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Publishing a comment or contacting the authors privately?
I have just read a recent paper in a well-respected journal. The work is technically sound and the results interesting. However, the authors comment their main results as unexpected and “extraordinary” (in the abstract and in the text), while it is an instance of a very generic and well-known phenomenon, which has been experimentally confirmed (and theoretically explained) in a large range of systems in the last decade. The author do not seem aware of the literature on this phenomenon.
Now, I am somewhat conflicted between two courses of action:

Raising the matter with them privately, making them aware of the literature they have missed so that they do not repeat the mistake, and telling them (nicely) that their claims of extraordinary behavior are not valid.
Doing the same thing, but through a formal “Comment” published in the same journal. This does not only bring the matter to their attention, but also to other readers of the journal. Right now, I favor this option, because I think it improves the scientific record.

The journal in question does publish comments, its policy on the matter is the following:

These are a medium for the discussion and exchange of scientific opinions […] For publication of a Comment or a Reply, they must be judged by the referees to present new insights and be of interest to our readership.

Moreover, a Comment in the journal will necessarily include a “Reply to the Comment” by the original authors, as per journal policy.

So, how do I choose between contacting the authors in private, or submitting a formal “Comment” to the journal? What factors should guide my choice?

@CharlesMorisset a formal Comment in the journal will necessarily include a “Reply to the Comment” by the original authors, as per journal policy. I will add that to the question.

@F'x there is also option 1.5: put the comment on your blog. This way your insight is not locked in email, and you promote open science.

@ArtemKaznatcheev I don't have a blog, and even if I had (or if I upload it to my website), the readership would be much smaller than that of the journal itself

I believe that these two choices are not mutually exclusive.
Authors should be given the benefit of the doubt. Contact them privately first, to see if they are aware of your concern, and if so, whether they have a reasonable response. You should say, in that first contact, that you think it's enough of a concern that you're preparing a formal comment to submit to the journal. Perhaps it's a bit too nice, but I would rather be allowed the opportunity to publish my own comment or even a retraction, rather than being publicly "called out" without warning.
However, I believe that if your faithful attempt to privately contact the authors fails—if they do not respond within a reasonable amount of time, or they blow you off without a satisfying explanation, or they say that they'll do something but don't—then you should move onto publishing a formal comment.
I agree that something needs to be put into the public record, and the sooner the better, but it doesn't need to be so quick that you don't even attempt to contact the original authors. Everyone should get the benefit of the doubt.

There is nothing stopping you from contacting the authors directly. In fact that might be polite. It may, however, be unfruitful. Submitting a comment is not considered less polite than contacting the authors directly first. Remember, the authors have, in your view, published poorly referenced/researched work (reviewers and editors are partly also to be blamed). By writing a letter/comment, you perform a scientific debate where you wish to correct a problem with said paper and that is clearly within the realm of what we can and should do as scientists without feeling impolite.
Before you do anything you should perhaps solicit colleagues to discuss the matter over. Since the results have been published, some form of publication discussing the problem must also appear in a publication. It is for this reason you should carefully discuss the matter, start writing a "letter to the editor" of the journal where it was published. The letter should contain the information that puts the "novelty" in perspective. Under such circumstances the authors will have the possibility of a rebuttal which typically is published at the same time as your letter, it is their opportunity to "defend" themselves. This is what typically is done.
Now several things might happen, for example, the authors get angry, the editor refuses to publish your letter. This is why you are better off not being alone behind anything you write. If the letter is refused, then publish it elsewhere. But, remember, the point of writing a letter is to set the faulty perspective of the paper in a more correct one so that the paper is not taking credit where not credit should be had. Do not stray from this endeavour.

I'll add here, for the record, what I ended up doing. After reading the advice here, and discussing with a few close colleagues, I decided to write and submit a comment, without first discussing it with the authors.
The reasons behind the choice are the following: I assume good faith on their part, and that they simply didn't know that the phenomenon they observe, and which might seem counter-intuitive, is actually a specific manifestation of a quite common behavior. They didn't know the literature well enough, or didn't realize it; at least two reviewers also didn't realize that. Thus, it is really good to “educate” the community on this, and publishing a comment in the same journal appeared to be the best aim to achieve it.
The reason I didn't contact them privately first is two-fold:

They will get the well-polished comment for them to reply, through the editor. A journal editor who is a friend of mine suggested that she (as editor) would prefer to see all communication go through her, rather than come at a later point and have to “referee” a dispute he hasn't seen half of.
If I wrote to them first, and they then wanted to write a correction to the paper themselves, I couldn't be sure exactly what they would say, and my message as relayed by them could be less clear than what I intended to say.

+1 For having asked the opinion of an editor.

I would advice you to be careful. Not citing other sources is quite common in the academia as a mean of making your result look more innovative, more important, and more appealing. Then, if you tell these researchers "Oooooh,  I know your dirty tricks!" (even if you do it in a polite way), they might feel offended and could probably take revenge when they come across one of your manuscripts as referees.
I understand your frustration since I often come across papers like the one you mention, written by reknown researchers and published in important journals, while they are basically reinventing the wheel. I have also come across papers where the authors do not cite their previous extremely related papers. C'est la vie.

What you describe is academic dishonesty, and (at least in my experience, in my own field, in top venues, etc.) is not very common in the blatant form you describe. At the very least, I would not at first assume that this is what was going on, but rather that the authors' were genuinely unfamiliar with some relevant literature.

@Aaron I would be very surprised if there is an area where this doesn't happen at all: Lima beans are cooked everywhere. But I am glad to see you still have hope for the human race.

I have no reason to suspect that it is done in bad faith: this is a decent team from a related field, and as far as I can see this paper is their first in my own field.

In a top journal of my field, note citing related work will soon be discovered either by referees or other peers, in more than 50% of cases.

authors: Алексей Демидчик


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What to do with papers after misconduct allegation was resolved?
I was alleged in scientific misconduct in form of authorship abuse. More details are in my previous questions
How to respond to allegations of misconduct in authorship dispute?
Should I put my supervisor as coauthor of a paper?
The good news is that the investigations have ended in the inquiry stage (the dean have informed me by email).
There are several probable reasons why they have stopped:

The article was indeed done with different methodology, which had nothing to do with the approach described in the grant application.
At the interview I have revealed several facts of abuse, namely I was ordered to work on the projects not connected to my funding project.
They are afraid I could become a whistleblower.

After receiving the confirmation from the dean, I immediately informed the editor of the journal. Unfortunately, the editor rejected the manuscript, stating that:

This is useful information for us, but the question before the journal is not one of personal scientific misconduct, but rather whether the authorship on the paper is the correct one, and whether we should proceed with the external review process, which may lead to its eventual acceptance and publication.
Based on the information available, we have decided not to go further with the review of your manuscript.  There are still significant concerns being raised about whether the manuscript should have been submitted with its current authorship, and we do not believe there is any clear path to removing these concerns.  The scientific reviews we have received are mixed and would place the manuscript in an unclear position regarding acceptance or rejection based on its content.  These two factors together give us sufficient cause to issue a rejection.  Because the manuscript did not reach the publication stage, no other action is necessary, and we would like to also consider the case closed.

My questions are:

Should I try to resubmit the manuscript as is into some other journal; should I redo all the calculations, reanalyze, and rewrite it first; or should I just abandon it?
I have another manuscript, for which my ex-supervisor sent me an email stating that "he assumed that I was going to publish it by my myself", in spite of the fact that he supported me. This seems to be the evidence that he resigns his authorship. Should I try to publish it also?
Can they reopen the misconduct case if they would like to do that?

If you would like an academic future, you should ask these questions your (former?) PI, and do your best to make up.
Some answers to related earlier questions you asked gave you advice that saw this only from a David taking on Goliath perspective, and wrote what I felt would only further egg you on. With additional information added in the newer questions, however, you really found yourself in the extremely rare case of your PI taking action against you at your own school. It is time to stop acting on guesses and interpretations, with some Internet forum feedback. You need to get a clear answer from that PI, ideally in writing: for 1 and 2, ask if this means he agrees you can go ahead and submit the 2 papers under your single-authored name?
However, that isn't what I would do. 2, at least, could be read as a conciliatory outreach by your PI: I assume you want to publish this by yourself? (...but do tell me that no, you would like to go together).
Even if that is not true, publishing something (anything) with your PI now matters more than a publication by yourself. You write they are "afraid" of you. They are not. Whistleblowers (if you even could blow a whistle) are a nuisance and embarrassment, rarely more; and in the cases in industry I know of (a friend was a fairly high profile one in banking), they eventually only come back to bite the whistler. It may take years and seem differently; but they eventually do.
Justly or not, the whole incident reflects poorly on all participants (a petty adviser; and a student setting off a petty adviser). For an academic future, in all cases I am familiar with you need your adviser's support. You had a falling out; you should try to mend it. The situation will not help the PI to recruit in the near future; and how are you going to get recommendations that matter? You both have an interest in making up: that is what you should focus on. It may be hard, it may be impossible; but it doesn't seem that you have tried, or tried hard enough. It's your life and future, and phyrric victories and a single publication don't matter in the big scheme.
If you really just want to know if you can ignore all this, and publish alone  based on that email and the result of the proceedings: I find it risky, but not very so as there is no way your PI is going through with another case...at least it's extremely unlikely. But I don't think that's what will serve you best.

+1 This. Sharing co-authorship on the paper you worked together should be the first step on mending your relationship with your supervisor. You messed up and so did he. So, although you will never be friends again, there is no need to be enemies either.

You should probably continue trying to publish it.  Presumably the results will be useful to somebody, and it will help your career.
Probably, but you should ask for explicit permission.
Surely this depends on your institution's policy.  Ask the dean.

If I were in your place, I would seek to repair relationships and maximize the number of publications.

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When should one include the proof of known results in a mathematical PhD thesis?
When writing a PhD thesis on mathematics one needs to quote many results by others, such as

The following theorem was proved by ABC in [1].
Theorem. Bla, bla, bla...

My question is when should one include a proof of the result in his/her PhD thesis, if it is basically the same as in the reference? I do not quite see the point of copy-pasting the proof by others. Of course if one has a completely different proof of the same result, it is probably suitable to include it.

A comment rather than an answer due to a physics perspective.  Some factors to take into account: How well-known are the theorem and the particular proof? How fundamental are they to your thesis?  Is it possible to summarise the proof (e.g. by reference to a better-known proof which was built on to do the bit you're interested in)?  I assume your supervisor will read the thesis and comment (the approach will of course vary between supervisors) but they are best placed to help you answer this for your specific case.  However you may as well do it especially if you cut/paste LaTeX a lot.

As a general rule, you can cite other people's theorems without explaining their proofs, and omitting a proof is a good idea if it would be a lengthy distraction.  However, there are several reasons why including such a proof could be helpful:

Including it may be convenient for the reader if the proof is short.  It's annoying to look up another paper and discover that you only needed a short argument that could easily have been explained in the original paper.  Extracting information from a reference can be cumbersome (you have to locate exactly what you're looking for, figure out what it depends on, sort out the notation, etc.), while giving your own explanation can help readers avoid some of these difficulties.
Even if the proof is not particularly short, it may serve as a warm-up for new applications of the same techniques.  Reminding the reader how they work may make your paper much easier to read than if you just dive into the newest and most complicated case.

Ph.D. dissertations are something of a special case, because your advisor may encourage you to include extra details in the background sections (beyond what you might include in a published paper).  This is partly a matter of demonstrating your mastery of the area and partly a matter of writing a useful survey for others.  Advisors differ in how they approach this: some think it's a waste of time and it's best just to focus on writing a published paper, while others think writing a more extensive dissertation is a valuable learning exercise.  This is an issue you should discuss with your advisor.

Thank you for your detailed answer! The information is very helpful. Usually a mathematical PhD thesis is over 100 pages long. I am curious usually what percentage of a typical thesis is "non-essential"; that is, containing definitions, results with or without proof by others, etc.? Of course the answer could be "it depends"; but I am looking for a general (unwritten?) rule.

Unfortunately I don't have a good feeling for this ratio.  Besides including more background and more details of new results, theses can also be longer because of inefficient formatting required by the university.

One of the things that commonly comes up in papers that I review is that the graduate student author has written up a version of the research for the thesis that has way too much background (such as proofs of previously published theorems.)  It may be appropriate to include these in a thesis, but they need to be edited out before submitting the material for publication as a paper.

You need/want to explicitly use/cite elements from the proof somebody else write, e.g. like "With c as defined in the proof of..." or "with a similar argument to ...".

@Zuriel Definitions are not "non-essential", unless the definition and associated notation are so well-known that the great majority of your readers will already know it. (For example, many papers redefine treewidth, to establish the notation that will be used.) If the definition is short, it doesn't take much space to repeat it; if it is long, you should include it because you can't expect your reder to remember all that detail.

@Zuriel To add to what David notes, many "well-known" notions are defined in many different ways in different sources, so you want to note which variant you use especially for these.

Thank you @DavidRicherby for your comment! I should have clarified a bit: by "non-essential", I mean those concepts and results which are already known. Basically I was asking what ratio of a PhD thesis in mathematics is the authors' original ideas, theorems, propositions, proofs, examples, comments, etc.?

Excellent answer. I think there are two main reasons for including a proof (or a summary of a proof) of previous work: (a) because the reader will have difficulty understanding your own original work if they are not familiar with this proof; (b) to demonstrate that you thoroughly understand it. For (b) you need to include some analysis or criticism or paraphrasing of your own. The occasional comment like "Note that X has made the unstated assumption here that N is finite", or an observation that the terminology differs from that of another author, can help to demonstrate your understanding.

This is a good question, and as Anonymous Mathematician indicates, it is well worth discussing with your advisor.
Essentially what you are asking is whether and when to include exposition in your PhD thesis.  The answer is that it is rarely strictly required, but it is often expected, in many cases encouraged, and in some cases not necessary.  There are a lot of nuances here and I don't foresee a comprehensive general answer being possible.  (Anonymous Mathematician's answer is excellent, and I am essentially corroborating it.)
Mathematics has a proud tradition of PhD theses having significant expository content.  (In my thesis, Chapter 0 is expository.  It occupies about half of the thesis.  This is a bit on the lengthy side, but not so unusual.)
One reason that this is done is because a PhD thesis is usually the last chance that your mentors get to lean on you and require that you show your mastery of highly difficult, technical concepts.  When I am a committee member on a math PhD thesis, I generally want to see at least enough exposition to convince me that the writer has mastered the concepts, definitions and objects used in the thesis.  Especially, I want to see key definitions in a lot of detail, even if they are long and taken from other sources.
Another reason this is done is that the cultural standard in mathematics is that PhD theses can be significantly more discursive than published papers.  When a PhD thesis gets converted to a paper, often there is a compression of 2:1 or more in terms of the page count, and often the results that appear in the paper are stronger than what appear in the thesis.  (In mathematics, I gather unlike some other fields, one most often publishes the lion's share of one's thesis work after completing the thesis, not before.)  Something's gotta give, and often math papers published in the strongest journals are written so that every single page contains an important new idea or truly difficult calculation.  This density of content is a point of pride of the top journals, but it can make the papers awfully difficult to read.  A lot of theses are famous for being the best sources of exposition for the topics they contain.
Having said all this, it seems clear that little value is added by "copy-pasting".  Taken literally: copying lengthy proofs verbatim from other sources would be plagiarism if carried too far.  Most exposition in a PhD thesis is filling a gap in the literature, not reproducing it.  Good exposition synthesizes several sources, offers new perspectives (including a bridge to the novel results, as AM mentions), chooses notation and hypotheses in a globally appropriate way, and so forth.
Finally: formal proof is often the least important part of good mathematical exposition.  Getting the definitions and statements just right and putting them in context is more important.  Most contemporary math PhD theses build on significant technical foundations, not all of which the student is expected to be personally conversant with.  A PhD thesis is not supposed to be "logically self-contained" in any formal sense, only to demonstrate mastery in the eyes of the committee members and to be a useful document for the reader in the eyes of the advisor and (most importantly) the writer.  If you are thinking of more or less copying a proof "for completeness", that may not be the way to go.

Generally, you should only need to reproduce the proof verbatim in cases where you need to dissect it, call out one part of the proof in particular, or you intend to extend it directly using similar arguments, otherwise, stating the theorem and citing a work where it is proved should be sufficient.

I don't see any reason to copy a proof found somewhere else. I think its fine to say that this result and its proof can be found on this article. In my opinion, the proofs in a dissertation should be your own.

Since you are just stating your opinion, could you tell us a bit about your background and experience with math PhD theses?

I don't have any. I have discussed people with PhD and they have been said that in every scientific papers you should put only new results that has not been done before. Otherwise it is plagiarism.

A PhD thesis is not quite a scientific paper, and the standards for how much exposition to include are variable.  More to the point, there are many circumstances in which scientific and mathematical papers contain results which are not new and/or due to others.  If you think that this is (inherently) plagiarism, you have a significant misunderstanding of this important concept.  I recommend that you discuss this with your advisor.

I didn't say that one's dissertation can't contain results found elsewhere. Of course you can, otherwise you can't really do mathematics. But I would not copy a proof found in elsewhere.

Restating somebody else's proof in your own words is not plagiarism. Nobody here (I hope) is recommending copying the proof verbatim from somebody else's paper. The OP says "basically the same", which I interpret as meaning not the same words, but the same basic mathematical argument.

@PeterShor Actually, there are plenty of circumstances in which a verbatim copy, properly acknowledged, would be reasonable. But I agree that, in the majority of cases, a paraphrase would be more appropriate.

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Must graphs in a mathematical PhD thesis be drawn nicely?
I am writing my PhD thesis in mathematics and there are several graphs to be included (on knots, braids, and other related objects). I know that there are several software available for drawing graphs like this, but I am not experienced with any one of those. Also I do not have much time to learn a new software to draw graphs. I have asked a related question before but am frustrated by the time that is needed in learning the drawing software. Am also considering using hand-drawn graphs.
My question: It is generally a requirement for the graphs to be drawn very nicely in a mathematical PhD thesis? (I know that different universities have different rules and here I am asking about the general principle.) Is it generally considered acceptable if I draw some graphs by hand, scan them and include them in the thesis?

Ask your advisor. Look at other theses in knot theory. Look at papers. If I was on your committee, I'd want them to be drawn by a computer not by hand.

Yes, I agree that all graphs in the papers/books that I have read in knot theory look like that they are drawn by a computer, except those which are written dozens of years ago. My difficulty is to learn drawing graph in very limited time.

As Bill Barth said, you need to ask your advisor.  Maybe he/she will be happy with hand-drawn knots, or have some advice about how to produce computer-drawn figures more quickly.  But if your advisor feels strongly that the figures should be computer-drawn, then it doesn't matter what random people on the internet tell you.

PhD thesis is your work, and you are supposed to make the decisions, both on research and presentation sides, and take the risks.
However, in my opinion, a nice picture produced by hand is much better than an ugly and unclear picture produced by a (badly used) computer software.

@NajibIdrissi, I didn't know this! How to retrieve the source?

If you're using LaTeX you can have a look at the packages knots, braids and pst-knot.

@MassimoOrtolano, I assume that the name of the knots and braids packages are self-explanatory. What is pst-knot for?

@Zuriel: It is also for drawing knots, but it is based on pstricks instead of TikZ.

@MassimoOrtolano, the graphs that I wish to draw are closed related to braids (see this post) but not quite the same. In this case, will those packages help?

Yes, I think so, especially the package braids (have a look at the doc). Moreover, you have the power of TikZ to modify the diagrams according to your specific needs. The learning curve, however, might be a bit long, but that depends on your LaTeX skills. To shorten the learning curve, you can start from a given example which is as close as possible to the simplest curve you need to draw.

Many thanks again @MassimoOrtolano for thy kind assistance!!

@MassimoOrtolano, do you happen to know how to draw a braid with n strands for general n (with \ldots or \cdots) with the braid package?

Unfortunately not, I haven't used those packages myself. Moreover we would be off-topic here. But if you start modifying a simple example, you can surely find help on TeX.Se.

@Zuriel On the arxiv page, go to Download → Other formats → Source → [Download source].  The file type is probably tgz, so you need to extract it.

Thank you everyone for all the suggestions! I have finally decided to ask my girlfriend to draw the graphs with inkscape for me and I will do the dishes instead.

Even if it's not a formal requirement, consider how important first impressions are. People will judge a paper with sloppy diagrams, and assume that the results and writing will also be sloppy. This is especially true for a PhD thesis. Since you've had 4-5 years to work on it, people will assume that a thesis is well-written and every aspect carefully planned. That includes the figures. A thesis with hand-drawn figures will not be seen as professional.
I personally recommend Inkscape for drawing things. I think it's easier than Illustrator. I believe for my undergraduate thesis I picked up most of the knowledge i needed in 2 hours of watching Youtube tutorials and trying them out. Fortunately, math diagrams usually only require knowledge of the most basic tools in a program.
If you are truly desperate, I believe it is usually acceptable to pay someone to take your pencil drawings and turn them into professional ones, as long as you give proper credit (check your university guidelines though). There is probably an undergrad at your university with experience in Inkscape or Illustrator who wants to make some extra money.

Hand-drawn does not equate sloppy (see e.g. this paper), so they may be an option. However, in most cases, computer drawing may be more time efficient to get good (enough) results, especially when there are done in bulk.

@PiotrMigdal While it's certainly possible, it takes a lot more skill to make excellent drawings by hand than with a computer. It's also more acceptable for established researchers like Penrose to not follow the standard (which computer generated images are).

@PiotrMigdal Sure but that paper is nearly 45 years old and, in those days, producing anything other than hand-drawn graphics basically involved hiring a professional to do it for you. Hand-drawn graphics (and even hand-written equations) were very much the norm in those days.

What about matlab? Its really easy to draw graphs using vectors. I am not sure what graps we are talking about but matlab can do 2d, 3d plotting.

@Kyslik Not those kinds of graphs :) In this case it's knot diagrams, which I don't think can be drawn with MatLab.

Since I'd hope that the OP is doing their Thesis in LaTeX since it's in maths; they might want to consider TikZ or one of the other LaTeX drawing packages as well.


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Maximum number of citations per sentence?
I'm working on a literature review for a masters thesis in the sciences, and I have a ton of sources that cover the topic.  Many specific points are covered ad nauseam, and many similar ideas can be cited multiple times.  My question is how many is acceptable?  Is there a general rule for citing sources per sentence/idea?  Does more look better?  Basically, is there a limit?

Once sentence in my PhD thesis has 19 citations; the corresponding sentence (also the first sentence) in the journal version of that chapter has 21 citations.  In retrospect, that might have been a little excessive.

I don't think I have near 19 or 21, but I know one has 9...  That work has been done independently in replication by 9 different sources, and they all came up with the same conclusion.  I thought that would strengthen my argument, but just want to make sure I'm not going overboard.

The short and somewhat unsatisfactory answer is: enough. There is no formal limit but obviously too many becomes impractical. If you can reference a huge number of references for a single statement (sentence) it is normal to pick one or possibly a few by using a format indicating these references are just examples:

(e.g., Smith et al., 1943; Turner and Anthony, 1963)
some statement by, for example, Smith et al. (1943) and Turner and Anthony (1963)

I am assuming Harvard style formatting in these examples.
Exactly when it is reasonable to show examples and when one actually have to show al references is a matter of context. If you, for example, have a series of references that together build up some matter and where none is more important than the other and none summarize the other, it could be necessary to list them all regardless of how many there are. I suggest you try to look at a number of different papers of a similar type (literature review) to the one you are writing to see how others handle such instances. You should also look at other masters thesis if you have the possibility.
The main point of this is to know when it is sufficient to list only (good) examples rather than all possible references. This is of course a matter of training and learning to assess when which format is appropriate. It is therefore necessary to assess when papers simply duplicate each other (from whatever view point you reference) or when  they each contribute something unique that merits their reference.

And to add to Peter Jansson, don't over do it. A literature review in an article is meant as a general reference, so the reader can get "up to speed" in the state of the art of the topic under discussion. In your thesis, you have to show that you are able to search the literature, you understand it, and are able to extract the important information.
If you put every single article, you are not fulfilling any. On the one hand, the reader will not know what are the most relevant articles for your work. On the other front, anyone can get all the articles published in a subfield in the last couple of years and write a sentence, based on the abstract and the figures, in just a few days.
In short, show that you have comprehended the literature by finding the most informative subset of articles.

While the referenced literature can certainly help to get the reader "up to speed" as a nice side-effect, isn't the primary reason for references to support one's statements? Following a rule of thumb like "Every statement that is not common knowledge is a claim that must either be proven in the article or by a reference." leads to including rather more references than less. Also, when reading a paper, I rarely look into a reference to understand the paper, but rather to understand or get more info on a particular detail mentioned in the paper - only referencing papers that are ...

... "on-topic" of the particular focus of the paper would not fulfil that goal.

@O.R.Mapper in the introduction there are few claims regarding the actual results. From the first paper on my desk: "We are studying this, that appears a lot [1,2,3,4]. Other people have tried to study this [5] or that [6]. The best attempt so far [7] does this and that, but fails when this happens [8]. We overcome these problems using the following strategy". Later in the article, there are other cites supporting claims "we used a=3.3 (developed by [16])", but outside the literature review.

Besides whether or not the citations themselves are necessary, it's also important to consider how they affect the flow of your writing.
If it is actually necessary to cite all those papers (see Is there such thing as too many references for one paper?, as well as the other excellent answers to this question), it would look much cleaner to place the citations in a footnote (especially if you use the author-year rather than numbered style).
If you use numbered citations and LaTeX, the sort&compress option in natbib can reduce clutter by citing a range (ie [7-16]) of sources rather than [7,8,9 ... ]. However its effectiveness depends on how your bibliography is ordered.
If you must cite many papers in a single sentence, you should at least make every effort to ensure it reads fluently and that the citations do not distract you from the main text.

Clutter was another thing I was worried about.  I'm using Zotero to manage my sources, and using Elsevier Harvard as the style.  I'm not averse to other other styles though, I just don't know them well, especially numbered inline citations...

@Krezyle If you use LaTeX to typeset your work, you would probably be better off with the more advanced biblatex package and biber frontend. There are usually packages for the most common citation styles already, for example here

That looks great, and I'll have to check it out!  I'm already waist deep in my thesis, but that sounds like a good switch for future work...

Some more concrete thoughts (background is biological sciences):

A "particular point" may be covered ad nauseum in backgrounds and introductions of papers in the field, but where did that idea originate?
Cite review papers sparingly. I generally cite reviews only when pointing out that there's a tangentially related body of work well covered in someone else's review.
The only time to cite MANY sources for a particular point is when the point is (or is considered) controversial.

Point 3 reminds me of grant applications. "The development of this has been considered a cornerstone for the field [1,2,3,4,5,6]". Another reason to cite two works may be if they use completely different methods, but agree on the results (e.g.: one does a mathematical derivation from first principles and the other uses machine learning to infer it from the data).


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How common is it that professors have their students write textbooks?
I keep hearing my teachers (high school and college) joke about how professors make their grad students write parts of textbooks for them.
For example, one high school teacher picked up a history textbook and joked that Spielvogel (the author) just made his grad students write all 1000 pages or so.
How common is this practice? Does this even have a grain of truth?

Why do your high school teachers have grad students?

Some used to be professors.

Exploiting their grad students might be why they are now teaching high school.

@RoboKaren now, I only wish exploiting grad students were enough reason to get them fired...

Yes, it does happen. It prompted me to ask the question, Why do universities support faculty writing textbooks?

The one case I know of where a graduate student helped write a textbook, he got his name on it as coauthor, gets a portion of the royalties, and got an academic job at a good school which cares about teaching. Not a bad outcome.

It certainly does happen in my university.

Still not clear what is being asked. Are students being told to write textbooks, or write stuff that would be the stuff of textbooks?

@Compass - edited to clarify.

Got it. I doubt professors can force students to write the textbooks (conflict of interest-y). I'd believe it'd be more of an "If you want to" thing.

Amongst the number of professors I have known who wrote textbooks, I have never known this to be the case.  Of course, I have only a small sample...
I have however, known professors to trial run their textbooks on the students in the appropriate class.  I would consider this entirely reasonable and appropriate, as in many cases it would probably be more accurate to say that, in fact, the textbook is a condensation and evolution of the lecture notes of the course that the professor has been developing in any case.

often, in the preface of the textbook, the author is thanking and crediting people who helped in the preparation of the work.  this includes editors and copy-editors, graphics people, and the like.  also, i remember reading, the prof thanking grad students who have worked out solutions to textbook problems at the chapter ends and solved problems/examples inside the chapter body.  sometimes these grad students find out that the premise to a problem is flawed or that a previous answer was mistaken.

Students can often point out errors or unclear passages in professors' notes before the notes become a textbook.  I would expect that, if a professor plans to turn his notes into a book, he would encourage students to point out anything in the notes that could stand improvement.

I can't provide you with general statistics on this, but I can relate what I have seen. In my undergrad I had a 3rd year project course where the professor had published a book that consisted of projects written by students in previous years. We were told that the projects we did would also be destined to be considered for future editions. I don't remember if credit to the student was given in the book, so let's just say that it was.
In any case, I voiced my objection to not being given a choice about it (and was shouted down by my colleagues :). The professor's response was that 'MIT does this all the time' - I think he had his PhD from MIT.
But this is the only time I have seen students being 'used' to write a book.

'MIT does this all the time'---certainly not in any portion that I interacted with.

When I was a master's student, I TAed for a course where we used a book written by a Yale professor as our main text. I entered the PhD student and met a student who did their undergrad in that Yale department.I mentioned the book and she said that she wrote the majority of the text for the book when she was an undergraduate RA. I was surprised she was not acknowledged more heavily in the text.

As a student, I studied from a great textbook, by Hewitt and Stromberg.  Hewitt was the senior professor, Stromberg was his Ph.D. student.  I met Stromberg years later.  He did not consider that Hewitt has "used" him unfairly.  On the contrary, writing this textbook was the start of his career.

Was Stromberg made to write it as part of his PhD, I think, would be the onus. I'm sure Stromberg wrote the textbook of his own volition and enjoyed it, seeing he has written many more.

This can be very common. Even some students rise the suggestion to cooperate with another professor to author a specific book. For example when I was involved in researching and writing a book about mathematics of cryptography, I thought it'll be a good opportunity to receive the advice of my teacher and therefore to work with him completing that book. I hope you would love such thing as this is very common and many books published yearly have authored even by 20 and more persons based on their chapters. It seems that such method of publication will be very popular in near future.

On my colleague, we got a new professor who started writing new textbook of Linear Algebra during the semester on-the-fly based on

previous version (written many years ago by prof. predecessor)
feedback from students (us) on how to better explain the topics

So from my experience, the student-professor collaboration on textbook is something from which both sides will profit.

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


text:
How to write teaching philosophy and research statement?
I am applying for faculty positions in the US. Almost all of them require teaching philosophy and research statements. I have read some examples, but still do not understand what should I write.

Should they be about my past experiences or future plans?
Should they be evidence-based or just my ideas?
How they should be categorized (e.g., different topics that I
taught or my teaching methods; different research topics or
research strategy)?

I know that this question is too broad, but honestly I am deeply confused. How can I highlight my teaching/research potential to attract their attention?

Please ask separate questions about teaching statement and research statements - the answers are completely independent, there's no reason to ask them in the same post and make this question broader than it needs to be.

And it may help to include also which type of school you are applying to: big research universities and small liberal arts colleges with emphasis on undergraduate research opportunities will have very different criteria used to evaluate both of the statements.

BTW, books such as this give quite some discussion about this topic. Your local institute's career office can probably also help.

There is already a lot of information on this site about teaching and research statements.  Please spend a little time browsing first.  (Incidentally, oughtn't we to have a research-statement tag?)

There's a lot of info about teaching statements in the tag wiki

@ff524 I think--based on the subquestions--that this question is not about the specifics of either statement, but about how they relate to each and how to go about writing both. Thus, if your view is that they are completely independent then I feel your first comment could be made into an answer ("Don't, write them separately"), rather than carving this up into subparts which are redundant to other questions and don't reflect the asker's intent.

I'd agree with @Tim that, both potentially and perhaps actually, the "teaching statement" and "research statement" are related, both in writing and in perception ... at least of some people on the receiving end. E.g., if I read two such statements that absolutely don't refer to each other, I am not as happy as when there's some connection...

Someone should turn this into an answer!

Many successful teaching and research statements do the same basic three things:

Describe broad themes or approaches that tie together your research or teaching.
Narrate specific relevant examples of your achievements related to these themes or approaches that illustrate your experience and qualifications.
Describe your aspirations and future directions in terms of your research or teaching.

It might help to think of the research and teaching statements in terms of other items in your packet. For example, your writing samples will provide concrete examples of your work as a scholar so don't need to prove this in a research statement. Similarly, your CV will show your publication and teaching record so you don't need to reiterate this either. Instead, provide a high-level overview of your approaches to research or teaching while referring to examples from your experience that help make the case for your excellence in each area.
Statements also provide a space for you to explain what you hope to do in the future. I used my teaching statement to describe examples of graduate and undergraduate classes I could teach that were on the books at the department I was applying to and that I would design from scratch. I used my research statement to explain the areas of research I was hoping to move into in the future.
Your goals with the statement may also be to address potential weaknesses in your application. For example, if you have little teaching experience, your teaching statement is an opportunity to show that you have thought deeply about teaching and that you have gained relevant skills through experience like mentorship that might not show up on your CV.
Specific expectations, in terms of of teaching and research statements, may vary from field to field and even within fields, but you can generally assume that authors have quite a bit of latitude. Look for examples online and, perhaps, more usefully, contact successful recent job market candidates you know to ask their materials.

No Name this seems like a pretty solid answer to me and it's been upvoted a few times as well.  If this isn't what you're looking for you might try explaining why in a comment.

I have recently come off the job market myself (I am ABD, soon to defend). By far the most useful information I came across was from The Academic Job Search Handbook. It has tons of useful information about Teaching Philosphy & Research Statements, plus tons of other information that might be useful to you, since it is geared toward US academic jobs. Good luck on your search!

One wonders whether the authors have been on hiring committees much...

@paulgarett Good point. The Chronicle of Higher Education trusts them with a career column, so I would assume they know their stuff.  Also, from their bio: "Julia Miller Vick is Senior Associate Director and Jennifer S. Furlong is Associate Director of Career Services at the University of Pennsylvania. They are coauthors of the Chronicle of Higher Education online column Career Talk."

Teaching philosophy examples: http://www.uwo.ca/tsc/resources/selected_teaching_topics/teaching_dossiers/guide_to_constructing/teaching_philosophy_examples.html
Nice suggested format for research statement: http://theprofessorisin.com/2012/08/30/dr-karens-rules-of-the-research-statement/

The second article begins with the advice to limit the research statement to one page or two at the most.  This is dangerous advice to give without indicating a scope: I gather that the author of the piece has experience in the humanities, and I am willing to believe that this advice is good for a lot of humanities jobs....

... I am in mathematics and have looked through over one thousand research statements in the last nine years.  I cannot recall seeing any that were a single page.  If I read a research statement that was two pages or less that did not describe obviously phenomenal work, I would be more than halfway to dismissing the candidate entirely.  Bottom line: talk to others to learn the norms of your field.  Especially, get multiple rounds of feedback from your advisor.  I got more feedback from my advisor on my research statement than any other one thing I did as a PhD student...and I needed it.


text:
API for Scientific Literature Search
I have to dig through a large number of scientific papers (~26K), all with DOI links. I've built a small Python script for searching through the papers. Now I want to have more data about those papers. For example, where the authors are from (country or university) or, at least, retrieving the DOI link for the papers (not all of them have metadata).
One approach might be as follows:
(1) Get the DOI link (from a library, for example)
(2) Retrieve the information about the author(s).

Is there an API or a Python library that could help with that? I've looked at the Elsevier API, but it seems to be just for Elsevier papers. Web of Science isn't helpful, as they haven't much papers for my field (Information Systems).
Mendeley, Citavi or Zotero aren't really the options, as I want to do that somehow "automatically".

For some options, see my answer to a related question. However, none of them will provide you with a perfect solution. At this point, expect to perform a lot of manual work in addition to some level of automation.

Check also ORCID API

CrossRef has an API, and this will resolve metadata for most papers. (Not all DOIs are registered through CrossRef, but it's going to cover most of the cases you want.)
However, it may not have all the detail you need - it won't always have author affiliation, for example.

I don't know that any scholarly citation database that covers all of science and provides an API that will give you author affiliations.
If you are working in biomedicine, though, you're in luck: PubMed has both an API with DOI search, and high-quality author affiliation data.

Here are some APIs you may want to consider. I found the pybliometrics one which uses Elsevier Scopus to be very useful.
https://github.com/pybliometrics-dev/pybliometrics
https://github.com/ElsevierDev/elsapy
https://github.com/OrganicIrradiation/scholarly

DBLP might be another option for you. There's a python wrapper to get data from it:
https://github.com/scholrly/dblp-python


text:
Where to find the most valid databases about the ranking of countries in research and scientific production?
Where to find the rankings of countries in research and scientific production?
For example, how can I find out the ranking of a particular country in the number of scholarly essays? What are the most credited websites for such data?
I need such data because I am doing a research on the rate of scientific production of a particular country.

I'm curious to know your interest in this. Are you doing specific research into this? Looking for a good place to study? Other?

@Buffy I am writing a paper on the rate of scientific production of a particular country.

Sounds interesting. Sorry I can't help you. But adding context like that to your question might draw answers that will.

It's a subjective question, so "most valid" isn't well defined.  For instance, you could look at the number of scientific articles (I don't think "scholarly essays" is the term you want), the number of Nobel prizes, the economic value of scientific patents, etc.  I'm guessing that you're willing to settle for "most popular" instead.

Please see my answer below. Note that it is focused on publications, which might or might not be a good proxy for scientific production, depending on various factors (e.g., scientific domain). For a more comprehensive review of the subject, you have to analyze other types of scientific artifacts, some of which are mentioned by @DavidKetcheson above.

It seems to me that you haven't made any effort to find information in question, which is easily available online. To illustrate, just a very brief Internet search resulted in the following arguably relevant sources: SCImago Journal & Country Rank - International Science Ranking as well as Nature Index - Country Outputs. Note that Nature Index is a much less comprehensive resource, since it is based on "selected group of 82 high-quality science journals". Thus, it is likely less representative, though it might still be representative enough, depending on how representative those 82 journals are. On the other hand, SCImago Ranking is based on Scopus database and advertises the coverage of 5000+ publishers and citations across 239 countries.
Obviously, if you are serious about your research, you have to perform a comprehensive search for relevant sources (as well as relevant papers) and analyze their quality before using any of them to draw any conclusions.

You can go to Web of Science and then search by author country. It unfortunately doesn't look like you can cover the entire database like this, but something like this would at least give partial results:

Go to Web of Science.
Enter a generic search term, such as "Science". If you're looking after a specific field, even better, use terms appropriate for that field. You can also refine by publication year if you wish.
From the results page (I hit 1,596,792 results in the Web of Science Core Collection), select "view all options" at the bottom, followed by Countries/Region.

As of time of writing, the top five countries for the above search are:

USA (460,271)
England (125,914)
Germany (116,557)
Japan (116,384)
People's Republic of China (94,438)

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


text:
I Plagiarised, what punishment can I expect?
I am a university student, doing a scientific bachelor study. I plagiarised multiple exercises from multiple homework sets for three different classes, all in all about 50% of all the homework for those three classes. I passed the final exams of those three classes. Realizing what I have done, I am considering turning myself in, unless the punishment would be too severe. What do you think?
Edit: I actually got caught once before for plagiarising on a single homework set.
Edit2: I calculated that redoing the courses would cost me at least $7000, this is also a consideration for me personally.
Edit3: I actually copied the homework of a friend who gave it to me because he trusted me. I broke this trust, and now he terminated our friendship. I asked him about it and turning myself in is the only way to earn back his respect.
I'd like to know from more people what kind of punishment I could expect. If I turn myself in, I would find it fair to only have to redo the three classes.

Did you pass the finals without cheating?  If so then you did something wrong, but you proved that you know the material.  Take that comment as you will.

I passed the finals without cheating. The homework did count for the grade (but I got decent grades for the exams).

In which country are you?

Why do you want to know? (I'm paranoid)

"Edit: I actually got caught once before for plagiarising on a single homework set." So what happened then?

Nothing much, I got a zero, the professor was (too) nice about it.

@user17965: Relaxed wants to know because punishments for plagiarism can vary greatly by country. Also, it would be helpful to have a better sense of what exactly you did wrong. Did you copy another student's work, lift solutions from a website, or something else? Also, what sort of "honor code" does your university have?

@Relaxed Edit two would indicate the USA (given $'s).

@aeismail The Netherlands. I copied it from other students homework.

Do you mean that, instead of doing homework, you simply copied from someone else who had done the assignment? I'm surprised another student (or other students) so readily let their work be copied. Not only are they doing work for someone else, but they could easily be implicated (and punished) if the copying is discovered.

http://blog.tanyakhovanova.com/?p=369

@Thomas The following are some countries which use the $ symbol: HK, Canada, Singapore, AU, US, NZ, (maybe others) and some like Chile use the $ sign even when they refer to pesos (I know, confusing).

@earthling Well, it makes sense, since the origin of the symbol is Spanish.

I suspect the worst of eventualities has already come to pass - you broke and subsequently lost the trust of a good friend. Regaining that will likely not be as simple as merely coming clean to the powers that be. That is a step in the right direction, of course, but its a long road to haul, after all.

This guy was caught: http://jyllands-posten.dk/aarhus/uddannelse/ECE6800720/ikke-mere-snyd-end-alle-andre/ (in Danish - Google Translate link: https://translate.google.com/translate?sl=da&tl=en&u=http%3A%2F%2Fjyllands-posten.dk%2Faarhus%2Fuddannelse%2FECE6800720%2Fikke-mere-snyd-end-alle-andre%2F )

I am going to show this post to my son. He is 14 and consistently cuts and pastes into his homework. He knows very well, from us, that plagiarising will only end up with him flipping burgers in some god forsaken burger store somewhere. Bad idea.

@horsehair: Every test is only a random sample of your knowledge, and not a proof thereof. A bad test isn't a proof that you are bad, and a good test is not a proof that you are good. Even more, the whole school life is not a test of your potential; a lot of ppl just failed at school because it's not their natural kind of learning; personally, I failed a lot, until I realised (myself, not by teachers) I am autodidact. If at all, school is more a lesson in empathy wrt. teachers and memorizing stuff, but not in intelligence. But I am going to far for just a comment :P

Your friend will be punished too, unless he claims he only gave you the homework to submit, but not look at or copy, which frankly sounds quite fishy to me (in itself an academic code violation?), and he might get punished anyway. So when he advises "turning myself in is the only way to earn back his respect", is he ok with being investigated and likely being punished too? Did you talk through the consequences of that with him?

@IanLewis kind of off topic, but have you asked on Parenting.SE how to stop that plagarism?

@OldBunny2800 Hi. No, I haven't asked. Do you think it would help someone if I posed the question there?

Yes. Parenting.SE has a lot of specific questions, but change a few details and it applies to someone else too.

I am considering turning myself in, unless the punishment would be too severe.

You are describing an extremely serious violation of most university's academic integrity policies.  The most likely punishment is that your credit for those classes would be revoked, your grades would be changed to Fs on your transcript, and you would be suspended or expelled.  (That would certainly be the most likely result at my university.)
Nevertheless, I believe you should turn yourself in.
Ari gives a good summary of the ethical argument, but there is also a selfish practical argument.  Since you mention being caught once, there is good reason to believe that your work will face additional scrutiny.  If you get caught before turning yourself in, the result is much more likely to be permanent expulsion.  If you admit your plagiarism, the punishment will be slightly less severe; in particular, even if they decide on expulsion, the university will be much more likely to readmit you after 2-3 years.
Even if you decide not to turn yourself in, I recommend taking a short break from university, if you can afford it.  The amount of cheating you describe indicates that something is very wrong — maybe you were overwhelmed, maybe you were scared, maybe you were lazy, maybe the homework were insultingly stupid, maybe you just didn't want to be there — but something was preventing you from engaging in those classes as a responsible student.  You need to figure out what that something is and address it, or you'll just fall into the same pattern again.

Thanks for the indication of the punishment. I know why I did this, I know it is a matter of my past, and I know I will never do it again.

I've also caught students clearly cheating as a grader, reported it, and found that the students in question got a slap on the wrist. So I don't know if I would agree with JeffE's assessment of the "most likely" punishment here.

Hell, as a grader I've caught people who were obviously cheating on multiple assignments, and the end response was to do nothing. (Granted the total HW was only 10% of the grade, but still...)

Also, the OP did not copy an entire masters thesis, but a subset of the homework assignments. Expelling a student for that seems too harsh.

In my department, the penalty for plagiarizing part of one assignment is a zero on that homework, for the first offense.  The penalty for a second offense in the same class is an F in the class.  All offenses are reported to department, college, and campus, to catch patterns across multiple classes.  Failing three classes for cheating normally results in suspension.  Plagiarizing on half of the homework in three different classes means about 10-15 separate offenses.  No, expulsion doesn't seem overly harsh at all.

Our department has an academic misconduct committee on it, which includes a couple students.  You should know that the students are by far the toughest on misconduct cases (especially those that are discovered, not volunteered), and I've personally witnessed a student not getting his degree over plagiarism.

I've personally witnessed a student not getting his degree over plagiarism. — So have I, more than once.  At least one such student also lost a visa and a job offer.

I always feel strange with this questions, since here in Spain nobody cares if you plagiarised or not (except one or two professors I had).

Oddly enough, in the US I know of a professor who told the graders to let the students know they see a lot of similarities in their work. The professor went on to say that he didn't want to deal with it.

As a student in the sciences, I see cheating all the time. My undergraduate institution had a strict honor code we had to sign; Many people cheated. I'm not sure how aware or unaware professors really are to the fact; I remember having one very strange conversation with one of the professors I'm closest too:
"There is good cheating and bad cheating"
is the exact phrase he said. He wasn't advocating to cheat, but what he said was that as long as the cheating didn't hurt anyone else directly (curved grades) or undermine the point of the class ( doing poorly on tests) then one could say that you cheated not because you weren't capable of doing the material, but moreover you cheated to save time. In undergrad, I think, many people get away this this type of cheating.
I would not turn myself in. I have never cheated, but I don't see why turning yourself in helps the university or yourself as long as you never cheat again. You obviously learned the material; make sure you try your best to be as honest with your work as possible from now on.
Not all lessons learned need to have punishment, having to learn is sometimes consequence enough.
Now, if your courses were curved, and you might have harmed someone else's grade, that is a totally different story.

I appreciate your honost comment. My grades were not curved, and no-one's grade has been harmed.

Don't take this as an excuse to cheat; If I were a coworker or your teacher and found out, I would find it very hard to trust you again.

+1: don't turn yourself in, and don't do this in the future. Turning yourself in is pretty much the end of your academic career at least, and quite possibly a big bump in your life's road. That said, with cheating commonplace in my phd in California (what honor code?) which appalled me, you at least show moral conscience, and suffer for it. It happened; don't again; and move on.

@gnometorule, the reason why I plagiarised was actually because I suffered intensely under psychological problems for a few years, the plagiarism was an aftershock under pressure to graduate. I think my past suffering would be a sufficient punishment for what I've done.

Doesn't your honor code contain a clause that if you don't report any observed cheating, you are cheating yourself?

It certainly does. But cheating in the 3 schools i've been to (state, small liberal arts, ivy league) cheating has been so rampant that you sort of hold your head down and do your work. The general type of cheating I'm talking about, for example, is looking up solutions online on problems sets or even take home tests. It has greatly colored my view of scholarship in this country (USA).

Related: http://academia.stackexchange.com/q/19256/18027

@TemplateRex I am not saying I disagree with whats said their, on the contrary, but many of us make unethical choices when we are between the ages of 18-22.

The OP has got enough punishment; mentally, in his heart. If he turns himself in, he may feel better ( and maybe worse, too ).

You should talk to an ombudsperson at the university or an academic dean and tell them the whole story.  They will likely punish you, but the punishment should be mitigated by the fact that you voluntarily provided the information even after "getting away with it".
If you keep this to yourself, it will either haunt your conscience for the rest of your life, or you will learn to be comfortable with wrong behavior.  If that's the type of person you want to be, you don't need me to tell you otherwise.  However, the fact that you've published this question suggests that you know that this needs to be rectified.
Either way, there is clearly an endemic problem at your university that the administration should know about.

Without wishing to get all judgemental about the practice of awarding course credit for homework: the number of questions on this site about catching and punishing homework cheats, and the prevalence of plagiarism detection software for that purpose, both suggest that a lot of universities have an endemic problem with it. If the administration doesn't already know then that's classic avoidance at an institutional level ;-) Which is not to say that another data point isn't useful to them.

@SteveJessop - It's also possible that staff are aware of the problem, but have chosen to manage it in other ways (eg, mandatory pass marks on final exams, low homework weightings, grading interviews where students have to explain their reasoning).  I'm not saying that's necessarily the most ethical solution, but it's one I've seen used a lot, and when you have 500+ students in a course, it's understandable.

I suggest you approach a guidance counselor at the school (or a school psychologist, or equivalent).  I think they are in the best position to help you in this case.  (You might want to check first if your conversations will be treated confidentially.)  The punishment you will receive for confessing will greatly depend on what the school policy is and I think the school's guidance counselor would know how cases like yours were handled in the past.

Your university likely has rules about academic misconduct. At my university the rules and penalties about academic misconduct are pretty clear. The minimum penalty we can apply to second offenses is a zero on the piece of work and the maximum penalty is a zero for the year. For third offenses the penalty starts at a zero for the class.
I sit on our academic misconduct committee and in general we try and be forgiving, especially to students who admit guilt. Other committee might simply expel you.
For our committee, you admitting copying 50% of the course work would make it difficult to conclude anything other than that you committed an academic offense. We would then be left with trying to mitigate the damage within the rules. We would likely argue that all the copying is a single offense (i.e., nothing falls into the third offense category) and that all the pieces of work that have copying should get a zero. We might be so lenient as to only penalize the first piece of work. Then again we could be mean and argue for multiple offenses and expulsion.
I think if you turn yourself in, the penalties could range from rather light (a zero on one piece of work) to expulsion. Getting caught without turning yourself in would likely increase the minimal penalty, potentially to a zero on all pieces of affected work. It is not clear if this additional penalty would have an affect on your ability to graduate or make a substantial change to your transcript.
That said, I would talk to a lawyer and figure out your legal responsibilities and weigh those against your moral/ethical responsibilities. It is not clear that a university would be able to retroactively amend a degree for academic misconduct related to homework, especially if, if all the affected pieces of  work were given a grade of zero and you would still pass.

Honestly, no one cares. I plagiarised in all 3 of my degrees and I am a doctor. Do NOT turn yourself in. Everyone does it. The lecturers did it. Your children will do it. Uni is a process to get to where you need to. Your real learning starts in your career. Not on an exam paper or essay that is double spaced, size 12 arial narrow font and referenced in Vancouver style. Seriously, it will not affect any part of your life going forward. To everyone else who is getting cut at this, move on. Assignments are there to reduce the workload of the lecturers. Our thesis was 100,000 words. I copied at least 30% from other people and made up half of the references. My lecturer (after uni and over a couple of beers) told me he reads the intro, picks 10 pages, adds comments and reads the conclusion.
Move on and enjoy your life.

"Honestly, no one cares" Ex-Doctor zu Guttenberg (http://en.wikipedia.org/wiki/Causa_Guttenberg) would disagree.

The question is jot about sweeter the student should or shouldn't tun himself in, it is about the possible penalty if he does. As such, I don't see how this answers the question.

To be fair, the text of the post states the question more generally: I am considering turning myself in, unless the punishment would be too severe. What do you think? and several other answers neglect to answer the titular question. I think this is an answer, albeit possibly a very bad one.

It would greatly contribute to the value and sincerity of this answer if you would tell us your full name.  If you are not willing to do so, then your answer simply seems to be a lie.

For whatever your reasons may be, you choose to submit someone else's homework as your own and received credit for being able to do so. In the real world that is not any different than benefitting from work given to you by a volunteer or an employee. These things happen thousands of times day in the normal course of life.
The important thing here is that you passed your exams on your own demonstrating that you had a mastery of the material, which is the purpose of education, isn't it? Your exams reflect your own ability and since those were done without cheating, you should simply continue on with your life.
If you've resolved not to continue this behavior and are done with it, I see no reason to submit yourself the school or any of its representatives.  They have your money, You have the knowledge. The transaction is complete.
Einstein was a "poor student" yet revolutionized physics. Henry Ford, had no college degree yet revolutionized the fledging auto industry. What matters here is not what school, "a self appointed authority" thinks of you, but what you think of yourself.
If you can resolve to work harder at your studies, or find something you're actually interested in and can change your behavior so as not to put yourself at risk, I suggest you are done and should quit punishing yourself for the past.
As much as they would like us to think otherwise, schools are a very poor place to learn most of the real knowledge you need to survive and prosper in real life.
Let it go.

Careful! The success of Einsteins and Fords (poor student/no college degree) does not negate the seriousness of cheating... Einstein and Ford persisted despite outside opposition, not the inward opposition of a guilty conscience.

In the workplace, it may be expected that a volunteer or employee gives you work. In academic settings, it is expressly forbidden to get work from others. I cringe when I see my peers cheat in engineering classes -- I wouldn't want to fly on a plane or drive over a bridge designed by somebody who couldn't do the homework themselves (whether for lack of time or lack of knowledge).

The Einstein argument is wrong on so many levels, I won't even start to explain.

"Homework is only to ensure that you are exposed to material not necessarily taught in class, or provides information not presented in class." - I disagree. At least at my institution, the statement is clearly that both exams and homework (which is the precondition to participate in the exam) have to be passed, and while only the exam is graded, it is the implicit understanding that passing the exam says something both about your skills in solving the exam tasks under exam conditions, and solving the homework under homework conditions (e.g. with reference material, within small teams etc.).

The whole idea of Einstein being a bad student is a myth (based on the fact that his first biographer confused the Swiss and German grading systems - in Switzerland a higher grade is better, in Germany the best grade is a 1).

The question is about possible penalties and not whether he should or should turn himself in. As such, I don't see how this answers the question.

To be fair, the text of the post states the question more generally: I am considering turning myself in, unless the punishment would be too severe. What do you think? and several other answers neglect to answer the titular question. I think this is an answer, albeit possibly a very bad one.


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Why do junior faculty serve on PhD admissions committees at American universities?
I only have knowledge of American universities:  I know of junior faculty that serve on graduate admissions committees in the STEM fields -- at top schools such as Harvard.  The things that I hear from them are quite interesting, for instance, how strong the recommendation letters are from the undergraduate applicants at top schools - that virtually all letters say that those students are the "best" that those professors have ever had.  But why do junior faculty such as "Assistant Professors" or "Titled Instructor" serve on graduate admissions committees? To me, the admissions process for graduate STEM programs are so important that I feel the committee should consist of senior faculty instead.

You do know that in the 5-8 years it takes for you to finish your PHD that those junior faculty will be tenured, right?

In many STEM departments, the new Ph.D. students will work under those very Assistant Professors.  Who better to vet their advisees-to-be?

Shouldn't all professors have a say in whom the students that may end up advising might be?

virtually all letters say that those students are the "best" that those professors have ever had — [citation needed]

Because assistant professors need PhD students to get tenure?

Because junior faculty get the boring jobs?

I don't know about Harvard specifically, but I strongly suspect the answer is "because the premise of the question is wrong". Both junior and senior faculty members serve on admissions committee, and junior faculty are still faculty, so they are 100% qualified to do the work and make good decisions -- your assumption that they're not is another incorrect assumption. As for "why" they do it, technically the reason is "because it's part of their job, which they were assigned to do by their department chair or whoever makes those assignments at their department".

What makes you think that senior faculty would do a better job than junior faculty? The junior faculty are often REALLY good (especially in the current job market), and they will have had a more recent/modern grad school experience.  I reckon the last thing you'd want is a grad admissions committee dominated by "dinosaurs."

When I was at U. Chicago as a doctoral student, I actually sat on the graduate admissions committee along with several other students (and a greater number of faculty).  Given our presence, having junior faculty on the committee seemed perfectly natural.  The main thing I remember about the pre-tenured faculty on the committee was that they never seemed to have enough time to read many applications, since they were too busy doing research and applying for grants...

If junior faculty members aren't allowed to sit on an admissions committee, then  by the time they become senior faculty they won't have had any experience of sitting on admissions committees. The junior members need to learn how to become senior members and this is just one part of it!
I also don't think that graduate admissions decisions are quite so monumentally important (or tricky) as you imply; for top institutions such as Harvard you will already have a self-selected pool of very good appplicants to choose from, and I imagine it's difficult to make a bad pick.

As an applicant the decisions of the admissions committee are critical, as a faculty member, they don't really matter as long as you get it close. In the worst case, a school passes up a future Nobel Prize winner for someone who fails their quals and life of the department goes on. In contrast, Assistant Professors also sit on faculty hiring committees where  a mistake means another faculty search and possibly the loss of a tenure line.
As for why they sit on the committees, there is a ton of admin work in a department, and some of it truly needs to be done by Full Professors (e.g., tenure and promotions) and you need to use people where they can contribute.

In addition to other excellent answers, I would add a pragmatic (and even cynical) viewpoint: serving on admissions panels includes a lot of boring paperwork which is not visible or recognised outside the university (e.g. does not lead to peer reviewed publications). Since the currency of academia is fame and prestige, senior members don't want to spend their time on admissions panels (and they have a lot of other administration duties to take care of). Since they usually have enough gravitas to say no, the unprestigeous task inevitably falls on younger colleagues.

As other people have said, tenure-track assistant professors have to do a certain amount of departmental service to get tenure, and being on the graduate admissions committee is a good way to do this.  Lots of committees require work thoughout the year, which ends up taking a lot of time.  Grad admissions basically means that you have to spend a day or two reading files and then attend a couple of meetings to hash out who gets admitted.  High impact, low commitment.
One thing from your question that hasn't been addressed is the fact that at some departments grad admissions is handled by "Titled Instructors", who are not on the tenure-track.  At least in mathematics, this does happen at a couple of places like Princeton (where the senior faculty are particularly effective at avoiding departmental service and which doesn't really have a tenure track), but it is very far from the norm.  In the vast majority of departments (including fancy ones like MIT and Chicago), non-tenure-track faculty are not expected to do any service at all.

+1: This is a key answer as it points out that postdocs should not be lumped together with tenure track faculty.  I also don't know a better answer than "Indeed it is kinda weird that non-tenure track faculty at a few elite departments have duties that would be explicitly against the rules at, say, a state research university."  Well, except to point out that some of these "Titled Instructors" are actually "Titled Assistant Professors."  The top drawer ones at Princeton can stay there for more than three years, right?   They're still not tenure track but there's more pretense than usual.

TLDR: A combination of self-interest and the pigeonhole principle.
As a junior faculty member in the sciences, I've been advised by a few mentors to be on the grad admissions committee. Junior faculty need to build up their research groups, and the graduate courses they teach will be populated by the incoming students. Choosing students who could fit in those two roles is highly valuable to a new faculty member - but less critical to well-established groups!
In addition, it is to some degree unavoidable. Everyone does some service work in a department - this can be acting as chair, serving on university-wide committees, reviewing tenure cases, organizing seminars, redesigning curriculum, hiring faculty, dealing with admissions, etc. Some of these are restricted from junior faculty (e.g. no one without tenure reviews tenure cases or chairs the department, I think), and others are merely inadvisable because they require huge time commitments and better knowledge of the department (curriculum redesign). This means things like hiring committees and admissions committees are often mixed junior/senior groups - there are not enough senior people to do all of this work alone!

In addition to the other excellent answers given, there's also a number of other considerations:

In programs with funding coming primarily from grants, programs with lab rotations, etc. these junior faculty will be expected to host and mentor these students as well as potentially serve as their advisors. How receptive do you think they're going to be to "Hey, you had absolutely no input in this decision, but this student is going to need to hang out in your lab for the next six months"?
Junior faculty can represent new directions for the department. For example, my department is currently hiring a number of more theoretical/computational faculty. They will all be "junior faculty" - and yet the department is hoping to recruit students who will work with them. Would you want to be evaluated by an admissions committee whose entirely unfamiliar with your field, qualifications, and what would be expected of you? Ones with entirely different expectations of what should be "required"?


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What is the closest alternative journal to journal X?
Does anyone know of a website or resource that identifies the nearest journal neighbours to journal X (any specific journal) in terms of content (perhaps defined by some distance metric defined on article keywords?). In other words, if I am rejected by journal X, which journals might consider the same paper?

Indeed, there are tools that create maps of journals in a given area. Most of them are based on citation data, i.e. they consider that citations between articles of journal A and journal B are a good indicator of proximity of the two journals (and it seems like a good definition of “proximity”). If you are interested in the topic of how such maps are created, and how they can be analyzed, you can read on the topic. For example, see “Seed journal citation network maps: A method based on network theory” and related papers.
Now, regarding online tools available, a search lead me to VOSViewer (paper), which looks like it contains exactly what you want:

A final note: while such journal maps can be useful in discovering new journals in a field you don't know well, I will add that each journal is unique, and you have to learn about the journals in your field in order to increase your chances of success at publishing articles. It may, for example, tell you that two journals are very close in scope when they actually have very different editorial policies. Read the editorial guidelines for the journals of your field and, at least as importantly, read papers of each journal to get a feeling of what the actual policy in place are.

If your institution has access to Journal Citation Reports, there is a feature called Related Journals that will provide a list of titles similar to your selected title, based on citing and cited relationships. Journal Citation Reports is a subscription database provided by Thomson Reuters


text:
Is the PNG file format acceptable for academic papers?
When I have to use Microsoft Word for writing a paper, I tend to export most my graphs and charts into the PNG image format since I find it the most convenient due to its smaller size (than TIFF) and higher quality (than JPEG).
However, when I wanted to submit papers for conferences, none of them (three in total) listed PNG as an acceptable format for figures. Two of them requested all figures in either JPEG or TIFF formats, and the other asked for (direct quote):

Use the following standard image formats: BMP, JPG, JPEG, TIF, WMF, or EPS.

Is there something inherently wrong with PNG figures for representing scientific data that I'm not aware of? Should I quit using it for everything?
I do understand the advantage of vector graphics. I use PDF to store the originals, which I then convert to PNG for use in Microsoft Word. As suggested in Peter's answer, I've sent an email to the support address for that journal to ask for more information.

Why do you convert to png at all?  Just use the pdf file in the paper.  Then readers can zoom in as much as they wish.

Agree with @DavidKetcheson, make your graphs etc. in vector format whenever you can (eps, svg, pdf, ...). Smaller and lossless.

@DavidKetcheson I'm using MS Word 2007. Inserting a PDF image automatically rasterizes it into a lower quality preview. EPS causes it to slow down and eventually crash

@Timmy In terms of vector graphics, Microsoft Word only plays well with Microsoft's own Windows Meta File (wmf) format.

Because they haven't updated those instructions since 1996.

Don't you ultimately have to send the graphics as separate files anyway?  Then you can still use the PDF (or EPS) originals.

Microsoft Word for Windows does not support .pdf vector graphics (my reason for abandoning it and moving to LaTeX). Microsoft Word for Mac OS does support it.

If you use a word processor for preparing scientific articles, choosing an image format is your least concern. That said, you should certainly not use JP(E)G for most figures (plots, charts, ...). It's compression algorithm destroys one-color areas. If you have to use pixel graphics, PNG is probably the right choice.

What is acceptable for an academic paper depends wholely on who is publishing that paper. Ask them.

It is a pity that many publishers want Microsoft Word .docx documents. However, Microsoft Word also supports formats such as SVG or WMF, so there is no necessity to convert to PNG or JPEG. If they state "Use the following standard image formats: BMP, JPG, JPEG, TIF, WMF, or EPS" then I would export graphics as WMF and EPS and let them choose.

Running a journal with Wiley as a publisher, Wiley's instructions state JPEG, TIFF and EPS are acceptable formats. Since many authors supply figures in PDF and PNG I started to pass these on to the type-setter and found that no issues erupted. It is therefore clear that publishers may lag behind with their recommendations while type-setters are quicker to adapt to "new" formats. I imagine the lag is possibly a lack of interest to update what works, but can also be because they work with many type-setters and printers and wish to maintain a largest common set of files that they know all can accept rather than having to constantly adapt to individual services' capabilities. I am fully aware that this thinking is a bit arcane and that any type-setter/printer that cannot handle almost everything has very little potential for survival in today's competitive world.
Anyway. I would suggest asking the journal if it is possible to use PNG in your case, or do as many authors have done in "my" journal, send them in anyway. It may, for example, be possible to send in a JPG and a PNG copy of the graphics asking them to use the PNG if possible.
As a side point: PNG is in my opinion the best pixel format because of its strong loss-less compression except for photographs, something it was never intended for anyway. Using PNG graphics will keep down the size of final PDFs of the article which is a good goal to have. So in my case, I encourage authors to provide PNG even though Wiley does not.

Why don't you, as an editor, ask Wiley to update the istructions on their website?

@FedericoPoloni. Why do you assume I have not tried to do so?

@PeterJansson Because you didn't mention it in your answer. :) In any case, what did they answer, if you wish to share this experience?

@Timmy, weird, since as far as I know the PNG standard does not support layers anyway.

Why does the answer say that PNG is lossy for photographs?  That's not accurate...

@MooingDuck - I think he was saying that PNG doesn't have "strong" compression for photos, not that it's not lossless.

This answer needs a strong statement about when (not) to use JP(E)G.

Don't think of standards and documents first: think of the guy who's running the press. These days they're using Photoshop, Illustrator, or other Adobe/similar software and can import any stuff that's in their version's import dialog. But they don't have time to faff with options for your own special self: they want stuff that imports without fuss. There's a load of options for layers, they don't want to look at them, ditto transparency. TIFF and EPS have modes for talking to aliens on a-Centuri with Aldis Lamps: off. With a bit of imagination it makes sense. No need to geek-lawyer up.

@A.Donda It's not unheard of for PNGs to have lots of extra data crammed into them: https://www.adobe.com/support/fireworks/export/fw_export_vs_sav/fw_export_vs_sav02.html  I imagine this is just a nicer way of saying “no Fireworks PNGs; only flat PNG exports”.

Another reason might be that vector formats (EPS, PDF, PS, SVG, ...) are first options if they make sense. If they do not make sense for a reason (for example for a photo) then that reason might influence what should be considered for a raster format. PNG is based on RGB color space while TIFF supports different color spaces, including CMYK which is the one being used in paper based publishing. So if one has an illustration let's use the vector version, if one has a photo then TIFF makes sense. JPEG has been around for a long time, and probably that is why they have it in their list.

@SlippD.Thompson from what I've gathered, the only software to do that is Fireworks. Frankly, before I had never heard about this application, and according to Wikipedia it is designed for "rapidly creating website prototypes and application interfaces". I'd expect academic authors to use Photoshop if they like the commercial and Gimp if they prefer open source, and to my knowledge neither of them produces layered PNGs. PNGs saved by Matlab don't have this problem either. So seriously, I think this is a marginal problem connected to a specific software, and not a problem of PNG per se.

Oops, the last comment, while responding to SlippD.Thompson, was partially inspired by the discussion under user1850420's answer.

I don't think there is anything wrong with PNG that makes it unsuitable, but it may be the case that the publisher's processing software does not support PNG files (or they never bothered to update their author's instructions). To avoid extra work it is usually best to stick to the publisher's instructions and submit using formats they recommend. I would recommend using whatever format you prefer internally to store high quality images, and only convert at the time of submission. Avoid converting as much as possible, since this will lead to quality degradation (for lossy formats, at least).
That being said, if possible you should try to use vector-based images (which EPS usually is) since they allow for higher quality scaling. For photos and the like the other formats are more suitable, so using vector images may not always be possible.

Is there a reason why you can't provide EPS files? Do you have original (for example .fig if you created the file in Matlab) files?
It can be irritating to constantly re-make your figures, but EPS are recommended by almost everyone because they store vector data, not pixels, when generated from applications/filetypes that support vector graphics. This means that, despite having very low file size, someone can zoom in semi-infinitely on your fonts and graphs. This makes for good quality of figures for publication -- much better than JPG or PNG, which can end up looking pixelated, especially around the labels.
Of course, there are times when you need an image -- like a photo of a lab setup -- and as other answers have mentioned, it's hard to tell whether the publisher can't process PNG files or just didn't update the instructions.
As a final tip, I learned the hard way how helpful it can be to save original (ie .fig) files of all my figures. This lets me manipulate them very easily and export them from the native format into whichever other format I need. So if a collaborator asked me to send a Word doc with figures included, I could easily export to PNG and include, and then later export the exact same figure to EPS for the publisher. This will of course depend on the program you use,  but I think it's a helpful idea to keep in mind.

EPS, and PDF, files can also store "pixels" and trivially converting PNG, BMP, and JPG files will not magically make them vector graphics.

"it's hard to tell whether the publisher can't process PNG files or just didn't update the instructions" It's trivial: send them an email and ask.

Good point, I meant that it was hard for me personally to tell

"it's hard to tell whether the publisher can't process PNG files or just didn't update the instructions": it's easy: they can process PNG files. Everyone who has a computer can process PNG files. There are plenty of software tools to convert them into anything else.

Better phrasing would have been to say that it's hard to say whether the publisher is willing to accept PNG, rather than whether they are able to process them. Lots of journals accept them but don't want them, even if it's for no good reason.

In my experience PNG and Multilayered TIFF formats are constructed using layers which in rare cases in some software to cause some layers not be be displayed or appear even when the layer(s) have been switched to invisible. It is recommended to use flat formats (non-layered) such as JPEG or if sizing is necessary then use Vector or resize friendly format such as EPS. My experience has been down to providing PNG to a T-Shirt printing business, the layers I had made invisible but their software made all layers visible. End result looked awful. If you really must use PNG, make a backup then flatten PNG.

PNG does not support layers, however, it may store color values for fully transparent pixels.

At the time I used Fireworks which used to be capable of multi-layer PNG, I don't know if it still can. According to forums, people say it is PNG is a hybrid proprietary format. GIMP does not support multi-layered PNG. There are some real oddball standard of standards formats out there.
Extra advice. If anyone wants to extract layers from multilayered TIFF, I recommend irfanview which is an awesome free Image viewer/converter/filter depending on the plugins you use.

@user1850420 The PNG standard allows to store "private chunks" of data in the file, where applications can store for example metadata, or in the case of Fireworks, also separate layers. These private chunks are not standardised, that's why other applications might not support them.

Thank you for your input. I believe we have all learned technical on the PNG and a rare reason not to use it in publications in the small chance that multilayer may cause problems, which in my experience it had. Working in a University, the Academics send JPEG files for publications. I think we can agree that JPEG 100% quality and reasonable resolution is probably more than ample for publications. For large poster printing then PNG 24 bit.

Unfortunately I can't agree. JPEG at "100%" (which is not clearly defined anyway but depends on the implementation) is still not lossless, and especially which sharp edges common in scientific illustrations artifacts are easily visible even at highest quality settings. Second, it doesn't make sense to blame the PNG standard for the side effects of a proprietary and incompatible software. So I would hope we can all agree ;-) that standard PNG is the best file format for the lossless transmission of bitmap images, with JPEG being a close second only for lossy transmission of photos.

PNG is a ISO/IEC standard designed not to use patented methods, and therefore is clearly not proprietary. https://en.wikipedia.org/wiki/Portable_Network_Graphics

The PNG format is superior to JPEG in a lot of ways.  Though I try to format my images in PDF/EPS for journals.

@A.Donda, probably off topic, but why PNG over TIFF or BMP?

@StrongBad, BMP is most of the time used uncompressed, and only supports the quite weak RLE (run-length encoding) compression anyway, so BMP files will be much larger than the corresponding PNGs. Moreover, while documented and also implemented in open source software, BMP is a proprietary format of Microsoft, developed originally for use with Windows. There is no public standard for this format.

TIFF is a time-honored (not to say: old ;) format, imho it had the place of PNG before that existed, and I would still use it for some specialist application which is not covered by PNG, e.g. layers. However, it is also a very complex file format with several extensions (one of which covers compression, base TIFF is uncompressed), and for this reason to my knowledge no single piece of software supports the full specification. Therefore incompatibilities like those described by user2379888 can happen. I'd say, if you can do it with the simpler PNG format, use that one, otherwise use TIFF.