text:
Can co-first authors’ positions be swapped in a CV?
Some papers have co-first authors, which are supposed to have contributed equally. However, there is still an order issue.
Imagine a paper co-authored by A, B, and C. The paper goes like:
                                     A Very Long Paper Title
                                         A*, B*, and C
Our work is good.
-----
* A and B contributed equally to the work.

In this case, is it acceptable for B to cite this paper as follows in his/her CV?

B*, A*, and C. A Very Long Paper Title. Journal of Stack Exchange.
  Jan. 2015. (* indicates the co-first authorship)

Note the position swap.

I think we had this discussion before, but I can't find it. Anyway, no, you really shouldn't do that. Even if you agree that a paper has joint first authors, the "signature" of the paper (title, authors including ordering, etc.) is fixed. You can't mix this up. You are of course free to add something like (joint first author), e.g., to the end of the citation.

I agree with xLeitix and yo'. If you were applying for a position and we (or more likely, our eagle-eyed deputy provost) noticed this, it would likely lead to concern about misrepresentation -- enough to tank an application at a stage where there is no room for rebuttal (i.e., we won't contact you to clarify, your application will just be dropped). Remember you're competing against scores of people equally qualified.

@xLeitix: Are you thinking of the question in which the OP, Mr. X, was co-first authors with coauthor Mr. Y, and Mr. Y wanted the author list to read Y,X,.....?  My answer to that question was that practice makes no sense: if authors are claimed to have contributed equally then they should be listed in alphabetical order.  That's not the same question as this one because the order has already been determined in the publication.  As others have said: you can't mess with that order, and trying to will make you look worse, not better.

Related, but no duplicate: How to display your own name in publications list when you are a middle-author on a publication with a large number of authors?.

No.  The reference is the reference, changing it to move yourself higher could be misinterpreted as willful deceit.
Add a parenthetical statement at the end of the references saying "first n authors are co-first authors, listed in this order because..."
On my "internal" CV I have parentheticals after many papers, for example, listing contributions, nominations for best paper, etc.

About what might this be interepreted as deceit?

You are changing the published author order to put yourself higher?  I can see some people interpreting this poorly ("they changed the author order to make themselves look more prominent.... Really?").  The published order is the published order.  In Computer Science, I have never heard of anyone doing this and I think it would raise eyebrows.  Perhaps it's common in other fields.

Put another way:  if it's already noted that it's co-first-author, what reasonable reason would there be to swap.  The published author order was chosen for a reason, so swapping it on your CV seems completely bizzare.  I'd interpret it poorly, because it's unnecessary and thus inexplicable.

I think there's some confusion about what co-first-author means here.

Not really.  I understand what it means (the poster was pretty clear).  My point is that every publication has a published author order; changing it on your CV might raise flags in people who read it.  Seems pretty simple.  I'm not saying it absolutely will, I'm simply saying it might.  I see it as possibly doing harm, and doing no real good.  Surely I could be missing something, though.  Please explain what I'm missing.

One thing you can do (and some people do), is that you omit the names at the beginning of the references and include them in the end, like:

List of Publications
Study of ABC in the context of DEF (with J. Doe and J. Soe). Journal
  of ABCDEF 45(5):170, 2013.
Note on DEF (with J. Doe and G. Surname). Communications of FooBar
10(1):1, 2014.

However, remember that this is more common in fields where the order of the authors is most usually alphabetic. In fields where First Author, Second Author and Last Author are significant, this would be really uncommon, and an academic committee of any type will likely consider it as that you credit work of others as yours.

I tried this style in my CV for a few years early in my career but was told by higher ups in the university that they preferred to see the conventional "first author, second author, ..." listing.  I don't think the battle is worth fighting at this point.

I list publications this way (with links) on my webpage: the point is that I am describing what I'm linking to (also, more than half of the publications are single-authored, so this is more efficient).  On a CV though I see no choice but to give the formal, correct bibliographic citation, and in this you are not allowed to move authors' names around.

@PeteL.Clark I think I've seen it this way in official documents like CV or thesis' list of publications. But as I say, I'm in a field where the order of authors has zero significance, so this is not a problem.

I have to resist posting this PHD comics ...


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Is it better to have no publication than having you as second author?
I am a post graduate engineering student (computer science). I have only one conference publication (not very good) as a first author.
One of my senior labmates worked on a very good research project a few months ago and wrote a paper. I have been approached by him to generate a few more results for his paper and proof reading and extending his paper with a literature survey and elaborate explanation of results. I have been offered co-authorship (second author) for this paper.
Now, though I can dedicate some time to do that work, I wonder whether being the second author is worth it.
I would like to ask in general as well, that is: Is it worth it to put effort in papers to become the second author, given that the paper is not related to my primary area of research or rather work, as opposed to dedicating time to one’s own research and getting papers as a first author?
Note: I have seen that in academia (where I want to go), usually advertisements call for applications from people having some number of papers as a first author.

Any lessons on this from the last eight years you picked up and can share? Probably valuable advice for someone else.

If the paper is well-written, contributes non-trivial knowledge to a particular field, is peer-reviewed, and you contributed significantly enough to the paper to be listed as an author, you should put your name on it. In the case of fields where pre-prints are common (i.e., it won't be peer-reviewed, at least initially), it is also worthwhile.
What you don't want is to be an author on a poorly written paper. In other words, you should be proud to list a publication on your CV even if it isn't exactly in your primary research area. Especially at this stage in the game, having a few good papers will help your case, even as a second author (and keep in mind that some fields, such as theoretical computer science, should have the authors listed alphabetically and all authors are considered primary).

I think the question was whether it's worth doing the work, rather than accepting the credit having already done the work.

In my opinion, I would evaluate the quality of that paper (so far) first. If the quality is good, I would join him and become the second author. If the quality is poor, then walk away.
You have only one publication thus far. Have another one, even the second authorship, is definitely better than nothing. Not to mention your first authorship paper is not very good by your own evaluation.

In the end, each paper counts. I would not hesitate to get second authorship unless I felt I deserved to be first author on the paper. What you need to consider is if the time you spend is worth it. If the paper is going to a good journal then is more acceptable than if it goes to a low rank journal. When your cv is evaluated, number of papers, journal impact, and citations on the papers are most frequently looked at. First authorship is an important factor as always but having second authorship (I am assuming among several co-authors) shows that you have been instrumental in the paper (I am again assuming authorship order reflects contribution). As long as you have first authorship on a sizable fraction of papers no-one will think twice about coauthoships, particularly not early in ones career.

I think you have to do a cost/benefit analysis. It's always good to have another paper, even if you are second author. A hiring or review committee may ask you to describe your own contribution to the paper. As long as you can do that honestly and point to some substantive contribution to the paper, it will be to your benefit. If it will take you a significant amount of time then it is probably a substantive contribution. The fact that it is not completely aligned with your own research may be an asset...it shows that you can collaborate and are willing to get outside your comfort zone.
So, what would you be doing instead if you did not contribute to your colleague's paper? If you have another paper that is at a critical stage then it may be reasonable to turn down your friend. Otherwise, I'd say go for it. It's hard to say what will catch the eye of a hiring committee.

It always depends on how much effort you need to put relative to the quality of the paper. HOWEVER -
This may be an urban myth, but I keep hearing from faculty that not having any second author papers is seen as a slight negative (this is in biology). Both in academia and in industry, the ability to collaborate and work in groups is seen as important. The only method they have of guessing what your teamwork skills are is - second author papers.

You can have collaborators even if you are first author, so I don't understand what you mean here.

As explained to me, it's the ability to BE a collaborator. Being willing to be second fiddle to help a project become better. Y'know, all that team-player stuff. Institutions supposedly like that because it increases the total available knowledge (say, you want someone who can help other labs do qPCR or something. Then there's qPCR for all!)

Ah. Ok, I see what you mean. Though I don't see how one can conclude that (or much of anything really) from being a second (or n for n>1) author. You could just be putting your name on something you haven't really contributed anything to. Happens all the time.

Am also working in a biology department currently, and have been told the very same thing (i.e. second authorship papers are considered valuable for different reasons than first) from more than one source. In this field at least then, it sounds like something people really do look for.

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text:
What is the difference between a magister and a master title in Austria?
After reading this question focusing on Austrian titles themselves, I still have a couple of open points that I would like to understand, especially around the relationship between Austrian titles and EU titles.

What is the difference between a magister title (“Mag.”, which would come before the name) and, for example, a master of science (”M.Sc.”, which comes after the name)?
Assuming one received a second-level Bologna degree (300 ECTS) – a master’s degree in mathematics, for example – from a German university, which one of the two titles would they use in Austria?

Note: As this post has been moved from the German SE, it contains a lot of German.  I can add translations on request, but I'll leave it as is for now.

The title you get is exactly the one official notification (in Austria: Bescheid) you receive from your university, which usually contains some information on using it.  I, for example, have one that says literally

[...] verleihe ich Ihnen den akademischen Grad Diplom-Ingenieur (Dipl.-Ing. oder DI). Der akademische Grad Diplom-Ingenieur/in, abgekürzt "Dipl.-Ing.", entspricht international dem "Master of Science", abgekürzt "MSc".

The English variant was introduced by the Bologna unification and is just a different name -- presumably the same holds in other countries.  That means I am officially allowed to use any of these variants (but only one at at time, of course -- unless I would have received another degree with the same designation!).  Since Austria is trivially part of "international", too, it is equally permissible, and nowadays not uncommon, to use the MSc instead of the Dipl.-Ing. even within the country.
Now, the above holds because I graduated from a Technische Universität, which distinguish themselves by the special degree of Dipl.-Ing.  What title you get is in fact just defined by the university regulations and your curriculum.  Regular universities before Bologna used to confer Magister, and still do, with the English equivalent of MA (Magister Artium).
These are not necessarily differentiated between subject families -- so one could, in principle, get a Mag. for both physics and law -- but also a specialized form like Mag. iur. or Mag. pharm..  In any case, you will receive a similar Bescheid telling you that you may use the German title, or one of the English equivalents -- which will likely be MSc for a technical subject, but could be MA if the university chooses to.
Similar things hold for doctorates.  Typically, technical universities confer Dr. techn., regular ones Dr. rer. nat. or Dr. iur. or Dr. rer. soc. oek. or whatever, but most will nowadays list PhD as an allowed equivalent form on some Bescheid. In contrast, from most medial universities you get a Dr. med. univ., but this is just a Berufsdoktorat (like an MD in the US, I guess).  It does not come with a PhD equivalent, and cannot usually be used outside the DACH region for potential of confusion.
So, it really just boils down what is literally said on the Bescheid. Sometimes this can get relevant: for example, until some point, Fachhochschulen were only allowed to confer Mag. (FH) degrees.  These have become equivalent to regular Mag., but you need an extra Bescheid to be allowed to just use Mag.!
This holds also for foreign degrees.  You can officially use them in their literal form (as originally conferred), with some privileges to degrees from EU countries (see here).  Beyond that, you can get an Anerkennungsbescheid, and then use whatever is specified in there.

Regarding doctorates: I don't know the general situation, but for some curricula and universities in Austria, you do not get a "Dr. rer. nat" anymore, but only a PhD.

Getting a "Bescheid" is new and kind of depressing. I remember the half-sqare-meter piece of heavy hand-made paper with an inscription in Latin, no less. These were the days!

@bakunin True, it's kind of sobering. And I got my degree during Covid, meaning I had my Masters exam online and then picked up the papers from the faculty secretary without any further ado :D Honestly, I kind of liked it this way, though. Not a huge fan of all that Brimborium.

@bakunin in addition mine had also wax seals

There is this Bologna Process which is a reform of European universities that started in 1999, with all EU-states (among them Austria) and some other states (like Norway and Switzerland) as foundation member states. Other countries in Europe and Asia joined later.
Among some other reforms (most notable the ECTS system), the national systems of academic degrees were altered, so that these degrees are easier to compare and easier to accept by other countries that are members of the Bologna Process.
Before 1999, there was no degree comparable to a Bachelor degree in Austria. The majority of university study programs lasted 10 semesters (5 years) and ended with a degree called »Magister«, but some programs named their degree different, like »Diplom-Ingenieur«.
After that you could add a second study course, to gain the degree »Doktor«. Only when you studied medicine, the first degree you could get was already »Doktor«, but the program lasted longer than 10 semesters (I'm not sure, but I think it was 16 semesters).
After the Bolognia Process was applied, the situation in Austria is this:
When you start to study on an Austrian University after you left school, you are in the first cycle, which usually lasts 6 semester. When you finish this cycle, you get one of these degrees:

»Bakkalaureus« if you are male and »Bakkalaurea« if you are female
Abbreviated as »Bakk.« (Examples: »Bakk. techn.«, »Bakk. rer. soc. oec.«)
»Bachelor«
Abbreviated as »B« (Examples: »BSc.« »BSc«, »BA«, »BA.«, »B.Eng.«)

Which of these two degrees you get depends on a decision of the university that was made when the study program was submitted to be accredited by the ministry of science. But both degrees (Bakkalaureus/Bakkalaurea and Bachelor) are fully equivalent, they are just different names for the same degree. When the abbreviation is written together with the persons name, it is added behind the name and separated from it by a comma. (Sandra Huber, BA)
After that is a second cycle that lasts only 4 semesters, and it ends with one of these degree:

»Magister« if you are male and »Magistra« if you are female
Abbreviated as »Mag.« and written before the persons name (Mag. Sandra Huber)
»Diplom-Ingenieur«
Abbreviated as »Dipl.-Ing.« or »DI« and written before the persons name (Dipl.-Ing. Sandra Huber).
»Master«
Abbreviated as »M«, always with some extra letters indicating the kind of study plrogram, similar to the abbreviation of the bachelor degree, ands always written behind the name, separated by a comma (Sandra Huber, MSc.)
»Doktor der gesamten Heilkunde«
When you studied Human medicine. Note, that this medicine "Doktor" is a degree of the second cycle, so it is not equivalent to the "Doktor" degrees of the third cycle, mentioned in the next block.
Abbreviated as »Dr. med. univ.« and written before the name (Dr. med. univ. Sandra Huber)
»Doktor der Zahnkunde«
Very similar to the medical doctor, but for dentists.
Abbreviated as »Dr. med. dent.« and written before the name (Dr. med. dent. Sandra Huber)

Which of these degrees you get, and which abbreviation is valid is again a decision made by the university when the study program was submitted to be accredited.
Also these degrees are fully equivalent. None of them is "stronger" or "more important" than the others, and all of them are accepted by all other countries that participate at the Bologna Process.
After that there is a third cycle, that lasts 6 semesters and ends with one of these academic degrees:

»Doktor« if you are male and »Doktorin« if you are female
Abbreviated as »Dr.« with an additional information about the stury program and written before the persons name (Dr. techn. Sandra Huber)
»Doctor of Philosophy«
Abbreviated as »PhD« or »Ph.D.« and written behind the name, separated by a comma (Sandra Huber, PhD)

And again, it is the decision of the university durign the process of accreditation, which of these degrees you will get. And also these degrees are fully equivalent.

In any case, when you successfully finish a study program, you will get an academic degree. For each finished program you get one degree, and you keep this degree for the rest of your life. It can not be altered in any way.
So, having a degree »Magister« and another degree »Master« just means, that you successfully finished two study programs of the second cycle. It is impossible to tell just from the titles, in which order you made them, because, although »Magister« existed in the old system, it still exists in the new system. So, you can get the degree »Master« in 2007, and later, in 2020, you get a »Magister« for finishing another study program.

Note, that all above is only about academic degrees but there are also a lot of titles that also can be added to names in Austria, like »Universitätsprofessor«, »Professor«, »Ingenieur«, »Ziviltechniker«, »Tierarzt«, »Kammersänger«, »Bergrat« and many more.
If a person has titles and and degrees, the titles are written before the degrees and degrees from second cycle are written before third cycle degrees (FH-Prof. FH-Hon.Prof. Priv.-Doz. Mag.rer.soc.oec. Dipl.-Ing. Dipl.-Ing. Dr.techn. Karl M. Göschka)

The "old" university system in Austria had several titles: "Magister", "Diplomingenieur" and "Doktor".
You finished you "normal" studies (usually 8-10 semesters) and wrote a sort-of "thesis" (the name was different, but otherwise it was the same). Then you got a "Magister" ("Mag." if you studied on a general university or a "Diplomingenieur" ("Dipl.-Ing.") if you studied on a technical university. Optionally you could do further studies (usually 2-3 years of slave labour for a Prof.), write your doctoral thesis, have some additional examinations ("Rigorosen") and you became a "Doktor" ("Dr.").
This was the "old" system. Since the Bologna process (an EU-wide process to make university-level education more (grammar) school-like, less valuable and more time-consuming) was also implemented on austrian universities there are now "bachelors" (roughly what was called "erster Studienabschnitt" before but requires a "mini-thesis") and "masters" (equivalent to "Magister" and "Diplomingenieur"). Notice that some departments (for instance: law) still have the old system in place - but only the departments in public universities.
There are some private universities with departments also offered in state-run universities which use the Bologna-system instead: for instance, studying law at the University of Vienna is done in the old system and your studies end with a "Sponsion" to "Magister juris" ("Mag. jur.") with the option of doing a "Doktoratsstudium" and become "Dr. jur." (or, rather, because you needed to do the normal studies before, "Dr. Mag. jur.") Studying law at the Sigmund Freud Privatuniversität Wien your studies will make you a "Master of Law" (LL.M) and you can add a "Doktoratsstudium" after that the same way.
PS: in addition to these titles there is also "Privatdozent" (former "Universitätsdozent") as the highest title one can achieve by writing an additional thesis, a "Habilitation". This is the usual qualification for becoming an "(außer-)ordentlicher Universitätsprofessor", a full professor. See more here.

Broadly speaking, Mag. is an older title which may still exist in some niche curricula but is mostly superseded by M. Sc. In the case someone has both a Mag. and a M. Sc., I would assume in title-hungry Austria they'd use both.

"In the case someone has both a Mag. and a M. Sc."
How would one get both? By having an "older" Austrian degree and a "newer" one?

@user1301428
Exactly: In the course of the Bologna process, the titles in university curricula were change step by step, starting in the early 2000s. I.e., if someone got a title before the change from Mag. to M. Sc., and another one afterwards, they'd have ended up with both.

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text:
How could I calculate my GPA?
I have my GPA in the 100 point system,
how could I calculate it in 4.0 point system?
I searched, and I didn't find a good answer,

You should ask your university if they could provide a mapping to a 4-point system. If they don't, you simply have to calculate GPA*4/100! In case you feel this undermines your prospects, ask your university for a rank certificate which will give the admissions committee a good idea of where you stood in your department.

well actually my university doesn't provide a mapping to a 4-point system, but as you suggested it is better to calculate using GPA*4/100,
thanks for the help

I would strongly recommend against doing this and just fill in your GPA as a number out of 100 if the school that gave you that grade has no official conversion.  My school, for instance, gave grades out of 100 but anything below 70 was a 65.  If you simply convert it as GPA/25 that would be a 2.6; a low--but passing--grade.

Unless it is specifically requested, do not do it. Some school even urge you not to do it. It is highly probable, that they know your scale and understand what level means you are smart and hard working. Be sure to include thing like cum laude, merit scholarships, ranking within the cohort, ... These things are easier for them to understand and help them to compare you to the other students.
Miscalculating your GPA may result in unintentional deception or undermining your actual achievements. Be careful.

I found the following conversion for Syria, 100 point systems differ so generally the conversion is not always the same. I would use this only as an indicator.

| Scale          | Grade Description   | US Grade | Notes
| 95.00 - 100.00 | الشرف       (Honor) | A+       | Arabic: Sharaf
|  85.00 - 94.99 | امتياز  (Excellent) | A        | Arabic: Imtiyaz
|  75.00 - 84.99 | جيد جداً (Very Good) | B+       | Arabic: Jayed Jeddan
|  65.00 - 74.99 | جيد          (Good) | B        | Arabic: Jayed
|  60.00 - 64.99 | مقبول   (Aceptable) | C        | Arabic: Maqboul
|   0.00 - 59.99 | راسب         (Fail) | F        | Arabic: Raseb; Lowest passing grade

According to this source: http://www.classbase.com/Countries/Syria/Grading-System

Hooray for grade inflation/compression.

I recently had to deal with this situation when applying. My University did not have an A/B/C... system and would not provide a GPA.
Some of the application forms that I filled out provided instructions for international students, eg: no not enter a GPA. So I would start by reading the application forms.
For those that do not, my strongest recommendation is to contact the person in charge of applications at the department that you are applying to. Ask them what you should do in your specific circumstance. There is usually an email address on the department website for application enquiries.
Unfortunately a few universities never replied to my emails. For their applications I left the GPA field blank if the form allowed. For forms that required a GPA for submission I simply made up what I thought was an appropriate system.
While this didn't seem to hurt my chances, I would only recommend this as a last resort if you can't get a straight answer from the department you are applying to.

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text:
What to do when visiting a lab or a university for prospective application?
In his famous and interesting article "Ten Simple Rules for Selecting a Postdoctoral Position", author Philippe Bourne states, in the 2nd point:

Rule 2: Select a Laboratory That Suits Your Work and Lifestyle
If at all possible, visit the laboratory before making a decision.
  [...]

I think that is definitively a good advice, not only for Post-Doc applicants, but for all applicants in general. But, what is the best way to arrange a lab visit?
What to do when you're there?
Whom to speak to?
What to ask?
What to do?

This question is mostly answered by "What are some good questions to ask current graduate students when visiting schools?".

The question of how to arrange a visit is a different issue.

Is this for prospective Ph.D students or prospective postdocs ?

@Suresh for both... what do you advice in the two cases?

Two options I can think of:

Simply email the professor and arrange a visit.
Some programs will have lab tours during the recruitment/orientation programs, so you can try to arrange to meet the professor on that visit.


text:
Separate books from papers in bibliography of a paper
Is there some automatic way to single out the books in bibliography of a paper in IEEE format?
For example, write some program or use some functionality of some editors to find out the books mentioned in this paper with 303 references in its bibliography?

Try brute force. Sit down by hand and examine each one. The last 100 seemed to be journal papers. I gave up then.

Write some code that starts with that paper on the ISI website and then crawls each reference link to determine the type. Probably ~ 20 to 50 lines of code in Python, would be a good exercise...

@mankoff: Thanks! (1) What is "ISI website"? (2) I am not familiar with Python and how to parse the text yet.

I agree with Dave Clarke; just do it.  It should take you about half a second per reference to identify the books, which is less than three minutes total.

ISI is the old name for Web Of Science.

This seems to be what you are looking for. Essential some bash scripting. But as @JeffE says, it probably takes ~1second to scan through a reference so you won't be losing more than 5-6 minutes for a 300 reference list. Of course you can bash script the cr@p out of your pdf using some cunning gs and such but thats perhaps a mini-mini-project (which if you get to, please do share! )


text:
How should students react to inaccuracies in professors' teaching without causing resentment
I am an undergraduate in the UC system.  I sometimes encounter situations where professors or TA's make errors, or there are inaccuracies in the material.  These situations tend to be quite awkward for both the student and the TA or professor.
It is painful for me not to speak up, but there is a fear, possibly exaggerated, that this could lead to resentment by the TA, or professor, or even future unfair treatment.
The most frequent response by senior students is that the professor is always right, and you should never attempt to argue with the professor. Confronting a professor about a misconception could end up being detrimental to the student in the long run.
What should a student do (and how?) when a teacher makes an error or gives inaccurate information or material?  Is there any reasonable way to anonymously point out mistakes?

Though I'm sure they exist, I've never actually met a professor that was offended when a student pointed out a legitimate mistake in his/her coursework that needed correcting. The issue, of course, is that 99.9% of the time, the student is wrong and just being stubborn.

I have had lecturers who've made mistakes in class. For example, my lecturer of classical mechanics would sometimes mix up sin() / cos() or something like that - it can happen when writting down on the blackboard. He just asked us to always correct him, as such a mistake is easily made - but much harder to notice personally than have a student notice it.
Lecturers can make mistakes, doesn't mean they are bad in their field at all, it's just human :)

I've edited the question, hopefully into better shape (removing the ranting part and focusing on the constructive parts). I've also cleared comments who did not apply to the question as it currently is.

I think your fears may be exaggerated.  I can't think of a professor I've ever met who I think would be offended by having a mistake (politely) pointed out, much less retaliate.
Accusing anyone flat-out of being wrong, or worse yet, lying, will certainly make them defensive; and if it turns out they were right, it will be more embarrassing for you.  So I don't suggest thinking of it as "confronting" the professor.  What I would suggest instead is to approach the question as something that you don't understand.  "Hi Professor Smith, in class today you said X.  But I'm confused, because I thought that Y."  Listen to her response.  Be open to the possibility that you are mistaken, or have misunderstood what she said, but if your doubts aren't cleared up, figure out what part still seems wrong to you, and ask about that.  "I still don't understand; what about...?"  Stay calm and polite.  If you find you are getting worked up (or she is), take a break.  "Let me think about that, and if I still have questions I'll come back later."  Hopefully in the end, everyone agrees on where the truth lies, and nobody feels too embarrassed.
If you think she's simply misspoken about something in class, or written something incorrectly on the board, point it out right away: "Is that X supposed to be a Y?"  If there's something deeper, it may be better to discuss it in office hours or by email; I know that when I'm teaching, if I think I may have a serious mistake, I get flustered and it throws off my rhythm.  I'd rather have time to think about it offline, and then correct the error in the next class.
I think the other comments saying "Be sure you are right!!!" are excessive.  It's not a bad idea to try to think carefully about your question; if you can clear it up yourself, you'll learn better.  But don't hesitate to talk to the professor.  Even if it's you that's confused, part of my job as a professor is to clear that up.  And if it turns out I'm wrong, of course I want to know.
Your suggestion of having some sort of middleman to anonymously forward queries strikes me as a bit extreme.  Again, I think you may be more intimidated by your professor than is really warranted.  It may help to try to get to know your professors better: early in the course, make it a habit to drop by their office hours.  Ask some trivial questions if you like.  "Are we going to study Z next week?"  Then later, if you have more substantive questions or concerns, you'll feel more comfortable approaching them.
Anonymity seems unnecessary and perhaps counterproductive.  If you come to me with something you don't understand, and I'm able to clear it up, I won't think less of you; instead, I'll be pleased that you now understand it better.  And if it turns out I was wrong, I won't resent you; I'll be impressed that you understand the issue deeply enough to spot the error, and grateful that you brought it up.  But if you're really timid, you could consider sending an email from an anonymous account. ("I'm sending this anonymously because I'm embarrassed that it may be a silly question."  Either way she'll probably assure you that it isn't.)
One final comment: If you have mentors suggesting that professors are never wrong, find better mentors!  I agree that it is not pleasant to argue with anyone, but that doesn't mean you can't discuss your question and try to sort it out.

I'd like to add that it's a good idea not to insist that they are wrong in the class. Often, if you ask the question in the class, they may realize they are wrong, but they don't want to lose face (and they shouldn't either). So they'd somehow give you a vague answer to finish the conversation. If you are not convinced, continue the talk after the class where they are not being judged by all the students.

You have met nice professors, this may not be the case for everybody. There are many countries, universities and professors in this world and if you consider that you can probably realize that your experience is not any close to the average.

@Trylks you appear to have a different experience, a somewhat bitter one, but why would it mean that your experience is any closer to the “average”?

That was the first time I upvoted an answer and at the same time voted to close the question…

+1 for "If you have mentors suggesting that professors are never wrong, find better mentors!"

@F'x my university is not any close to top rankings in the world, it's ranked in the top of Spain. I'd say that makes it pretty average. But that is irrelevant, my experience doesn't need to be any close to the average to be able to point out that one nice and expensive university in USA is probably not a good sample about how things are in general in the world. You are making a straw man here.

I suppose there are some insecure professors who resent having mistakes pointed out, but in my experience they are relatively rare.  I'm impressed when a student catches a mistake, and I'm happy to learn they were paying close attention.  I'm certainly not alone in having this reaction, and I'd say it's a pretty standard response.
Of course, it depends on how you raise the issue: if you act like you are pained by the falsehood, or you question the professor's competence, then it's easy to cause offense.  Instead, it's safer to take a neutral tone, with an understanding attitude (based on the fact that it's difficult to teach a semester-long course without ever misspeaking).
For some errors, you should mention them as soon as you detect them.  For example, if your professor drops a sign in a calculation, then the earlier it gets corrected, the better.  No reasonable person could take offense at having this pointed out, so the only danger is being too eager to point out mistakes and inadvertently complaining about correct calculations.  That would be annoying if done frequently.
Sometimes it's hard to tell whether a statement is an error or an intentional simplification or approximation.  For example, if someone does a calculation using Newtonian gravity, then it's almost certainly unhelpful to interrupt to complain that general relativity would be more accurate.  If you can imagine that the statement might be deliberate, then it's probably better to raise the issue outside of class.  It's helpful to phrase it in the form of a question: "I was wondering why we neglected relativistic effects.  Do they matter at the scale we're working with?  Do you know of any good books where I could read about these corrections?"
Sometimes you just have to understand that the discipline in question is based on an approach you don't like.  For example, you might complain that your biology professor is always talking about evolution, or that your philosophy professor doesn't use an Ayn Rand-approved definition of freedom, or that your economics professor studies models that assume people are rational utility maximizers.  You should definitely not start a conversation by saying "Why are you teaching this nonsense?  Surely you know it's all wrong."  It's reasonable to ask foundational questions about the field and why the standard approaches have become standard, and you might learn something interesting (for example, that behavioral economics exists).  But you should approach the issue respectfully, with the goal of improving your own understanding rather than condemning the field itself.
In your particular case, I'd try to handle things delicately.  The fact that you frequently run into these situations makes me wonder whether you are taking a very literal approach to truth, and perhaps counting many models or simplifying assumptions as outright falsehoods.  There's nothing wrong with that philosophically, but approximations are a fact of life.  If you start complaining whenever anything falls short of the literal and exact truth, then you won't be happy anywhere outside of pure mathematics.  Furthermore, when you talk about how painful you find falsehoods taught in class, I wonder whether you make that pain apparent when asking questions.  I certainly don't want to discourage you from challenging falsehoods or from asking questions, since both activities are crucial parts of academia.  However, it's worth making sure your strong feelings aren't playing an unproductive role in your interactions with professors.

I would imagine that if you're unhappy with anything except the literal and exact truth, you might be unhappy inside pure math as well :). After all, some of the most interesting questions resist exact answers.

Falsities is a strong word--be very sure that the teaching is actually inaccurate before confronting your professor. And if you feel that you MUST say something, it is best handled in an area less public than a lecture hall. Also, a professor is far more likely to admit to having been mistaken if you approach them with the attitude of trying to understand their viewpoint and/or teaching, rather than trying to point out where they are mistaken. You may discover that you have misunderstood, and the professor is actually   correct. On the other hand, your humble, 'trying-to-learn' question may impel the professor to  take a second look, and discover where s/he has been inaccurate or mistaken.
I don't believe that there are many (if any) professors who will deliberately teach falsehoods to their students, especially in a course where, as you say, the material is of a technical nature and mistakes easily provable. So when you approach your professor, do so with an intent to discover where YOU are mistaken. You may both learn something.

This is good advice, but my concern is that I will be resented by the professor, and I am quite nervous in such a confrontation.  I would like to be able to let the professor know when I am certain they are wrong, without them knowing it was me who pointed it out.

Good answer. You type much faster than I do. I saw the message there is an answer while I was typing mine. Yours is clearer and better. So, I gave up mine.

@MVTC, Point being, go to her/him, with the intent to find out how you are wrong! Makes it a little less intimidating than going with intent to prove them wrong...

Approach with the intent to discover where you are mistaken, or where the misunderstanding is between what they say and what you hold to be true... Good advice for approaching anyone you believe to be wrong. Teacher, manager, subordinate, spouse...

There is a difference between having a discussion and having an argument. Once you know the difference you then need to be able to recognize when the two parties appear to have a different view of which applies.Once you know that you need to know how to change the situation to one of agreement. Once you know that your question will not bother you.


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How to get the most out of a period in another university during PhD?
Many PhD programs envisage for every candidate a period (3, 6 months or more) in another university, in order to carry on research in another institution, acquire new skills and (maybe) lay the foundations for a postdoctoral fellowship.
The task could be useful, but involves some problems, too. Often the PhD student is not able to familiarize with the new scientific environment and start working efficiently with the new group. Also, it is often difficult to find a research group that suites one's scientific fields and projects.
More over, sometimes the supervisor from the hosting institution agrees in welcoming a PhD student from outside (also to get his/her lab more international), but he/she has no time to dedicate to him/her...
For all these reasons, and more, sometimes a period abroad for a PhD could be very useless and ineffectual.
What do you think makes a period abroad successful?
Do you have any advice for PhD students going to face this career phase?

I would like to answer this question by asking one myself: would you go to a three-star Michelin restaurant, with a respectable but established clientele, with posh and smart diners, who do not need to meet their cooks or maitre's but just enjoy the glamour of the settings? Or would you prefer to visit a 1-star, striving to get a second star, where you have the occasional tourist and the owner is more keen on explaining to you the philosophy of their recipes?
I have been visiting both types (restaurants and universities!) and I prefer the second one, but it's probably due to age. In the latter you have more flexibility and contact with the main person you're interested in. Also, the first period acts as a "showcase", and it's very likely that more will be possible in the future.
My main advice would be to be a good networker. That implies "work hard" but also being prepared to "party hard", if you see what I mean. You should not be afraid to "ask people out" as much as in asking to share some research: you're likely to be in touch more often with the "second tier" (the first being the professor and her peers), and they will be the next generation of professors, so it's good to have a number of relationships with the post-docs and researchers of any institutions, at your stage of career. So don't close yourself in a shell of hard work for six months: I have seen that happening, and it does not make a good impression (to me)


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How to approach principal investigators for internship/job positions

What would you recommend as the best way of approach principal investigators for internship/job positions? I'm undergrad, with a planned graduation this winter and I want to get some experience before grad school.

Should I try 'cold' messaging? I want to go abroad and I'm not well networked there.
I've been on exchange and performed rather well. Can I use this experience to my benefit?

(Somewhat less important) Ideally I'm looking for research experience in Computational Neuroscience. I already have some research experience, I've done graduate work and I majored in cognitive science and mathematics but I come from a Liberal Arts & Sciences college. Will my LAS background be seen as a disadvantage?

The absolute best way to approach someone to work in his group is to be recommended by another researcher in his field, preferably someone he has heard off previously. So, either a big name or someone with close or overlapping research interests.
So, I would advise you to approach some of the professors in the field you are interested in, at your current institution, and ask them if they know a research group or a professor meeting your criteria. Try to be flexible when you discuss possible names/places with them, to gather a relatively large list, even if you later decide against some of these names. Once you have decided on a few names, either you can get your professors to contact them for you or, barring that, you can contact the abroad PI and mention your shared acquaintance.

Tried that, the department I'm working in is poorly connected with Computational Neuroscience departments, especially abroad. My thesis supervisor is a moderately big figure in the field, but our cooperation was poor ('difference of characters', to put it euphemistically), so I cannot count on his recommendation.

@Peter this is only tangentially related to your question, but regarding “difference of characters”, it is too bad that you let it hurt your later chances… that would have been the best way to go. As an undergrad, it might be a little early to start burn one’s bridges and make “enemies” in the staff.

I didn't really burn my bridges, I just got depressed and didn't communicate enough after the supervisor discarded my hard work. At first he gave me free choice in what I did and then he decided it wasn't sufficiently interesting.

Well, now that his help would be valuable, you apparently can't ask for it… which is why I called it that. But recommendations for internships are among the easiest to get, so maybe you can still ask him…

It's good to hear, I didn't dare ask him for any recommendations after the not so smooth cooperation.

Regarding (1), the answer is if you're "not well networked", you'll have to find someone who is. I would try the following, in order of potential usefulness:

Ask professors in your department to introduce you to other researchers you want to work with. They may be familiar with other researchers in your field and may be a good source of contacts.
Speak with any other faculty you think may be able to help you, outside of your department.
Talk to your department's administrators and see whether they can help you find an internship.
Try to contact students in the department you wish to intern and see whether they can help you get in touch with an advisor.

Regarding (2), it likely won't have much of an effect. Once you've actually performed research, the quality of your research output is primarily what's used to gauge your usefulness and potential. University and grades are a good proxy before then, but they're only a proxy.

@erykanal obviously networking seemed like the way to go, but it's difficult to find connections between my university and computational neuroscience labs.

@Peter - Are you sure there's no one in your university who does similar research? Computational neuroscience is a highly cross-disciplinary field; check the faculty pages of the math, statistics, comp sci, biology, neuroscience (if you have one), bioengineering (if you have one), and psychology... more than likely at least someone will have a connection that you can take advantage of.

As someone who has done exactly what you're looking for (an international PI hiring an undergrad as an intern), I can tell you that the circumstances are pretty unique, and it's not an easy road, unless you follow eykanal's or F'x's recommendations, and get a referral from someone who's worked with you and who can vouch for you to the person you want to work for.
In this personal case, the reason why I even gave this individual the time of day was that his "cover letter" email was compelling enough and well-researched enough to get me to take notice. I requested letters of recommendation and got good feedback on those, and had a similarly positive phone interview. More importantly, I already had a research project in mind where I could take advantage of the extra manpower, as well as the resources to commit to paying for the work.
Had any of those fallen through, I wouldn't have done it. But everything was properly aligned, and the experience has been successful.


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Use "parts" in a master thesis report
I am writing a master thesis of about 80-100 pages and want to know a good way of structuring my document either using only chapters or chapters and "parts". f first wanted to post this question to the TeX Stack Exchange but realized that it was too philosophical.
As most thesis writers I use LaTeX and I have seen thesis templates that use \part (classicthesis) and ones that do not (master thesis template from a university). I think that classicthesis is mostly aimed at PhD thesis documents that are longer and will become a "book".
So when is it appropriate to use \part? Any specific document length in pages or number of chapters?
When you use \part then a page is cleared after the text. Is this a style that is used in American PhD thesis documents? Why is this done?
I have also looked at some textbooks and they often do not have something similar to part. Instead these books only use chapters. One of my favorite textbooks (Artificial Intelligence: A modern approach by Russel) uses parts but no actual pages that show the parts name. Instead they are only visible in the table of contents.
My two competing ideas are with and without parts:
   \chapter{Introduction}
\part{Concepts}
   \chapter{Background}
   \chapter{Related work}
\part{Methods and systems}
   \chapter{Proposed method}
   \chapter{Implementation}
\part{Evaluation}
   \chapter{Experiments}
   \chapter{Analysis}
\part{Conclusions}
   \chapter{Conclusions}
   \chapter{Future work}

This would fit on tex.sx better than here.

And welcome to academia.sx

I would advise you to ask at writers.sx (http://writers.stackexchange.com/). I think it's a better fit there and you might get a sound advice with references to style manuals (The Chicago manual of style, etc.)

What does your advisor/grad school say? Thats perhaps one of the most important factors that decide the style of your report..

@drN - there is no style advice and when I ask They say I can do it the way I want. Other similar universities and master programs have good style guidelines however...

Apart from my advice in comments above to ask at writers.sx, I think you might want to consult manuals of style. E.g., The Chicago Manual of Style, speaks about division of a work in chapter 1, subsection 1.47 on division of a text into parts. I do not have the book besides me, so try to take a look at your library. Also The Oxford Guide to Style in subsection 1.3.2 speaks about this and says the following:

Arranging a work into parts is useful when a lengthy text falls easily and sensibly into logical divisions of similar length.

My personal opinion is, that for a work of 80-100 pages, division into parts is a waste of paper and imposes a too high cognitive load on the reader. Such a text is not lengthy enough to be eligible for such a crude division into multi-chapter parts. Do you have something like 3 times (parts) of at least 3 chapters each in your thesis? If so, and your thesis is about 80-100 pages, then IMHO, something is wrong with your structure to start with. Parts would make sense for a dissertation, or a similar manuscript if you would for example attack a problem from several aspects, each of a size and structure of several chapters.
My personal advice: Keep it simple! This is a master thesis, not a memoir.

When you use \part then a page is cleared after the text. Is this a style that is used in American PhD thesis documents? Why is this done?

Actually, the primary reason for this, I believe, is related to traditions in bookbinding. In the "old" days, it was accepted practice to begin each major new section with a right-hand page. Even now, some books are published in such a way that every chapter will start on a right-hand page, whether or not the previous chapter ended on a left-hand page.
Given that, the assumption would be that you'd want to have a blank page after the "part" page, and that the "part" page, as well as the first page of the ensuing chapter would both be "right-handed" when the thesis is printed in two-sided format. If you have to submit it in one-sided form, this becomes a bit of a nuisance, but I suspect this is an option that can be turned off in LaTeX.


text:
Vertices & edges vs. nodes & links
I'm writing a paper on graphs. Personally, I've always disliked the vertices/edges terminology. I found it very confusing when I started working with graphs, and I much prefer the alternative names nodes and links respectively. These terms are used, but far less than vertices/edges, and it depends highly on the field. I think nodes/links is more intuitive (to a modern audience) and I would like to see people move to this convention.
Now, I have a habit of choosing less common conventions if I don't like the common ones, sometimes to my own detriment. On the other hand, if nobody ever bucks the trend, there's no chance of poor conventions ever improving.
So my question is, specifically, is it acceptable to use nodes/links, and would it give a reader/reviewer that immediate slight sense of distrust towards the paper? Are there fields where it would simply be unacceptable? My paper is somewhere in between practical computer science and machine learning, but I'd be interested in the unwritten rules of other fields as well.
As a secondary question (if you care to elaborate), how should these situations be judged in general? Is it ever smart go against the most common convention, just because you don't like the common way? Are there good heuristics for such decisions?
EDIT: I edited the question to make it a bit more subtle. The original phrasing suggested that I'd made up the nodes/links terminology myself, when it's more about choosing between a popular and an unpopular convention, rather than introducing a new one. Apologies for changing the question after answers have been given.

"I much prefer to call them nodes and links", "I have a habit of refusing to follow conventions", "get rid of all the poor choices made in the past". And the reviewers will have the habit of rejecting your papers, when you do not follow the norms of your discipline and to avoid publishing papers that instead of focusing on actual content are more interested in shaking the norm for feeding egos.

"poor choices" Do you have any evidence that your choice is better?

This may depend on the field, but my perception was that "nodes and links" is a pretty widely followed convention, comparably wide-spread, like the other, maybe older convention of "vertices and edges". And of course, what about "nodes and edges"? Note that Wikipedia further suggests "points and arcs".

@O.R.Mapper You can easily use the terms nodes and edges on a paper with no problem. The OP's problem is that he is considering that this is a big issue and that he is proving a point, whereas he should focus more on the paper's scientific content and how to reach its target audience, instead of a trying to fight the scientific "status quo" and waste his energy on silly things.

Is this question in scope here?

Different terminology is prevalent in different communities.  "Graph theory" people tend to prefer "vertices and edges", but "network science" people tend to prefer "nodes and links".  Early 20th century topologists called them "points and lines".  The definitions strongly suggest "things and pairs of things".  You say potato, I say potato.

@Alexandros well that's sort of what this question was about: to figure out what the norms of my (or any) field are. As JeffE noted, there are people using nodes/links already, but not uniformly across fields. I see my attitude has rubbed some people the wrong way and they've focused more on my desire to give the conventions a nudge, so I guess that's now what the question is about (which is fine, that's interesting too). But originally, I just wanted to poll how people would respond to slightly idiosyncratic terminology.

@AustinHenley Only personal experience. I remember finding vertices/edges hard to read way back when I started on the subject. Sort of like there was nothing to hold on to. I don't know that it's uniformly better, but I figure there's a kind of democracy: you pick the form you like best from the available contenders. Of course, it it's between something you came up with and something that everybody else follows it would be silly. But what if it's 30/70, or 20/80... where do you draw the line?

@JeffE Except nobody says potato.

I tend to think of "vertices" and "edges" as the abstract graph theory concepts, and keep "nodes" and "links" for one of the data structures that can represent a graph, a node object for each vertex, with a link pointer for each edge.

You're right. "Nodes" and "links" is a way better nomenclature. "Vertices" and "edges" already have specific spatial/geometric meanings, and so the vast majority of people who've learned those terms in another context will be rightfully confused to discovered that an "edge" in graph theory is not actually a literal "edge" at all. The original names are simply really badly chosen and the community should work together to change the terms of art.

Your Case
Candidly speaking, I really like your terminology better than the established terminology, and hope it catches on!
Because the convention is established, you should at least acknowledge it, perhaps as follows:

In this manuscript, we will refer to what are conventionally called vertices as nodes, and what are called edges we will call links. We believe that this terminology is superior to the conventional terminology because ... [briefly support your claim].

General Case
If you submit a paper with your own convention, acknowledge it and support it! Give a reason to convince your readers that your way is superior, but don't belabor the point. If the reviewers don't like it, they have an obligation to say so.
Bucking the convention without acknowledging it might make it look as though you aren't familiar with the convention (or even the field?) in a slight way. As you said, there might be an element of mistrust.
The wise reader/reviewer will be able to to sense the mistrust and ignore it. If they prefer the conventional terminology, they will be able to mentally replace your terms with their preferred terms. While this would certainly annoy some readers, it might please other readers—especially those less "set in their ways" (particularly those newer to the field).
Value of a Convention (generally speaking)
Conventions usually—but not always—become established for a reason: perhaps they better avoid confusion, say more for less, or they just express something "better" —compared to the alternatives. Certain terms and phrases can serve as quick aliases for larger issues, and following conventional terminology usually help prevent confusion or misunderstandings.
If you go against the convention, you ought to have a really good reason for doing so—one that outweighs your readers' annoyance and risk of confusion.
Of course, not all conventions are the best. There's often room to improve or replace them, though changing conventions is uphill work. If you feel your convention is better than the established convention, discuss it with those who are familiar with it to see if you can build support.
Conclusion
While my discussion has been primarily general, I suggest that you discuss this with several colleagues and collaborators whose opinions your respect. Perhaps there's a good reason to prefer "edges" and "vertices" over "links" and "nodes"?
If your terminology has the support of your peers, then—by all means—submit your paper with it. If your peers don't approve, then maybe you can introduce your terminology in more subtle ways (e.g. a footnote or parenthetical statement, or even in conversations with peers), but publish according to the established convention.

Lastly, every once in a while, there's a paper that comes out that presents a superior convention or (more often) disambiguates several competing terminologies that together are confusing, misleading or erroneous. These often have great merit. (For an example, see "Meaning of ionospheric Joule heating" by Vasyliūnas and Song (2005), here). Your case probably isn't worthy of its own paper...yet...unless you can find truly strong and compelling evidence that it is.

And what if the next author likes neither your terminology nor the previous one and decides to call these elements bars and joints? And then the next one goes for arms and knees?
I'm an electronic engineer: what if I decide that I don't like the terms resistance, capacitance and inductance, and I decide to use the terms opposance, tankance and springance?
Readers should not struggle to follow author's idiosyncrasies about terminology, the effort is already enough to understand the new concepts that are typically introduced in a paper. And recall that the first readers of your papers are the reviewers, and sometimes the reviewers complain for even more conventional terminologies. Moreover, if you are free to make your terminology choices, they have even more freedom in rejecting your paper.
Here is an example. As I said in the above, I'm an electronic engineer. However, due to the tradition of the field in which I work, most of my readers are physicists. When I write a paper, I typically use terms and symbols that are widely employed by the engineering community, and are even defined by standards. For at least three papers, the reviewers complained that I haven't used standard symbols or terms (standard for them). And so I had to reply with references to standards, literature etc. It's annoying, but at least I had references to provide, and eventually symbols and terms were accepted. What do you have to backup your choice of terminology?

I think it's more intuitive (to a modern audience) and it would be better if people adopted this convention

Aren't you generalizing too much?

we'll never get rid of all the poor choices made in the past.

Are you sure that there are so many poor choices?

So my question is, is it acceptable to use nodes/links?

I think not or, better, as I explained above, I think there is no sound reason to use nodes and links in place of the accepted terminology.

Is it ever smart go against convention, just because you don't like how things are done?

It is seldom smart, unless there are good scientific reasons or the existing terminology is really misleading, but before going against an established convention, you have to provide evidence that that convention is wrong or misleading. An example in this sense is that of relativistic mass, a term which was introduced at the beginning of the theory of relativity. In later years, however, the concept has been criticized [see e.g. Adler(1986)] and the term is now considered utterly misleading, and modern books on relativity avoid it altogether.

Lol... arms and knees... I've messed the body up!

I'm pretty sure that, if you used the term "springance", all other electrical engineers would find it so awesome that they'd call it springance, too.

You worry about two words you don't like. Your question does not even explain why you would think that "nodes" is a better choice than "vertex" (I find both perfectly understandable, and certainly can't see why you'd think that "vertex" and "edge" would be a "poor choice").
In other words, you're trying to fight a really small, unimportant battle. Save your argumentative powers for the things in your paper that really matter.


text:
What prevents reviewers from providing biased and very negative reviews?
One of the fundamental features of science, maybe even the most important, is that publication of scientific results is peer-reviewed.
I want to understand why peer review is effective in the scientific community, because I want to apply principles of peer review to a different domain.
As I understand it, a researcher is reviewing work of a competitor who is producing scientific results in exchange for grant funds and reputation, usually same as the reviewing researcher does. Of course, this competition may not be very direct, but the reviewer is in an overlapping area of research. In addition, there is some natural bias of every human being to groom their own ego. Based on this, I expect most reviews to be very negative. However, it seems that biased and extremely negative reviews are rare for decent submissions.
What stops reviewers from providing biased negative reviews?

Comments are not for extended discussion; this conversation has been moved to chat.

The term competitors does not really describe the relationship between different scientists in the same field. Of course there is some competition for grants or such, or even to put one's name in a new result, but some aspects are deeply different:

A publication in your field is a good thing, even if it's not from yourself. It makes your area important, and alive. It's actually very important when it comes to applying for grants.
You cannot benefit from someone else's work by writing negative reviews. There is no way to simply slow down publication of one paper in order to publish the result first.
A rejected paper will not slow down the "competitors" research. Sure they will have to improve it and submit it elsewhere, but this takes a marginal time compared to the research process itself.
Dishonest reviews are clearly dangerous, as some people will see your review with your name on it (I'm thinking of other reviewers on such systems as Easychair). These people might very well be the ones reviewing your grant application a few weeks later.
why would one risk being exposed as dishonest, when anyway there are several reviews for the same paper, and any deep difference should trigger an in-depth investigation by the editor?

The most frequent bias I have seen are review of the form "you should cite those 5 obscure and vaguely related papers all from the same author", which clearly indicate reviewers in need of citation, but nothing much worse.

Vis your second point, I've recently heard an anecdote that von Neumann was the referee for a paper in which Birkhoff proved his ergodic theorem, and after reading it, he sat on the review for such a long time that by the time he returned it, he had published his own related, but less general result (the mean ergodic theorem).

@tomasz do you have a reference for this anecdote?

@DanRomik: Not really, as I have said, I have only heard it recently. May be completely apocryphal. I am not a specialist, but as far as I understand, von Neumann's result, while less impressive and closely related, is still an important result on its own right (it's called the mean ergodic theorem), not some kind of trivial corollary.

@tomasz There is a story, but it's different, and AFAIK isn't about peer review. Rather it was von Neumann who initially came up with his proof, communicated this to Birkhoff, who proved his theorem. Then Birkhoff quickly wrote a paper and had it published in December 1931, whereas von Neumann had to race to publish his in January 1932. See this perspective by Calvin Moore, as well as a first-hand account from Birkhoff and Koopman.

I think the main factor that makes the peer-review system to not fall in the trap you described is that academics are finally interested in the advance of science. If I have to review a good paper, then I enjoy it and want to see it published. If I review an almost good paper, I suggest some improvements and enjoy if these are incorporated and the work is published. The very mild advantage I may have if I reject more papers does not really seem to be worth it, if I have to act unfair and unreasonable to get this advantage.
Another factor may be: The reviewer is not anonymous for the editor. Editors are often influential people and writing consistently bad and unfair reviews will make you look like a mean and unfair person. Also, the editor will not choose you again as a reviewer if you write such reviews and you will be effectively eliminating yourself from the review system for that journal (while you can still submit papers).
In view of the bounty I gave the question another thought and here is one more thing: Community. Science is well organized in communities (e.g. I consider myself as part of the mathematical community, the applied math community, the community on mathematical imaging, the optimization community and some more). As part of a community one has a sense that there are some rules one should follow to be a valuable member of the community and of these rules is fairness. Being unfair is misconduct by the unwritten community rules. So even though one may get away with several cases of unfair behavior, it feels like one is cheating the system. But staying a respected member of the communities is very important both for the scientific standing and also for productivity. This reasoning also explains that bad behavior sometimes happens, when several competing communities form which are somehow "enemies of each other": One can stay a respected member of one of the communities while still treating members from the other community unfair.

I think the main factor... is that academics are finally interested in the advance of science. - I think the main reason is that most academics are decent human beings.

You might add an additional concept to your otherwise excellent answer: if multiple reviewers, say for instance 3 review the same paper, but 2 give an excellent review and the 3rd gives a very bad review that seems to contradict the others, this can have an effect on the 3rd reviewer's good name. If that person consistently provides biased reviews, the chance is high that their bias will come out, which in turn means their name will be tarnished

Many academics are interested in the advance of their own career (views, theories), not of science as a whole. That's pretty obvious on social sciences like economics.

I have nothing to do with academy, so take my answer just as something that I'd expect based on my understanding of human interaction and behaviour.
Reputation
The main resource you have is your own reputation, and that will be severely harmed if people are accusing you of being unfair, biased or "not objective enough". You might be able to get away with it once in a while, but overall, it's quite enough for the system to work. Worst case scenario, you slow down the propagation of the work in question, but in practice, the paper will find another way (another reviewer, journal...). Even if you succeed, you risk harming your reputation, which is extremely important in a field centered around collaboration with peers and promising understudies.
Competition
You only considered competition between individual scientists, which is mostly a thing of (1) competing for grants and (2) competing for reputation. I've already dealt with reputation. Competition for grants might be important for you if you're trying to adapt the process for something like performance reviews - it's the clearest cut case where hurting others can help you. However, it doesn't have much to do with the peer review process - that would indeed introduce a very strong motivation to be "as unfair as you can be without actually appearing unfair".
However, there's also another competition going on - that between individual reviewers and their journals. If your paper was rejected based on grounds that are seen as fair and objective, you'll likely also be rejected by other journals. If not, the other journals might jump on the opportunity to publish your paper, while also implying that another journal has treated the paper unfairly. You can't do this very often if you want your journal/reviewers to keep being relevant!
Points to take away
If you want to use a similar system for another domain, make sure that similar incentives are at play.

Have multiple independent reviewers, and let people choose their reviewer (while the reviewer has a chance to decline).
Make sure there's not a lot of "authority" in play - for example, superior-underling relation doesn't make for good peers. Peer review works best with consensus and with reasonably objective / shared values.
Make everything public (in the team / company). No anonymity, no "hidden" reviews. This is necessary for the reputation-based controls to work. In a way, it's a redundancy in the peer review system - it allows people to "review" the reviews themselves.

It works best in mostly flat hierarchies. Thinking in terms of a performance review in a company, peer review will be a poor choice if managers order people around. On the other hand, if managers have to persuade others to follow with their plan, it might work great :)

In addition to the mechanisms listed by others, most journals I've published in so far allow the authors to list people who they feel have competing interests and thus should not be considered as reviewers. So if there's someone who you know is working on competing research, you can put them on that list.
Of course, this isn't perfect, but if you get three reviews out of which two are largely positive and one is deeply negative, the editor is likely to decide in your favor anyway.
(I'm in biology, specifically plant genetics. I'm sure it varies a lot between fields.)

Double-blind review (neither reviewers nor the reviewed are shown who the opposite parties are) was invented to help with some of these issues. It's used almost exclusively in some fields for conference and journal peer review (various parts of CS comes to mind). Mostly, it's to help prevent unconscious bias against underrepresented minorities and women cropping up and tainting reviews. Given that it's relatively easy to spot women and foreigners from names, double-blind review tries to stop these biases from creeping in by hiding the names from reviewers, too.

True, but 1) if someone is doing research similar to yours and the field is small, they're likely to be able to tell it's your paper anyway, and 2) if they're just generally trying to keep their "competitors" down, they'd write bad reviews for "competing" research regardless of who the authors are. So in this particular case it's not likely to help much.

@weronika I'd note that, at least personally, "they're likely to be able to tell it's your paper anyway" isn't nearly as reliable as some people think, at least personally. I've been wrong both times I've been "positive" about it, and missed that I was reviewing the paper of someone whose work I was fairly familiar with once.

Double-blind review only takes away some of the bias, but it does not remove the incentives described in the OP (i.e. the reviewer is still giving a competitor's work the go-ahead, at least from the OP's viewpoint). It is still an important part of the peer-review toolbox and it may work well in other environments, though. In such a case, it should also be mentioned that double-blind reviews are much harder to implement than single-blinds, particularly in an academic setting where e.g. papers will tend to acknowledge previous work by the same group. In other settings that may or may not hold.

@E.P. and weronika, yes, and? I didn't say it was a panacea, just that there had been some work on reviewer bias that OP should be familiar with. Fomite is dead on that it's not as easy to unblind papers as you think, even in small fields. This is a reasonably well-studied area, and Computer Science sticks with it despite arguments like yours.

Yeah, I'm not saying that your answer is wrong, I'm just saying that there's more to be said. If the OP wants to port peer-review to other scenarios, and they want to port double-blinds, it is likely that it will be significantly more work, at the very least on the mechanics of the thing. (It's not easy to unblind properly blinded papers. If the authors say "As we showed on a previous manuscript..." and provide a full citation, the game is up. Nothing that can't be worked correctly, but it is more work.)

While it is good that double blind masks the authors, in my discipline (CS, systems) it unfortunately often also masks much of the content. In order to be not trivially unmasked, I frequently have to remove all links to our live systems, where reviewers may rerun the experiments and examine the tools.

@Daniel, maybe you should set up an anonymized live system in AWS on some VMs while your papers are under review and then just swap in the non-anonymous URL when preparing the camera ready version.

@BillBarth: Unfortunately it is not that easy. We do low-level systems stuff (operating systems and hypervisors, at times augmented by custom hardware) that one cannot just put inside a VM. However, even if so, our tools and techniques are pretty special, so providing them would also unmask out identity.

@DavidRicherby, fair point. I figured that was covered under "almost exclusively". I don't have room in this margin to list the subfields of CS that do or do not use it. It's common enough in CS to be worth listing broadly. Most of the research about it and the big push for it in technical work seems to have originated in CS as best as I can tell.

@DavidRicherby, don't parse too closely. This is just the web. Every other CS sub field I've submitted in required double-blind submission and review. I'm not a CS person per se, so I may miss some of the subtleties. My apologies if I got you riled up. Any idea why theoretical CS didn't join the bandwagon?

@BillBarth No worries. I guess that theoretical CS uses single-blind because it grew out of maths.

@DavidRicherby, which obviously has no oldboys to be unconsciously biased towards.

There is one aspect that has been mentioned in @weronika's answer, but not been stressed enough in my opinion and probably not obvious to the author: There is usually more than one reviewer.
In my area there will normally be three different reviews, which seems to be a good compromise of keeping total workload low and allowing to identify "outliers". An editor may not be able to see if a single review is biased, but if they see reviews contradict each other considerably, an unfair review might become noticeable.

Added for clarification: Three reviewers are certainly not enough to get meaningful statistics (that's why I wrote "outlier" in quotes), and only multiple choice or numerical ratings in the reviewers' sheets could be compared in a statistical way. But there are several critical factors that can reduce the quality of a review, and their possible impact can at least be reduced by having more than one reviewer:

inadequate knowledge in the field of expertise,
negligence or missing time, and
bias or malicious intent.

Is this is somewhat the "statistical game" to provide a review that is likely consistent with the other reviews of this article?

@h22 I'm not sure I understand your comment, but I tried to clarify my answer with some more text.

We've seen randomly generated papers accepted, Universities acting like paper mills, and researchers being scored soley on the number of papers published.
The review system is based almost soley on the wish that everyone has good intentions. Unfortunately this doesn't make the system work flawlessly.
The most common complaint is that a lot of reviewers don't take enough time to review the material. Making people invest precious time in a peer-review system might be a harder problem than making them behave honestly.
I haven't heard of cases where reviewers intentionall gave bad reviews. Though I have heard of feuds between authors. This is especially problematic in small fields where the reviewer isn't as anonymous as we would like. Note that feedback might identify a reviewer. Also note that the author is never anonymous (and is hard to make anonymous) which makes the system more suspectable to malicious reviewers.
The partially mitigating factor might be the editor. Which acts as a sort of referee. But what if the editor is malicious?
To answer your question: there is no definitive factor that prevents malicious use of the academic peer review system. There are instances where the system has been abused. I also do not believe that scientists are less often malicious than any other person :).

To be honest, it is very hard to justify (or in this matter to generalize) the behavior of a group of people (reviewers). I'm sure some of us were victims of irrational and unfair reviewing process i.e., getting reviews after 4-5 months with poor questions, harsh language or the most obvious case where you can find a very similar work to your paper published couple of weeks of your article that you received after a delayed review!!
Even with double-blind peer review process, a reviewer can guess who are the authors of a certain paper based on their research topic, wording, experimental set-up and/or even funding account/agency (usually mentioned in the acknowledgement section). So, it is very PERSON dependent! Think of it like athletes who compete in sports, all of them are subjected to the same rules, however some will always try to cheat the system!! whether with drugs or with exploding loop holes!
The good news is there are more reviewers who are genuinely interested in advancing science than those who are eager to unfairly compete with other researchers. Don't let any of this put you down, think of it like this.. You must have been doing some very interesting research!!

Your methodology itself is biased.  Anytime you are doing something to alter the review process you are creating a biased review.  This could be as simple as wording before or during the review process and at the other end of the spectrum leaving out some potential reviewers.
My advice:

worry more about your science than your review
welcome the biased reviewer.  I would rather see the flaws that my research/science has as soon as possible, not after it has been fully publicized.
understand that there is an element of risk or wasted time involved.  If someone is biased and using corrupt review tactics this is more time consuming. But and big but this also allows you to learn more about the outside forces you are going against and how to refute them better.
and a further point is an obviously biased review will be easily refuted.  As it is, it will lower the reviewer's stance/reputation and highlight the work that you are doing.  People are far more passionate when there is an A vs. Z dynamic than just hearing about A.

So really the only thing that you need to do (and I write review/survey systems) is to have a mechanism of review rebuttal and make sure the person writing the review understands this.  If I cared about my name I would not write an untrue/biased review about something if I knew that someone could refute my stance directed at me.  Transparency is key.

This answer does not seem to address the question. There is nothing OP said about altering the review process, only about implementing it, and it is not at all clear what "methodology" you are claiming is biased. It is also not clear that there is any sort of science involved (except in the meta level, perhaps).

@tomasz - asking the question is an indication of trying to formulate a biased review.  You are not understanding my answer and that is fine, maybe it is too meta for you.

@blankip The asker clearly states that they are trying to implement a system equivalent to peer review, outside academia. They are not trying to change academic peer review. As far as I can see, tomasz understands your answer just fine: it's you who seems to be misunderstanding the question.


text:
Why do some publication venues prefer TIFF over some vector formats?
Why do some publication venues prefer TIFF over some vector formats?
Example:

Most figure file formats are acceptable, although TIFF is preferable.

Comments are not for extended discussion; this conversation has been moved to chat.

TIFF is the preferred pixel format for print due to being able to use CMYK (the colour format relevant to printing) and being lossless in typical use (using lossy compression cannot happen without clear intention in most programs). Moreover, this was already the case long ago, when formats such as PNG and PDF were only beginning to emerge or not even created and creating a good vector graphics was not feasible for your average scientist.
On the other hand, today where online publication is standard and graphics software has advanced a lot, TIFFs cannot really compete with vector graphics for most applications. Either the TIFF is of good quality, but then its usually huge, which is not desirable for online dissemination. Or the TIFF is reasonably sized but rasterisation shows. Moreover, almost all problems in vector graphics can be easily repaired by the production department, whereas repairing pixel graphics can be much more cumbersome. There are some exceptions where a TIFF is the best choice but even this requires, e.g., that the authors and their programs are CMYK-aware to gain an advantage over formats such as PNG.
So, I cannot imagine that any reasonable production department would prefer over TIFFs over vector formats in most cases, let alone allow TIFF as the only format. Thus, the reason, why the journal is preferring or requesting TIFFs is probably is probably one of the following or somewhere in between:

It was a reasonable requirement twenty years ago, and they never changed it.
The person making the specifications asked the production department which format they prefer for graphics, and they answered with TIFF. The actual question, namely which format they prefer scientists to use for submitting graphics, would have probably received a different answer, but was never asked.

Note that the specifications you linked seem pretty reasonable to me at first glance and also marks EPS as a preferred format alongside TIFF. Moreover, it mentions embedding fonts, which only makes sense for embedding text as a vector object, which is not possible with the TIFF format at all.

"It was a reasonable requirement twenty years ago, and they never changed it." This seems most likely. After all, it doesn't say they prefer TIFF over vector graphics, they just prefer it over "other formats", which at the time of writing might have meant BMP and JPEG.

TIFF is an image file with all elements of the image in a fixed position relative to one another(assuming layers are flattened). As such, it is easy to ensure consistency regardless of differences between the software used to create and display.
With files where the elements are separate, there can be alignment and compatibility issues if a file is opened in a different piece of software. A very clear example of this can be found with written documents. A .docx file opened in Microsoft Word, Apple's Pages, or LibreOffice, even something like a two-page essay with minimal formatting, can look quite different in each of these applications.
When compared to JPG, TIFF is a much higher quality format. JPG compression greatly reduces the quality of text and blurs hard edges between solid colours that are not exactly horizontal or vertical.

Thanks, interesting, do you mean that vector formats don't ensure the location of each elements of the image?

@Frank They're pretty good, but not as reliably as TIFFs. There can also be issues like these which fair number of people do not know to check for.

A very clear example of this is opening a .docx file in Microsoft Word, Apple's Pages, or LibreOffice. – I do not think that graphics made in this or a comparably unsuited format are the alternative we have to consider here. — JPG compression greatly reduces the quality of text – If you want a good text quality, you should not use pixel graphics at all. — PNG files […] tend not to print very well and have frequent colour shift issues. – Sure, but these issues come from using RGB over CMYK. Except for the rare CMYK-aware author, you better let the production department worry about this.

I meant that as a general example of a minor formatting error, not as one specific to this context. I've edited the post a bit in an attempt to clarify. You're entirely right about .PNGs.

@Wrzlprmft If you want a good text quality, you should not use pixel graphics at all. Except when the image is actually originally captured and best presented as pixel graphics, e.g., microscope images, screen shots.  Even some extremely high-density data is better presented as pixel graphics than vector graphics.

@jakebeal: Except when the image is actually originally captured and best presented as pixel graphics, e.g., microscope images, screen shots – Even in that case, you should not (and need not) use pixel graphics to render labels and similar, as vector graphics can contain pixel graphics.

@Wrzlprmft I would generally agree --- in that case, you are producing a composite graphic, one component of which is a vector graphic.  I frequently find myself presenting pixel graphics that have no need for labels, however, only for captions.