to use instead of academic 'we' when describing an experiment?
My research is in software engineering, but in a sub-field which is very close to social science. My papers normally contain sentences like "We conducted a study with 56 participants." and "Our previous study showed that [some assumptions are true]" and "We chose to use Cramer's V as the association measure, because [explanation why we thought it is better than other association measures]".
Now that I am close to my Ph.D. thesis, I am writing more texts alone, and the thesis is legally required to be my own work. So "we" is factually wrong. But using "I" feels immodest, and it is certainly unusual. But I don't know how to change my texts to avoid it.
I can't imagine how to apply the advice from that other answer to my case. "One conducted a study with 56 participants"? "The conducted study had 56 participants"? "A study was conducted, with 56 participants"? Unlike describing a mathematical proof, these sentences sound terrible. And how to explain my decision to use Cramer's V, when it is based on personal opinion?
Any advice how to deal with the matter outside of the world of mathematical proofs?

Another example why "I" might be needed. It is not only vanity; in the not-so-exact sciences there is sometimes lots of leeway involved. Say that I code some data. This is a very subjective process, and can be error prone. It is important for the readers to know that a coding was done by a single person, as this is considered less reliable than having somebody else repeat it and discuss any differences, and also because the coder has to take responsibility for any unusual decisions or errors.

There is a more general question on the same topic. But the accepted and highly-upvoted answer is from the point of view of a mathematician, it says that the writing style is best constrained to declarative sentences such as "Since p, it follows that q.".

I am almost sure this is duplicate of http://academia.stackexchange.com/q/2945/546. The only difference I can tell is that you're working on PhD thesis. Have you talked to your advisor yet?

@scaaahu it is a dupe, thank you for pointing it out. But the answers there don't help me, as the highly upvoted one assumes that I am making a proof. I can't say "One performed a study with 56 participants", etc. :( Maybe I will think of ways to re-write my question.

@scaahu I rewrote it completely, to point out how it differs from the situation to which the answer of the other question applies

The study included 56 participants. For each sentence, identify the key verb. You are off track because you have focused on conducted as the key verb. Maybe you can aso avoid mentioning a person if you make the subject the study or the paper.

The use of the authorial 'we' is very common in academia even for single-author papers, as argued by many and properly referenced in the other question that you mention.
Personally, I would keep 'we' also for the thesis without bothering. I doubt anyone would misunderstand, but if you wish you can include a quick remark in the introduction: something like Despite the use of the 'authorial we', common in academia, this thesis is the sole work of its author. In many cases you are required to state that you are the only author anyway in some boilerplate forms in the front matter.
This looks much better to my eye than changing every sentence to a contorted passive form. Readability matters.

Related: http://math.stackexchange.com/questions/1305775/why-do-single-author-math-papers-use-we-instead-of-i

There are customs and habits that differ between disciplines, between research groups and between individuals. I would endeavour to claim that the trend is away from passive phrased (e.g. "was made" etc.) to active we and I but perhaps also from royal we's and expressions such as "this author" in favour for being to the point using "I". The key, however, lies in how the "I" is used. (in fact, "this author" may even be confused by the author of the latest referenced paper)
If you write a paper you can safely use I whenever you report on things you in particular have done. In methods sections, it concerns the choices of methods you (and nobody else) has made and in the results section it concerns the results you (and nobody else) has obtained and your choice which ones to highlight. In the discussion section you can use "I" whenever you make a point that you stand by, you can use we in parts where you perform a discussion with the reader; we meaning you and the reader. In short, the "I" signals your contributions and puts you (and nobody else) on the spot for criticism. So as I see it "I" is not a way to brag (which seems to scare many), it is exposing the fact that you alone stand for what is written.
I suggest you try to find good (recommended by peers) papers written in different styles and think about the styles with the aim of finding your own comfort zone. It is a matter of style, not right and wrong.
To cap off I want to highlight a couple of books that I personally, being a non-native English speaker, have found very useful:

Glasman-Deal, H., 2012. Science research writing for non-native speakers of English. Imperial College Press, London

and

Day, R.A. & Sakaduski, N., 2011. Scientific English. A guide for scientists and other professionals. Greenwood, Santa Barbara CA

I'm not sure about the conventions in social science, but the problem seems to be very close to what natural scientists face when writing a methods section, i.e., how an experiment was performed. If you look into the publications, you will see that these sections are almost exclusively written in the passive voice. The idea behind it is to take away the focus from the subject performing the experiment, putting more emphasis on tthe process instead. So you examples would become:

A study with 56 participants was conducted.
Cramer's V was chosen as the association measure, because...

"Our previous study" is still fine, when the previous study has several authors.

Yes, that is, "passive voice" in verbs avoids first-person pronouns altogether.

Interestingly there is a parallel debate(?) in screenwriting, whether it is appropriate or proper or not to use "we see [character] suddenly jump back." in action text or screen direction.

I want to add two thoughts based on APA style. While the passive voice may help in some circumstances (as demonstrated in other answers), overuse of the passive is sometimes considered bad style. The Publication Manual of the APA (6th) even says on page 77:

Prefer the active voice.

Furthermore, the APA manual contains something about attribution on page 69.

Inappropriately or illogically attributing action in an effort to be objective
  can be misleading.

Thus, if you did something, it may even be misleading if this information is hidden using some stilted writing. And APA explicitly mentions the usage of I for single-author pieces on page 69:

For clarity, restrict your use of we to refer only to yourself and your
  coauthors (use I if you are the sole author of the paper).

In summary, I think a good balance of passive and active is considered good style, and the usage of I (where appropriate) is slowly becoming acceptable.

I am in cognitive psychology and frequently use, "In the present investigation." There are sometimes workarounds you can use to avoid passive voice such as, "56 adults participated in this study."

If any co-authors, you need to use we since the readers don't know who the I is.
Use I, as needed for sole author pubs.  I like I because it is a strong statement--there is a definite person to hold responsible.  Don't use "we" if there are no co-authors (what you got a mouse in your pocket?)  If you feel too hesitant about a bold I (or get static) than go to passive voice.  But a "we" for a sole article is distracting.
Do not use I when it makes more sense to make the objects of the research, the subject of the sentences.  For example NOT "I observed pitching as the stall angle was approached", but "the model started pitching near the listed stall angle, about 35 degrees".  The reason is not for modesty but because (a) it is tighter writing and (b) the proper attention is on the model in the wind tunnel--your observation is not the point, here.
I recommend to avoid the passive voice, but some people will recommend it or expect it.  Certainly if an editor requires it, just do it, don't argue.  "The reactants were combined in a boiling flask..."  Note, it does have the benefit of putting the attention on the science, not on you as an actor.
Some math writing uses we because the reader is included as an observer in a derivation, "after completing the square, we see...blabla".

We in PhD thesis typically mean: I am as an author and you as the reader. It is used in the sense that we together explore the topic. And it is just a kind of writing style to incorporate the reader.
Writing "We conducted a study with 56 participants" or "our previous study" can be considered as a bad writing style. Since it has not the same meaning and could be easily transferred in passive voice.

I asked my supervisor directly. She said that she is OK with using "I" in the dissertation, but that it is "uncommon" to use it in articles. As she is always a co-author on our papers, I guess none of her students had to deal with the problem in the context of an article anyway :) And because she did not mention internal reports even though I specifically asked about them, I think that she doesn't care what I use in them.
This is just the opinion of one professor, and the answers here show me that there doesn't seem to be a good convention. So, my take-home message from the whole problem would be: ask your professor, he will probably have a position on it and it is wise for you as a student to follow it.

I'm facing the same problem, though in German language/natural science (conventions may vary somewhat).
The main problem with the passive construction is that it doesn't say at all who did it. Consider:

The algorithm was implemented.

How can the reader be sure it was you as opposed to your colleague giving you his code (particulary, if the corresponding paper is authored by multiple coauthors)? I'm told I cannot expect the reader to look up the source where the author is explicitly stated.
So for some (ver key points where I need to make really sure everyone gets the fact that I actually did work myself that is fairly common (e.g. in other groups in my field) to be done by colleagues, collaboration partners, students or technicians I use "I" even though is so uncommon that I get comments about the use of "I".
Assuming that commonly studies like the one with 56 participants have someone planning it, someone (else) doing the experiments/collecting the data, and someone (yet else) analyzing the data: make sure you properly acknowledge the contributions of your collaborators in the acknowledgements.
You can also use constructions like:

A study with 56 participants was conducted [ref]. This thesis focuses on [whichever part you did]

Otherwise, "This thesis shows that..." or

Throughout this thesis, Cramer's V is used as the association measure, because ...

get you a long way.

For disciplines where passive voice is used, there's an English grammar convention that tells whether you or somebody else performed the work. You: The algorithm was implemented. Somebody else (or you, in a previous paper): The algorithm has been implemented. And of course, if you reference other people's work properly, this will also answer the question.

@PeterShor: good to know. Not knowing this, I've produced papers for a decade that may be misleading... That being said, I'll try to remember this, but considering how many non-native English speakers publish (and not knowing which native languages have a similar concept of using time to denote contributions) I will not rely on this convention when reading papers. I'm anyways a big fan of a "contributions" paragraph at the end of the paper.


text:
Can I use a Google map in my PhD thesis?
I want to use a map downloaded from Google maps in my PhD thesis. Does Google allow me to do this? Do I need permission from Google?

Same here, have you found an easy way to do that?

Related: https://academia.stackexchange.com/questions/77933/permission-to-include-a-segment-from-google-maps-as-a-figure-in-a-publication


text:
Should I tell my advisor that our paper is full of mistakes?
Okay, I'm in a nasty situation. I'm about to receive my master's degree in two months. Also, I am a third author on my advisor's paper, and the paper is completely awful and full of mistakes. Contradicting results not reported etc., it has it all. The thing is, my advisor will take it personally if I give comments that would put him to a bad light in front of the other co-authors. Very probably, he would let his anger to be seen in the evaluation of my master's thesis.
Really, I have no idea what to do. Should I be quiet, hope the paper gets rejected, and then RUN FAST, or just write a long email about every error there is? Which one is less harmful? I really don't want my name on that paper, nor a biased evaluation of my master's thesis.
(For background, my previous advisor left the university about 6 months ago, and then I got this new one. So, I could probably get a letter of recommendation from the previous advisor.)

why your advisor doesn't want to correct the paper mistakes?

Must the paper be submitted before your thesis?  Do you have other faculty mentors besides your advisor?

You do not want to be associated with an awful, incorrect paper at this stage of your career. That is, unless you plan to leave academia for good or the paper is published in a place where nobody will ever read it.

If the paper is really bad, it will get rejected. What reputation harm does happen to you because of that? Nobody knows you were one of the co-authors right?

What about the other authors of the paper? Do they share your opinion or can you at least talk to them about the issues?

Isn't your thesis evaluated by a faculty committee? If not, how is there any mechanism to protect students against spiteful (or overly generous) advisors? And if it is, have your old advisor write to your committee on your behalf, if you do expect your new one to try and tank your defense.

Your name is on the paper; you should be able to take a look at the draft, and suggest improvements.

The paper is completely awful and full of mistakes. The thing is, my advisor will take it personally if I give comments that would put him to a bad light in front of the other co-authors.

Okay, there are two ways to address this. You can pubically say, "This paper is awful and full of mistakes," paint your advisor in a bad light, and face his ire.
Or, you can take each of the mistakes, and tactfully offer an improvement. That is, you could privately say, "I think the paper might have a better chance of acceptance if we made these changes."
In other words, don't edit as a critic; rather, put some work into the paper as a co-author.
There's a fine art to editing work in a way that isn't off-putting for the primary author. People tend to get defensive when their writing is critiqued – it's a very natural reaction. However, if each of your suggested changes is offered constructively, as an improvement to an initial draft, rather than an indictment of it, you stand a better chance of incurring thanks instead of wrath.
On the other hand, if the paper is so bad that it's not salvagable, then I'd suggest requesting that your name simply be removed from the author list.

@VahidShirbisheh I don't think being a scientist makes a person any less likely to get defensive when he is critiqued.  The word for that is maturity.  Some scientists have it and others don't.  Maturity seems to be correlated only weakly (if positively at all) with scientific ability.

You wouldn’t be asking this question if, instead of errors on a document, your dilemma involved a source of personal injury, such as a hole outside the front entrance folks could fall in and never crawl out of!   (Facetious I know, please accept my apology.)
Aren’t you asking “At what point should I point out errors?"  Below that arbitrary point I find errors acceptable, above that point, prohibited.    Unfortunately, our conscience doesn’t come with a warning lamp.  :)


text:
When can I make assumptions in scientific papers?
I would like to know if assumptions are accepted among the scientific community. especially in the field of theoretical computer science.
To be more specific, is it OK to say something like: "The behavior X might be explained by . . ." when you are not 100% sure that it is the correct explanation, or you are not able to explain it mathematically or statistically.
Edit:
Indeed the possible explanation I'm talking about is not the main point of the paper, but a small part of results discussion that is, from my point of view, important for future investigations. Also, if I take the time to run some additional tests it would be off-topic and very time-consuming.

@L What about "Possible explanations include, but are not restricted to, ..."?

It depends on what you mean by "is it OK".  If you write "The behavior X might be explained by...", it's certainly OK in the sense that nobody will be offended or automatically reject your paper.  You are acknowledging some uncertainty, so there's nothing to object to (while there would be if you claimed greater certainty than your work justified).  On the other hand, speculating about possible explanations is not as good as giving a compelling explanation.  It's reasonable if this is not the main point of your paper, or if the speculative explanation is awfully clever.  However, if the main point of your paper comes down to speculation that you just haven't investigated carefully enough to resolve, then it will probably not impress readers.  You could end up with a paper that's not objectionable but still isn't very good.

This is not so much an assumption, but a hypothesis. If this is the bulk of the work, then it is not likely to be acceptable. But if this is part of the discussion of a larger piece of work, then it may well be acceptable. Your paper needs a contribution beyond the hypothesis.
Ultimately, hypotheses are fine in papers. Good questions drive research forward.

Just make sure you call it a hypothesis. State the main claim of the paper (the one you prove) clearly as such, and do the same for the hypotheses and assumptions.


text:
How do I deal with an extremely difficult master thesis with poor basics?
I am a master physics student in a German univerisity. I started with my master thesis topic in May 2019 and at that time I had wrong evaluation about the pre-requisite and difficulty of the topic I chose. Later on, I found most of the problems/papers that I need to solve/read, I almost do not have any pre-requisite knowledge for them and I have to learn from the basics each time by myself, and I encountered many problems while self-learning the basics which I do not know whom to ask (due to the pandemic, I have to work alone in my hometown in my country and I do not have a suitable friend I could think of to ask questions) and I felt my interest for the master thesis topic got wiped out after these very difficult processes.
I have long time depression, and had been taking anti-depressant regularly before, but then I stopped taking them due to the negative effect of being sleepy and other negative symptoms which makes me hard to concentrate on study.
I also face a lot of pressure from my parents, and I am often told to finish the thesis as soon as possible though I have explained that it is too difficult, so I currently moved out from my home and live outside in order to get more concentrated on study and avoid receiving the pressure from my parents.
My current situation is that I have already taken more than 2 years in the thesis (where normally it lasts for 1 year) and I have applied several extensions for my thesis topic but I felt the extension is not bringing too much help for me, as I am still depressed and the problems are still difficult. Each day I cannot control myself well and waste a lot of time doing other non-related things, and I feel very demotivated and I do not see any hope to solve the endless difficult problems in order to complete this thesis.
I wish to know if any of you could give me some advice/share your experience in how to dealing with my situation. Thank you very much for reading.

Firstly, I'm sorry to hear you are in such a bad spot.  Your question strongly depends on individual factors (which is why people are voting to close).  Given your circumstance, it would be a shame for us to give you no advice, so I am going to sneak in an answer before this gets closed.  The most important thing to do here is to speak to your supervisor and lay out all these problems and see what your options are.  Universities commonly face cases where students are out of their depth, and dealing with concurrent depression.
There are a lot of separate issues here, but the aggregate effect seems to be that you are no longer making substantial forward progress on your topic, and you are unlikely to be able to complete your thesis.  Postgraduate university degrees sometimes have a mechanism to allow you to "drop back" to a lower level program in cases where you are unable to complete the requirements of your present program.  In this case, it might be possible to negotiate to drop back from a Masters degree by research to a lower-level coursework program (e.g., Graduate Diploma, Masters by coursework, etc.).  If such an option exists, I recommend you take it eagerly and don't worry about the drop in level.  If such an option does not exist, you should ask about options for taking extended leave from the program.  If this is not possible, you will have to make a difficult decision about leaving the program entirely.
Given your circumstances, I see little point in trying fruitlessly to progress on problems that are too advanced for you; the likely effect is to aggravate your depression, waste your time, and damage your status in your program.  You should consider putting aside your advanced research topic and dropping back to learning introductory and intermediate material that is within your present capabilities.  Try to remain active, go for walks, eat healthy, get enough sleep, and do what you need to do to make your life more manageable and enjoyable.  And again, talk to your supervisor.  Good luck.
(Please feel free to email me if you would like further general advice or just a sympathetic chat.)

Thank you very much Ben! I am grateful that you took your time reading my post and gave me these tips and I am willing to take some of them to try to improve my current situation. All the best wishes to you!

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


text:
Do social behavorial and economics (SBE) PhD students get funding in the US?
I am a Banking and Insurance graduate from India with 7.5 years of banking experience. I wish to pursue a combined MS and PhD in the SBE field. Do universities in the US fund such PhDs? By the way, I am on an H4 visa.

Yes, U.S. universities often fund these Ph.D. positions, though my sense is that there are fewer funded positions than in STEM fields. It would be very rare for a MS to be funded, as far as I know, and often opportunities for teaching assistantships (funding through teaching classes to (usually) undergraduates) are reserved for people in doctoral programs as opposed to master's programs.
Also, usually I hear these fields referred to as "social science," with the NSF being the only entity I associate with the term "SBE".

Thanks a lot. Can you point some "social science" disciplines that are more in demand than others? I was thinking about psychology.

@user65003 In the context of your question, I believe you should decide your field of study based on what you're most knowledgeable and passionate about, rather than what's in demand. Funded graduate study usually requires a lot of demonstrated potential for doing research in that specific field.

If I were to apply for a combined MS phd, would the intake for both of these be separate? Or acceptance to the MS equals acceptance to the phd program?

Acceptance to a master's program would almost never imply acceptance to the PhD program in U.S. social science programs I've heard about. (Usually you'd apply to the master's program, then afterwards apply to a lot of places for Ph.D. programs, or you would apply directly to a Ph.D. program, and potentially (maybe) get a related master's degree on the way to the Ph.D. For instance if you're in an Econ Ph.D. program, there may be an opportunity to get a Sociology Master's degree based on additional coursework.)


text:
How to cite a modified figure?
I took Figure 1 from this article
and made a few changes to it.
How should I cite it?
Do I have to cite it?
Should I cite it like "from [source] (modified)"?

You should indicate that the figure was taken from an existing article and that you have modified the figure. My usual means of doing so includes

Figure adapted from Fig X. in Ref. YY.

inserted at the end of the caption.
You should also make sure to include whatever copyright notice the journal or repository in question expects to be added.


text:
Resubmission - Dealing with rude reviewer
I submitted an article in September 2016; after that, I got an invitation to submit at a conference. In January 2017, I got my first round of reviews. The first reviewer had "no comments" as his sole input and the second reviewer was very positive, so my submission is rated as "Minor corrections needed." Meanwhile, I graduated (March 2017).
In July 2017, I got my second round of reviews. The first reviewer “woke up” and shot down my article by vetoing it. Of the 12 points he mentioned:
•   5 were previously addressed in the first round of reviews.
•   4 asked for origin of data clearly labeled (i.e. references were already provided and clearly labeled)
•   2 were ad-hominem attacks.
•   1 highlights a lack of understanding of elementary principles.
(The second reviewer was positive and said that the modifications following the first round were acceptable.) It feels really, really unfair to be dismissed like this, on no scientific grounds, and I was not even given the chance to defend myself!
How is this even possible? How:
•   Can an article go from "Minor corrections needed" to "resubmission required" without any checks?
•   Can the first reviewer say nothing on the first round of reviews, only to come out with guns blazing?
•   Can the editor let the borderline remarks pass?
•   Can the editor not have a critical thought on this second round of review?
I’ve reached out several times to the editor and to the senior editor, and any of them won’t even answer my mails. I’m not in a position to resubmit the article myself in the immediate future as:
•   I’ve started a (non-academic) full-time job.
•   I don’t have access anymore to the computer framework to run additional simulations or refine existing ones.
My former advisor says that another student will rework it, but I will not be primary author anymore. As it will mostly remain the same (my work), I also see that as unfair. I have an amicable relationship with my former laboratory, but I will oppose the decision of removing me from primary authorship if the modifications are only cosmetic.

I'm not sure what the (major) question is. Perhaps "how can I still get this paper published"?

It is possible that reviewer #1 had confidential comments during the first round that were not at all positive, and still wasn't positive about the paper in the second round. Or it could be that he mixed up the "comments to editor" and "comments to author" fields, hence the first review had no comments.

It's not clear that it's actually the same reviewer as before. Sometimes journals will bring in additional referees on a revised paper; I know that I have certainly been asked to do so on a few occasions.
That said, if your review was so biased as you state, then you should be able to write a convincing response to the criticisms made by the reviewer. Be firm but also polite—trading insults or being rude will get you nowhere.
Overall, though, it seems that the editor is not a very good one, and you may find more luck submitting to a different venue. (I also don't see why you have to be in an academic position to be the one to resubmit the paper!)


text:
Changing university and advisor midway through PhD
I have read several posts regarding this question such as "Is transferring to another university an option for an unhappy PhD student?" and
"Changing University in First year of Phd", but none of them apply to my situation.
Background: I am a first-year computer science Ph.D. student, I started my Ph.D. in the spring semester and so I am in the second semester. I am fully funded, but the problem is that the income I get from the university is very low and I did not know that I have to pay about 2000 each semester for insurance. My mind is always busy thinking about how can I provide this money. It's hard, as I have the potential to do really well but most of the time I am struggling with financial issues.
The second but minor issue is my advisor, she isn't an expert in her field, we just go forward with trial and error, and I am the kind of person who needs to read deeply to understand all aspects before trying. We have to have a strong reason to test an approach so before testing we should take a good amount of time, but she just likes to force me to test without in-depth understanding. It's disappointing for me. Most of the time the results are not good. I said this is a minor issue as I am self-learner and I will find a way to do the way I like.
I talked with my advisor regarding this, she said we have to survive in this time, and I don't have any other sources, she tried to make me happy by not giving me the TA of a subject that I don't like, but it does not work for me. I need to make my mind free and focus on the research.
With these explanations, how can I convince another university and professor to accept me?

Given the possible conflict with your advisor, may I first suggest you to change your SE profile, name and picture, to avoid being recognized?

@MassimoOrtolano thanks yea I have to do it, but I have heard that saying conflictit with the professor has the negative context and should not do it, they may think I am not some one put up with the situations, or someone that complain all the time, but really I am not. I am very patient but found myself really broken and helpless, though even my professor likes the way I am thinking and most of the time I have something to offer in terms of idea

I think the advisor part is less of a concern, assuming she is an experienced  researcher with quality publications.  For example, my students quickly become more of an expert in a topic than me after 6-12 months.  Trial-n-error is fine but you can minimize going down a rabbit hole by first getting a better understanding of the method/problem yourself.   Then provide evidences to your supervisor why it is good/bad.  As for the financial issue, there is no easy fix.   Best of luck.

@Prof.SantaClaus many thanks for your advice, yea I agree with you that supervisor part is really not important and I mentioned that. I just said that to give you a big picture of the situation.

@Prof.SantaClaus also somehow she isn't very experienced in publications, though she has been a professor for many years. but its not like a concern as far as im self-learner, do you think I can explain about the financial difficulties here to professors and convince them>? or its unreasonable


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Tools for data organising and processing
Suppose we perform experiments with input parameters (temperature, humidity, processing time...) and collect resulting data (thickness, structure, mech. properties...).
Is there a tool (or set of tools) to organize, process and export data from such experiments?
Key features are:

Structured files decomposition (raw text files).
Basic math operations.
Filter and sort by given parameters (show/export data from samples treated at given temperature and humidity for various times).
Generating tables with given parameters and list of "constants" (table of times, mech. properties and thicknesses and list containing temperature, humidity...).
Vector graphics output and/or output suitable for MATLAB (graph of thickness as function of time).
Automated (or easy-to-create) LaTeX output (report sheet).

If not, any idea, hint or recommendation how to create it is appreciated. Right now I'm thinking of a spreadsheet (Excel) as core database and MATLAB as the processor (filters, sorting, graphics).

Check out R and one of its function Sweave, which can integrate R analytic command into LaTeX codes. Users can run the code first in R, and then LaTeX to obtain a report with all tables, statistics, and graphics already nicely embedded.

Org mode lets you combine the data, text, and processing. The processing can be done in whatever language you want, and even in multiple languages (i.e. wrangle data with awk, process with Python, display with R, all in the same file). Everything (or everything you want) can then be exported to LaTeX, or various other formats too.

I would store data in CSV (i.e. text file with a table, with values separated by commas) rather than XLS files (the first is easier to import from and export to anything). Otherwise many tools will do the job (if you are familiar with MATLAB - why not using it)?
For general data processing and manipulation, Python (with SciPy stack) is capable of everything you mentioned. In particular IPython Notebook is great for data exploration and presentation (you can use code, comments and LaTeX in such notebook - also for reports). For tabular data, use Pandas (R-like DataFrames).
For reports also you can create files in Markdown (with LaTeX), and then convert them to pdf with Pandoc - may be much easier than generation of LaTeX code. (To get you some taste what is Markdown - look at StackEdit.)
And alternative to Python is R, with knitr for report generation. If you are not sure, if to choose R or Python, then for your task R seems to be an easier and better way to start (especially with RStudio as an interface).
For a bigger list and links to tutorials, take a look at a list of software for scientists.

Having worked with R and Python, I'd suggest using R for the bulk of the data analysis, building an <input> -> csv shim that's as thin as possible in python. For some munging tasks, python is much better, but for data processing R is often much stronger (especially when combined with ggplot2).

So the answer is NO... I thought of .csv, but with MATLAB I can't use it as table with head (meanings of columns) and MATLAB can read .xls and .xlsx files easily.

@Crowley http://stackoverflow.com/questions/19613232/reading-csv-files-with-matlab

@PiotrMigdal Thanks. I'll look closer at RStudio. It seems powerful enough and I like it's licence and OS mobility.

I find Google Sheets is easier and more powerful in many ways than excel. I have done a couple of projects with a sheet of raw data coming in via csv, then other sheets to process it. If you're clever, it can be done so that when the raw data are updated, everything else falls into place. Google Charts is basic but has some neat features for looking at data. The Transpose, Filter, Sort and even query (SQL) is very cool if you have lots of data.
You can collaborate in teams, commenting on interesting findings, etc. Graphs output to PNG or PDF look great in latex. Data are available in the cloud, not just on some file server in a lab. Tables are a special kind of graph that can be shared on web pages and have user-selectable options for sorting, etc.

Before starting with google docs make sure their terms of service (http://www.google.com/intl/en/policies/terms/), particularly the section "Your Content in our Services" agrees with your needs.

I should have mentioned I use google apps for education (my uni has a domain) so those terms are likely different than the "free" services.


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Which discrete math journal should I choose to publish my findings?
I have some results, related to imposing group structures on subspaces of finite fields with a metric, and I would like to publish my work. My advisor asked me to choose a journal, but I have no idea how to decide.
I have some further results on a paper published in Linear Algebra and its Applications. I have resolved a few open question they pose in their paper.
Is it advisable that I publish my results in the same journal? What other options do I have? How do I know if it is a good journal?

possible duplicate of How do you judge the quality of a journal?

Why not putting it on http://arxiv.org/ and then asking question (more people would be able to give advice). Maybe asking on https://scirate.com/ under your post won't hurt. But in case of doubt, why not journal which you cite the most, or one from which comes the result you push further?

One good place to start is the journals in which your most important references were published. (The authors of those references would be good candidates if the journal asks you to propose referees.)
Or: ask other people that work in the same field what journal they would suggest. (While you are at it, send them the manuscript and ask them for comments, nicely.) Have you presented your results at a conference? Do you recall anyone there working on a similar topic? Ideally someone who sat in on your presentation?
Your advisor should have at least a passing acquaintance with your field, so he should be able to suggest something. That he does not do so suggests to me that he is watching how you cope with this situation :-) How about other students of your advisor, does anyone work in this field?
It is not easy to judge whether a given journal is good. @EnergyNumbers' comment is helpful.

No one in my lab works in my field, including my advisor. He is very reputed in other fields and he is extremely sharp. Perhaps he is testing me! Thank you for your comment.

"Perhaps he is testing me!"  I'm not exactly sure what that means, but I don't like the sound of it: you don't want to be playing mind games with your advisor, I promise you.

@PeteL.Clark: It was in reference to Stephan's comment:"That he does not do so suggests to me that he is watching how you cope with this situation :-)".
In all likelihood, I think my advisor believes I have a better idea (which I dont), since I worked on the problem alone. I will talk with him anyway;And, also there is no mind games with him, he is very cool.

Helping you choose a journal is exactly the sort of aid your advisor should be giving you.  Often in the relationship between an advisor and a graduate student there is a lack of clarity and/or a miscommunication about what the student should be doing on his own and what his advisor could be helping him out with.  I remember that one of my students gave as part of an oral exam a talk on an important paper.  He asked me about it a little bit, but not as much as I was expecting.  When he gave the talk it was excellent, except that at one point he presented a sort of black box and said "unfortunately I didn't understand this".  It was (to me) no big deal, but I had to wonder, "If you understood everything except this one thing, why didn't you ask me about that thing before the exam?"  He must have had different ideas about the amount of independence that was being asked of him.
The point of the above story is this: given what little you've said, I am not yet persuaded that your advisor is unwilling to help you choose a journal for your paper: why wouldn't he be willing to help?  In general, here is a good strategy for getting help from any faculty member: rather than saying "I'm stumped; please advise," try something and then get feedback on the merits of what you tried.  In your case you have the idea of submitting to Linear Algebra and its Applications because you answer some open questions raised in a previous paper in that journal.  To me that sounds like an excellent idea: I have several times submitted to journals with the same idea (unfortunately, acknowledging that you have successfully answered questions from a prior paper does not guarantee that they'll want to publish your paper; I've had it happen both ways) and most of the journals that I've submitted to have been for less logical reasons than this (the other common strategy, related to yours, is to look through your bibliography and see whether any journal comes up more than once; if it does, if your paper is similar in subject matter and scope to any of those journals, then it's at least reasonable to submit there).
Here's an idea: why don't you come up with one or two more ideas for where to submit your paper which feel different from Linear Algebra and its Applications: e.g. try a journal which does not specialize in a mathematical subfield; try a journal which is of significantly higher quality -- e.g. Discrete Mathematics; if it doesn't sound ridiculous, maybe try something like the American Mathematical Monthly.  Then bring these specific journal suggestions back to your advisor and ask for feedback.  If you don't get any feedback from this, that's strange, and it is probably worth asking (as sunnily as you can possibly muster) why you're not getting help on this.

Thank you for your insightful comments, especially the idea of trying a journal of 'significantly higher quality'. If that means better peer review, I would love to send it there.

To be clear, when I suggested trying a journal of significantly higher quality, I meant trying the idea of submitting to such a journal out in front of your advisor.  This will help you to find out what he thinks about your work.

Yeah, of course. I first submit my draft to him anyway.


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Conference management software (preferably open source) with custom fields
I've been told to set up software to organize a workshop. Is there (preferably an open source) conference solution that allows for:

Abstract Submission
Event Planning
Arbitrary user data-fields

Apparently managing "dietary requirements" is a really big deal for the organizers.

According to the developer, the non-free version of easychair can support something like this:

We have a similar functionality in the registration module (non-free).
  All your requirements are related to conference registration, not to
  paper submission.

However, the "registration module" is very difficult to find.

Open conference systems supports a nuanced registration module.
While arbitrary checkboxes are not supported out of the box, there is an area for "optional registration types" which we have repurposes into an area for us to track the various optional things we need.
The rest of the system supports abstract management and scheduling.
Also, this forum post has literal instructions of how to hack registration.

SAdly this software doesn't work anymore, it's archived at https://pkp.sfu.ca/software/retired/ --- it's "retired" as you see from the URL, has old security problems, and doesn't run on PHP7 (maximum is PHP5.6). So, Indico or OpenConf it is seemingly. I once had a (paid-for) WP plugin but that was a nightmare.

I just found out the existence of Indico, an open-source conference management software developed at CERN for their own needs. I have just played with the sandbox for now, but it seems impressive.
EDIT: six years later, I have used Indico as an organizer for two small conferences and as a user for 3-4 more. I confirm that it is powerful and simple to use; for my needs (in applied mathematics) it seems the best choice. I confirm it supports custom fields in registration, in particular, as OP requested.

How did you "use" it? i.e., did you have to set up a dedicated instance on your own web server, or were you able to piggy-back on someone else's?

@LouKnee I used it on self-hosted servers in our university, but small events can be hosted for free on CERN's public server, upon request. This lets you try Indico without installing your own instance.

You can use OpenConf for your purpose. It is free but you have to buy license for upgraded features. Going through the demo, it seems impressive. Bear in mind that you have to host this on your event website.

does OpenConf have abritrary registration fields?

I think it has that option, you better take a demo tour - http://www.openconf.com/demo/openconf4/openconf.php

The link from @ShadowWarrior doesn't work. You can find the demo at https://www.openconf.com/demo/


text:
How are graduate students funded over the summer (in US)?
I know that there are often summer courses through TAing, but those are much rarer. Many departments don't even offer summer courses.
In that case, are graduate students over summer always supported by RAships? And does an adviser have to have funding in order to support these students (in US)?
Do these standards also vary between professors at public schools and those at private schools? Especially schools that have guaranteed five-year funding?

Do these standards also vary between professors at public schools and those at private schools? — Yes.  Also between schools with an even number of letters and schools with an odd number of letters.  Every department is different.

Please specify whether it is US, UK, Europe or sth different. I think that it may change situation wildly... (and then, JeffE's comment).

In my experience in math in the US it is not expected that the school or the advisor provide summer funding.  Many people do make money in the summer in a variety of ways, but it's much less formalized than during the year.  Personally, I was funded by the NSF half the summers I was in grad school and worked at a summer math program for the other half.

Depends on the field. In engineering, the expectation was that students were fully funded for the entire year, including summers.

In an engineering discipline, it is not hard to be funded for most/all of grad school. I was a research assistant almost my entire time (at 2 different universities), minus one semester as a TA. Most of the time this was working for grants that my professors had already secured. While TAs may not have as much work in the summer, RAs can work whenever as long as the advisor has money. This works best if you have an advisor who is well-connected and has a large group with several grants from which he can shuffle money around. Newer professors may simply not have available funds for all of their students.


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How many weeks of break (per year) should a graduate student reasonably expect to have?
Here are the details for one of my schools so far:
At UChicago, my prospective adviser said that I should expect to have around a month off per year (probably 2 weeks in winter and 2 weeks in summer).
It's probably fairly reasonabl, though it came as a bit of a shock at first but that was because I was used to being an undergrad where I had at least 2 months off EVEN if I included courses during summer quarter.
I'm on a fellowship for my first two years, but I'll still be pushed to produce results (I'm basically being trusted to do a highly ambitious project).

Well, I suppose I take about 4 weeks or so per year, so that's pretty accurate.

When it comes to the comparison, rather take as a reference a 'normal' job than undergraduate studies (it is unlikely that you 2+ months of holidays). However, often it is case-dependent and somehow flexible (see e.g. http://www.phdcomics.com/comics/archive.php?comicid=1459).

The official answer depends on where you are located, and the applicable laws in your jurisdiction. For instance, in Germany, graduate students are almost always employees of the government, and are therefore accorded vacation benefits commensurate to that (between 23 and 29 days per year, depending upon age). In contrast, the United States technically does not have any requirements on annual paid leave, so the answer in principle could be as little as zero, but normally is two weeks per year.
Unofficially, that's a matter to be worked out between you and your advisor. Some advisors will be willing to let you take days off here and there as needed, so long as they don't interfere with either your long-term progress or meeting your day-to-day responsibilities. Most advisors will be rightfully displeased if you ask to take two months of leave all at once, but most will not mind a three-day weekend here and there as needed.

aeismail's answer is very good. Just to extend it a little, you should not expect to take breaks with the undergraduate schedule; spring/summer/winter break does not apply to graduate students. Almost all (US) graduate students will take off the week of 12/25-1/1 or thereabouts. At the end of the day, it really depends on your advisor's dispositions towards your taking time off from lab.

I guess one can take 4 weeks off per year if they want to and can. But you hardly have the time to do so, especially if you are working in a wet lab. I probably took 2 weeks max per year, and that also not all at once (more like one of two days here and there to fit my experiment schedules).

Having this small amount of time off seems very unhealthy to me

Unhealthy, but very common in the lab sciences.

This answer is very anecdotal… maybe you could expand it a bit, or link to external resources on the point you highlight (which is interesting)?

What is a wet lab?