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What is the advantage of being a Math/CS double major in graduate admissions for someone who wants to work in TCS?
Doing original research in Theoretical Computer Science requires a quite good understanding of almost all areas of Mathematics.
I think double majoring in Mathematics and Computer science for someone who wants to do research in Theory is very important.(Or at least having a knowledge of Algebra, Analysis, Logic, Topology etc.)
I'm wondering how do graduate admission offices take this as an advantage?( Specifically in comparison with other good applicants which have publications or higher GPAs.)
Thanks.

Anything that "requires a quite good understanding of almost all areas of mathematics" would require multiple lifetimes of preparation.  Unless you mean almost all areas of undergraduate mathematics.  But do you really need to know, say, differential equations for TCS?

I'm not aware of any applications of Differential Equations in TCS but maybe that's because there are a few people knowing both Differential Equations and let's say Complexity Theory. Of course understanding all areas of mathematics can't go further than undergrad mathematics, but in some areas we need much more than that.

Doing original research in theoretical computer science requires a good understanding of some areas of mathematics; which areas it requires obviously depend on what kind of theoretical computer science you want to do.  Every area of mathematics is useful for TCS (yes, even differential equations), but unless you're Terry Tao, you can't master everything.

@JeffE Definitely, But my point is that a theoretician(including PhD students) must have a knowledge of almost all areas of mathematics at undergrad level(like Analysis, Algebra, Logic, Topology, Set Theory, Number Theory, Algebraic Geometry & Topology). The least advantage is that you can talk to math people, see what they're doing and get ideas from them.

I understand your point, but I disagree.  It's enough to be familiar with some areas of math; some TCS folks do quite well with no expertise in math (except, of course, TCS itself).

To split the difference here, you need to know enough to recognize things ("Oh wait, that might be a variety"), but you don't need to know enough to apply a theorem from the top of your head ("Let's throw theorem XYZ at it") - the latter can be obtained if you have the former by reading and talking when needed. JeffE's point is to do lazy querying (to use a CS term :))

I personally rate strong math skills as a major plus when it comes to looking at applicants. This is not superior to having actual research experience, but it definitely helps an application. For many areas of TCS, a strong math background can be more valuable than a strong CS background that is weak on TCS.
But students with a strong math background AND a weaker TCS background tend to need a little reprogramming when it comes to asking questions :) - they are good at answering them though.

I agree.  But it really doesn't matter whether an applicant actually majored in math.  I'd personally prefer an applicant who didn't double major, but instead took some interesting grad-level math classes.

@JeffE Why do you prefer non-double majors?

@Kaave: It's a mild preference.  Satisfying the requirements of a second major requires jumping a lot of administrative hurdles, which potentially distract from learning interesting math and doing research.

Studying mathematics is great, and I agree that many theoretical computer science students would benefit from studying more mathematics.  However, double majoring is definitely not a must, and it will help only slightly with admission.  It could serve as a tie-breaker, but it is less important than getting good grades and much less important than doing research.  Ultimately, a double major is worthwhile if you would enjoy it or find it useful, but the learning will have to be its own reward.

Yes, I should relax my claim a little bit but I think it's better to point it out in an extreme way :)


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How to approach a professor for research?
There is a similar question posted here, but the answers don't exactly fulfill my needs, as will become obvious in this post.

I just graduated from an undergraduate program in engineering and in September will be beginning my Masters program at the same university. The Masters program is advertised as coursework-only, with the official website saying that students can "contact professors for research opportunities to augment coursework."
That's all well and good, but I'm not sure how exactly to contact a professor. I had a high undergraduate GPA, completed internships in industry, not academia, and took one course each with the professors I'm interested in - I did well in their courses, but they probably don't remember me since I didn't often attend office hours (other commitments).
There are certain topics I'm interested in researching, and I've casually read some PhD theses produced by students of the labs I'm interested in, but I've clearly never done formal research work.
So, the general question is, how should I contact a professor about joining his/her lab? It's currently the summer, so should I email him/her? Should I wait until September to talk to him/her in-person? Do professors generally just look at resumes, or do they expect prior research experience? Should I indicate the topics I'm interested in, even though my knowledge is gated by the courses I've taken and papers I've read?
I haven't decided about whether I'd like to do a PhD, so does my indecision make it harder for me to get a position at a lab for the 1-2 years it'll take for my Masters program?

Different situation, same advice. Read their papers, email them asking to set up a time to talk about them, ask good questions about their work. Finish up asking if you could work with them on whatever to gain experience.

How should I contact a professor about joining his/her lab?

Email now. Express interest and see if they're willing to talk via Skype or would be willing to meet in person when you're both in the same city. You want to talk face to face. This is also a good spot to ask if they have any advice on what to read to get up to speed on their work if it's going to be a while until you can meet them.

Do professors generally just look at resumes, or do they expect prior research experience?

No to both. Research experience is a plus, but you have to start somewhere.

Should I indicate the topics I'm interested in?

You should be interested in the topics that the professor works on and should identify what those are in your initial email.

I haven't decided about whether I'd like to do a PhD, so does my
  indecision make it harder for me to get a position at a lab for the
  1-2 years it'll take for my Masters program?

If you end up wanting to do a PhD you should go somewhere other that where you did your Masters and undergrad work. Any decent professor shouldn't expect you to stick around.
There are some professors who won't work with Masters students. There's nothing you can do about that. Others will want you to take their class first. Take it, ace it, and then remind them that you're still interested and now have other ideas from their interesting and wonderfully taught class.
Now for Ric's guide for getting into research

Go to your department's website and find the page listing all professors (hopefully with links to their websites).
Skim each professor's bio and see if their research areas interest you.
For every professor that sounds interesting, read through some of their current papers. Focus on more recent works. Read abstracts and intros. Use this to get a better idea of what they're working on.
For every professor you're still interested in, find a recent paper or two that you like and read it fully. In this step you want to try and figure out what they did, why they did it, and how their work fits into the current work in the field. This is the hard part, but the more effort you put in here, the better. Besides, you want to get into research, right? You need to learn to read papers =)
Send a short email to each professor. Something like:

Professor Webb,
My name is Francis Thurston and I am a first year Masters student interested in meta-physical topology. I was reading through your recent paper on non-Euclidean architecture ("His House at R'lyeh: Modern architecture of Greenland cults") and was wondering if you had considered Professor Atwood's claims on the subject ("Mountains of Madness: The innate wrongness of the city") in light of your recent work. I think that combining his claims with some of the results of your recent experiments would be interesting. Would it be possible for me to come by your office next week to discuss your work and any possible research opportunities?
Thank you,
Francis Thurston

When you meet with a professor. Ask questions that show you're interested in the subject and have put in some work. Extra points if you have ideas about directions their work might go in (e.g. areas to explore, experiments to run, &c.). Ask if they're taking students, if they would consider you, and what the workload would be like.

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Affiliation and address when writing under a pseudonym
Quite a few threads have already discussed the issue of publishing articles under a pseudonym, such as
Is pseudonymous publication ethical?
If I publish under a pseudonym, can I still take credit for my work?
among others.  My question is:  with journal submission being what it is today, what should one write under e.g. "Address" and "Affiliation" when writing under a pseudonym?  For most journals, one has to write something in that field.

Ask the journal. This is the sort of thing that is entirely within editorial discretion. It's very unlikely we can give a general answer here - this is so rare and so niche that all we could do is guess or handwave...

You have to make your own decision on that issue and accept the impact it may have on your chances of publication.
My recommendation would depend on your field. If you are dealing with a cryptography journal you might be able to share your PGP information (or encrypted email address) and "anonymous researcher of topic XYZ"
For other Journals you may be forced to provide the name of an actual organization with a mailing address where you can actually receive mail. Whether or not a pseudonym is acceptable will depend on the Journal and whether your organization will vouch for you in some manner (perhaps least by accepting mail addressed to your pseudonym and confirming your affiliation with the organization without revealing your identity).
If you want specific advice, the name of the Journal may help (if someone here is knowledgeable about their policies). What you want to do may or may not be possible.
I will ignore any taking credit and ethical concerns since you have already read those discussions.
Of course I am assuming you have a good reason to do this, otherwise you are making things much harder on yourself than they need to be.

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Could a second masters hurt my PhD application because expectations will be higher?
I would like to do a second masters, because I would like to change focus to a certain subfield within my field (not changing fields) and have the best shot of getting into my favourite program. I also had some personal problems both during my BA and my first MA, and think I could do much better.
I am worried though that having 2 masters will set the bars slightly higher for me in the application process. Is this true? Phrased differently: are admissions people more likely to look at the my CV in a 'absolute' way, or do they judge it 'relative' to the amount of time spent in academia maybe?

In the parts of academia I'm most familiar with (mathematics, US), even one master's degree is not a necessary prerequisite for a PhD program.  Some students do improve their application and chances by doing a separate master's degree, but (when a master's degree is not a necessary prerequisite) I would advise any student to also apply for PhD programs and see what they get into.
In your case, having completed one master's degree in your field and having the desire to go on to a PhD program, I think you should certainly apply to PhD programs.  If there is a second master's program that you are extremely excited about -- in particular that you think is prestigious, would improve your academic record and offer you critical new skills that you would not necessarily pick up in the PhD program -- then you should apply to it as well.
If you get into a solid PhD program with funding, I advise you to take that over any master's program.  This is your life, and at some point you will want to have your student days behind you while you are still somewhat spry.  However, if you get in only to PhD programs that are substandard and you get into a very good master's program, then yes, taking that is probably a good investment for the future.
All this is definitely something to discuss with your current thesis advisor, by the way.

I would echo Pete Clark's answer and also add, succinctly: it won't necessarily hurt, and it won't necessarily help. Depending on your field and the program, admissions committees are far more likely to put stock in exam scores and samples of prior work before anything else. Whether or not additional accolades give you that precious edge over some other candidate will really depend on the attitudes of the admissions committee members, which are impossible to know in advance. You could certainly approach people in the department you want to get into and ask, but it's always a bit of a mystery (and a bit political) how individual opinions and preferences are transmuted into a collective decision. It may make a difference if you're working on something relevant to the interests of the department's research activities. It may not. In any case, the better programs are not necessarily going to give you "credit" for your masters work anyway, which is something you may want to look into before you end up doing a whole bunch of redundant course work.


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Could it be more productive to work independently after PhD?
Picture the following scenario:
X finished his PhD. X is also quite rich and can support himself (as well as his research) independently.
What do you think about this:
Would X's time after the PhD be well spent if he would just work 'independently'? Would this make things more difficult for him if he ever wanted to move back to an institution?
Is it in a way, in this particular scenario, not actually a very good idea, to focus solely on research and not bother with teaching and all the administrative stuff? Wouldn't he be more productive? What would hold him back?
Note: I am assuming that X is in the Humanities, that is, he does not require a lab or anything & has access to a academic library / or has his own etc.

Call me naive, but If I were that rich I'd search for a part-time position and then use the money to travel around the world! ;-)

It could be more difficult to advance upwards after such an adventure maybe. But there do exist other positions, for example "research engineers" who seem to get to help professors do cool technical research related stuff in research groups. But also, maybe the academic life is not for you if you already feel that way.

In academia, he might have

more exposure to interesting ideas (especially cross-field pollination),
better access to students and colleagues to exchange and refine ideas with,
as well as external pressure to be productive (which might be a good thing.)

While administrative work has never inspired me to have an interesting idea, teaching and mentoring students certainly has.
It all depends on the context he's able to set up for himself as an independent researcher. If he works better in isolation, maybe he'd be better off. If he can afford to hire other researchers and create an interesting intellectual environment, that might help.

I did not want to write it into the question, but say he has not been able to find TT after his PhD. Would working independently then be a viable option (provided X is rich) and could X get 'back' into the university system afterwards, or does it look rather bad and is frowned upon?

@Chris see http://academia.stackexchange.com/questions/40725/humanities-taking-a-year-off-between-phd-completion-and-academic-job

If this person wants to move to an institution later, having a strong research record (since he didn't have other duties, research expectations might be high) is important and, depending on the school, some teaching experience would be valued.  (This is more important if the person is out as an independent for many years.)
In addition to the issue ff524 mentions, being independent may be counter-productive for some people.  I have had no teaching/administrative duties at different points in time, and the lack of structure can make fit harder to be consistently productive at research.  In addition, you can start to feel a bit isolated without a good academic community to be a part of.  Personally, I think the ideal teaching load for research for me would be one course per semester most semesters, and then occasionally 0/semester for long trips etc.
I know a couple successful research mathematicians who do not have research positions, but they do have some sort of affiliations (one I think with no requirements, but can teach classes if he wants).  I would say if you don't need the salary, something like this would be ideal, and you could teach a little, with minimal service requirements.

this is very interesting. regarding your last point, how are these positions called / how does one become affiliated in this sense?

@ChrisDoyle I think the department will just make up a name for the position like some kind of adjunct or "research professor."  I suppose the thing to do would be to contact departments (chair or faculty who would be interested in you) to see if it would be possible to arrange such an affiliation.  Certainly one can get part-time adjunct/lecturer positions this way.

Yes, definitely. If he has set a clear course and has a vision. In academia he will be dragged down / have to split his focus between many duties not related to research :

Administration.
Teaching - many who are employed at universities have teaching as part of their duty. Almost everyone except self-funded post-docs have some teaching duties.
Representation - representing his group for example.
Acquiring grants.
Supervising MSc and PhD students.

All of these eat away some time, energy and focus each.

and 5. can be fruitful and bring new ideas.

So can walking around randomly, visiting new places, learning new things and talking to new people. All which can also be done outside of academia, whenever there is a lack of inspiration or motivation.


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How can a masters student compensate for lack of solid foundation in basic math and CS fundamentals?
I am a graduate student in Computer Science (in the U.S). I did my undergraduate study in India.
My fundamentals in Math and CS importantly are shaky. I often feel insecure in class where my peers seem to understand in depth about fundamentals that I have been taught differently (now I think about it -- mediocre standard at best).
I have been working my way through math using Khan academy. For CS I study them as and when needed. But I still feel a major gap in my approach and would like to get some suggestions on this.

I was/am in a somewhat similar situation: I chose not to go to grad school, despite having an opportunity, because I came to realize that my math intuition is mediocre. I only realized that towards the end of my undergrad studies when I started reading high-profile research papers. What I've been doing to improve the situation is learning from video lectures (namely MIT OpenCourseWare - there's a YouTube channel) while taking my own notes, and investigating additional examples and exercises on specific subtopics found around the web.

@jackbeal has an interesting answer relating to this question

If you can spare the time, you could just go through some of the elementary textbooks by yourself (e.g. CLRS Intro to Algorithms would be a good start).

That you realize this is good, but the appropriate approach depends on lots of individual factors.  The people who are likely to be able to give you the best advice are your professors/advisor.  They probably know best where you are at and what is most important for you to succeed in their program.  Also, informing them that you are aware of your deficiencies and are trying to make up for them should improve their opinions of you, and also make them more willing to help you succeed in the program.
That said, here are some things that can help: start tutoring or TAing for lower level math/CS classes (I first really understood eigenvectors when I was tutoring other students in linear algebra), going through texts on your own (exercises are the most important!), taking/sitting in on undergrad classes (some of our grad students with weak backgrounds do this), typing up your own notes on this fundamental material, finding people (students or faculty) you can ask specific questions.
Also: read up on the impostor syndrome (on wiki-p and here, say).  You may have it.

Take the relevant (even low-level) courses to fill out your knowledge is probably best. You might consider asking the teacher to attend classes without grading, or ask them to suggest material for self-study and self-assessment.
There are lots of freely available lecture notes, even classes with complete homework and exams (sometimes over several years) and often complete solutions.
One thing I found out the hard way about self study is that (as far as viable) just-in-time learning is best. Seeing where you will apply the material helps with motivation, avoids getting lost in unproductive side branches, and "hands-on" learning is more fruitful. Besides, "learn this because I might need it" can be a mistake (it is never used), happens too soon (when the use comes around, you have all but forgotten about it), or (even worse) a better technique comes by, and you'll have to learn that on-the-job anyway.
Yes, this will take time. Perhaps even lots of it. But as I tell my students, better leave late with a degree than soon with nothing.


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Trying to transition into different undergrad research area, how to approach professors in new area?
I am currently an undergraduate studying Physics and Aerospace Engineering. For most of my time I have been doing research in Applied Physics (optics, lasers, light-matter interactions stuff along those lines) and am looking to transition into propulsion or astrodynamics.
Unfortunately I have emailed a couple professors and have not gotten anything back from them (a few months ago). I don't know where to go now. What's your advice to get into one of these labs?
I am not keen on visiting face to face because I feel like as if I am invading his or her privacy and/or bugging them when they have such busy schedules.

Some suggestions in no particular order:

Try getting in touch with one of the grad students working in the
labs you're interested in, they may be more responsive and they can
potentially be your "in." Or they can give you very specific, individual, advice on how best to reach these professors.
Take courses with the professors whose labs you are interested in,
and impress them with your ability and your diligence in their
course.
Ask your current research advisor if they'd be willing to talk to the other professors you're interested in working with about possibly taking you on.
Find out when their office hours are from students in the class(es) they're currently teaching. Visit them during office hours and ask if they have a few minutes to talk about research. Talk to them about research, and impress them.


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How will academic misconduct as a first year undergraduate affect graduate studies admission?
I am a 1st year undergraduate student and I just put myself in trouble this week by cheating in a midterm exam.
This is my first offence, so I still have a 2nd chance and, trust me, I will learn from this stupid mistake. However, I am very worried as to whether I still stand a chance to be admitted to graduate studies in the future with this permanent notation in my record.
I plan to apply for the MA in about 5 years, so I still have time to take my redemption and do well in school and get some field experience, but I don't know if they will consider my efforts.
Will they even consider my application?

Which country are you in? (The spelling looks British...) In the U.S. any disciplinary action pertaining to cheating would be an internal university matter and would not normally be shown on your transcript. No one wants to ruin your entire career because of one mistake. You may have to repeat the class or serve some other reasonable punishment, but after that the case will be closed and no one will know or care.

I second Dan's statement. Usually, the first offence will not leave a permanent stain if it is not reinforced by further contraventions. However, I very strongly recommend that you never, ever be tempted to test the system again (you already say that you won't do it), as I must impress on you that punishment for repeat offenders can be expulsion from the studies. The philosophy behind this is that students may not know what they are doing in the first offence, but if they repeat it, they are seen as trying to game the system, putting an extra cost on the system to enforce fairness.

Some institutions in the US will certainly include disciplinary actions (e.g. disciplinary suspension for a semester) on academic transcripts.  Usually the first offense won't result in any punishment that serious.

One offense, if in early years and followed with solid achievements later on, will probably be forgiven. But someone with your exact same qualifications and no black mark would probably have an advantage.

Thank you,  everyone for your answer. I am from Canada, so I think the system might be the same as in the US...I think...Do you know if the notation in the record can be removed? I have been told that I can write a letter to the president of the institution, but it is usually dismissed...what can I say in the letter?

@T.Tran As Dan Romik says, it will probably not be on your transcript.  It's not even clear from the question if this is already on your official university record or the professor is just keeping this information "in-house."

It will appear in my unofficial transcript, also called "academic record", but not in my official transcript. The unofficial transcript is the one that is required for the MA application...so that means they will see the notation...I think the official transcript is only for employment.

@T.Tran At least in the US, an unofficial transcript doesn't usually have anything not listed on the official transcript.  It's usually just something free you can print yourself, rather than paying the university to issue a certified copy.  "Academic record" to me means the internal file the university keeps on you which is typically never released to external parties.  Though maybe things are different in your system.


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Professor will not write a letter of recommendation because I have restricted access to my records under FERPA, is this legitimate?
I am preparing my tenure-track faculty application materials for the current hiring cycle, and I'm thinking of replacing one of my reference writers with one of my PhD committee members (I'll call him Dr. Z). In addition to serving on my committee (I successfully defended my dissertation earlier this year), Dr. Z was a co-author on several journal/conference papers and a former instructor for several classes in which I did very well.
I sent an email to Dr. Z asking him if he would be willing to provide a letter of recommendation for me. His reply:

I have been informed that you have FERPA restrictions on your academic
   records.  I cannot provide reference letters for you or speak on your behalf to any potential employers with FERPA restrictions in place.

When I first enrolled at my PhD-granting institution, I placed FERPA restrictions on my academic records. Specifically, I chose to have my directory information removed from my school's online directory. I'm not a control freak, but I do tend to take advantage of mechanisms which help to prevent any of my personal information (such as home address, etc.) falling into unknown hands.
I have no reason not to remove the FERPA restrictions, but I hate the thought of removing them under these circumstances. However, I also understand, and appreciate, anyone's right to provide (or not) a reference for whatever reason(s) they choose.
I am left wondering, though:
Is there a legitimate reason that someone in Dr. Z's position would have for wanting to see my academic records prior to providing a reference?

Edit — For what it's worth, I am seeking out reference writers, such as Dr. Z, who can speak to my research capabilities, not about how well I did in their class.

Any recommendation letter Dr. Z may write will necessarily talk about your academic performance, because that's a large part of the context in which he knows you. It seems to me that he is saying the FERPA restriction prohibits him from sharing what he knows about your academic performance - which is FERPA-protected information - with the recipient of the letter. It doesn't necessarily mean he needs or wants to see your academic records. (IANAL and I don't have any FERPA-specific expertise, this is just speculation.)

I'm confused.  FERPA restricts who can see your educational records by default, unless you explicitly given them permission.  You shouldn't have needed to "place" any restrictions.  (Unless you're talking about "directory information", which is not restricted by default.)

Following on what David Z wrote, the professor may already have access to your records, but university policy might forbid him from commenting on you at all while you a FERPA hold. Some universities go a little overboard in their conservative interpretations of FERPA.

Not sure if Dr. Z is on the right track... if I am to write a letter for a faculty position applicant school grades will not be in the picture.

@Penguin_Knight: Dr. Z. is on the right track.  My (non-lawyer) understanding of FERPA is that nearly everything written about a student, including such things as Dr. Z's comments on MadJack's dissertation progress, is an "education record" and so covered by FERPA.

It sounds like there may be two issues here.  No matter whether or not you've placed additional restrictions on release of your directory information, he shouldn't be saying anything about your academic record (and this would include vague comments like "one of the best students in the class.") without a signed waiver from you.  A separate issue is whether he wants to see your academic transcript.  I won't write a letter of recommendation without both a signed waiver of FERPA rights and a transcript.

@BobBrown, oh, that makes sense...

If possible, it may be worth checking Dr. Z's university's policy on the matter. Dr. Z may feel constrained by that policy, rather than FERPA directly.

This document says by default a school can divulge "directory" info about a student. This may include date of birth, height & weight, address, phone number, and more. A student has the legal right under FERPA to forbid any directory disclosures without prior permission. This may be the "FERPA restriction" mentioned above. If the student has forbidden disclosure, then perhaps any reference by a professor of this student as a student to any outside person or organization may be a crime. (But I'm no lawyer or FERPA expert.)

You need to clarify whether he is asking you to authorize the school to release your records to him, or to authorize him to release your records to the recipient of the letter.

@JeffE You are correct. I went back and looked at what I had selected a few years ago: I chose to have my directory information removed from my school's online directory.

In that case, the professor is right to be cautious.  By hiding your directory information, you are making it illegal for anyone to even identify you as a student, much less write a letter about your performance or research potential, without an explicit written waiver.  You are asking for the same privacy protections as a student who is a victim of serious harassment or violence, or who needs protection from an abusive spouse, abusive parents, abusive paparazzi, or 4chan.

Thanks, @JeffE. Really puts a new perspective on something that I did not consider to be a big deal (i.e. not wanting my home address blasted across the internets).

By "FERPA restrictions" I assume you mean additional restrictions on the release of directory information, since these are the only extra restrictions I'm aware of.  If so, then the professor's reluctance may have little to do with your academic track record per se.
Many professors take a fairly laid back approach to FERPA and consider that an e-mail request for a recommendation constitutes sufficient written permission to release information.  However, some universities take restrictions on releasing directory information very seriously indeed.  As I understand it (keep in mind that I am not a lawyer), when you invoke these restrictions the university is not even allowed to confirm to anyone that you have ever been a student there.  A few students deeply care about this, such as celebrities, the ultra wealthy, or anyone trying to avoid a stalker or abuser.  These students have good reason to worry about invasions of privacy, and they want universities to place absolute restrictions on even apparently innocuous information.  For example, you can imagine social engineering attacks in which a private investigator, tabloid reporter, or stalker forges an e-mail to a professor asking them to serve as a reference for a job or internship, and then calls them to dig for information.
For most other students, FERPA restrictions can be problematic.  For example, if a company contacts the university to try to verify your resume, the university isn't allowed to drop any hints.  They are supposed to give exactly the same response as if you had never been there, so your resume should fail to verify, and the company may not give you a chance to explain.  (You'd think they should, and they might if they really want to hire you, but big companies can be pretty callous about quickly dumping applicants whose resumes fail to check out.)
In my experience, universities differ in how vigorously they enforce these rules.  For example, lawyers are more influential in some administrations than others, and some universities simply have more celebrities enrolled and thus face greater pressure to be strict.
As for how the professor could find out you have these restrictions in place, I'd guess it was from looking at your records.  However, there are other possibilities.  Some universities specifically notify everyone whose class contains a student with extra FERPA restrictions, to remind them not to reveal that this student is in their class, so the professor might remember receiving these warnings.
So my interpretation is that your university has you on a short list of students for whom everything is supposed to be completely confidential, and this professor doesn't want to risk upsetting the administration by violating these restrictions (while your other letter writers may not have been paying attention or may be more relaxed about such things).

As far as I know, the student choice of restricting release of directory information (stuff like name, field of study, degrees awarded, etc.)  is the only way in which a student can place restrictions on the release of information- the restriction on the release of academic records (such as grades) is automatic and must be explicitly waived by the student.  It may be that Dr. Z. is confused on this point.

It is more likely that Dr. Z. has (correctly) interpreted that things like his comments on dissertation progress are "academic records."

David Z's comment is dead on: it is an unpleasant technicality that under FERPA regulations, one should not discuss the student's performance in any quantitatively specific way.  E.g., one should not say "Mr. X got an A in all my courses" or even "Mr. X was the top student in the course".  The exact rules are confusing to many faculty members, to the point where one feels like if one took FERPA too seriously one might not be able to write a suitable letter.
In my university there is, in theory, a form that a student can fill out to waive the FERPA regulations on a letter-by-letter basis.  In theory this means that if the letter is getting mailed to N institutions, one should fill out N forms.
(The above considerations apply to all students, not just those who have asked for special protection.  However, a student who places further restrictions on their records is precisely going on the record as being especially concerned about their privacy, so in practice it makes a lot of sense to take the FERPA restrictions much more seriously for these students.)
It may or may not be the case that Dr. Z is himself trying to access or view any of your academic records.  (I guess he must have done something to find out that your records are FERPA-restricted though.)  Whether someone would look up a student's grades in courses taken by other faculty members must depend on the people and the institution.  For instance, at my institution I have access to the grades of all undergraduate students -- and I have been informed of the FERPA requirement that I access them only for legitimate, educational purposes -- but I do not have access to the grades of any graduate students, even my own advisees.  So in practice when I write letters for students I speak only about their performance in my courses -- but again, if they were FERPA-restricted and I was being suitably conscientious then I would even then have to be extremely careful about what I could say and likely be forbidden from including a certain amount of positive information about the student.
Also:

I have no reason not to remove the FERPA restrictions, but I hate the thought of removing them under these circumstances; this tastes a little too much like blackmail to me.

Even assuming that Dr. Z wants permission to access your records and not just to talk about them, I think you are not viewing this in the right way.  "Blackmail" seems ridiculous to me: one of the conditions for that is that the blackmailer must have something to gain!  What does Dr. Z gain if you waive or even entirely remove your FERPA restrictions?  The pleasure of viewing some of your academic records??
For my part, I am curious as to why you chose to place restrictions on your academic records at all: what are you protecting yourself from, really?  It sounds like you may not completely understand what FERPA restrictions mean and may have just taken them on as a sort of free insurance.  If I were you I would learn more about this.  In my opinion, one could argue that "I have FERPA restricted my records" and "Please write me a strong recommendation letter" is already a bit of a mixed message.

Thanks, Pete. I agree that "blackmail" is too extreme, but I couldn't think of a better word to describe my feeling. I'm going to remove it from my post.

one could argue that "I have FERPA restricted my records" and "Please write me a strong recommendation letter" is already a bit of a mixed message. — I don't see it that way. I'm interested in letter writers who can speak to my research capabilities, not how well I did their course.

@MadJack: Letters written for former PhD students by faculty in their program usually talk at least a little bit about their coursework.  This is a way to provide new information and an independent perspective.  Also, if performance in courses had nothing to do with research success, why would we have courses at all?  I recently wrote a letter for an NSF postdoc, and I explained how his superior problem-solving abilities in my courses were directly related to his research strengths (and to a paper that we wrote together).

If you feel strongly that your letter writers should not write about your coursework, there's an easy solution: get letters from people who haven't taught you in courses or better yet, from outside of your university.

@Mad Jack: you can certainly suggest to the letter writers which aspects you'd like them to mention, but you can't really micromanage the exact topics they write about. They have the freedom to write about anything that they think is relevant to helping you get a job. And they have probably seen many letters of recommendation from others, so they have a sense of what is commonly included.

@MadJack: Also note that your research is also part of your educational history at the institution. (I bet you signed up for a bunch of ungraded "Independent Research" courses, right?)  So your professor may think (rightly or wrongly, I am not a lawyer) the FERPA restriction also prohibits him from discussing your research.  In fact, as some of the other answers mention, it may prohibit him from confirming that you were a student at all!

get letters from people who haven't taught you in courses or better yet, from outside of your university — That is exactly what I have done for a majority of my letters. @PeteL.Clark

Here is what I tell my own students; my guess is that Dr. Z. is thinking along much the same lines:
"Federal law requires that I have a FERPA (Family Educational Rights and Privacy Act) release from you before I tell anyone other than a school to which you have applied anything about your education at this institution. For most of you, all I know about you is your performance as a student, so without that release, the most I can say is that you were my student, period. Because those asking about you are likely to interpret such a stark statement negatively, I won't provide any reference at all (except to other schools) without that FERPA release."

Good point that providing a reference which has obvious holes (and thus might be interpreted as "damning with faint praise") could be worse for someone than no reference at all.

Is there a legitimate reason that someone in Dr. Z's position would have for wanting to see my academic records prior to providing a reference?

Yes - I usually look up the academic records of students when I write a letter for them. This is so that I have more data about their academic success when writing the letter.  For example, if they did well in classes that I know are particularly difficult, I can mention that somewhere, and if they have a high GPA, I can mention that somewhere.
In general, you should try to give your letter writers as much info as possible. This includes not just access to your academic records (which they likely have anyway) but also at least your CV. If you have them, it doesn't hurt to send your personal statement, teaching statement, research statement, etc. as well. Not every reviewer will be able to speak to all of these in their letter, of course.
Remember you have already trusted the person to write a confidential letter  about you which you are very unlikely to ever see. This requires some amount of trust in the letter writer. For that reason, if a student told me "I would like you to write a letter of recommendation, but please don't look at my academic history", I would find it very unusual.

From that quote, it seems like that person is not on friendly terms with you. If s/he had the good will in him/her to recommend you, s/he would write something like "Oh, I'd gladly oblige you, but you have this FERPA restriction we would need to get past because of blah blah blah; so why don't you do XYZ to take care of it?"... but s/he did the opposite of that basically.
I'd seriously reconsider whether I want his/her recommendation in the first place.

Thank you for your answer, and +1. I don't understand the downvotes here: this is a perfectly legitimate take on the situation.

@MadJack: Just had to say it, since I know sometimes people are stressed out about getting a recommendation, since they N of them and they only have N-1, so they tend to overlook the (hypothetical but probable) possibility that it will do mor eharm than good.


text:
Is it well-received to thank the assignment author at the end of a course?
Institutional Background
I'm currently taking a programming course as part of my computer science studies at a rather small German university.
The course is done by the professor, who's holding the lecture, and three assistants who do the lab with us, prepare / correct the assignments and update and maintain the sample code base / documentation.
Actual question background
Now I've liked the assignments a lot and even posted them on CodeGolf.SE (after the assignments expired) after having obtained permission from my professor. They have done quite well over there (usually a lot of answers, upvotes and views). To be clear: The assignments were not "good" in the sense that they were trivial or easy, they just required an appropriate understanding of the materials and were quite enjoyable to do.
Because I and apparently others have enjoyed these assignments, or the ideas behind them, so much, I'd link to thank the author of the assignments in a nice email with links to the relevant CodeGolf posts.
As an inexperienced student I don't know whether it would be awkward for him to get such a "thanks" for "just getting his job done".
Is it generally considered appropriate / acceptable to thank members of the team besides the primary instructor for a good and enjoyable course experience, like good assignments)?
As for the relation between the assignment author and me: We had near to no interaction except him pushing the new assignments into everybody's SVN folders and then correcting all solutions, usually without many comments, after the students have pushed them back into the repository.
To distinguish this question from "Is it appropriate to send an email to a professor at the end of the semester thanking them for their teaching?": To my knowledge, the assignment author has no authority whatsoever about my grade and I already have my qualification for the exam and I've never met / seen him in person.

"Is it well received to thank [helpful person/people] for [helpful action]?" I can't think of many examples where the answer is "No". How and when to do so might take a little more consideration.

It would be even more beneficial to the assistants if you have the opportunity to formally evaluate them, and praise them with your comments.

@MatthewLeingang we had this this semester for this course and I already dropped a nice comment about the assignments in there.

Yes, I think it would be fine. Everybody likes to know their work is appreciated. Teaching assistants are often not appreciated enough  by their students (and sometimes not enough by their professors!).
Just a short concise form of thanks would be enough:

Thanks for those exercises you set for course xyz. They were really interesting, and I enjoyed solving them. I hope you liked creating them as much as I appreciated their contents.

Something along those lines perhaps. If you make it too long it might sound obsequious or sycophantic.

"Teaching assistants are often not appreciated enough by their students (and sometimes not enough by their professors!)" This alone is reason enough to offer a kind thank-you. It doesn't cost much to offer sincere thanks, but it can mean the world on the receiving end.

+1 and emphasis on the length; if I got a short email like this from a student, I would really appreciate it, as I do put some effort into the assignments.  If it was longer, I would assume an ulterior motive, and be irritated (even if they didn't ask for anything at the time).

You might even add a "working on them helped me..."  Just be sure everything is truly sincere.

In Germany
From my point of view, being a German computer scientist, I would also deem it appropriate to thank the team. From my point of view it is perfectly fine.
In General
Most certainly it would leave me smiling for the rest of the day. Everybody likes to hear that he/ she did well, as Brian already wrote.
Feedback
To give another angle why this is ok: Let's think about Feedback.
When designing courses and assignments, feedback from the students can be extremely helpful. It is not easy to judge how an assignment is received and nobody learns from assignments that are way too hard or way too easy. So if you tell them the assignments worked well you are providing important information to further improve the class.
In my experience, negative feedback is more readily given than positive. On the other hand, it is often not useful hearing that the course was too hard, from someone who skipped half of the sessions.
That said, I think your point of view matters here and can help shaping the next iteration of the course. Share it.

Having run the gamut of responsibility in my numerous TA assignments in graduate school -- all the way from glorified grader to total responsibility for the course, I absolutely endorse this answer.  It's very easy to come up with assignments and tests that are too easy, too difficult, too unfair, or otherwise unworthy of appreciation.  Crafting assignments and tests that are engaging and appropriately challenging is far more difficult than it appears.  Feedback in any form is useful.  Positive feedback would send me over the moon.

+1; as a teacher you rarely hear about things that went well, so it can be tough to make sure you're not losing anything important when you change from year to year. Specific positive feedback is greatly appreciated and useful.

My opinion is that if you feel thankful toward someone for something, just express it. Sometimes it might seem awkward, but so what? The thanks can be very simple, or more elaborate, depending on the size of the act, among other things. Don't overthink it.

Of course! No one dislikes having their hard work acknowledged and appreciated. This is even more true in academia, where the feedback loop is incredibly long and the feedback is mostly negative. At the very worst, a few people might demur and say, "Just doing my job." or something, but I suspect most of those people are still secretly pleased and I would be shocked if any were actually offended.
You can even do this in a way that helps the assistant.
Provide concrete examples of what you liked. For example: "I really appreciate the detailed comments I received on my assignments. My internship supervisor keeps commenting on how much my code has improved recently, so thank you for all the advice." or "Balanced binary trees finally clicked for me after we made that silly model from straws and sellotape during a tutorial." This may help the professor and/or assistants improve their teaching in the future.
Get your feedback "on the record." A personalized note or email would definitely brighten my day, so by all means, send one. However, if there is an official course evaluation, please fill that out too. Scores on those may be used to determine future teaching assignments, internal awards, etc. and they may also make the professor aware of the assistants' good work. This can be very helpful if the professor is ever in a position to recommend the assistant for a teaching position somewhere. In fact, it would not be totally out of line to mention this to the professor, if the occasion arises, or cc them on an email.

YOU DID WHAT?!?!?

In general, thanking people is perfectly appropriate.

I've liked the assignments ... and even posted them on Programming Puzzles and Cold Golf (CodeGolf.SE) (after the assignments expired) after having obtained permission from my professor.

Basically, what this indicates is that the instructor doesn't object.  The instructor's job, of course, is to run the course.

I'd link to thank the author of the assignments in a nice email with links to the relevant CodeGolf posts.

If I made the puzzles, I might appreciate knowing that my work has been shared with many people in the world, and that it was well-received.
However, there is another possibility.  Hypothetically, if I was a TA, I may have thought long and hard about this, and finally come up with a great puzzle that will challenge students.  I submit my code to the professor, and he agrees to use it for this class.  I think about how my contribution has benefited this department now, and how this benefit can happen for years to come thanks to the possibility of re-using material.
Then, the professor okayed a student's request to post this onto CodeGolf.  The professor has probably heard of Stack Overflow and might have some vague idea that Stack Exchange is somehow somewhat related, but may not be familiar with just how popular Code Golf is.  (I know, this hypothetical scenario is getting painted by making quite a lot of assumptions here.  What is being said here might closely match reality, or may differ significantly.)
As a TA who may be more familiar with Code Golf (especially after you show the hyperlink), I might be a bit disappointed that the professor ruined the ability to re-use the work in an academic setting.  Another possibility is that you may have taken my chance for fame.  After all, if I really thought that posting the puzzle was a good idea, I may have done so myself (and received whatever resulting reputation benefits I could).  Now, you've kinda ruined the author's ability to do that.
Overall, this might be bad news that might disappoint some people more than what it enhances their life.  The professor probably won't be disappointed at all, since the professor did give the okay for this.  The TA's may have a different perspective.
In summary: I say again, thanking them would be perfectly appropriate.  Letting the person know that you've used the code in such a public way (and even providing the hyperlinks) might work out quite well as this may cause the authors to appreciate your actions and their results, but there's also the possibility that they might not like that.  I simply advise you to be prepared for that possibility before you do that.


text:
Is there a definitive list of style guides?
Almost every publication, journal or conference series seems to have its own style guide. Is anyone keeping track of these ? IE, is there a website which keeps a list of style guides - specifically citation styles - for various publications ? The most definitive (ie all-encompassing) list would be what I'm after.

Why do you need the list. Why not just grab the style guide when you know where you really going to submit?

Well, my question is somewhat rhetorical - I want to know how many different formats their are and see how they differ. It's related to bibliometric studies, not necessary for submission purposes.

Perhaps a good starter.

Also go to your school library and ask the research librarian.  You'll learn more than you ever thought possible.

https://github.com/citation-style-language/styles

This Wikipedia may be a good starting point.
There are the international ISO series. And just in the US there are style guides for general writing, legal documents, academic papers, journalism, electronic publishing, business, and computer industry. It may be better to limit your scope of study.

Many reference managers can format citation styles automatically. This is a case where LaTeX is probably not your friend. A search of CTAN reveals around 43 styles for Biblatex and my TeX Live 2016 install has 404 bst files for Bibtex. In contrast, Endnote offers more than 6000 styles and Zotero has 8341 styles. I believe Mendeley uses data from CitationStyles.org which claims to have over 8000 styles.

A dedicated literature reference software may help you to keep track of the publications already accessed, as well in cross-linking them together (for example with a mind map; like docear), as well as easing insertion of the citations in your word processor / editing software.  Beside an article about it, wikipedia holds a list to compare them.
After collection of your readings, you will benefit from their style library, simply select "this publication is for Nature", and the citations will be formatted accordingly.  If you you want to use the citations again, for a different journal, reformatting is just a click away.
Personally, as working in an environment of different operating systems, I prefer zotero with a large -- and extensible -- library of styles, and "connectors" to Microsoft Word, LibreOffice Write, Apple's office, and LaTeX.
In addition, university / research libraries often offer workshops how to work with such tools.  Because of personal preferences, I recommend exploring them, side-by-side for some time prior to make a decission in favour for one or/and the other.


text:
Graduate program focusing on DevOps
I was asked the following question by someone who was interested in pursuing a career in devops, but wanted to learn things in a more formal environment such as a masters degree. Is there / Can anyone recommend any graduate program in the US that would help prepare said person for a career in DevOps? He already has a Bachelor in Computer Science in India.

Schools in the US operate on a department basis. Almost all big research institutions will offer research work in the subject field. If your friend doesn't know anything about where the subject he is trying to study is thought, I think he is wasting his time on a graduate degree. Graduate study is research intensive work that requires more commitment on the student's side then it does on the professor's or school's side.

Computer Science departments focus on various areas of Computer Science such as Operating Systems, Graphics, Artificial Intelligence, etc. The problem is that DevOps is a relatively new focus and not enough schools teach the practical aspects of setting up and working in a data center. He is trying to find a department that would give him a theoretical knowledge of large scale systems, and some practical experience in working in an ops environment. Basically, he is looking for recommendations.

hmmm like you stated DevOps is relatively new.  I have not seen DevOps being taught as a specific discipline; usually the DevOp skill set comes from the software engineering side of the fence in the US. Is he in the US or in India? See if any of these tickle his fancy:
http://unomaha.smartcatalogiq.com/en/2013-2014/Graduate-Catalog/Graduate-Degree-Programs-Certificates-Minors/Management-Information-Systems/Management-Information-Systems-MS
http://unomaha.smartcatalogiq.com/en/2013-2014/Graduate-Catalog/Graduate-Degree-Programs-Certificates-Minors/Computer-Science/Computer-Science-Concentrations
There's two versions of this degree, a professional one and a research one; the link below is of the research variety.  This institution also has campuses in London, Brussels, Dubai, Paris and Sydney along with a few other locations:
http://www.bu.edu/eng/admissions/grad/
The University of Illinois has a partnership with State Farm Insurance
http://www.ece.illinois.edu/students/grad/overview/ms.html
http://www.cdm.depaul.edu/academics/Pages/MastersDegrees.aspx
The University of Wisconsin has a partnership with Microsoft:
http://www.cs.wisc.edu/academic-programs/graduate-program


text:
Referee made a mistake but recommended acceptance, what to do?
I recently received a referee report on a math paper in a mid-tier journal.
In this paper I proved (to give an example avoiding technicalities) that all dogs are cute.
But the referee claimed in his report that I claimed that all animals are cute (that is, he claimed that I proved something much stronger than what I really proved).
There is no way to understand the more general statement from my paper, and my guess is that the referee simply did not read the paper carefuly.
Now, the referee recommended acceptance, and the editor accepted his recommendation.
Should I do something about it? should I explain this to the editor?

I would not do something about it, but just leave it.  Congratulations on the acceptance.

How many referees commented on your paper in total? If it was only one, the issue would be greater than with two or three.

@lighthouse: In mathematics, it is quite common to have only one referee.

Science is not about getting published no matter what. You should most definitely clarify the misunderstanding of the referee.

That's what you get for reading the comments on an acceptance. Don't do that.

It is entirely possible that the editor understands the distinction between "dogs" and "animals", noticed and understood the referee's error, and then accepted the paper anyway based on their own expert judgement.  (Of course, the only way to know whether this happened is to ask the editor.)

Is the title of your paper something like "All dogs are cute: A proof"? If so, I would assume that the editor knows what your paper is about, and read right past the reviewer's error.

After mulling this over for some hours today, I really think that more context would be helpful.  If there's just one wrong word "animal" instead of "dog," and of course if the paper itself is clear and correct about the distinction, I think it's really likely that this was just a misspeaking on the referee's part.  Depending upon the situation, I might choose to assume the best and let it drop without much worry.  But if the report calls attention to the stronger result, and especially if there is any evidence that the weaker result would yield a different outcome: that's something else.

@Pete: in particular, the "something else" is similar to "suppose you submitted a paper and were offered the choice whether it's reviewed or just published in the same venue without peer review at all". Because a review that's gravely misunderstood the paper is in a way worse than no review: (a) you don't have the benefits of review; (b) you know for a fact that your paper is capable of being completely misunderstood. Scary stuff ;-) It's not even "just" an ethical matter: it's a real risk your paper is bad.

Adding to @JeffE, from the information we have it could also be that the referee thought "some animals" and the fingers typed "all animals" out of a momentary distraction, although the referee actually did understand the paper. I wouldn't jump to conclusions without talking with said referee (which might be impossible).

@Steve: I'm not sure how much experience you have with refereeing of mathematics papers.  I have a lot at this point, and I'm sorry to tell you that the quality control is just not there: while some referee reports are heroically terrific and more than half are fine, a sizable chunk are either manifestly bad or might be the result of a referee who put essentially no time or effort in and there is no way of knowing.  Upshot: if you're worried that your math paper is bad, you'd better do something about it yourself rather than relying on the referee.

Actually, @Pete makes a good point. My experience with writing proofs (of unimportant things) is that no one reads them. This includes the coauthors, supervisor/boss, and the reviewers. I guess, this may (or may not, as OP's case suggests) be different when a proof is the whole point of a paper.

@PeteL.Clark: out of interest, then, is there much momentum in the mathematical community to formally do away with peer review entirely? Or, if it amounts to the same thing, to formally stop reading journals and rely solely on arXiv, each others' web pages, and recommendations what to read from people who currently are journal editors but perhaps more productively could just curate recommended reading lists?

@Steve: I don't think there is much interest in doing away with the journal publication process.  It still plays the role of determining how much value the community places on each particular work (quite imperfectly, of course, but a lot better than nothing).  It doesn't play much of a role in certifying correctness, and so far as I know most mathematicians are willing to rely on results from arxiv preprints as published papers.

This is not so great, because the journal refereeing process definitely plays some role in vetting papers for accuracy and improving them.  As a referee, I have pointed out small mistakes in papers many times, and major mistakes a few times.  As an author I've often received referee feedback improving the paper.  I think it comes down to this: gross errors are easy to catch, and often the experts are not fooled for a second.  Subtle errors are caught only by those who put time and effort into finding them.  The referee may not do so, and someone who is not the referee may do so.

I would probably mention it, but not make a big deal out of it.  The referee here was lazy (by not reading carefully), the editor was lazy (by not looking at the main result of the paper), so my plan would be to be lazy too.  I'd write an email back with the final revisions and mention casually in the text of the email "just to correct the record the referee wrote animals, but they must have meant dogs which is what's actually in the paper."  Odds are the editor won't read your email carefully and won't even notice your comment, but you'll feel better.
Peer review is such a random crapshoot anyway, and you obviously thought this journal was appropriate, so there's very little actual harm here.  You can be sure that at some point the same thing will happen in the opposite direction and you'll have a paper unfairly rejected by a referee who didn't bother to read the main result and the editor almost certainly won't do anything to correct the error.

This answer is the one I agree with most.  Mention it, but don't yourself delay the publication process or indicate that something needs to be done to delay the process.

Mention to whom? If two persons nearby you fail to see or pretend not to see someone is in trouble, perhaps because that would imply them to do something about it, would you also pretend not to have seen it? What if, in the end, the author is the person in trouble?

I'd mention it to the editor in my reply to the editor.  As I explained in the second paragraph, there's very little harm here, and nothing analogous to an injured person.

@NoahSnyder even if the editor does not read the email carefully but they realize the mistake, won't it be likely that the referee will end up knowing it as well? Since it was his fault in the first place, won't they try to push that responsibility? I made an analogy with physical injury, but in this case someone's reputation may be injured by a carefree (in)action. I understand that there are unfair situations in the review process, but is that an excuse to ignore responsibility and twist this situation in someone's favor?

No, you don't have to do anything.
However, if you have the chance to do a minor revision, try to see where the misunderstanding of the referee came from and rewrite these parts so that it is clearer, that you are really only proving things about dogs and not all animals. In addition, I would not suggest to put such a clarification in the title or abstract, but only in the introduction (or wherever in the text this is appropriate) - I think an abstract that stresses that you do not treat a case and that you never intended to, may read strange in the end.
The case would be different, if there is an actual serious error in your paper that the referee did not catch. If that would be the case, e.g. if the proof of your main result has a gap, or the result does actually not hold, you should stop the publication of the paper by withdrawing the paper.

I'm sorry but this is just some terrible advice. They know the referee made a mistake when reviewing their paper. Saying nothing is highly unethical.

@Gabriel I don't find it obviously unethical, and clearly the OP and this poster didn't either.  Maybe make an answer explaining why you think so, rather than a brief comment.

@Gabriel: When the mistake is in the other direction, we're the ones who gets screwed over, and editors ignore the matter. Somehow that's OK, yet it's unethical when submitters do it?

@Mehrdad: carelessly giving a wrong review is incompetent. Perhaps to the point of unethical negligence, but perhaps only incompetent. Unethical is the name for doing something bad when you know it's bad, so the ethical issue for the questioner is not, "are other people sometimes frustratingly incompetent to my detriment", it is "would it be bad to allow a paper to be published without competent peer review, and am I knowingly making that bad thing happen for my benefit?"

... or in other words, it is unethical to just decide to keep a mobile phone that you found on the table in a bar, even if your phone was nicked yesterday and the thief wasn't prosecuted. Of course, one might think it's good, not bad, to publish a good paper that wasn't properly reviewed. But the fact of papers being wrongly rejected isn't what makes it good.

@SteveJessop: I wasn't talking about the reviewer being unethical, I was talking about the editor to whom you subsequently complain and who ends up completely ignoring you about 99.9% of the time being unethical. They don't even care enough to reply, let alone address your complaint. So if that's OK, then I don't see why submitters should go out of their way in the reverse direction.

"I don't see why submitters should go out of their way in the reverse direction", because it's unethical not to do so.

@Mehrdad: so you see no point in taking the ethical path here, OK. But that doesn't make the thing you're resigned to lower yourself to, in order to be successful, suddenly not unethical after all. That said, it might not be very unethical: opinion is quite divided as to whether it's the author's responsibility to seek peer review at all. I don't think it's totally unreasonable to address it as an adversarial system in which you have no responsibility other than to advocate for your paper without actively lying, but a lot of people don't think publishing should be that way.

@SteveJessop: Well, I don't think it should be that way either. In my ideal world I would definitely bring this up to the editor's attention, and the editor would also definitely not ignore me when I was bringing the opposite to their attention. In my ideal world a lot of things would work out nicely and cards wouldn't be heavily stacked against one side. I just wish I lived in that world.

If you care about being a person of integrity (not everybody does), then yes, you should explain this to the editor. Your paper was accepted based on a misunderstanding of its contribution; do you really want to have this "achievement" on your record, and forever have to feel a pang of guilt every time you discuss the paper with someone and they ask you where it was published and then nod with approval when you tell them the name of the journal?
The ethical thing to do is to clear up the misunderstanding. Hopefully the result that all dogs are cute (far from an obvious fact if you ask my opinion ;-)) is impressive enough that your paper will still be accepted, and then you can have the satisfaction of knowing that this happened for the paper's actual merits. And you will score major points with the editor and referee for your honesty, which may offer its own practical benefits someday.

I actually think, unfortunately, that this advice may be a smidge overly-ethical.  I don't have time to talk about it in detail now, but the gist of it is: the whole system is not under the submitter's control or even transparent to the submitter, but it often happens that a faulty negative opinion leads to a rejection, and then most of the time the editor is not very interested in revisiting the matter.  I think it is too much to ask for those in positions of lesser authority to be more ethical than those in positions of greater authority.

...Also: "forever have to feel a pang of guilt every time you discuss the paper with someone..." I think this takes too seriously the meaning of any one published paper in any one journal.  We all know that papers get published or not published for many contingent reasons.  Just because the referee (apparently) didn't understand the paper doesn't mean that it's not as good as other papers published in the journal, and I'm not convinced it increases the likelihood of that.  Ultimately an author has a feeling about whether her work is good or not; that's what counts.

@Pete whether it is a smidge over-ethical, under-ethical, or just-right ethical, is really a personal matter of conscience (but I am glad we agree up to a smidge). You do make a good point, and I think for precisely the reason you pointed out -- the asymmetry between faulty negative opinions and faulty positive opinions from referees -- the editor is unlikely to wish to revisit the matter, as a way of correcting the asymmetry. But you are suggesting for OP to take it into their own hands to correct the asymmetry through somewhat dishonest (in)action. I still say let the editor handle it.

@Pete as for your second comment, the point is OP knows that the referee misunderstood the strength of their result. Of course there were many contingent reasons, but if you are aware that one of them was a pure accident - say, the editor clicking "accept" instead of "reject" in an online publication system - it is unethical to carry on pretending that never happened; maybe only a "smidge" unethical, but still unethical. And I'm not taking anything too seriously - obviously OP can decide however he/she wishes and the world will keep turning either way. Just offering my opinion FWIW.

@DanRomik Your answer says that an author in this situation boldface-should talk to the editor; your comment says that it's just a matter of personal conscience. Which is it?

Again, sorry to only have the time to quickly comment, but: based on the OP's description it is not completely clear (to me) how serious was the refereee's misunderstanding.  "Animal" might have been a typo for "dog."  In my experience exactly how much the referee understands is one of the things that is not always made sufficiently clear.  If it is clear that both the referee and the editor thought it was "animal" and also that it being "animal" and not "dog" played a role in the decision, then for me the ethical issue becomes more serious.

@DavidRicherby Which is it? Both. OP should talk to the editor if he cares about being a person of integrity (as I wrote in the answer) and if he agrees with my analysis according to which being a person of integrity requires clearing up the misunderstanding. Ergo, this is a matter of personal conscience as I said in the comment (for example, Pete Clark apparently disagrees with me somewhat, and he is certainly a reasonable person). I'm not claiming that my answer is some sort of universal truth.

@PeteL.Clark OP wrote: "he claimed that I proved something much stronger than what I really proved". Seems pretty clear cut to me that the strength of the result would play a role in the decision to accept the paper. Would you consider revising your verdict based on this?

@PeteL.Clark it occurred to me that your "many contingent reasons" argument could be used to justify all kinds of unethical behaviors. For example, would it be acceptable for someone to say "Stock investments yield a good or poor return based on many contingent reasons. I think you are taking too seriously the meaning of any one investment." in the context of an accusation that they engaged in insider trading of stocks?

@Dan: "he claimed that I proved something much stronger than what I really proved" Right, I find that a bit ambiguous.  Also, I don't find your stock analogy a very good one.  Still without time to fully respond but: if one only thinks ethically it is possible to get carried away.  I agree that it is a matter of personal conscience, but I don't think it is only a matter of personal conscience.  For instance, what if someone misses out on an academic career because of the delay in re-refereeing the paper to come to the same conclusion?

I guess I would say the following is the principle at work here: if you participate in a lengthy, multi-step process that is opaque to you, but you have some reason to believe that a mistake was made at some stage, do you have an ethical obligation to start it over no matter what, or only when you think the wrong outcome was reached?  If you apply for a visa and you think they thought you lived in place X rather than place Y at a certain time, do you have to ask them about it even if you think you deserve a visa?  I don't think one has unlimited obligation to correct other's mistakes.

@PeteL.Clark That argument reads as "the end justify the means", and could potentially be used to justify virtually any academic misconduct. "I don't think one has unlimited obligation to correct other's mistakes". That's a misleading exaggeration of the situation.

@Gabriel: The proposed action of letting it go is not illegal (unlike insider trading) and it is at the least not clear that it is academic misconduct.  But yes, in real life one does sometimes not take the maximally ethical or academically proper action because of the possible consequences.  If you've spent X hours doing a literature search, it would be more academically proper to spend X+1 hours: you can't be sure you won't find something else.  One does have to take practical considerations into account at some point.

Except that by spending X hours reading instead of X+1 I'm not exploiting any weakness in the scientific process of research+publish. You most definitely are if you agree to be published knowing the referee accepted your manuscript under a wrong impression.

@PeteL.Clark you make some good and valid points. In particular your principle that one is not obligated to always take the maximally ethical action regardless of practical considerations is very reasonable and I've applied it myself in other answers. Anyway, to the extent that we disagree here, it's a very minor disagreement. Thank you for a fun debate. :-)

Yes, you should explain this to the editor.
Science publishing should not rely upon taking advantage of a referee making a mistake. Your ultimate goal should be the advancement of science, not how many papers you can push through the refereeing process at any cost.
If the referee approved your article based on an improper understanding of it, it invalidates the entire purpose of refereeing in the first place.
A referee is not an obstacle to conquer at any cost. It's an allied, a colleague, pursuing the same goal you are (or at least should be) pursuing.

Yes, this, very much. The referee understood that the paper was proving a much bigger result than actually proved, and still failed to spot the fact that the proof does not support the stronger statement. It follows that the referee would be unable to detect any actual errors in the weaker statement, should they be present. The referee is failing the author at the one thing they're meant to be doing.

I agree with the principle that referees should be your allies, but I find it very common that a paper will be accepted based on reviews which are clearly not sufficiently deep to ensure that the reviewers would have spotted any serious problems if there had been some. In such cases, by your logic, should one refuse to publish and ask the editor for better reviews? I think reviewer feedback should be taken seriously, but I don't think it is the authors' responsibility to obtain deeper reviews if their paper was accepted based on superficial or even erroneous reviews.

Are you sure that the reviewer made a mistake? As a reviewer I usually say something like "The author proved that all animals are cute, which is interesting." or "The author proved that all dogs are cute, which is boring because cats are much more interesting." The editors cannot be expected to understand the difference, in particular if you submit to a general journal, so in the first case it is not necessary to give too much detail. The author on the other hand wants to know why his article got rejected, so in the second case I have to be much more precise.
So if the short description is followed by a list of small remarks, then it might be that the reviewer was deliberately vague. If there are no detailed remarks, the reviewer either didn't read the article or your style of writing is outstanding.

Would you have explained to the editor when the referee made a mistake that would lead them to reject the paper? If yes, then I think you should do so here as well. Then it's up to the editor to leave this be if he/she would have done the same in case of a reject.

Before you decide, get a second opinion or two.
Select one or two people knowledgeable in the area, and ask them to evaluate your paper.  If one of them comes up with the same inflated wrong view of your claim and proof, then you have a problem and need to think about bringing it up with the editor, rewriting, etc.
If the second opinion is that the paper proves what you think it does, and that the paper is worth publishing in the target journal, then you can rest easy and look forward to seeing the project in print soon.


text:
Is it acceptable to copy verbatim the description of a software package?
I just read an article where the description of a software package was lifted verbatim from the package's site itself.
It's a whole paragraph where not a single comma was changed. There are no quotations, nothing to indicate that this is a verbatim transcription of text. The site of the package is properly cited though, nothing is being hidden.
I understand that the description of a package created by the author is the best source to understand what that package does, but copy/pasting about 12 lines of text (single column) seems a bit excessive.
To what extent is this acceptable?

What do you mean, "an article". Is this a journal paper, an advertorial, something else?

It is a scientific paper in a well known indexed journal.

It is quite acceptable, provided it is stated where it came from, so the reader knows it is not due to the authors of the paper.

As long as a proper reference and quotation indications are provided, there is nothing wrong with it - as with any other type of verbatim text copy. However; it is debatable whether this is a desirable approach, and this may vary with the traditions in individual fields.
If no reference is given it is (a mild form of) plagiarism.

There are no quotations. Nothing to indicate that this is a verbatim transcription of text. But there is a link to the package's site. Just added this to the question.

In that case, it is plagiarism, albeit a mild form (a reference is given).

There are no mild forms of plagiarism...

There are a vast number of different citation standards, I assume the journal in question adheres to one of them. In most journals' implementation of the citation standards, it is denoted how a direct quote should be demarked, eg. with "" or >><< or italics etc.
If the article fails to live up to that, they are guilty of breaching the citation standard. Since we are talking about a full paragraph, but not anything were they present any deep thoughts, it is probably severe enough that it should be avoided, but definitely not severe enough to be punishable by any standards.


text:
Research assistant, associate, fellow?
I completed my PhD and post-PhD. Since last year I am working as a researcher in my country, at the lowest level of hierarchy (first out of five) It usually takes no less than 4 years of steady research to advance to the next level. These levels are named (translated to English)

Assistant researcher
Associate/Adjunct researcher
Independent researcher
Principal researcher
Superior/Top researcher

My employer is the government (Argentina), and I work at a government-funded institute.
Although I understand that this likely varies for different countries, what designation do you believe describes my position more accurately?

What does the title in your contract state?

The literal translation to english would be Assistant researcher.

I see your point. Could you just list the diff. 5 levels (as translated to English)? Maybe it will help others.

Could you provide the country?

In the US, a "research assistant" is typically a graduate student, or occasionally an undergraduate. A "fellow" is somebody funded by a scholarship - it indicates you aren't being funded because of the merits of your research project but primarily because of your personal merits as a scholar. Research Associate is the same title given to post docs, and including the information from your previous post I think it is most appropriate for you.

My suggestion if you were wanting your CV to be most understandable to someone in the US or familiar with the US system would be to write your title from your contract, untranslated, and in parentheses you could translate it as "Research Associate."

Thank you @BryanKrause! Do you want to turn your cmmts into an answer so I can accept it?

In the US, a "research assistant" is typically a graduate student, or occasionally an undergraduate. A "fellow" is somebody funded by a scholarship - it indicates you aren't being funded because of the merits of your research project but primarily because of your personal merits as a scholar. Sometimes "fellows" are also more senior positions (senior non-professor PhD roles in academic laboratories, or some PhD researchers outside academia) and there the title implies some additional autonomy beyond other employees.
Research Associate is the title typically given to post docs, but can be more broad than "post doc" which implies a training position. Including the information from your previous post I think it is the title that would be used in a US context that is most equivalent to the position you describe. Note that all of these designations apply mostly to academia: titles in industry can be completely different and vary a lot by field.
My suggestion if you were wanting your CV to be most understandable to someone in the US or familiar with the US system would be to write your title from your contract, untranslated, and in parentheses you could translate it as "Research Associate."

No- invert the order - Research Associate or Research Assistant still give strong connotation of a 'student' title in US and as reader would first assume it is a student and t I would have to spend time perusing for other clues. Using the order inverted - Associate Researcher or Assistant Researcher, works better as the 'person is the researcher,  - I might assume it is non-academia title,  but at that point, I'm looking for 'where' the person is a researcher, not whether they are a student or not.


text:
Cases when old references are valid?
Some guides say to limit the references to up to 5-6 years old.
But I've speculated as to, whether it's possible that research would become "deviated to pursuits for which in the history there existed multiple paths". I.e. since old research may suggest new research, but not all new research is necessarily "all research", then wouldn't it be possible to grasp an old article and then do new work on that?
I'd assume that this could be very feasible in mathematical papers for example. What about computer science papers? Something else?

Please indicate the field you are working in. As a mathematician, to me such a rule seems to be completely ridiculous.

Throw away those guides ;-)

Can you link to such guides? This sounds preposterous.

@user2705196 Out of curiosity, I found one such guide: "Be careful about citing old references. The rule of thumb is to go back at most five to six years" the 3rd line of  the section "Some dos and don’ts of using references"

There's some published research on citation age - here's a recent paper for the subfield of computational linguistics (https://www.aclweb.org/anthology/2020.acl-main.699.pdf); in the top venues of the field the mean age of citations is 5-7 years, with a significant number of citations being to 10+ year old; and the recent decrease of the mean from 7 to 5 years is considered troubling - so you definitely should not limit yourself to at most five to six years. On the other hand it would be very troubling if you have only old references.

In my experience (physics), it is generally considered proper to cite the original work on a specific topic, which is why certain seminal papers garner thousands of citations over many decades. For example, consider Polyakov's original paper (1976) showing that QED is confining in 2+1 dimensions. This is considered basic knowledge now, and the article has nearly 1500 citations because of that, with at least 19 citations in 2020 so far.

Related: How old can references or sources in a thesis be? AND How can I tell if a paper is too old to be a reference for my research? AND Is there any requirement to cite recent literature in publications?

@scaaahu How old is that guide? ;)

Just to flex my muscle: I cited a paper that was more than 150 years old in a biomed context. Mathematicians have no problems citing Gauss from late 1700s. It still makes sense sometimes to cite Euclid from 300 BC.

If you don't have ANY references that are less than 5-6 years old, it would look weird (if only to say that they investigated an avenue that is similar but different to yours).

@Peteris It's worth noting that computational linguistics moves at a different pace from many other academic fields and often involves big improvements and changes in approach very quickly. For instance, in theoretical linguistics, it would not be unusual to have a ton of older citations for the origins of your current approach, but in computational linguistics it's likely that your approach has quite recent origins (unless you're deliberately taking a more retro approach than mainstream NLP currently is).

In a Wikipedia article I once had good reason to cite Tacitus (56-120AD). I was proud of that one!

Taken at face-value, these guides are useless or even harmful, as they would promote an organized loss of memory and lead to multiple reinventions of the wheel.
It is also important, however, to show that your research is moving at the cutting edge of the field. This is probably where the advice you mention is coming from. You should demonstrate the topicality of your project by discussing the most recent literature to the extent that it is adequate for your research problem. Strategically, it may be useful to highlight your project's contribution to the latest research, including new trends, especially in the introductory section. But take care not to exaggerate this tactic, as it cannot compensate for substantive shortcomings and might even come across as superficial.
To explicitly answer the question in your title: References remain valid until superseded by later research with respect to the aspect they are cited for. To make that judgement, you have to know the field; to know the field, you have to read. Looking at the age of the reference cannot replace making that judgement, it can only give you a rough indication as to whether the reference is likely to have been superseded. The fact that different (sub-)fields move at different speeds makes it even less reasonable to put a number on a reference's shelf-life.

"References remain valid until superseded by later research." - I would add "with respect to the aspect they are cited for" to that sentence. With that addition, the statement is beautifully accurate for all cases, including the one where the reference is specifically cited for being old (think "The problem of thingsadoodling was of interest as early as in the 1870s (Mugglevich et al.)." With respect to its age, this reference never gets superseded by later research and thus always remains valid.

@O. R. Mapper Thanks, that's a welcome addition

As a mathematician, this sounds like terrible advice to me.
I would be slightly wary of a paper where every citation is 10 or more years old; but even then, I have seen cases where such a situation makes perfect sense, because someone found a way to pick up the slack on a research avenue that had stopped 10 or 20 or more years prior.
In a good research paper the results should build upon previous work, so some recent citations are expected. But I would also expect a decent review of previous work. If all citations are less than six years old, then the paper is likely either too technical or too shallow.

Thanks for the edits, guys. The first I thought I had corrected it myself, but I guess I didn't.

As another mathematician, I have cited papers from the 1800s. If a paper is correct, then it is correct. If it's relevant for your research, cite it.

"because someone found a way to pick up the slack on a research avenue that had stopped 10 or 20 years prior" - very true. It's not the authors' fault no-one has looked into a particular question in the meantime and they should not be punished for it.

It depends on the purpose of your reference. If you cite a paper to show the state-of-the-art, then older papers might be only acceptable for very niche fields, without too many publications. If you compare your results with an older paper, than you have to have a good explanation why such comparison is insightful.
If you refer to some general theory or idea, than older papers are still acceptable. I personally like to include the original paper for a given idea if the page limit allows it.

I strongly disagree that "older papers might only be acceptable for very niche fields, without too many publications". Hard open problems can stand for decades or centuries, even in fields with active research.

@NathanS. Sure, if you remove the first conditional part of the sentence than I would disagree with it as well. In any practical discipline where something is realized, comparison should be made with the best results published so far. Comparing a the computational performance of the newest processors with one from the 80s have hardly any value of information. Similarly in medicine and psychology it would be strange as well to compare a result with one from the 70s. In very theoretical or descriptive fields that is not the case, but in such fields nobody would tell OP to forget any old article.

"comparison should be made with the best results published so far" - and sometimes, those best results are one or two decades old, even in practical disciplines. What do you want the authors to do in such a case? Compare with something else that is more recent, even if it is beside the point? Indeed, the computational performance of the newest processors is quite likely not an example of such a situation.

If you read it, and you relied on it for your research, then you have to cite it. To not cite it would be plagiarism.
Can you do good research without looking at anyone else's research that was published more than six years ago? Almost certainly not. Even if you were doing a review article on research from the last five years, you would want to contextualise that five years' research with the five/ten/fifty years before it.

As others have mentioned, this broad-stroke advice is sufficiently wrong in many disciplines to be useless as general guidance. Yes, of course you need to ensure you're up to date in your subfield, but above all you need to cite whatever is needed to ground your research conceptually and empirically, whatever its datestamp might be.
With that in mind, it's worth asking: when is such guidance valid in a nontrivial way? I have encountered it most often in the humanities or in interdisciplinary work with a humanities or social sciences element. A strong caution about old references is actually warranted in fields which have undergone major paradigmatic shift, especially where the old paradigms have been criticized for being biased or rooted in privilege.
If you run around quoting "old-school", Euro-centric papers on "Primitive Art" or South Asian civilizations, especially without engaging with the paradigmatic shift in (e.g.) postcolonial theory since then, you will (rightly) get skewered. Similarly, I have read then-respected scholarship in linguistics and psychology from a few decades ago that now makes us cringe. And woe betide you if you rely blindly on psychiatric research implicitly grounded in DSM versions <=4 (6 being most recent, I believe).
That doesn't mean you can't dig up something meaningful from the historical vaults even in such fields; just that you better know what you're doing and engage deliberately with material shifts since then. Therefore a simple heuristic of "don't do it" is, in those instances, helpful.
With that in mind (and in agreement with others answering), I'd actually turn your last paragraph around. Math is pretty simple in this regard; the only issue in quoting an old paper will be the obvious one: have you failed to note a more recent substantive advance; otherwise it's fine.  It's not my field, but I would expect the shifts in computer science to be more significant. While not as big a deal as in many fields in the humanities, I think your risk of coming across as anachronistically irrelevant if you're relying significantly on old references are higher in C.S. than in math.

Speaking about computer science: it always amazed me, how certain books there do not age gracefully. As for the papers, they seem Ok. Either it's completely outdated (and then you would not read or cite it) or the idea is well and living (in which case it makes sense to stumble through ancient notation and such). Of course, mathematics is more for eternity, but many parts of CS age well.

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