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Aftermath of rightfully submitting a solo paper without my advisor's name
After reading this question and this I haven't find my answer.
My advisor hasn't contributed to my work and I know that my work isn't significant and it won't publish in top journals. But I want to publish it without my advisor's name in a conference.
So my question is not about automatically coauthor my advisor or having high hopes on my individual work.
The Problem arise from here. We have to enroll in some seminar classes before starting to work on our thesis.
In one of those classes our teacher said:

"No matter what you do, you have to enlist your advisor's name in your papers because unless it would considered as a work with no supervisor and it can not be trusted."
"In interview we have for PhD students, if the person who is applying hasn't written the name of his suprevisor we doubt him. Either he is a genius or he is hiding something or he is too active in his field."
"In some companies and research labs everyone add the name of their fundraiser to show him their gratitude, so should we.".

So based on what I heard I'm going to face serious problems if I publish my work individually as a student. The question is:

Apart from being unethical including a name of person who didn't contribute to work as a coauthor, does it have any academic weight? I mean, does it value my work if I say I did it alone or it does not have any different until coauthor isn't a student.
Is it true that I am going to be accused as a not genuine person if I don't add my advisor's name? Because our teacher told us that he and his colleagues don't consider these kind of submitted papers trustworthy and genuine, so don't look at them carefully and mostly reject them on sight.

Edit:
Conclusion: Thank you all. I think my vision is more clear now. The right way is not the opposite of the wrong way. It means despite "spoon-fed" "a very distorted view", the right thing to do is not doing the opposite.
I decided to do my best to play as a team, because of its mentioned benefits, especially for my first paper. But if working as a team doesn't go well, there is no harm in solo publishing or getting some new advisers.

If your adviser really hasn't contributed to your work, then you really do need to get some new advisers as soon as possible.

What would it mean to be "too active" in one's field?  That sounds like a nice problem to have.

@Trevor Wilson It means the student is working with multiple advisors and teachers or working simultaneously on diffrent projects, whether academic or industrial.

Actually, I heard the exact opposite to be said a lot (quite often on this website): during their PhD studies, it is often expected of the student to publish at least one paper without his adviser. This is supposed to demonstrate that the work done was not actually adviser's work, and that the PhD candidate is indeed capable of doing research and publishing on his own.

What discipline are you in, and what country? It makes a difference.

@EnergyNumbers I strongly disagree. I wrote two papers as a graduate student that were fairly far afield from my advisor's interests, and while he read them and provided some comments, neither one of us thought he came anywhere near authorship - the papers basically arrived fully formed and written. Side projects are a thing that happens.

@EnergyNumbers is almost correct. If your adviser really hasn't contributed to your work, and they still insist on being a coauthor on your papers, then you really do need to get some new advisers as soon as poosible.

this is an old and classic problem in modern academia.  sometimes you have to dance with the person who brought you and sometimes you have to stand on principle.

I don't think your problem is with your advisor. Your real problem is with teachers in classes who say things like:

No matter what you do, you have to enlist your advisor's name in your
  papers because unless it would considered as a work with no supervisor
  and it can not be trusted."
"In interview we have for PhD students, if the person who is applying
  hasn't written the name of his suprevisor we doubt him. Either he is a
  genius or he is hiding something or he is too active in his field."
"In some companies and research labs everyone add the name of their
  fundraiser to show him their gratitude, so should we.".

In light of all the recent debate about whether we are too idealized and rosy in our views of academia, let me at least say this:
Whether or not this is common practice in the areas you work in, the problem here is the rationale being used to justify author inclusion. In no way is the decision being made based on some notion of contribution by the advisor (either financial or moral, or in any form). It's being based purely on a notion of patronage or bias.
The person making these claims has either a very distorted view of how authorship works, or is misleading new students in a terrible way.

Just to make things clear. Does it value my work if I say I did it alone or it does not have any different until coauthor isn't a student. If not, I'd rather not pickup a fight and just go with the fund raiser for publishing my paper.

All I'm saying is that you really have to look at the authoring conventions in your area. If it is the case that PIs funding your research are typically added on, you should have a good reason for not doing so.

I agree with what you've written. But I'm not sure it actually answers the question(s) asked (in the last 4 sentences of the OP), does it?

I had a supervisor who insisted on being listed as the primary author on every paper written by his students. I presented a paper at a conference, and afterwards a senior researcher from another establishment queried my contribution, and I accurately stated that I had done everything involved in this project. He informed me my advisor being listed not just as an author, but as primary author, was considered to be fraud. In conclusion, I disagree that the problem is not with the advisor. Sometimes the advisor is the problem.

Apart from being unethical including a name of person who didn't
  contribute to work as a coauthor, does it have any academic weight?

You use very strong words, but things are not black and white. You are a student and most likely you do not know how to write a good paper. Why not involve your supervisor in the writing process? You can write the original manuscript and he will make the final version, since he is more experienced than you. In that setting you are still first author, he does contribute and he is co-author, your paper has more chances to be published and everyone is happy.

Is it true that I am going to be accused as a not genuine person if I
  don't add my advisor's name?

You are exaggerating again. If your paper will be rejected it will most likely be because it is not good enough and not because of your name. There is always the possibility that someone with no previous experience is easier to get his paper rejected (I believe many reviewers do a Google search on the person they are reviewing) but that mostly applies to big conferences. For smaller conferences or workshops criteria are not that strict.
But you have not thought the most critical factor. What if your paper gets accepted? Who will then pay for your conference registration and trip? Usually it is the advisor that provides such funding. If you submit it solo, you must do the entire process with the university bureaucracy alone and without support from some faculty member it will be much harder for the university to actually cover your expenses.
So, although I disagree with some of the comments your seminar tried to spoon-feed you, in the long run it will be better to play as a team member. So, involve your supervisor, make him actually contribute on the notion that you will still be first author. This cooperation might even vastly improve your paper and then it might get accepted even in a top conference or journal. In this setting, you will have more to win than to lose.

Thanks for advice. I think I've found my way now :) It's not about authorship, it's about using the maximum potentials that are available in every situation.

"You are a student and most likely you do not know how to write a good paper." Er, what?

The OP admits this is his first paper. He also admits "my work isn't significant". So, isolating the "You are a student and most likely you do not know how to write a good paper.." without actually reading the OP's question is misleading.

The advice is to find a way to make his adviser a co-author because 1) The adviser can help write a better paper, 2) your paper is more likely to be reviewed positively with a well-known name, and 3) you are more likely to get funding if you add your adviser. And people wonder why academia has such a bad reputation! Reason 1) is the closest to an ethical argument (depending on the field), reasons 2 and 3 are absolutely corrupt.

In scientific publications, at least, "author contribution" statements are becoming more and more common. These statements list the exact contributions that each author on the paper made. A number of excellent examples are provided on this Nature blog post: http://blogs.nature.com/nautilus/2007/11/post_12.html
If you included your supervisor as an author on the paper, providing such a statement would allow you to clarify the nature of your roles.

It might be worth pointing out the existence of the Vancouver Protocol (first described by the International Committee of Medical Journal Editors, this is becoming more widely accepted). This protocol states

Authorship credit should be based only on substantial contributions to
  1) conception and design, or analysis and interpretation of data; and
  to 2) drafting the article or revising it critically for important
  intellectual content; and on 3) final approval of the version to be
  published. Conditions 1, 2, and 3 must all be met. Participation
  solely in the acquisition of funding or the collection of data does
  not justify authorship. General supervision of the research group is
  not sufficient for authorship. Any part of an article critical to its
  main conclusions must be the responsibility of at least one author.

This is quite restrictive, and clearly discourages some of the attributions that your teachers appear to encourage.
That said, it is important for a scientist at the start of his/her career to be very aware of the value of collaboration - working closely with your advisor (to the point where their contribution warrants co-authorship) is quite likely to improve the quality of your paper. If you believe it would not, then maybe you need to question your choice of advisor.
It is no doubt true that a person with a good publications record carries more weight in their chosen field, and that their papers will be read more carefully and cited more frequently. Because of this it is often considered a good idea to start out in this mode.
Personal note: in the 80s when I did my PhD, email wasn't yet a thing. My advisor was abroad for almost an entire year, and I did in fact independently write and publish a paper. The work in this paper was very good (I can say so in retrospect after more than 20 years), but I was a complete unknown - and it had incredibly narrow applicability. To this date, it has received just one citation. I still believe I was correct (given the circumstance) not to include my advisor's name on the paper, but it did nothing for my career (or the field). It would have been better if I had waited until he returned, discussed and improved the paper, and published jointly.
There is a lot that an experienced person can do merit co-authorship - but you have to create the opportunity for them to do so.

First of all, pretty much all the justifications your teacher gave to you are lies. This person is trying to encourage you to put your supervisors' names on your papers, but avoiding telling you that you have to do so because it is the rule.
Secondly, there are roughly three ways a paper can be written as a grad student.

The student does some work and publishes it, but the supervisor is responsible for lots of guidance, planning, editing, making sure the work gets done, suggesting the original question, helping to place the paper, etc. This is how almost everyone's first paper gets written. The supervisor will almost always be an author, and everyone accepts that this is fair. (However, I have known some generous supervisors who decline an author credit in such cases, since they regard what they did as part of supervising, and not a specific contribution to authoring the paper).
The student and supervisor collaborate, similarly to how to colleagues would collaborate (but perhaps with the student doing more of the 'grunt work' and the supervisor making more of the decisions). Both are authors.
The student does work independently, perhaps asking for some limited advice or proofreading. The supervisor should not be an author, but often is in practice.

Most people except the very gifted start off with the first type, and everyone except those who don't progress very far should have some of the latter two types by the end of a PhD.
So if someone has only publications with their supervisor, it could be taken as meaning that they didn't do much independent work, but it could also be that they had to 'give credit' to their supervisor, or that they work in an area where most papers are collaborative.
If someone has only publications without their supervisor, it might be seen as positive, but it could also be assumed that their supervisor was generous in not taking credit, therefore neutral. If you are known to be a genius, the fact that your early publications were on your own will be mentioned, but it won't prove that you are a genius if this isn't already accepted.
The implied lack of credibility 'that your supervisor didn't approve of your work' would be a very strange reaction. It's only something you should worry about if there's some other reason you might come across as a maverick - for example all your papers are serious work about some topic beloved of conspiracy theorists, or you went straight into grad school from high school, etc. In these cases, you might want to make sure that some form of reflected legitimacy is evident.
If some has a combination of supervisor-included and -not-included work, it would be seem as normal.
In other words, no case is really a strong indicator of your strength.
Your last problem is what you should do. Your teachers are behaving unethically, but your best option is probably to go along with it. Just make sure that you can justify your authorship of the papers you consider yours, if asked in an interview. If so, anyone who takes the time to do so will probably figure out what your supervisor's contribution was, and won't assume that you were playing the same game.

If your advisor has substantially contributed to the work described in the paper, of course they should be listed as a co-author. If they did less in the way of contribution, but did at least read the paper and suggest improvements, they could be a secondary author. If they just taught you (in general) and didn't work with you on the research/paper, I would think a dedication or "thank you" note in the paper would sufficiently recognize them for what they've done for you. Unless your school insists on listing advisors as co-authors (it's the custom there), leave them off if they did nothing.

@PhilPerry - the custom of the school ought not to come into the discussion. The journal in which you publish usually has guidelines for authorship - those are the only ones you should follow. If the school insists on "guest authorship" (recognition without contribution) then you have to find journals that accept that standard.

@Floris, well, which is it then? You say to ignore what the school demands, and then to find a journal that meets those demands. If your school or advisor insists on guest authorship, you'll have to decide if you want to continue your association with them (accede to their unreasonable demand), or if the paper is important enough to you to be worth fighting them by switching advisors or even schools.

@PhilPerry - in my comment I distinguished between "custom" of the school vs "insisting": I consider the former a suggestion, and the latter a condition of belonging to the school. It is hard to see how a school can actually force you to include the name of a non-contributing author; I don't think they have the legal authority (especially in the US). Still - I advocate finding ways to get the advisor to merit being listed as co-author, for all the reasons I outline in my answer (which I wrote a little after my comment, after giving the matter some further thought).

@Floris They didn't literally force me to include the name of a non-contributing author, but they did told us that the paper won't accomplish anything. The thing that made me doubt was one of my friends in another university. He told me he is going to solo publish his work and I was worried that he might destroy his efforts. Now I think both he and I have more options to consider.

@user263485 - if anything I said has made you consider your options more carefully, I consider that a success. Remember - almost any endeavor can be made better by working together with someone who has better or complementary skills. See my "personal note" in the answer I wrote.

@jwg It's not about me claiming to be a genius. Where did I imply this? It's about ridiculed and dismissed of not being honest when you apply for your PhD degree.


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Discreet way to establish priority
After finishing a paper, I'd like to show it to a few people for review. I'd like to establish publication priority somehow. The site arXiv won't do because my paper hasn't been reviewed to that level of quality. On the other hand, viXra won't do because I don't want to look like a crackpot.
Here are some desirable functions. The site:

Lets me upload a file
Lets me share the URL so that anyone can see it who has the URL
Shows the time I uploaded the file in a trustworthy way
Prevents others from modifying it-- it's view only

Bonus:
5. Shows versions of the file, together with their upload times
How many of these can be satisfied? Would a file sharing site suffice? Thanks for your advice.

The site arXiv won't do because my paper hasn't been reviewed to that level of quality. — What? ArXiv doesn't review anything, except to make sure submissions are well-formed (abstract, bibliography, etc.) and not blatantly out of scope.  (I'm a moderator.)

ShyPerson All of your four requirements and bonus are satisfied by arXiv. You can send the url of arXiv paper to anyone to review your paper. What are you looking for?

If my paper is wrong and I put it on arXiv, I'll look like a crackpot. I want something a lot more obscure than arXiv while my paper is in its formative stages. I thought arXiv was really intended as a pre-publication site-- wouldn't it be misleading for me to put a paper far below pre-publication quality there when people are assuming otherwise?

Private repository on Bitbucket? You can keep the TeX sources there too, which is useful for collaboration.

So, you're looking for a site between arXiv and viXra? I have seen many poor quality papers on arXiv. I also saw some good(not a whole lot) papers on viXra. Endorsement requirement is a reason people shy away from arXiv. You should be able to put your paper on arXiv and then revise it after review.

I'm confused by 4. prevents others from modifying it - it's view only. There is no such thing as "view-only" for a text - you can always re-type it.

@JeffE Arxiv does require an established researcher as endorser

You cannot establish priority without circulating your paper widely.  Or, more precisely, you can prove that you had the idea first, but that won't help you much.  Academic credit is awarded for contributing to the research community.  If you have an idea and don't publicize it (so few people find out or learn from it), and someone else rediscovers the idea and tells everyone, then they will get most or all of the credit, because the community will have learned far more from them than from you.  Even if you can prove you made the discovery first, you may end up as a footnote or side comment in the background sections of future papers.
This is not always fair, but it's a pretty good system.  In particular, it avoids the nightmare scenario of researchers trying to establish priority while deliberately telling as few people as possible (to preserve their head start for follow-up work).
The fact that the arXiv has time stamps and keeps old versions available is potentially useful for resolving disputes, but the important aspect is that papers on the arXiv get noticed.  That's why the arXiv is a good way to establish priority: the community doesn't consider "Oh, I had no idea that paper was on the arXiv" to be a good excuse.  By contrast, if you post the paper somewhere much more obscure, then not noticing it would not be surprising or frowned upon.
How to handle this depends on the threat you are worried about.  If you are concerned that someone you ask to look over the paper might steal your ideas, then you could cc a trusted mentor who could vouch for you if there were a dispute.  On the other hand, I wouldn't worry about this too much: outright theft of ideas is rare, and why would you even want advice from someone you think might plausibly be a thief?  If you are concerned about staking out credit in case someone else is independently working on similar ideas, then there's nothing you can do except get your paper in good shape and then distribute it.

If my paper is wrong and I put it on arXiv, I'll look like a crackpot. I want something a lot more obscure than arXiv while my paper is in its formative stages.

Of course it's hard to say without more information, but these comments suggest to me that worrying about credit may be premature.  I'd recommend revising/polishing the paper until it is no longer potentially embarrassing or in a state of flux, and then posting it to the arXiv.

This "nightmare scenario" isn't just abstract, it's how things actually worked in the distant past, and it was bad.  See the cubic formula insanity, the Newton/Liebnitz dispute, or Galileo's observation of the rings of Saturn.

I've heard that it's bad etiquette to share a pre-print widely. Is that true? If a paper is on viXra or arXiv or any such pre-print repository, it's proof of precedence. Even if people give credit to the wrong person due to publicity, history will sort out that error because the pre-print repository has given a timestamp to the original author.

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What to do when you have two manuscripts under review where one cites the other, but the citing paper gets accepted before the cited paper?
I submitted an article around 11 months ago to a SCI journal and another article around 5 months ago in another SCI journal. The second article cited the first article which was under review for 6 months at the time of submission of second article. Recently, we got acceptance letter for 2nd article while 1st article is still under review.
What action should we take? remove the citation in 2nd article and cite the 2nd article in 1st article or we stay with the current situation. but what if our 1st article got rejection?

I don't think the "self-plagiarism" tag is appropriate. It is not self-plagiarism to cite another paper you have written

Can you post a public preprint of the first article?  If so, then you can simply cite the preprint.

It would be helpful to know what field you’re in, since citation culture is very field-dependent.  In my field (mathematical logic), it’s accepted and reasonably common for preprints to be cited before even being submitted.  But I have friends in experimental sciences who are shocked by this — in their fields, it’s unacceptable for published work to cite anything not yet peer-reviewed.

@NateEldredge I just confirmation from editor office  that I can submit preprint  of article in arxiv. I think you suggested a good solution. Thanks

If the second article depends in some substantive way in the material from the first, the second should cite the first, according to the journal's policy for material under review.  (Different journals tend to handle such matters in different ways.)  If there is no real dependence, I would suggest omitting the citation, and having the first paper, when it gets published, cite the second.
Having each paper cite the others might be deemed less than optimal, but that does happen.  If you don't have a problem with the circular citation arrangement, I would include a citation to the second, published article in the first, even if the second already cites the first.

The traditional method to avoid these messes was to refer to any work as forthcoming until such a time as the work having definitely and definitively entered the literature. So yes, it did happen that certain papers were eternally immortalised as "forthcoming" - and as a reader you could be in for a bit of detective work (this was back when you had to physically schlepp to an actual brick and mortar library). A fun and not infrequent intermediate case arose when a promise was made or a claim was staked for the forthcoming paper, which, once it did come forth, was never made good on! Preprints were always a patchwork solution (as physical copies could be hard to track down), but luckily now we have archiv, BioArchiv and the like. Authors' personal webpages may help, but beware, as different authors may link to different versions of the work.

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Why do universities place so much importance on citation counts and impact factors when evaluating researchers?
Impact factors and citation counts are widely used metrics to judge the reputation of researchers. However, these metrics can be misleading, and in some cases can be manipulated.
Why do universities place so much importance on citation counts and accumulative impact factors?

Why do you think a "majority of universities" really care much about this? Citation needed.

I don't have experience of job applications in north America, but in Australia, UK, and several other EU countries gives a lot of importance to publication count, impact factor and citation. I know the person in UK who become reader within 4 years because of his large number of publications. He published 270+ articles in 3 years. I don't think someone can justify contribution in such a large number of articles, but there are 100s of such examples, and universities decorating them.

You mention exceptional cases. I doubt that promotion was due only to "bean counting", though it may have alerted people to take a look. And "majority" seems far too strong.

In A number of European countries, you can't get a PhD unless you've published x so many papers with impact factor higher than y. I know that in Spain, application forms for postdocs and faculty jobs specifically ask for impact factors. In the UK the research excellence framework ranks the quality if papers and decides university funding. Its claims not use IF (but will use citation counts), however university planning for REF generally does use IF. My academic probation criteria said i needed 1 paper IF>10 or 2 papers > 5.

I hate to say it... but it's because the people who set these KPIs tend to be dumb business types rather than academics who have no idea how to effectively run a research institution

@IanSudbery They must have different standards for different departments, because I don't think my field has any journal with IF > 5.

@Persistence sounds like some kind of "blindly trust the data" problem, kinda reminds me of this video. Measurement of success != actual success because "it's not a problem with human beings that they don't think like mathematical machines". It just ends up separating the productive things you do, from what you do to have funding to keep being productive. Though, a complete elimination of metrics would mean scaling back a lot, and spending more time reading an individual's papers and judging them on their own merits.

I hate to say it, but they don't.  The thing that is really important is grant income.

While these metrics may be biased (and easily gamed) the alternative is usually evaluation by a small panel of experts.  The problem with that its that it can have a high variance.  Reviewers of top conferences do not give highly consistent reviews (http://inverseprobability.com/talks/notes/the-neurips-experiment.html ) so the approach taken by e.g. REF may not be any more reliable (as well as being extremely expensive).  Citation count is probably better than impact factor, but is very variable from one field to another.

When my department proposes to promote a faculty member, the  college requires that we provide information about how we use citation metrics to evaluate research. The answer that I've used when preparing many promotion files begins with "The short answer is that we don't." There follows a paragraph about the unreliability of such metrics and the availability of far better ones.

Google does the same thing regarding evaluating web pages for how good they are (and ranked accordingly in a search result).  Works pretty good for them.

Answering "why" is no problem: as @Allure says, because it's easy (and it's hard to find better metrics). But you're right to point out that it's a flawed metric, and like any metric it suffers from Goodhart's Law: when a measure becomes a target, it ceases to be a good measure. Solving that isn't easy.

@ThorbjørnRavnAndersen it's also gamed heavily, look at all the "SEO optimization" pages and keyword / link stuffer scam sites

@jrh Yes, it is an art to identify malice.

@kimball yeah, sure, the actual numeric target will vary from department to department. See also the recent situation at Liverpool life sciences where faculty across the school were ranked on citation count, and the bottom 50 selected for sacking. It was only a months long campaign of industrial action, including no marking for nearly a year that saved the jobs in the end.

Because it's easy
Let's say you got 100 researchers to evaluate. How would you go about doing it? You could read their papers in sufficient detail to understand them (would take months or years, especially if they're not in your field). You could rely on peer evaluations and recommendation letters (already done extensively). You could look at prizes and awards won (also already done extensively). Or you could look at citation counts and impact factors. The last is easy to do, and while it's not perfect, it is objective and there is a correlation with research quality (citation counts is the standard method to measure excellence in bibliometrics).
Besides, many non-specialists care about citation counts and impact factors, e.g. all the major university rankings use it, and students look at rankings. Doing badly on those rankings can make one less attractive to students, with all its negative consequences.
See also this:

But. Faculty candidates are necessarily judged by people who are not experts in their field. Without the expertise to judge whether your work is really good, those people must look at secondary data that correlate strongly with successful researchers. One of those secondary characteristics is "pedigree". Did you get your degree at MIT, Berkeley, Stanford, CMU, another top-10 department, or somewhere else? (What's an "Ivy League"?) How good/famous is your advisor? If they're really paying attention: Where did your advisor's other PhD students get jobs, and how well are they doing now?
Fortunately, most good departments do make a serious effort to understand the quality and impact of applicants' results, instead of relying only on secondary data. Also, secondary data matters considerably less once you actually have an interview.

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Because many funding agencies give a lot of weight to citations and impact factor,
Because many ranking agencies (of all sorts) will give higher rankings to institutions with research-active and well-funded faculty, as measured by such metrics,
Because stating in a recruitment brochure that your faculty publish on average so-many papers a year will make you look better than so-few papers a year.

Yeah it’s all marketing, but in these days where governments are funding a decreasing proportion of the cost of education,  where universities compete for students, and where the ratio of administration to faculty keeps increasing, the administration needs new revenues.  See this article in Forbes magazine for additional context and financial pressures on institutions.

I agree with you its all because of faulty methodologies adopted by funding agencies, but academia didn't resist rather becoming part of it.

@MBK it is a self-evident truth that most universities are perfectly happy to just  “follow the money”… principle of least resistance.

Question: "Why do we give so much importance to citations and impact factor?"; Answer: "Because some people give so much importance to citations and impact factor". OK, but this just displaces the question a bit, it doesn't really answer it.

@Stef no and yes.  If the people who give such importance hold the $$  then yes it does place the ball in their court, but they would argue it’s their preferred way of allocating resources.  Would you rather send your kids to a top-ranked school or a lower-ranked one (cost notwithstanding )?

Question is impossible to answer since the premise is false, or at least has no proof. Specifically,

why majority of universities give too much importance to citation
count and accumulative impact factor

No university I am aware of cares at all about impact factors, which are in most cases fake (the ones reported by journals).
Citation count is slightly more important, and is used at times as a proxy of "impact" of a scientist, but even this is not universally recognized, and most universities do not explicitly check this measure.
In fact, promotion and hiring is based more on:

reference letters and peer evaluation
places of publications: prestigious or not.
acquaintance of existing faculty members with the candidate
number of publications in selective places (not number of citations)

In the US, at least, promotion is largely a result of peer evaluation and peers have a more sophisticated view of the accomplishments of a candidate. True, the advice of a promotions committee isn't the final word, but is nearly always respected - or chaos results.

"impact factors, which are in most cases fake (the ones reported by journals). Citation count is slightly more important, and is a proxy of "impact" of a scientis" Your these sentences are contradictory.  Citations determines the impact factor. So, if impact factor is unreliable, then how citations can be a reliable metric? As I mentioned in my previous comment publishing 100s of articles in a year  cant be justified so as the citations of such researchers.

In the systems I’m more familiar with, not all journal publications can be included in the CVs.  This is certainly true when it comes to PTR, or when it comes to grant applications; lower-tiered journals are thus filtered out of where applicants would publish.    In addition, lower publication counts can be compensated by higher citations counts, i.e. two papers in Nature with high citations may well be considered equivalent to or better than  5 papers with low citations in a middle-tier journal.

Because of the rise of predatory journals, pure publication count is not as important as it used to be, in the sense that predatory publications are very often discounted; in this sense the “prestige” of the journal does matter.  The false permise is that a single score can capture the “value-added” of a faculty member.

@MBK, I didn't say citation counting is "reliable", I said it's more important in the process of being promoted, because it's something that people and committees and peers look at. No one I know of looks at "Impact factors", and moreover IFs stated by publishers are unreliable (or "fake").

@Buffy, thanks, I've added "peer evaluation" now.

@ZeroTheHero Predatory journals are irrelevant. All citation counts, impact factors and h-indexes are taken directly from WOS and most predatory journals never make it there. If they do, they remain somewhere at the bottom of the ranking with low IF. They generate few citation from other WOS journals. Only WOS to WOS citations count.

@VladimirF WOS is not the sole supplier of metrics (there are enough questions here in GoogleScholar for you to know that).  My point is that the total number of papers is now no longer accepted as a metric.

@ZeroTheHer No one cares about Google Scholar, it includes too much crap. Those who have the power to disttibute money care about WOS and sometimes, but only sometimes, about Scopus (but even then only as a secondary piece of information). Whenwe care about the number of papers we, of course, only count those in journals that have a WOS impact factor. Other papers do not count, noone cares about them. For some purposes, like money in our uni, only papers in journals in IF ranking above the median count.

@VladimirF your experience is apparently very different from mine in this matter.

I agree with Vladimir about not counting journals/conference that are predatory or below a certain IF threshold. Of course, no body counts these for most purposes. But it seems that ZeroTheHero says precisely this, so I don't see where's the disagreement between you two.

I have no idea about "majority" either, but we are occasionally discussing what a "fair metric" would be for counting publications. Everyone agrees that the evaluation of the true scientific merit is impractical (or even impossible) for a variety of reasons from impossibility to carefully read and evaluate all papers in a variety of completely different areas to the mere fact that to estimate a true impact of something, one has to wait for 10+ years at the very least.
Our current system (as far as I remember it) is to have tier 1 and tier 2 journals with 2 points for a publication in a former and 1 in the latter (there are also some fancy rules about sole publications vs. co-authored ones I was too lazy to read properly, so I'd rather skip them here). It is far from ideal and is constantly critiqued from all sides, but it is a not too bad compromise after all. I've heard of much worse arrangements where the formalization was brought to something completely absurd (from my perspective, at least). The tiers are determined by "general agreement" (and there is some fight here) with the impact factor playing some role, but not the decisive one. In general, it is believed that the individual citation metrics (like h-index) reflect the true impact of a researcher much better than the sum of journal impact factors times the number of papers in that journal.
The main reason for the very existence of this point system seems to be that neither we would like to explain to the administration what is worth what on the routine basis, not the administration would like to hear such explanations more often than absolutely necessary, so everything should be reduced to a single number. When really important cases arise (like promotion to tenure, etc.) the number merely needs to be above a certain (fairly low) threshold and the decision is made based mostly on the recommendation letters and such, but for trivial issues like annual merit salary raise that number suffices and everybody can see how the awards are made. Transparency here is at least as important as fairness and since the latter can be hardly achieved even in theory, resorting to the famous KISS principle is a reasonable idea. As long as the point system (whatever it is) doesn't acquire life and power of its own that overrides common sense, it is harmless and even useful.
Of course, the situation varies from place to place, but what should be remembered is that many rules like that are not creations of the universities, but rather of the faculty in the particular departments, and the ugliest monsters are born when people do not want to agree on anything or even to listen to each other. Various "rankings" by independent agencies also play some role, of course, and the citation factors play noticeable role there, sometimes in a rather weird (again, IMHO) way.
As I said, the current system is far from ideal, but if you ever come up with a bright idea of a really good way (fair, transparent, and practical), let me know and I'll be happy to advocate for it locally :-)

Nice points raised, but this is not an answer to the question.

@Dilworth Agreed, but, as it has been already said in the comments, the very premise of the question is "questionable", so I just described what is going on at one particular place I can speak about with some certainty. The point is that we do put some importance on those metrics (and I tried to explain why) though not so much. If somebody works at the place where "so much" is a rule, they might be able to provide more relevant information, of course.

A major issue in my view is the concept of "objectivity" and the issues with it. Objectivity can mean many things, but often it is taken to be the result of a transparent and reproducible measurement procedure, and associated with the removal of the influence of personal interests and opinions.
The essential dilemma with this is that the ability and potential of a researcher and the value of their work are so complex (and surely not one-dimensional, as any ranking needs to be) that chances are that no "objective" measurement procedure can do them justice. In some places there is a tendency to prioritise straight numerical measurements despite being obviously deficient (I'm not necessarily saying the citation counts and impact factors are the best of those). In some other places decisions are made in intransparent manners by commission members, taking into account reference letters and other information from peers. This can work well, but also is connected to favouritism and old networks protecting their field.

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

authors: Vladimir F Героям слава


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Is it reasonable to collaborate with a professor when you are employed by a different professor?
How wise is it to collaborate with another professor while working as a staff under one professor? Is there a ethical conflict in doing so even if the other professor is from a slightly different area?
Also, how should one develop his/her own expertise while working as a postdoc under one professor? Is it wise to also work with other professor with slightly different research interest?

It depends totally on your status, and what exactly this collaboration entails. You say “working as a staff under one professor”. If you're on a short-term contract (say, post-doc), then it's probably not okay to do independent research on something completely different. You were hired on a project and it's unlikely that you have any significant time left for something else. On the other hand, if this new collaboration is related to your project and you involve your professor in it, it is okay (and he will welcome this initiative from which everyone involved benefits).
To the above, there are a few exceptions:

People who just arrived usually have some unfinished business with their previous institution, and they are given a bit more leeway in finishing it: revisions to make to papers on track for publication, conference attendance, etc.
People who are leaving due to their contract ending have to get involved with other projects to get a new job. They have to go fishing around, and this sometime requires a bit of extra work.
Finally, if your activity on the side is quite unrelated to your main job, and you manage to do it on your own time without prejudice to your employer, you may do so. Some people write books, some get involved in open source software unrelated to their employment, etc.

If you're working as an longer-term staff researcher in someone's group, then it is expected that they respect your academic freedom. To a reasonable extent, you are free to engage in new collaborations with other people, and not necessarily involve your group leader.

"it's probably not okay to do independent research" - our definitions of what post-docs do are widely different. In my institution, if you are a postdoc and you don't do independent research, you are not doing your job.

In contrast to F'x's opinion, I think collaboration with people outside your group is not just wise, but actually necessary, at least if you are working toward an academic career.  You must develop both a wide professional network and broad independent research experience.  As long as everything is out in the open, with everyone's knowledge and agreement, there is absolutely no ethical conflict.
This does not mean that you should shirk your paid job; any outside projects must be on your own time and must not interfere with your official duties.  Similarly, you can't use your supervisor's resources without their explicit advance permission.  And your supervisor may be happier if there's some chance of involving them in your outside projects.  But ultimately, how you use your own time is your own business.  (Any supervisor who tells you otherwise, or insists that you don't have "your own time", is simply abusing you.  Run.)

I agree partly. I would say, however, that if there is substantial overlap between your “day” work and your “own time” work, it may be unethical (unless you get approval for your outside work). To give one example I’m familiar with, a staff researcher in a French institution is not allowed to do consulting on matters related to his own work, without explicit authorization from his employer. There are exceptions (“intellectual work”: books, software, some stuff like that).

Ah, I see the difference.  In my field, research is "intellectual work".

Nice one. To expand: “intellectual work” is the translation of a French legal term, “œuvres de l'esprit”, which in fact does not cover one can consider intellectual work (without the quotes). My point is: there are limitations to what you can do in your free time, depending on your contract and your jurisdiction. Better safe than sorry. That's all. Some exaggerated example: if your day job is being a researcher at the WeCureCancer chemicals company, and you discover a new anti-cancer molecule one evening in your basement, you can hardly expect to be allowed to patent it for yourself.

And this exactly is why I work in academia, and not  for the WeCureCancer chemicals company.

Well, the law is the law, and whether your employer is a University or WeCureCancer, it applies the same (at least here in France). Also, I suspect that with current budgets, any university will want in on the patent :)

And this is exactly why I don't work in a field where people fight over patents.  Even in France, the mere suggestion that a PhD student or postdoc in mathematics or theoretical computer science might be legally forbidden from working with someone other than their advisor would be considered offensive.  (At least, so I infer from the French PhD students and postdocs I've worked with.)  It may very well be the law, but sometimes the law is an ass.

If you are perfectly honest with all parties involved, then it shouldn't be a problem. Everyone involved knows where they stand.
One small point. In the UK, post-doc positions are funded by grant income. It would be strange if a post-doc had enough "free time" for other duties.

Let me give an answer from my own viewpoint - that of someone who hires and 'supervises' postdocs on a regular basis (in my field, mathematics).
I consider that a postdoc coming to my group comes for two reasons: (a) to bring new knowledge to our group, and (b) to learn things from our group. Both are good for the postdoc and good for the group - everybody profits from this arrangement. Learning things from our group is best done in close collaboration with the supervisor (me), while contributing to the group often benefits from a much wider scope.
So I tell my postdocs that I expect them to work half of their time on the project they are formally appointed for, and the other half on something of their own choosing - and I suggest that for this part they might also look for other connections within our group or department.
What this means for the OP is (as has already been said): discuss it with your supervisor, and ask yourself the question whether the 'outside' collaboration might also have benefits for your supervisor.


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What to check when examining paper proofs?
When you receive a paper proof and review it prior to publication, what exactly should you be looking for?
The things that come to mind are any changes in the annotation of author list and the corresponding author. What else is there?

This is basically the last chance to fix anything (non-substantial) in the paper, so in addition to the things you mentioned, I usually check for spelling or grammatical errors, misprints in formulas, etc. Sometimes one might want to add a sentence to clarify something.
Finally, if the journal did any copy-editing, you should check its job. Some journals provide a list of changes they made for that purpose. You should also check if the pictures and formulas are still in the right places.
Added: sometimes it's necessary to update the literature list, for example if preprints cited there have been published in the meantime.

Often it is no longer possible to fix your own errors, only errors introduced in copy-editing.

Ok, I have never had that experience. But I am talking about small corrections like spelling mistakes, not anything that changes the content of the paper.

@JukkaSuomela a few times I have been told that I can fix minor typos, even if they are my own fault, and that more extensive changes can be done for a fee.

For example: I had several instances of {l-1\choose 2} in my paper, and the copy editor removed all instances of "\choose" so my paper suddenly had many instances of "l-12". This copy-writing change was a significant issue to the correctness of the paper (we fixed it).

I (as a journal typesetter "=" copy editor) would stress: (1) Update literature -- usually some preprints there have already changed their status. (2) Verify formulas -- both inline and display ones; that's where I most likely make a mistake (and it happens, I'm just a human as you are, after all). When submitting in Word, check every smallest bit of your paper, because bad things happen in word2latex conversion, and it's not my fault if you submit in Word to a LaTeX-only journal.

One other thing to be concerned about is overzealous copy editors, particularly when it comes to highly mathematical papers. In one of the first manuscripts I ever submitted, the copy editor in question decided that what I wrote as (1/2)x really ought to be 1/(2x). This would have completely altered the intent and the results of the derivation and everything that followed!
So, the lesson of this is that you need to check everything that was changed by the copy editors. If they give you a "mark-up," review that first, and then make sure everything has been transferred correctly to the paper. If not, you'll need to go side-by-side with the submitted manuscript and the final proof, and make sure eveyrhing is as you intended it to be.

Yikes.  That is worse than the urban legend about the copy editor who fixed all the places where "if" was spelled with an extra "f"...

Yep. And I can't imagine how many other papers that copy editor might have tried to butcher. . . .

It is not even sufficient to so that: the same kind of error have been introduced after the proofs in my very first paper...

@BenoîtKloeckner: If the corrections to your proof are not made correctly, or additional errors are introduced afterward, then you have the right to ask the journal to correct the flaws, and republish the article. (I've done this as well when the title of an article was screwed up, and published unfixed, even though they were informed of the problem.)

I always proofread the full paper, but not necessarily by comparing it word by word with the original. However, I give particular attention to:

Title, authors, affiliations
Abstract, introduction and conclusion
Figures and figure captions. In particular:

quality of the graphics produced
do color and symbols mentioned in the caption match the figure?
if the journal has black & white figures in print, is the figure understandable in black and white?
if the journal has color figures only in the online version: does the caption make sense for both version (color and B&W)?

Equations: most problems I saw introduced during typesetting were in equations. For many publishers, the text is transformed semi-automatically from your original file, but equations are re-keyed by an operator. People make mistakes.
Numbers: all tables, all inline numbers. Units (a “kJ/mol” might become a “kJ mol”).
References (citations are a key part of doing research):

if references are hyperlinked (using DOI number), click on each to check that they match the right online paper
if a paper is “in press” or “accepted for publication” or something else, update its status if it has been published

Acknowledgment: somehow, I often find that I might have missed someone in the acknowledgment when writing the initial paper, and for most publishers it is not too late to add them :)

I once had a journal publish my paper with the inclusion of the sentence "I thank the anonymous referee for his/her comments" in my acknowledgments without my knowledge.  I thought that was a bit rude.  (If I had been asked to include that statement, I would have gladly included it.)

Between your manuscript being accepted and the proofs being created two things are likely to happen: a copy editor may make changes and portions of the manuscript (e.g., tables) may be retyped (as the manuscript is converted from the format you submitted into the journal format). I know a number of PIs who get two people to look at the proofs. One person reads the proof out loud while the other person compares what was in the submitted version. I know one group that goes sentence-by-sentence backwards. The idea is you never know what will get screwed up in the conversion process. While I like the concept, I spend a lot less time going through the proofs.

One more thing to watch for if the format has changed, say if you submitted the paper in some garden-variety LaTeX style and the journal converted it to its own style: The new line breaks can create hyphenation errors.  In general, TeX is amazingly good at getting hyphenation right, but it's not infallible.  One of my papers had the misfortune that "colimit" landed on a line break and was hyphenated "col-imit".


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What's the etiquette for a short visit to a US university department by a faculty member from another university?
In May, I'll be visiting a department at Columbia University in the US for a few days. What's the etiquette on visiting (answers relevant to US in general are welcome, to prevent this question getting too localised)?
I'd like to spend some time with quite a few of the researchers, and compare notes on ongoing work. I'll read their recent publications in advance. Should I be inviting staff out for a coffee and a chat; or dinner; or a talk in the lab?
Context: I'm a faculty researcher, and would be looking to spend a bit of time with postdoc researchers, and those professors whose jobs are primarily research, rather than admin or teaching.

Not from the US, but in our group we often go for lunch with guests (I think usually from our groups budget), they are asked (but not forced) to give a short talk about their work for everyone who is interested, they are introduced to the PhD students and postdocs, if one side is interested, they can always ask for a chat. Sometimes we have BBQ together or go hiking (that depends on how long they stay and how close friends they already are with people from the group). And they of course might set up appointments to talk to people not from the group, while they are here. They are guests.

I think you are the person who would be invited out to lunch, dinner etc. as you are the guest :) ! However, there is nothing wrong with inviting your opposite number to talk in an informal setting. The only consideration is that you know the lay of the land!
Depending on how many days you would be spending at the US university, you might want to make a strategy on conversations and prospective collaborations.
I am assuming you would have results to show and tell and with a punchline at that. That generally helps.

Your host has a responsibility to make your schedule in such a way that it will be full and engaging.
Sometimes, it can be difficult to fill the schedule - it requires that people respond to the hosts invitations to meet with you. Your input can be helpful both in filling out the schedule and making sure that your visit is productive.
You can request to meet with specific people and ask for feedback from your host on who you might want to speak to.
I think it would be a good idea to request to meet with graduate students in addition to postdocs and senior scientists.

sometimes the opposite happens: and your schedule becomes unreasonably busy, where you are running from one short meeting to another with no chance to sit down for a few hours and talk/explore.


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What do statements of interest, teaching, and research mean when applying for an academic job?
I'm looking at a job application that asks for the following:

C.V. (required)
Statement of Interests (required)
Cover letter (optional)
Statement of Research (optional)
Statement of Teaching (optional)

I find this confusing because I don't understand what a "Statement of Interests" is supposed to be, relative to the others.  Does anyone know what's expected in a document of this kind?  I'm a bit shy to ask the institution in question just yet, for fear that it's something well-known.

It might essentially be what you would put in a cover letter with a focus on why you are interested in the department and who you would be interested in collaborating with on a university level. But this is just a guess.

Are you sure the second item on the list says "Statement of InterestS" in the plural? If it were "statement of interest" in the singular, I might take that to essentially mean a cover letter--a statement of your interest in applying for the position.

That is a rather confusing request, actually. However, what I think the job offer is looking for in a "statement of interests" is a description of the research areas you are interested in, while the "statement of research" would be a listing of projects you'd plan to start if you were hired.
However, in many job postings, those two items would potentially be conflated into a single statement. So I'd recommend that you contact the department. I'd recommend doing this by phone, if possible—that way, you don't have to give as much identifying information.

Generally I agree, but would add that "statement of interests" could be broader than just research interests.

It's also worth considering if they meant that Statement of Interest is what you would like to pursue, given that you have the money and staff; and Statement of Research is after what you have done so far and what you are currently working with, in more detail than what fits in the CV.

The fact that multiple interpretations are possible—and viable—reinforces my main point: contact the department.

Since I assume it is an academic job you apply for the letters will cover aspects of that type of work. The job profile could possibly also reveal how to interpret the requested information. My general advice concerning the confusion is to contact the employer to get additional information (they may also keep such information on a web-page). It seems the instructions are sub-par in this case, which is annoying.
View the CV as the back-bone and the statements as an opportunity to provide some meat.
aeismail has already covered two of the letters/statements well. How the research statement should be interpreted is less clear, but posdef's comment is good because it may concern what you have already done. If it is then it is common to go through previosu research and highlight what you consider are your major contributions out of your production and how you consider your work original and contributing to development in the field(s) of concern. I would strongly advice asking about the focus for this letter.
The statement of teaching is usually detailing your views on teaching. The purpose is to  get a sense of your ideas and understanding of pedagogical aspects of the work. This may nclude techniques/methods you have already used or ideas on such that you wish to develop. It could also include ideas on courses you would like to develop (if you have a sense of your possible coming mandate at the place at which yo apply. If your position is not concerning teaching, such a statement may not be necessary (I assume you received a form letter?). But, if you are pplying for a position which includes teaching then such a statement may be quite important and provide the job committee with a firm picture of your teaching philosophy.


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Why do universities have to spend money on journals?
Obviously this is a question in the light of the recent Elsevier boycott. Currently we do have an arXiv, maintained by academia and where researchers regularly upload parts of their work. In such a case,

Why do universities spend lots of money to publish in third-party journals?

The question especially applies to journals that operate with a rigorous profit motive. The subscription is very high, so wouldn't publishing in such journals affect the paper's citation count and deter the spread of knowledge about the work within academic circles?

Why should not universities collaborate to create free, open access, peer-reviewed journals?

Moreover, given the need to conserve paper, why should journals spend on printing research papers? Wouldn't an online version suffice, as most people use only local computer printouts anyway? In other words, why can't we have a Wikipedia-like system of sharing research knowledge, having properly established standards for such journals?

In my opinion, this question is on the borderline of "not constructive", as the question is valid but the topic is inflammatory. Please ensure that all answers address the directly asked questions and do not veer off into soapbox speeches on "open journals" and whatnot.

@eykanal: I will be happy to edit or have the question edited appropriately. I do not understand for whom the topic could be inflammatory.

The topic of "open access journals" is a hot one, and can evoke emotional responses which often end up lambasting publishing companies. The question as worded is fine, I posted this more as a pre-emptive warning to those answering to stay on topic.

The question doesn't make sense to me as worded.  Universities have to spend money on journals they run themselves, just as they spend money on journals run by other publishers.

@F'x: Splurge: to indulge oneself in some luxury or pleasure, especially a costly one: They splurged on a trip to Europe.
2.to show off. (from http://dictionary.reference.com/browse/splurge)

My edit has nothing to do with connotation and everything to do with meaning.  To splurge is to spend money on things that are not needed.  If you can show me a respected university that does not spend money on journals (thus demonstrating that they are a luxury), I will concede the point.

@DavidKetcheson: My Chambers says "spend a lot of money on" and it is a standard dictionary. I do not think "spend" captures the essence of the question too.

If you ask why universities have to splurge, then you are NOT asking why they have to spend.  It's a different question.  All the answers given answer the question of why they have to spend.  The answer to "why they have to splurge" is simple: they don't.

@Bravo: link for My Chambers?

Please note that the usage "splurge lots of money" is pure nonsense.  Inserting the supposed definition from @Bravo, it gives "spend a lot of money on lots of money".  I am a signee of the Elsevier boycott and I have no beef with any "opinions" expressed here.  I'm just trying to save the English language from a rather unfortunate assault.

@DavidKetcheson: Substituting dictionary definitions directly into sentences does not work always in English. Anyway let us please discontinue undue discussions on this question - I have accepted a worthy answer long time back and that's that.

@CharlesMorisset What do you think extravagant means?  Bravo: do you really believe that "splurge money" makes sense?  I give up.

This is a really big question, which unfortunately has no simple answer.  Some short comments:
Universities have very little choice about subscribing to journals, as long they publish good papers, since faculty need access to those papers to do their research.  The solution has to start on the publishing side.
Collaborating to create free, open access, peer-reviewed journals is a fine idea, but either you need to convince universities to support this financially, or you need to recruit enormous numbers of dedicated volunteers.  (Whenever this topic comes up, someone is sure to point out that volunteers run some free, high-quality online journals.  Of course they do, but the question is how to recruit hundreds of times as many volunteers.)
Printing is a non-issue.  Everything is already available online, with printed copies only for those who want them.
In a mathematics context, see http://gowers.files.wordpress.com/2012/02/elsevierstatementfinal.pdf and http://arxiv.org/abs/1204.1351 for more details.

See also http://blogs.law.harvard.edu/pamphlet/2012/03/06/an-efficient-journal/ for a careful breakdown of the actual (minimal) costs for one high-profile computer science journal.

I downvoted because I think other answers are more correct and because phrase The solution has to start on the publishing side. is wrong.

My take on parts of your question:

Currently we do have an arXiv, maintained by academia and where researchers regularly upload parts of their work.

I may be on something of a crusade against arXiv users who believe arXiv is more than it is, more more widely adopted than it is. "We" don't have arXiv - certain disciplines have it. Other disciplines, equally valid as those which support arXiv, both don't use it and have understandable issues with the reliance on a pre-print site as a way to disseminate findings.

Why do universities splurge lots of money to publish in third-party journals?
  The question especially applies to journals that operate with a rigorous profit motive.

First, they're not paying money to publish in the journals. They're paying money to be able to read said journals. I've published in for-profit journals, even ones my university didn't subscribe to, for free.

The subscription is very high, so wouldn't publishing in such journals affect the paper's citation count and deter the spread of knowledge about the work within academic circles?

Not necessarily. Papers are often available from the author, inter-library loans, etc. Beyond that, how a paper gets cited is a far more complex question than just "Do you have to pay for a subscription", and I don't think Open Access journals have compellingly showed that the citation counts are higher for open journals. The readership and downloads? Probably, but in terms of citation the Open Access journals are still struggling with a perceived gap between their prestige and the prestige of the "leading" for-profit journals. Perhaps that will change in time, but there are ways to get journal articles that your institution doesn't subscribe to, and those ways are often fairly trivial.

Why should not universities collaborate to create free, open access, peer-reviewed journals?

Some do - but for many the cost of laying out and producing a twice monthly journal would be distracting from the core mission of the university (or more likely, particular departments), and they'd run into staffing and budget concerns. Most don't have the money to fund what they actually need to do, let alone add a publishing arm that may or may not ever make money.
And those groups that are interested, like professional societies and the occasional university? They often turn to for-profit publishers to outsource it. For example Epidemiology, a publication of The International Society for Environmental Epidemiology is published by Lippincott. The American Journal of Epidemiology, which is put out by Johns Hopkins and sponsored by the Society for Epidemiologic Research? Published by Oxford.

Moreover, given the need to conserve paper, why should journals spend on printing research papers? Wouldn't an online version suffice, as most people use only local computer printouts anyway?

Because some readers want the paper versions. Seriously, nearly every journal I know has an "online only" subscription for less money. But if you want a paper version, why shouldn't you be able to get it?

"understandable issues" — Like what?

@JeffE An inherent distrust of anything supporters say there is no issue with ;). Less flippantly, the pre-print arXiv system was designed around a core of fields, and makes sense for those fields. But consider a clinical trial - there's valid reason to question whether a non-reviewed, potentially revised result should be made public. Preprints are something of an unresolved issue for meta-analysis as well - preprints are a tempting, but potentially biasing, source of documents. Mainly the issue is that arXiv is an interesting supplement, not a replacement, to journals.

@JeffE Keep in mind the notion of a "preprint culture" where papers are widely circulated before publication - or at conferences before they appear in proceedings - is not necessarily a general mode for academia.

True, but I think it's medicine that's really a special case here, because of the public health consequences of publicizing results.  (I'm skeptical that the meta-analysis issue is crucial, since publication bias is itself a major problem.)  I agree that preprint culture is by no means universal, but this is largely for contingent, historical reasons, and sites like SSRN are expanding rapidly in areas that once had very little of this sort of activity.  I don't think it will ever be fully universal, because of exceptions like medicine, but I think it will get much closer than it has so far.

@AnonymousMathematician Medicine may be a special case, but its a big special case (and its my special case, which means I care). The meta-analysis issue is probably a topic for another day, but the issue is that generally, if you don't think you can draw all unpublished papers, its probably wise not to draw any of them. That's why authors shouldn't use their own unpublished data. arXiv represents a tantalizing source of "grey literature", but especially for non-arXiv dominated fields, a biased one. The summary is that arXiv is neat, and useful, but not a magical fix.

This looks lke an orthogonal issue to me.  I agree that posting pre-refereed papers is not always wise, but preprints can be refereed before posting. (Preprint just means "before printing".)

Unfortunately, biomedical research drives everything.  If we were to have a totally free system for all other subjects, schools would still have to subscribe to Elsevier's Big Deal to get biomedical journals and Elsevier would still charge exactly the same as they would with all the other journals included.  That's how they run their business: you can drop of keep whatever subscriptions you want as long as you pay 6% more than you did last year.

Your second point is false. Page charges exist for some non-open access journals! Some university students/faculty pay this with University money. So some universities pay to publish in these journals. Even if the money comes out of a grant, that money sometimes could have been spent on more research. In such cases the university pays an opportunity cost.

@WetLabStudent Page charges have nothing to do with subscription fees. They may also have to pay to publish in them, but subscribing to them does not "unlock" the ability to publish.

@Fomite I never said anything about subscription fees. You said " they're not paying money to publish in the journals" which is false. Yes these fees are unrelated, but they do exist, despite having nothing to do with journal subscriptions and access. You should edit your answer to indicate that what you mean is that universities paying or not paying to publish in a journal is unrelated to access to reading articles in that journal, rather than saying universities don't pay to publish (which is false).

@WetLabStudent Subscription fees are what universities pay for. I have yet to be at an institution where page fees weren't something born by individual labs.

"if you want a paper version, why shouldn't you be able to get it" => sure: on-demand printing. Why on Earth would the company printing the journal also own the articles, the journal's name, and all intellectual property attached to it?

Nothing actually comes for free.  Expensive journals tend to have established their merit with a long history, and managing / maintaining that quality across decades and editors has traditionally been the job of publishers.  Why?
Although publishing can be a pain, but it is absolutely key to academic progress.  We need to be able to rank contributions if for no other reason than to determine what to spend our precious time reading.  Like all systems with power, publication is potentially subject to corruption.  Publishers are traditionally seen as more objective than authors or universities, since their reputation and income is entirely determined by how good a job they do of publishing selectively.
You could imagine a situation where a bunch of universities got together, dedicated their resources (paid their staff's time) to make an objective publishing system that was not controlled by any one academic institution.  But that is actually what most academic publishers are.  In fact, many academic publishers are associated with individual universities.
The problem remains, who pays?  Currently, in general readers / consumers pay, and they probably are really in the best place to know whether research is worth purchasing. But under open access, the authors pay.  This can actually be immensely more expensive for universities than paying subscriptions, since they produce a lot of research.  For example, my university spends less than the cost of two PLoS open-access articles per year per academic on subscriptions, but most academics are expected to publish a lot more than two articles a year.  The other problem with authors paying is that there is then a moral hazard.  Journals are effectively bribed to take papers, which may result in compromising the selective process that underlies academic progress.  This would be a terrible cost.
Many academics self-publish by putting their papers on line or just writing blogs.  This can be effective, but note that it returns to the problem of knowing what is worth reading.  Generally, successful academic blogs are run by people who also prove themselves as academics by publishing in highly-rated journals, so this is not really an independent solution.
The short answer then is: because paying to read publications is the best system we currently know.

+1, but note that the description of "most academic publishers" here does not describe the biggest ones: Elsevier, Springer, Wiley.

And of course "most academic publishers" is not the same thing as "the publishers of most academic journals."

Another (admittedly cynical) viewpoint is that the reason there are so many journals out there, and so many high-priced third-party journals, is that academics want to publish, and the system in which they work more or less demands publications in exchange for career advancement. The need of so many researchers from so many countries, as well as the fractionation of existing research fields into many sub-specialties, allows for this kind of behavior.
Although I would argue that "splurge" is the wrong word—researchers want access to as many journals as possible, and as a result, libraries are forced to spend substantial parts of their acquisition budgets on journals, which, with policies like Elsevier's, mean many of them will go largely unused in exchange for a handful of high-quality journals that aren't quite worth collectively what Elsevier charges for them.
The solution will be for the university libraries to join forces together and bargain collectively with the publishers. Working individually, they have no leverage. A hundred or a thousand libraries working together will have an impact.

One of the big factors driving the traditional publishing model is the tenure and promotion process. To win tenure and promotion, faculty members must publish in peer-reviewed journals... and journal reputation counts. Thus, many top researchers will strive to publish in journals with high reputation and university libraries will want to maintain collections that feature journals of high reputation (especially if those journals feature the work of its faculty).
Journal publishers point to the value added during the traditional publishing process, including peer review, editing and layout. This argument, however, is controversial, as many editorial and peer review panels are voluntary, unpaid positions.
Finally, electronic journals are not necessarily cheaper than print journals. Often, electronic journals are sold in expensive bundles and libraries are not allowed to select individual titles (this is how, say, EBSCO operates). Thus, libraries have to pay to subscribe to the whole database, which will include journals that are of little interest to the university.

Regarding to tenure and promotion process, I don't see the issue, citation count, H-Index and other metrics can be used.

I strongly disagree with user454322's comment.  Those measures are extremely unreliable when applied to individual papers and individual researchers.

Why do universities splurge lots of money to publish in third-party
  journals?

Because researchers ask for these journals, and the money is given by the university, and most researchers just recently discovered the cost of all this stuff. Now that we are all aware of the cost, and now that universities are running out of money, we, at last, want to change the way publishing is done.

Why should not universities collaborate to create free, open access,
  peer-reviewed journals?

Because to run a journal, you need people whose jobs are to run a journal. This is not the work of researchers or actual faculty staff. At the moment, hiring new profiles in universities is unlikely. Moreover, maybe this should be done at a higher level (funding agency or state level?).

Could you elaborate on the second point? After all even in top journals it is the professors who do the hard work of selecting papers. If no printing is involved, why can't the panel professors decide about the selected papers and simply upload them?

@Bravo: Some journals do work exactly like that—I'm on the editorial board of one—but with a few exceptions, they're slow to catch on.  Perception of journal quality is no more rational and no easier  to change than attitudes about car companies or brands of beer.

You need a website, a server to run the website, a back-office to handle the submissions, at least someone to work the templates and to solve the occasional problems that the authors will encounter with these templates, etc. This is not a big deal, but someone have to do it, and the burden on editors and reviewers is heavy enough.

@Bravo "If no printing is involved" is a big if, and there's matters of copyediting, layout, etc. I've found the help of editorial and graphics departments at major journals invaluable at times, and "just upload them" means at this stage being shackled to LaTeX-type document formatting. I'd rather avoid that. Scientists, brilliant or not, are not designers.

"Scientists, brilliant or not, are not designers." Except in mathematics, physics, and computer science?

It should be noted that ArXiv does not require TeX, you can use anything that can save the document as a PDF. Why should all the papers be slaved to the same format? Similar to presenting a poster at conference, you can focus on the design if you want (or not).

This is a very big, multi-faceted question. A hidden undertone is whether academic publishers make too much money, which is not something I want to discuss in this answer. Some thoughts on the rest of the question:
Do we need journals? If arXiv is so good, do we need journals at all? Can we do away with journals and just have everyone upload their papers onto arXiv? If you believe we don't need journals entirely then we can also do away with most of the publication costs.
arXiv does have operational costs, so presumably there'd still be a small (say ~$10) charge per uploaded paper, which is a far cry from typical OA costs. On the other hand this would be the end of peer review (at least organized peer review), it would make science communication more difficult, and authors from developing countries could really struggle. Whether or not this is worth it regardless is up to your perspective. This is the most drastic option; for everything below I assume "yes we do need journals".
Assuming we need journals, costs are to be expected. Who pays for these then? Realistically there're only a few options:

Authors. This is open access. OA has the fundamental problem of conflict of interest. Since only accepted papers generate revenue for the publisher, the publisher (and by extension the editorial board) is incentivized to accept papers. The COI can potentially be sidestepped by charging a (substantial) submission fee. Is the academic community willing to accept this, knowing there is a nontrivial chance of rejection? I don't know the answer to this; your guess is as good as mine.
Readers, i.e. pay-per-view, if you want to view the paper then you pay for it. This is likely doable but an administrative hassle. It's much easier to log in to your university's library and then access every paper, rather than work through payment every time you want to read something. (Also usage statistics for most papers are very low indeed.)
Universities. This is the current arrangement for subscription journals. A potential cost is that the university also pays for papers that its academics don't read (however you can be sure your library tracks usage statistics, which it uses to decide which journals to subscribe to).
Advertisers. Does not work in practice since demand for advertising in academic journals is too low to sustain the journal.
The general public. This is how things work for non-academic books: the author writes, gets paid a royalty, and the general public pays for the books. The problem with this is that academic papers are pretty bloody impossible to sell to the general public. They're so dense that undergraduates can't understand them, let alone the general public.
Funding agencies. "Someone" pays the publisher, which then operates the journal with free submission and free access. This is the diamond open access model. The problem is who that "someone" should be. If it's a university, then we're effectively back at option #3, worded differently. If it's an academic society, then the question shifts to where they are getting the money from, and likely means they have less money to do other activities like outreach. If it's the government, then unless they put more money into academia, they'll have to move money away from somewhere else, most likely research funding. Is the community willing to take a collective funding cut so there's money to use for this? Again, your guess is as good as mine.

Ultimately, if you can think of a stronger business model, you can put it into practice and it'll probably supplant the former one. The fact that the status quo has largely remained is, I would say, an indication the current business model is the most reliable, however flawed it might be.

Universities do not have to splurge on journals.  If you think your university is splurging, then you must consider journals to be a luxury.  However, a university with no journal subscriptions would not be able to attract faculty or students.

In this answer I tried to describe the main strategies of the Open Access movement.
I would though address few points in your question:

Why do universities spend lots of money to publish in third-party journals?

Fomite says, "First, they're not paying money to publish in the journals. They're paying money to be able to read said journals.".
This is an important distiction.
Why universities don't always publish journals (not necessarily OA, for that matter) is more of an organizational issues. Not all departments have time and resources to do teaching, research and also publish peer reviewed journals.
Many do, now, also thanks to free software like Open Journals System(as a mere example, these are the open access journals I used to manage for University of Bologna).
Peer-review is a crucial point here.
The self-archiving strategy of publishing pre-prints in repositories like archive is very important for OA, but doesn't address the need of a validation of publication. The only decent system that academia has found to evaluate publications is the review of its peers (there are also scientometric indicators like Impact Factor, but they do not substitute peer review).

Why should not universities collaborate to create free, open access, peer-reviewed journals?

Why shouldn't they? No reasons, if you ask me.
But read this great joke from Scott Aaronson.
Collaboration is the most crucial issue here.
Academia is a highly competitive social structure. You compete for your PhD, for grant research, for tenure, for gear lab, for everything.
I'm no expert in "history of academia", but I do know that different disciplines (aka, different communities) have different attitude to collaboration.
And I'm merely thinking about scholars collaboration between themselves in writing articles or doing research.
When you need a particle collider in order to do research, you are in the need of different scholars, different universities, different nations to collaborate at very different levels. This is the main reason, for example, why the field of High Energy Physics is one of the most advanced in Open Access (i.e. "SCOAP3 is a partnership of thousands of libraries and key funding agencies and research centers. Working with publishers, they converted key journals in the field of High-Energy Physics to Open Access at no cost for authors").
Collaboration is difficult, and it is not what academia is doing best.
Academia is a very complex social and economic structure. You cannot fund a system in competition and then ask the same system to set up an mass-scale collaboration to take over the publishers that took advantage of the scattered monadism of academia in the first place.

Publishing journals costs money.  If a university publishes journals itself, it bears the direct costs.  If a university subscribes to journals, it pays for those costs indirectly.  Either way, universities must spend money on journals.
A discussion of why universities pay fees for some journals that are much higher than what is required to run the journal would be useful but not in the scope of the question as written.


text:
Apply to PhD after expulsion from another
I was in a math PhD program for one year during the 2009-2010 year in US (with funding by school). I was expelled due to low grades (nothing related to violence/cheating). During the Fall of 2010, I took some classes at a local university and applied to Master's programs during that time. I went to a Master's program in math in Canada from 2011-2013 (currently there).
My plan is to apply to top PhD programs in the US in math this Fall and enter at the Fall of 2013. I have a 4.0 Masters GPA, >95% GRE math scores, publications, and excellent relations with Master's advisors. I have developed great focus and motivation and have rid myself of procrastination which plagued me the past. I am also sure I want to continue doing mathematical research.
I am sure that when applying to PhDs, mentioning the expulsion from years ago will only hurt me so I intend to not mention it (I have not told anyone about this either). My question is if PhD programs will discover this hidden information when I apply? What if when I apply for fellowships?

Was it technically called "expulsion" or were you "asked to leave" or "not allowed to continue"? Expulsion sounds rather extreme, whereas the others don't have the same strong connotation.

I would strongly recommend mentioning it briefly somewhere in your application, with a very short explanation of why it is irrelevant (for example: you were less mature and motivated, so you procrastinated and your grades suffered, but your performance over the last few years proves that these issues are no longer a problem).  Don't emphasize it too much, but your best strategy is not to hide anything.
You are right that it might hurt your chances, but I do not think it will hurt them much.  If it came up in a committee I was on, I would argue against worrying about it, if the rest of your application was compelling.  If you do not mention it, then you'll have an unexplained gap of a year in your CV, and that will also raise suspicions, since such a gap is usually a sign of something that did not work well.  If you don't want to mention it or have a gap, then the alternative is lying.
You should definitely not lie, by giving an incomplete list of previous schools attended if asked for a complete list, or by giving a different explanation of what you were doing during that year.  You might get away with the lie, since it can be difficult to detect missing information or disprove vague excuses, but if the lie is detected then it will ruin your chances of admission.  (And committee members might even mention it to friends at other schools, if they are irritated enough about the lie.)  Even if you get admitted, the lie may also come up again to haunt you in the future.  For example, a faculty member from your old school may someday visit to give a talk, recognize you, and mention the connection to your advisor.  Or you and your advisor may someday end up attending a conference at that university.  You probably won't get kicked out of grad school if the lie is discovered later, but it's technically possible (at least at some universities), and in any case you do not want to be known among the faculty as someone who lied about his/her past.
You've already done the hard part of moving beyond this issue and demonstrating that it is no longer a problem, and that will minimize the risks of honesty.  By contrast, the risks of dishonesty may follow you for years.

Once again, this answer pretty much says it all. The best strategy is honesty—although downplaying it would also be a good option (don't dwell on it, just state that it happened, won't happen again, and move on).

If I was a Federal Title IV Financial Assistance recipients during the 1st phd, will them knowing affect the possibility of me being funded since there is also a federal component and not just the school?

@user717: Sorry, I don't know.  My guess is that it wouldn't hurt you, but I really don't understand the technicalities of these programs.  (Under some circumstances, withdrawing from school requires you to pay back some of the financial aid or loans you were given.  I don't have a reason to think it eliminates future eligibility, but I have never looked into this.)  I'd be very careful with this: you really don't want to get in trouble for fraud with federal student aid, which is much more serious legally than what you tell the university.

I think if you owed anything in the past, they would have told you, so you should be safe there.  The fraud issue would be if you apply for financial assistance without mentioning this and end up getting funding you aren't eligible for, and then the government discovers it later.  (I don't think this is a real concern - as far as I know, there is no eligibility issue in the first place - but there is no sense in taking chances.)

Got cut off before finishing above.
I was not told to pay anything back. I hope I don't get into trouble for fraud; I never had any intention of going down that route.
But if I were to mention the expulsion in the statement of purpose, how should I phrase it to best downplay the past(i.e. what kind of reasons are considered least severe). I heard online somewhere else that one should never mention negative events or just the bare minimum if required(e.g. send bad gre score but no explanation of why) even if they were beyond my control.
Thank you for your advice.

As for how to downplay it, I'd recommend listing the school you attended for one year in your CV (but you don't need to go into detail there about what happened or why you left), and putting two sentences in your statement: one that explains that you left because of procrastination/poor grades [or whatever], and one that points out that your track record since then proves that these issues are no longer a concern.  I'd avoid putting this at the beginning of the statement, which would emphasize it, or the very end, since the end may stick in the reader's head.  Somewhere in the middle is good.

If the faculty do not know about it at my current master's program, is it best to not tell them now?

You also don't have to say explicitly that you were expelled.  For example, you can say something like "You'll see from my CV that I studied for a year at X, before leaving when it became clear that I was not yet ready for graduate school.  I took a few courses at Y to strengthen my background, and then I entered the master's program at Z, where I have received excellent grades and published several papers."

I'd suggest giving anyone writing a letter of recommendation a copy of your application materials.  People at your current school may learn about it from that, but I don't think it will be a big deal.  (If you just left it off your previous application, without lying about it, then don't worry.  If you told them something that was explicitly untrue, then you'll have to figure out how to handle that - for example, then it might be easiest just not to give them that information.  But one advantage of mentioning it briefly on your next application would be never having to worry about this again.)

I completely agree that you don't have to go into details. Just mention very briefly that you did a phd for one year but you were not ready for it so you decided to strengthen your background and lay a good foundation for a good phd program and you're ready and highly motivated now. Only go into details when someone asks for them. And try not to focust on that fact. Sometimes when we know something, we think,  that others are also focused on that fact, but frankly nobody cares that much. So, leave that behind but simultaneously be honest.