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How to address a mistake in an old paper in a very prestigious scientific journal?
A Nature paper published in 2000 currently has around 400 citations, but there is a mistake in the paper and surprisingly, still it gets citations. The mistake affects the result of the paper in a way that half of the arguments in the paper are invalid.
I warned the authors two years ago and they confirmed the mistake. I expected them to put some announcement that there is a mistake in the paper to avoid misleading researchers, but unfortunately they have not done so.
How should we address these situations? Should we send a comment and report it to the editor? Is it rude? Or should we simply dismiss it because it is an old paper?

I cannot add comments yes, so this by no means is meant to be the actual answer. Have you tried contacting Retraction Watch? Alternatively, a more direct approach would be to contact the editor and outline the reasons you believe there is an error, including proof of your communications with the authors, admitting they were incorrect.

@I Heart Beats, Thank you for your comment and the weblog. The annoying part is that in science community, in many cases a Nature, Science, or Cell publication (or any high impact factor journal) can change a life; people get job, promotion, and more research funds by these publications. They should be more responsible about what they have published.

@S.A. is this also something you can approach this blog with? http://www.iflscience.com/
I think the main focus is the integrity of the past research and any future investigations that may have been impacted. If you have proof of wrong doing, and clearly this is bothering you or you would not be posting here, is there a way to draw attention to this using scientifically minded social media outlets?

@I Heart Beats, Actually, I prefer the authors of the paper do this by themselves or in an anonymous way. That is why I informed them directly. I do not like to make it public by myself as it does not build any reputation for me. I will look more carefully into the new weblog, looks interesting. Thank you.

Are the authors are reluctant to take action? If so, does this bother you? If it seems that your ideal outcome is not possible, perhaps either you need to let it go (you did mention that the publication is old) or to take action yourself so it can be off your chest. Have there been publications that essentially corrected the original paper with their new knowledge?

One option: correct their method, redo the experiment, prove them wrong, publish the results in Nature and collect the "job, promotion, and more research funds" that you mentioned in your comment.

@I Heart Beats, Yes, they do not like to do that! I guess, they think it damages their reputation as it was one of the first papers in this field. The only reason that I would like it to be corrected is that I spent 2 months on some project based on their results and after that I realised it has some problem. It prevents people to fall into the same wrong loop. Although in their future papers, somehow indirectly, they recovered the mistake, still people refer to the original paper as well.

@Jigg, Sounds great, but I am theoretician :( and the experiment needs quite advanced facilities.

@Gobinath, I guess, they think it damages their reputation as it was one of the first papers in this field, but as you mentioned, it is the best option for them.

@ Jigg, they may also be interested in knowing about it, or perhaps starting a side forum for questionable results etc. The logic was that these people are interested in documenting and exposing scientific injustice, which seems to be the case here.

This answer is low quality. Retraction Watch is not going to get into a dispute over the quality of a paper; they care only about retracted papers, and it is clear that the authors are not retracting the paper, so I feel like the Retraction Watch suggestion is a complete misunderstanding of their focus.  As far as contacting the editor, in my personal experience I do not think this is going to lead anywhere useful. The best outcome you can hope for is for the editor to tell you "submit a short response paper and I'll have it refereed"; so why wait to contact the editor? Just do that now.

@IHeartBeats, why did you delete your answer? It was very useful :'(

Have you checked with other people in the subject about this? It happens that some errors in past papers are folklore, well-known to specialist in the field, and that they stay that way for a long time without being documented. This is very unfortunate as it wastes newcomers to the field time and efforts, but you should know the precise unofficial status of the thing before taking action.

Some journals accept a type of short correspondence or comment in which objections to some published material can be submitted. If you can articulate your objections in a scientific way suitable for publishing you may try this approach. For example, imagine the original analysis has some error. Reanalyzing the data gives different results and invalidates the previous publication. Conversely in this approach the authors of the original study have the opportunity to reply to your complaints.
An example of this is a commentary published in Nature Genetics, where the authors highlight important deficiencies in the design of the experiments in an earlier publication that can lead to incorrect conclusions. Of course, the authors of the original paper are allowed to respond to the comments.
Correspondences have the advantage that can be very short. I am not sure at this moment if Nature also accepts this format.
If the material that demonstrates the error in the original publication is substantial it may grant an additional publication. This is for example what happened with the paper that demonstrated the divergence between human and mice inflammatory responses, which led to a response paper analyzing the same data, and arriving at the opposite results.

Thank you, good examples. What about the fact that the paper that I have mentioned published 14 years ago?! Does anyone feel it is pointless to comment on such an old paper? Gravedigging!

@S.A.: I guess "old" is a relative term. In my field (mathematics) a 14 year old paper would be considered pretty recent. "Old" would start at maybe 40 or 50 years.

@NateEldredge, You are right, mathematics never ages! but natural sciences are ageing too fast until they mature really well. I should ask editor to force the authors to write the erratum.

I think the fact that is an old paper should not be considered. If the paper is highly cited and people still cite the paper then it means it has a significant impact. If the impact is based on some wrong conclusions then it is important to point that out. I would say it is ethically the right thing to do.

A related comment. If the paper is old, chances are that someone else has tried to replicate the experiments or the conclusions. So far no one has been able to find anything wrong? It is possible that even with their mistake their conclusions turned out to be correct...

There was a famous case in biology a few years ago in which a paper was retracted six years after it was first published. The decision to retract was taken by the PLOS Pathology editors, not the original authors, who would have preferred to update the original paper with an erratum.

In addition to the excellent suggestions above, I'd also suggest blogging about it. A recent study found that corrections to the literature were 8x as likely to occur if blogged about, as opposed to corrections that had gone the traditional route (contacting editors, authors, etc).

Very interesting; the web is so frightening!

In this case I would say the web is a good thing. It means wrongdoers cannot hide because everyone will know what they did anyway. Well, the problem would be when there are false accusations...


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What should I include as "evidence of effective teaching methods?"
I'm in literature and applying for a tenure-track position.
One of my job applications is asking for "evidence of effective teaching methods" as one of the documents I am to submit.
Does anyone have any idea of what this should be?
Research to date has given me very little. My usual go-to sources for job application information and help have not had anything to address this sort of thing.
Sure, there are teaching philosophies and teaching statements, both of which I've written in the past.
Evidence of teaching ability, in my field at least, includes your teaching evaluations and letters, your teaching philosophy, and a few syllabi relevant to the job search at hand. But, there is no clear-cut answer to that one either. And it varies a lot, depending on who you ask.
As for my own pedagogical experience, I would imagine this could include some sample assignments? Perhaps a narrative of what innovative teaching methods I've used in the past, perhaps some student comments from evaluations that speak to methodology in particular?
But, I'm really guessing here, and I was hoping someone who has dealt with this particular item in job applications would have some idea of what this might be.
Thanks for the suggestions on how to clarify the question.

These kinds of requirements are typically written very broadly so that the search committee can use its judgement in determining who the best qualified candidates are.  I would provide teaching evaluations, sample syllabi, and a statement of teaching philosophy.

So, in essence, no different from Evidence of Teaching Ability?

@Pupahava: The two seem synonymous to me (although I am  an engineer and do not work in the humanities). Also, I've edited the title of the question to better reflect the content.

From the perspective of someone who has been on a search committee this would normally mean your teaching evaluations -- either as a TA or as the instructor on record. Any teaching awards you might have won in this regard would also count
But we also recognize that not everyone has had TA/IOR experience. So it could also include:

Evidence of having taken teacher training / professionalization seminars
Sample syllabi and assignments
Student/faculty/participant feedback from guest lectures and guest talks

This question is deliberately broadly worded so as to not exclude people who haven't had to teach. You can include a cover sheet to this item category (i.e., when you upload your PDFs you include or prepend a cover sheet) that notes how you have interpreted this and let the committee know that you are willing to send more material if requested.
Why is this material requested? After the search committee makes its decision, your file goes to the Provost's office. The Provost will want to see "evidence of teaching effectiveness" as well as "evidence of research" as part of the portfolio. It's simpler for the committee if you can make this case for them ahead of time.

I'm also guessing that this is not for an R1 since we're not really that interested in good teaching .  But when I was applying to SLACs, they were very interested in teaching effectiveness and evidence of such.

That's right. Not an R1 school.

Here's a follow up question: This is a literature job. I have teaching experience in language instruction. Should I include those evaluations in this document?

Whatever strengthens your application.

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Reapplying for a PhD with a Master's degree
I am a senior undergrad studying internationally and majoring in electronics. I applied to graduate physics programs in the US. I was able to get into some schools, but not the top ones. I have accepted the offer from University of Minnesota for the PhD along with a Master's.
However, I got a few great positions in the upcoming summer and a couple of papers which seem to be completely deal breaking. I also have a feeling that my undergrad major might have been a problem so getting a master's could be helpful.
I wanted to reapply for grad school with my Master's (along with good GPA). There is a lot of negativity in academia about transfer students. However, I want to make it absolutely clear that I am not talking about transfer student. I want to reapply as a first-year graduate student. And, I am also not bothered by getting recommendation letters from UMN. I can get sufficient letters from other professors.
I contacted a few schools asking about it. They said I can obviously reapply as a first-year graduate student (that's what I want). But many people (on the internet) say that it is something that is highly frowned upon, and this decreases the chances of admission (even with Masters). I want to get some perspective as to what extent is it common, and how much is it frowned upon?

Hi, and welcome to Academia.SE!  Can you explain a bit more about why you want to take such a radical action?  University of Minnesota may not be MIT or CalTech, but it's still a very good graduate school for physics.  I'm assuming, BTW, that you don't really mean "freshman," which generally refers only to undergraduate.

Yeah sure....First of all Freshman refers to grad school freshman. May be I am a little worried about my opportunities. I feel like I screwed up my grad applications. Stanford and Berkeley told me that I was rejected because of my "SOP". I want to rectify that. I just feel that I may deserve a little better.

What is your goal for grad school?  Do you want an academic career, or are you doing Ph.D. and out to industry, or something else entirely?

I want to go into academia.

Given that the statement of purpose is largely bs, to hear that you were rejected for that makes me sad. But I agree with @jakebeal that, location aside, Minnesota is a very good school.

@gnometorule I have some colleagues who would take severe issue with that statement about location... :-)

Applying to another program without letters from Minnesota profs will probably look very bad.

@Potato I agree. May be if I go there and do well in few advanced courses, one of the Profs may give reco. Moreover UMN does have a terminal Masters program, but I am a part of Masters en route Phd. So, I am guessing many students would go to other univ. after their masters.

Since you, in part, ask how much this type of thing is frowned upon, I can provide a data point (or at least an anecdote). For the purposes of this question/answer I am going to pretend there is an absolute ranking of all U.S. PhD programs in my area (since you are concerned about moving to a "top" school).
The first PhD program I entered was one that does not even appear on the listed of schools that I typically see ranked by various reports. So let's say for my absolute ranking of grad schools that my first program was ranked not even in the top 100.
After a year (or 1.5 years) in this first program, I decided I did not want to get my PhD from there, so I applied to other schools. In the statement that I gave my advisor to help him write me a letter of recommendation, I included 2 reasons that I wanted to leave, which were basically the following

The program I was in did not match my interests. Basically the department was more applied-oriented (almost exclusively so) than I wanted to be.
I basically said that I wasn't a great undergraduate and that now that I had some successful grad courses under my belt, I wanted to re-apply to grad school and get to a better school.

After reading this statement, my advisor said almost verbatim,
"Please tell me you have not shown this to anyone else. You can't show this to anyone else without removing [item 2. from above]."
The major moral here is that there are reasons for switching PhD programs that will be perceived as legitimate, but prestige may not be one of them. I came from a liberal arts background with not much knowledge of the different types of research, and learned after a year in grad school that I was not in a location that would support my research interests. This is perfectly reasonable (in my opinion), and it was also plausible, given the department I was in.
I don't know anything about your field, but I imagine that if you enter a rather top-notch* program like Minnesota and then want to go to a different school to somehow start your actual PhD, I think you will cartainly have to explain your reasons for switching.
You want to go to the higher-ranked school for prestige? Probably this reason will not be well received.
You couldn't find a match for any of your research interests in Minnesota's department? Well, Minnesota is a great department that many tenure-track seeking new PhD's would love to work in. If you can't be a successful researcher there, what kind of researcher are you?
Of course I'm inventing the answers to these questions, and there are many reason's one might switch grad schools. But the point is that you should have a good (by some measure) reason for switching grad programs. If such a reason exists, I think there is nothing negative about changing programs, and I doubt getting into your second program will be more difficult with your Minnesota Masters degree.
*I'm assuming this department is perceived as top-notch based only on jakebeal's comment to the question.

"Great answer" comments are discouraged, but this is such a thoughtful answer. :) Welcome to academia stackexchange!

Thanks for ur reply. I agree that recommendation can be bit tricky. But like I said, I don't need reco from UMN profs. I am not sure if this will be against me or not.

@user33283, not having a recommendation from anyone in your current program will almost certainly be bad for your application.

Question: Why is reason 2 so frowned upon? Every single student I know (I am a student, also) want to go to the best possible school. What's wrong with that?

If you want to be in academia, you are making a mistake of treating graduate school as the end of your academic career, rather than the start.  Getting into a really good school is all you need at this point: there are professors who are just as world-class at a place like University of Minnesota as there are at MIT or CalTech, just less of them or in more focused sub-disciplines.
Your goal now should be to have a damned good graduate school career in the school where you are accepted (which, again, is a very good school and highly selective), and eventually line yourself up for the best postdoc that you can get.  In Physics, as in many other disciplines, you are expected to do a significant amount of postdoctoral work: postdocs come from all over, and it is the work you do as a postdoc that will have the most effect on your application for faculty positions.
So: don't waste your time now trying to optimize the wrong phase of your career.  Buckle down, do some excellent graduate work, and line yourself up for the right next step.

Thanks for the insight. But still, the question is unanswered. I wanted to know if this is possible and how rare or common is it ?

@user33283 Sure, it's possible, but it's pretty rare, partly because it's a bad idea.

I guess I'm out of the loop. I knew a handful of PhD students in grad school at the University of Texas who had gotten their Master's degree elsewhere first. There was no shame in it, but they also didn't start completely over. They came in having done their Master's, had the vast majority of their coursework requirements waived, prepped for their qualifying exams, took them, and then went straight into research. Some of them took several classes along the way to catch things they had missed, learn some exciting things, interact with eminent professors, etc. They did fine. It's not that uncommon to take a Master's at one US university and then a PhD at another. But, there's no need to completely reboot your career to do it.

Thanks so much Bill. Its good to hear that. May I ask, those students at U. Texas, Which major did they belong to ?

The primary one's I was thinking of were in a computational and applied math major which has since changed its name but is still run by the Institute for Computational Engineering and Sciences. There might also have been an Aerospace Engineer or two (which was my major).

I can't speak to physics, but in my field the master's you receive on your way to a Ph.D. is not equivalent to a standalone master's---and coming from a school with (primarily) a nonterminal master's program is often viewed as "couldn't cut it for the Ph.D." I'm under the impression from the original question that this is the sort of master's she'd be pursuing. I mention it because your answer is a little unclear regarding what sort of master's degrees you're talking about.

@kyle, exactly. UMN does have a terminal master program. But I am a part of masters en route Phd. I am afraid, I may be looked down bcoz of that.

@user33283, I think that admissions committees can tell the difference between those who couldn't hack it in a PhD program and those who could. Those who can't hack it don't apply from a lower-ranked school to a higher one. If you get admitted to MIT after a year and a half at UMN, who cares what other people think about your time at MIT? If you're really concerned about the perception, switch to UMN's terminal master's now.

JFK said, "Ask not what your country can do for you, ask what you can do for your country."  User33283, don't be a snobbish leech.  Don't turn down the meatballs before trying one, just because you think the Angus steak is more prestigious.
Go into your new school with the best possible attitude you can: you are a smart, curious, thoughtful, hardworking person; the school you will be attending has a great deal to offer; if you come across a professor there that doesn't appeal to you, just steer clear of that person; and gravitate to the people you find stimulating, helpful, ethical; etc.
If the school turns out not to be the right fit, despite your best efforts, then you'll have your reasons to move elsewhere.  And you'll have your recent recommendations (which WILL be needed, as @Potato pointed out).
Now, here's a point that will help you swallow the above: if Minnesota is not among the top-ranked schools, then you'll be able to be a big fish in a medium pond!
Just make sure you're a big fish with integrity.

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Advisor pushing for dead end topics
I am new to this forum. I am encountering a problem in my doctoral studies that I haven't been able to find in an existing thread so I wanted to ask here. Any advice on how to navigate this would be very welcome.
I'm 2.5 years into my doctoral studies (geography) working under two co-advisors. Their areas of expertise broadly overlap with my dissertation topic, but the topic is my own, and I know the study area better than both of them. One advisor has been pressing for me to conduct a certain methods for social data collection that I knew wouldn't work (research fatigue is high in this area, distrust towards scientists without existing connections in these communities is a huge - if not insurmountable - obstacle). I tried to explain that these issues would make this type of social data collection very hard to pull off. I suppose I failed at this communication, because he pressed for this method all the same (with the rebuttal "science is hard"). Because he's an advisor I assumed he knew something I didn't, and I wrote up a dissertation proposal with this approach being used to answer one of my research questions (in my program a "dissertation" consists of three publication-ready papers). I emailed a few groups engaged in work in these communities. The reply I got was what I expected: they strongly advised against attempting to collect household surveys for the reasons I had tried to explain to my advisor before. I just got this reply today, I have not yet discussed it with my advisors.
This does not sink my entire research proposal necessarily, but only a portion of it. There are other methods of data collection and analysis I'm still working on to answer the other research questions. Furthermore I spoke to my other co-advisor earlier in the fall (not a social scientist) asking what my recourse is if the social data collection component falls through for the reasons I feared. I was told not to worry necessarily, that we could figure out a way to work around it.
That being said, I'm still worried. I'm worried that the advisor who pushed for the an approach that was ultimately dead-on-arrival doesn't fully understand my research. He's suggested approaches in the past that have turned out to be dead ends too. I'm also worried that I wasn't able to recognize this as a problem until I am 2.5 years into my program. The heavy initial course-load (full graduate course-load for the first two years) and first few research dead ends had me seeing the individual trees, not the forest. I'm sure a lot of this is my fault; I should have communicated better, I should have been more clear on what the expectations were. But now that I'm waking up to the fact that this is a problem, I'm not sure what to do about it. I have (excuse the lack of modesty) a good topic, and I think there's still a lot of value in seeing it through. I suppose I will have a better idea of what to do about this when we all meet next week, but an outsider perspective would be really valuable to me right now.
Thank you in advance

It would help to clarify roughly where you are (particularly US vs Europe) and how long you expect your PhD to take ( / have funding for). In the UK, at least in most physical sciences I know, you'd be expected to be wrapping up or well on your way by the 2.5 year mark, but obviously Academia is a varied place. With that in mind, having more information about how much breathing room your timeline has will help get you answers that are more useful.

More of an interpersonal answer, but if told "you should do X", a direct dismissal, e.g. "that won't work because of Y", could very well make them defensive and harder to convince. Phrasing your objection as questions, e.g. "wouldn't Y be a problem?" or "how would we solve problem Y?", is more likely to be well-received and lead to them seeing things your way.

I've read this twice and still can't find a question anywhere. What's the actual problem to solve here?

@pipe how should op respond to professor, given that research proposal is DOA

One piece of useful advice my thesis supervisors gave me was:

We're going to throw a lot of ideas at you. You need to figure out which ones are worthwhile and which ones aren't.

If you know that something isn't going to work, then you need to figure out how to communicate to your advisor that it's not feasible. If you've tried and didn't succeed in making your case, try again using a different means of communication. Remember that the ability to make a convincing argument is crucial to success in research.

If I may elaborate on the last sentence: either there are objective reasons why it is a dead end, then you should identify them and use them in your argumentation; either there are none, and maybe your advisor is right.

How would OP respond if his/her adviser is adamant on a dead end? Stand his/her ground?

@FrankFYC If the advisor is insistent, then do enough work to show the approach won’t work, while making progress on other fronts.

@aeismail but at the end of the day, the final decision is OP's correct?

A few (hopefully) practical measures:

Talk to your co-advisor about this, asking him to accept your position and, assuming he has, to call for a three-way discussion of this matter.
This is not always possible, but if you can - schedule the dead-end work last, i.e. after other endeavors about whose success you're more certain. Why do this? More opportunities to change the advisor's mind; time for him to learn to better value your judgment; or perhaps even time for you to theoretically reconsider your opinion.
Regrading your "failure at communication" I: Write up your objection - Write either a methodological survey paper, or something less formal such as a blog post, arguing the shortcomings/dead-endedness of the collection method.
Regrading your "failure at communication" II: It sounds like you feel ashamed/afraid/embarrassed to bring up the subject again with your advisor after it was supposedly settled. Try to accept the danger of appearing foolish/obstinate etc. and have another go at convincing your advisor, being better prepared for it, perhaps with material you can pull from some folder you've compiled etc.
Consider whether you can't do research on the failing methodology. You could employ both collection method A (the poor one you disapprove of) and collection method B (a better one), documenting your preparations for both and the process of collection, more closely than you would do when interested in just the results. Then, besides a paper about the actual subject matter, you could write a methodological paper about the comparative failings of the method you disapprove of. In other words, make lemonade from the lemons.
Consult your advisor's other graduate students, current or former, about this matter. Maybe they've had similar issues and can share their experience of how they handled it. Hey, maybe one of them has had the exact same issue regarding data collection, which would help you even more.

It goes without saying you shouldn't try all of these at the same time (but some of these do fit well together).

Not all advisors are up to the task, and sometimes they are wrong. I've personally encountered situations where advisors were wrong and guided (or misguided) their students down a failing path. Depending on your university, and your financial situation (are you beholden to a particular advisor for your grant funding?) it might be necessary to find another advisor.  You indicated you already have two, perhaps a 3rd?
That said, remember your goal is to get the PhD.  Share this feedback from the outside groups with both of your advisors and discuss it with them. I'd start first with the one more likely to agree with you, then the other.  If he/she still insists, then politely toss the ball into their court: "Professor, I don't understand how this (survey stuff) is going to work given the limited time and resources, can you please show me how we can do this."   I used "we" on purpose - it draws them in as a collaborator not an opponent in an argument.
Part of the PhD process is learning how to manage people, your advisors in this case.
Also consider the possibility your advisor is correct.  It's not easy for the student to call out the master, and you have to be pretty darn sure if you do.  If the advisor is wrong, find a way for him/her to gracefully back down rather than challenging them directly.
Been there, done that.

Some further practical points in addition to @einpoklum's answer, in particular the advise of having another go at convincing the advisor (and too long for a comment)
Directly trying to convince your advisor (who is convinced of the opposite) may just result in more communication chaos. So instead, I'd

ask the advisor for an appointment to discuss (again) the choice of method: Ask the supervisor to let you first present your point of view so that once they know your understanding of the situation they can convince you of their point of view.
present your arguments
keep in mind that practical arguments are not necessarily scientific arguments. IMHO, they should be marked as such and then practicality considered separately from scientific arguments*.
Practical arguments against doing something share the disadvangate for you with negative results that there's always the latent question lurking of you being lazy or not good enough. So make sure your presentation of arguments will not look as trying to avoid hard work.
Now listen to their arguments.
Actually, you should also prepare a list with the advantages of the method. Doing this in preparation for the discussion would put you into a much stronger position, and it is actually an important working technique to be able to identify advantages of methods you dislike. Take the role of the Devil's Advocate.
The important point for the discussion with your advisor is: you need to be willing to be convinced! Be curious how they come to the opposite conclusion you came to.
Otherwise, no communication to solve the scientific/practical problem can happen.

* I have in mind several situations where computational feasibility was a question. I found that quantifying the effort goes a long way: computation time of 1 h (single occasion) may be unpleasant in an interactive session, but is certainly feasible in general. A final calculation taking a couple of months on a desktop computer would IMHO be quite inside what can be expected for a PhD thesis (I mostly deal with calculations where a "sneak preview" will give you a rough idea what is going on and then lots of computational effort goes into refining the results). So would be a couple of months of unpleasant final data collection given that pilot experiments/a small pilot survey shows that this is actually the way to go with the data collection. Whereas a computation that would take several years of Rosetta@home would clearly be outside a single PhD thesis and there would be no discussion whether this is feasible or not.

Building on cbeleites’s answer - ask for a couple of recent examples relevant to your work where your advisor’s approach was used to good effect.
It may be that your advisor has more insight on how to do this properly, and you can learn something from the examples. In that case, your advisor would likely be able to rattle off a few references off the top of his head. Studying those examples should give you some idea of how to do what your advisor is advising (which, incidentally, may not be exactly what you’re objecting to).
On the other hand, it may be that your advisor is too busy / is distracted / etc, and makes the same suggestion to all his students. In that case, it might be harder for him to come up with relevant positive examples, and you can then suggest a few relevant positive examples you’ve found that follow your preferred methodology. (Naturally, you’ll have to do some work to find those examples first.)


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Having a low tier publication as an undergraduate student?
Is it a good thing for an undergraduate student to publish in a low-tier conference as first author? Or should the student avoid such places and only publish in at least reputable places? If it is a good thing, how should the student present his study in the graduate admissions process to admissions members (since the conference name is mostly unknown to much of them)?
Note that, by low tier, I mean the conferences which are ranked at "C level" according to ERA (Excellence in Research for Australia).

"low-tier" is not the opposite of "at least reputable".

Let me answer the important parts of your question:

Is a good thing for an undergraduate student to publish in a low-tier conference as first author ? Or should the student avoid from such places and only publish in at least reputable places ?

Yes, especially if the venue is peer-reviewed.
As the answers to this question suggest, graduate schools look for evidence of research potential. The undergraduate research experience is about developing some basic skills and demonstrating that you are capable of handling a research project. Publishing at a third-tier conference, so long as there is some level of peer review, is better than no publications. Would publishing at a higher tier conference be better? Sure, but it might not be worth the effort or the risk of rejection. Publishing at a third-tier conference would look better than being rejected from a first-tier conference. Being first author on a paper at a lower tier conference should hold more weight than being a middle author on a paper at a higher-ranked conference.
Your research adviser probably has some wisdom about the level of conference at which your work should be presented. Choosing a lower tier conference is not about making your work seem less important. The choice might be about guaranteeing you get the change to present it at all.

If it is a good thing, how should the student present his study in graduate admissions process to admissions members, since the conference name is mostly unknown to much of them?

Present your work and conference presentation the same way you would present any other similar experiences. If you have to provide a personal statement as part of your application, write about the experience and how it benefited you. If they ask for a list of relevant accomplishments, include this presentation in that list. Put it in on your resumé. Ask your research adviser for a letter of recommendation.
Do not use any negative language or derogatory language when describing your experience. For example, don't mention that the conference is lower tier or that you thought you could have presented at a better one. If the admissions committee knows about the conference, then they already know about its ranking. If they do not, then you should not be the one to give any hint that you think your experience might have been sub-par.

Just to add to extensive Ben Norris's answer - as far as I know, ERA has been discontinued, but, Brazilian CS community did a conference ranking for their internal evaluation purposes. Here is the list (explanations are in Portuguese, but the names of the conferences are from all over the world) - http://www.capes.gov.br/images/stories/download/avaliacao/Comunicado_004_2012_Ciencia_da_Computacao.pdf, A1 is the best, B5 is worse - that is essentially based on h-index of a conference computed via this tool: http://shine.icomp.ufam.edu.br/index.php
May be the conference where you published is of better position there:)? There are also several community-driven rankings but I cannot post links to them as my reputation is not enough for posting more than 2 links;)

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Submission changed to a different status, but with the same explanation as the previous status
(this line is added later ) : The length of the paper is only 3 pages.
Soon After Submission

Article Status:  Reviewing
Your paper is being reviewed by the journal’s editors and you will be contacted as soon as we have news.

After a month changed to

Article Status:  Under Review
Your paper is being reviewed by the journal’s editors and you will be contacted as soon as we have news.

See: https://academia.stackexchange.com/questions/55665/what-does-the-typical-workflow-of-a-journal-look-like. These two likely mean editorial assessment and peer review respectively, i.e. in the first case it's the editor checking it, and in the second reviewers have been invited.

Just one note, the status of my paper has been changed from  Reviewing to Under Review after three month and now is the Under Review too.  I suggest you to wait and concentrate on your next research.

@user0410 : thanks. May I know the journal name? Did the status explanation say editors or peer reviewers?

For your first question, my answer is No. For the second question: My status of paper is the same as your paper. Therefore,  please be patient.

Thats a valuble info. Thanks @user0410 . Looks like this status is the normal thing for this journal.

Initial answer: (This answer assumes a regular type of full-length paper submission in the standard journal workflow.) This is probably an error in their explanation of the current status. The explanation is not in line with the typical journal workflow, especially the highlighted part:

Article Status: Under Review
Your paper is being reviewed by the journal’s editors and you will be contacted as soon as we have news.

In the typical journal workflow, the review is performed by the invited reviewers, rather than by the journal's editors.
You may contact the journal to task for clarification, but it probably won't matter in the end, as the process doesn't depend on this (incorrect) explanation.
Updated answer: (This update takes into account that the submission only has three pages, and that the journal uses a decision-making step based on consensus between the editorial board members.)  In this case, it's plausible that they're wont be additional reviewers involved. I speculate that the first status refers to the assigned editor handling the paper, and the second status refers to the editorial board making the decision. In this case, the status would not have any implication for the decision, other than removing the possibility of a desk-reject.

In that link (workflow), it is mentioned that, editorial assesment phase also can use the status "under review".

@RajeshDachiraju One particular system does that (and it arguably uses a slightly confusing terminology). However, unlike the system here, it doesn't have two separate status "Reviewing" and "Under review" with the same explanation.

This journal has a voting system by all members of the editorial board to make a decision. Can it be related to this?

@RajeshDachiraju Could be, even though this kind of decision process seems rather nonstandard in the first place. To be honest, in combination, these nonstandard procedures and erroneous/misleading descriptions don't cast the best possible light on the journal.

Its fairly reputed. Moreover the paper submitted is only of 3 pages. Would that cast any more light.

@RajeshDachiraju That is fairly relevant context. In this case (which is rather exceptional), it's plausible that they're wont be additional reviewers involved.

In that case, which makes sense, whats the need of a status change?

Do you also mean/think its going to be a rejection for sure?

@RajeshDachiraju I speculate that the first status refers to the assigned editor handling the paper, and the second status refers to the editorial board making the decision. In this case, the status would not have any implication for the decision, other than removing the possibility of a desk-reject.

a small mistake, its not voting but consensus.

Could you edit your answer in the new context?

@RajeshDachiraju Done

It means that your paper is being reviewed by the journal's editors, and you will be contacted as soon as they have news.
...
What kind of answer were you expecting?

I know that. What Iam asking is what is  the indication of that change in the status when they both convey same meaning?

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Is it appropriate to ask a professor via e-mail for a letter of recommendation?
I have been out of school since May now, and I am considering applying for graduate school. I currently live nowhere near the university I attended.
Would it be appropriate for me to ask for a letter of recommendation via e-mail? If not, what would be the best option?
[Suggestions as to how I should approach such a communication would be appreciated as well.]

I don't see why not, but we can always entertain the possible outcomes. Scenario 1 - It is appropriate. Professor has no issues. Scenario 2 - It is inappropriate. Professor emails you back a stinging rebuke remarking on your poor etiquette and demands that a formal request be penned in black ink and sealed with a red stamp featuring your family crest. Alternatively, if you have his number, you can call him.

Yes, of course it is appropriate. Why wouldn't it be?

@JukkaSuomela - I ask since a particular friend of mine says to request in-person, which I would do, but it's not possible currently.

If you're on-campus, then it doesn't hurt since the professor can put a face to a name, but realistically speaking, if your professor can remember who you are by name and face without seeing you, the email is fine.

In-person requests are always the best route, because you can gauge willingness and eagerness to write the letters much more directly than via telephone or email.
However, if you can't be there, because you've moved away, then it is of course appropriate to ask for letters by email. Whether or not the professor will grant the request or not is of course a question. However, I would mention that you've moved (and where you currently are) as part of your request, so that the professor knows why you're not able to come in for a meeting if asked.


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Can I work on old manuscripts using personal time?
I submitted few manuscripts to some journals during my PhD and moved to other institute for postdoc (full-time) in few months before. Now one manuscript has come for revision and other manuscripts may come soon. I have following many questions in my mind.
I am wondering is it ethical to spend some time to make revision of my old manuscripts in holidays/weekends in my house without using any resources from Institute?
Should I need to discuss this matter to my present supervisor or Institute?
Should I acknowledge my present Institute? Is it also necessary to change my affiliation?

In addition to what's been said in the answers very few supervisors will mind you spending a little time during the working day on it, especially for things like communicating with your old group while they're in work.

What ethics do you feel are being challenged here?

I expect the post-docs in my group to spend time finishing up manuscripts from their graduate work, with their affiliation that of their university (with a 'current address' footnote). In return, I expect them to spend time on their next job finishing up manuscripts from the post-doc. I suspect your current advisor would like all their manuscripts treated as such.

Let's address your questions one by one.

I am wondering is it ethical to spend some time to make revision of my old manuscripts in holidays/weekends in my house without using any resources from Institute?

What you do on your free time is entirely up to you: no job, boss, or conditions, can take that away from you...
(Well, almost… as noted in comments, there can be clauses that limit your abilities to work on other projects, but I would think that the principal case in which it causes problem / conflicts of interest, is when that "side activity" is paid, which, I assume, is not your case.)

Should I need to discuss this matter to my present supervisor or Institute?

...yet, depending on the sensibilities and particular conditions of your employment, you may want to tell your supervisor. You don't have to make it super formal, as it is rather usual for a young post-doc to have ongoing work that follows publications made during the Ph.D. Just mention that you'll be working on some revisions on your free time, and that should be fine.
If your supervisor shows interest ("Great, you should make a presentation", "Tell me more", "What are the connections with our current project?"), you can try to make fruitful connections, but that may not arise.

Should I acknowledge my present Institute? Is it also necessary to change my affiliation?

I would think that this will depends on the country, institute, kind of supervisor, and many other aspects. Listing your former institution as the "main institute", and your current institute as your current address would probably be the safest option.

If the work was performed without resources of the new job, then the best way to address the affiliation is to use the old affiliation, and list the new address as a "Present address"-type footnote. Most journals routinely allow this.

I would acknowledge the institution where the majority of the work was carried out, unless significant reworking was needed and this was done during 'work time' at a different workplace.

"What you do on your free time is entirely up to you: no job, boss, or conditions, can take that away from you...". I don't think that's correct, or at least not universally. Most work contracts (and in some cases even legislation) include implicit or explicit non-compete clauses.

@jcaron Yeah, was thinking about the same thing. In general a lot of those non compete clauses are unenforcable for the most part in most places around the world, but a contract can definitely limit what you can do in your free time.

@jcaron Good point. I edited my answer. I would think that non-complete clauses involves paid activities, but this might not universal either.

In many employments, one thing that's done at the time which the contract/in-processing is signed/done is list prior work which is not yet public/protected (i.e. published, patented, etc.). This is done to protect your rights to the work (i.e. exclude it from any rights which you are assigning to your employer). Often, you can list on-going projects/papers/ideas/etc. Depending on the jurisdiction/contract, the employer could end up having an interest in anything not explicitly disclosed. What happens varies greatly based on the jurisdiction/contract. Consult a lawyer if you want advice.

This is one of those things about academia that likely varies across disciplines. The answer below pertains to norms in mathematics. (It might help if you provide more information about your discipline so people can give more accurate answers.)
In mathematics it is customary to sign any paper you write while employed at institution X as "[name of author], Institution X". The distinction between "personal time" and "work time" is essentially nonexistent in the context of paper authorship, nor is there any discussion of the physical location where the paper was written or whether work "resources" were used.
In your situation, as I said I would sign the paper with my name and current affiliation, and add in the acknowledgements a note along the lines of "Part of this work was done while the author was at Institution Y", where Y is the name of my old institution.
As for discussing your plans with your supervisor, yes, in mathematics it would be expected that you discuss such projects with them, at least to the same extent that they would generally expect you to discuss with them what you are working on (which is not necessarily a very high extent - postdoctoral researchers in mathematics are generally pretty free to work on what they want and there isn't a high expectation on the part of the supervisor that the researcher spend all their time on things that are directly useful to the supervisor). Again, the fact that the projects are continuations of things you started elsewhere or that you plan to work on them during time that you consider as "personal time" is immaterial to the question.

If you do the revisions entirely in your free time without resources from your current job, then your official address should be the institute where you did the Ph.D. work. Your new address would be indicated as "current address." It would not be absolutely necessary to discuss the matter with your current supervisor, but it would be polite to do so.
If, on the other hand, you use work time or resources from your current job, then you should get your current supervisor's approval.  I can't imagine a reasonable supervisor denying you this approval unless the revisions were so extensive and your work on your current project so urgent that you just can't spare any work time for the revisions. Assuming you get your supervisor's permission, you should either list your current institute as a second address (if the revisions were quite extensive, so that a substantial part of the paper resulted from work at your new address) or put a footnote on the first page indicating what part of the work was done at the new address (if that part was not so extensive).
I should add that I'm answering from the point of view of a mathematician in the U.S. (except for the part about "your work on your current project is so urgent ..." which is extremely unlikely in mathematics but can easily occur in a lab science where you're the one who keeps the lab functioning).  Other fields and other countries might have different ideas of what's appropriate.


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Co-authors are not responding due to their very very busy schedule, How should I handle it?
I prepared a manuscript along with two co-authors and submitted the manuscript to a journal in January 2016. However, the manuscript was rejected in April 2016 and given another chance to resubmit after addressing the reviewers' comments.
I did all the revisions and submitted to my co-authors since August 2016 to check the revision. But none of the co-authors have responded to my emails, even after seven or eight gentle reminders at regular intervals. As both of them are top-level professors at very reputable institutes and heads of their department, so I understand their very busy schedule.
How should I handle this situation?
I found another question similar to mine: How to handle Co-author who is not listening the suggestions to improve the paper quality, but I did not find my answer there.

My approach to this kind of situations is the following: set a deadline, send a reminder a few days before the deadline, resubmit. That's it.

@MassimoOrtolano And soon, the co-authors will say that you submitted a paper without their approval. You should always get everyone's approval before submitting, especially after major changes have been done (i.e. everything that exceed spell checking).

@Mark It's hever happened. When I set the deadline I state clearly that if I don't get feedback for that date, I'll assume that they agree. If they don't, and they don't answer, too bad for them. In all the collaborations I've been part of, this was usually the expected behaviour from the first author.

Ask them if they'd like their names removed from the manuscript. I'll bet you'll hear back promptly.

Related post: https://academia.stackexchange.com/questions/14146/what-do-i-do-when-a-co-author-takes-too-long-to-give-feedback-during-the-peer-re

In general, you are the lead author. If you are keen to progress a paper, then you need take the lead. This may mean that you wont get as much feedback from your co-authors as you might want. But this is generally better than delaying a publication for months and months. I also find there is a real cost in having to get back in the zone on a paper that I'm leading when it is put on hold because of such issues.
I would typically give co-authors a specific timeframe to make a contribution. For example, I might say that I am going to submit the paper in four weeks, and thus, any feedback they can provide in the next two weeks would be most welcome. I'd also try to get feedback from them about when they might have time to have a look at it, and I'd try to arrange my own schedule for working on the paper so that I'm able to send something through for when they might be free.
Of course, this is something to be negotiated. Sometimes, co-authors may want or expect to have greater involvement. Or you may think that their input is worth waiting for.
The case where a student is the lead author is also another variant. In that case, the supervisor would have more influence over timelines. In this case, the student may also be relying on the supervisor more to make sure that the manuscript is ready for submission.
What about co-author consent?  Nate Eldredge raised the following issue in comments:

Don't you need the consent of all co-authors in order to submit a paper? So if they don't respond by your deadline, I don't see how you can ethically go ahead and submit anyway.

I agree that co-authors need to consent to having their name listed on a paper. That is very important. And you can imagine situations where consent would be an issue.
However, from my experience, in many situations the consent is implied. First, co-authors have usually already agreed to be involved in a publication at the start of the project. And in the above case, the co-authors have already submitted a paper and now they are revising it to submit it again. It's common for one author to take the lead on these kinds of revisions.
Then in the usual case, the lead author will send  emails to co-authors outlining a publication plan with a timeline as well as follow-up emails as it gets closer to submission. The lead author would also send emails about when a submission occurs and when the status of the manuscript changes. At every stage, co-authors are free to negotiate the timeline, their input, and whether they wish to remain a co-author.
In most cases, co-authors respond to emails. Busy co-authors may not have time to actually make a contribution to the paper at that time, but any reasonable co-author will reply to emails in a reasonable time at least indicating their intentions about the paper (or they should have an auto-reply to say they are on leave). Furthermore, a submission is not the final word on authorship. For example, if a co-author didn't respond to emails for four weeks and then finds out their name was put on a submission that they did not approve of, there will still usually be plenty of time to withdraw their name, or make sufficient changes at the revisions stage.
So, I think if the lead author engages in reasonable correspondence about the publication plan and the submission process, then the issue can be navigated.

Don't you need the consent of all co-authors in order to submit a paper?  So if they don't respond by your deadline, I don't see how you can ethically go ahead and submit anyway.

@NateEldredge see response.

@NateEldredge As I said in another comment, e.g., I set a deadline and I state that I'll assume consent if I don't get feedback. This was quite common in all the collaborations I've been part of.

Especially after the first submission, it feels much more kosher to give a deadline for a revision (i.e. they've already approved the majority of the paper).


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Rehearse or memorise to improve my presentations?
This may be a dumb question. I would like to improve my presentation skills.
So should I rehearse my presentation at least 5-10-20 times? Or should I memorise my presentation and practice it enough?
When rehearsing, I make my presentation in front of a mirror and observe that I deliver the same messages in a different way in each time, while if I memorise what to say for each slide of my presentation, then I deliver the same messages in same way very confidently each time I practice in front of a mirror.
So I am getting confused which one is the better method to deliver an effective presentation?

You should use whatever method works for you. That method will most likely change over time. Personally, I prefer hearing presentations that are rehearsed, rather than memorised.

Have you seen https://academia.stackexchange.com/questions/17984/how-to-do-a-flawless-and-natural-presentation?rq=1?

The best are presentations based on understanding : these can easily change direction due to questions or interest from the audience.

My clues are: don't memorise, don't read from a sheet of paper, rehearse, like 5 times, try to remember a general red thread and speak naturally. Manage your time.

Well, you can get some ideas from at least one guy who was known for being an okay presenter. Whether and to what extent his methods translate to the setting of academia is somewhat debatable.

A further nuance: Practice the first few minutes more often and with a more polished/definitive wording than the remainder of your talk. The first few minutes are special, because you need to grab the audience's attention and make them feel comfortable listening to you. This is the part where you need to project confidence.

There's no right answer here.
I had a colleague who would rehearse her presentation to the point of memorization. (Important detail: this was in the days when transparencies were still used in preference to laptops.) During her presentation, she discovered her slides got messed up in traveling, and had a very hard time recovering from the problem. So the problem with memorization is that you may or may not be able to deal with it if you're thrown off your script somehow.
However, some people get so nervous about the idea of a presentation that they can't handle it without memorizing what they're going to say. The reason why this works for them is that recitation uses a fundamentally different part of your brain than normal conversation. (This is why people who stutter in normal life don't stutter when acting.)
Personally, I try to just have a list of major points for the slides, and then work "with the audience" to get my points across. (For instance, if I'm talking to a room full of chemists, I'll give a different talk than when I'm presenting to an audience of chemical engineers or computational scientists.)
But you just have to experiment and find what works best for you.

It's not "either rehearse or memorize". Also, your sentence "In rehearse, every time I make presentations in front of mirror and observe that I am delivering same messages in a different way in each time." got me thinking that you probably rehearse inefficiently.
The purpose of rehearsal is to improve your presentation. So after every rehearsal you should reflect about your performance, think about points that did not come across right, and about ways to improve the presentation. If you just start over again without reflection and without a new, improved plan, you do a weird mix of "not really rehearsing" and "not really memorizing".
I'd say, a good rehearsal includes quite some memorization for the crucial parts. However, if you rehearse long enough, you may get to some point where do not even memorize your lines, but where the presentation has a natural flow such that your previously memorized phrases come out naturally.
I'd say, bare memorization is ok, but may be dangerous if you don't know the story line of your presentation as a whole. Imagine that you loose you lines and get stuck in the middle of the presentation. So also rehearse to speak freely but memorize some lines that you find particularly good at crucial points. A good structure of the presentation and a good story is very helpful here (and for a badly structured presentation, neither memorizing nor rehearsal will lead to a good presentation, anyway).

Prepare on your own first and then -- this is the key -- give a practice talk to a small group.  Ask a friend to jot down notes from the feedback people give you at the end.  Make sure the people you invite to listen to your practice talk know how to give constructive feedback in a supportive way.
If you are fairly inexperienced, you may want to do some rinsing and repeating -- but don't overdo it or the talk will lose its freshness.

I cannot memorise and so would always rehearse. At first I was very nervous  and practiced many times, but over the years I learned to care less. These days, I am confident enough in my knowledge of a subject to trust that the slides will queue me to say what is needed to get the message across. Anyhow, I do not know if this applies to you, but I would recommend that you sometimes talk without preparation. The quality of the presentation will suffer and it becomes more difficult to manage your time (so save this for an informal presentation), but it is a liberating experience and I find that it removes most of the stress involved.


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Going from co-advisors to just one advisor
I'm 2.5 years in to a 4 year PhD with possibility of a 5th year of funding. I started with one advisor, but research interests started shifting, so we brought on a co-advisor. My research interests have continued to shift in the new co-advisor's direction. The research components that the original advisor can guide me on are hitting speed bump after speed bump and never really getting off the ground. I've been making steady progress with the research components of the new advisor. I want to have the "new" co-advisor  (not so new by now) just be my main advisor, and have my original advisor just serve as a committee member. Feels like a cold move, seeing as he was the one that brought me on in the first place. But he recently mentioned he's no longer sure how to advise me anymore, so I think he might be thinking the same thing.
I worry I'm too far into my program to make such a move. My comprehensive exams are coming up this semester, which complicates the timing of this as well. I want to suggest this move to my co-advisor in a way that is tactful and won't cause waves. But I'm not sure how to go about it - you can't un-ring a bell.
My questions are:

How unusual is it to go from two advisors to one after 2.5 years, and am I better off making this change or doing the best I can with the situation I'm in?
If making this change is better, do you have any advice with regards to how to do it so that I don't make a mess?

I am not being directly funded by either advisor, like with a grant. Funding comes through university assistantships. Additionally, keeping the original advisor on in a co-supervisory role is not an acceptable solution, because the original advisor is adamant about research approaches that don't work, and - at this point - also fall outside my interests.

I think the optimal answer depends mostly on your situation and university. However, I try to give you some general advice. From what I have seen in your question, you might already be one step to far into the decision. I would rather start an open discussion with your first advisor and express your concern. All further steps, such as switching advisors, can be the outcome of your discussion, but there might be different and better solutions.
It is quite normal that research interests shift after some time into your PhD. Since you are making progress, you see which ideas are working out and which don't. You will get to know new topics and new questions will arise. This will have an influence on your research, of course.
Your advisor seems to see that, too:

But he recently mentioned he's no longer sure how to advise me anymore, so I think he might be thinking the same thing.

By expressing his concern, he already shows some awareness of this issue. You should try to talk to him and find a solution together. I would not approach him like "I want to replace you with advisor Y". This can come across as very rude since this is on a personal level. Start a discussion that focuses on your research. Talk about your concerns that your interest have drifted apart and try to come up with possible solutions. When you are further into discussion you could also include the co-advisor. As already mentioned, switching advisors might be one solution but it might not be the best one.
The more you integrate your advisors into the discussion, the less conflicts I would expect. Do not push your decisions onto them as this could really affect your current position. Talk to them and find a solution together.

I believe you have asked an X-Y question. Or rather, you are tacking an X-Y problem.
You see, it actually doesn't matter who's listed as your advisor. Your actual issue seems to be:

... co-advisor is adamant about research approaches that don't work, and - at this point - also fall outside my interests.

If he were magically removed as a co-advisor, then you will have circumvented this issue. And then you ask yourself "so how do I remove him?"
I'd suggest tackling the actual problem. First, I'd talk with your newer co-advisor about the situation, and see what he suggests. Perhaps he'll offer a meeting of all of you three regarding your progress, at which your older co-advisor would have to convince your newer one; or they might come with an idea you haven't thought of.
Another possible avenue of action is using the fact that your older co-advisor  says "he's no longer sure how to advise me anymore". Perhaps he himself realizes that the course of action on which he's been pushing you is not leading somewhere useful? It seems contradictory to insist on your advisee doing certain things but at the same time express doubts about your ability to advise him/her further. You haven't given too many details, but it sounds like there's a sort of a "crack in his defense". @J-Kun's answer makes some pertinent suggestions in this context.


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Is It OK for an academic to have broad research interests?
First of all I am a second year M.Sc. Student in Computer science, working on information networks and enjoy my research a lot. In my B.Sc. final Project I had worked on intrusion detection systems, which was actually a computer network protocol related area and irrelevant to my current field.
I should mention that actually I am not frustrated with my current research or topics that I was working during B.Sc. But the problem is that I am also so excited about other nearly irrelevant topics.
For example I have passed about two courses in signal processing and now sometimes I am thinking about continue my PhD in that field. I am also interested in algorithms and CS theory, etc.
I want to know is It OK to have such broad activity in your resume or this can flag me as picky person regard that I finished successfully every project that I had been started and it can be verified in Recommendation Letters and so on.

It may depend on place/discipline. But as a PhD student (in quantum information) people were surprised that I had other interests than my PhD thesis (and that I do know anything at research-level on things not related to my thesis). While surprise was (usually) positive it was telling a lot that it's weird for me to know things from other disciplines (and I felt "not belonging"). And I have feeling that anything by smooth transitions between closely-related fields is looked down (for one being non-serious, shallow, etc) and may harm application chances.

@PiotrMigdal This is how science dies, people digging trenches around their field, and pretending that outside knowledge is useless. The truth is, the broader your knowledge, the better the chance of making new discoveries and connections.

There is nothing wrong in showing interest in various topics, as long as you obtain deep results in at least some of them.
Without having any deep results in some of the fields, it really looks bad, because it looks like that you are unable to advance enough in something to push the topic forward. It more looks like you chicken out of any serious job, because, frankly, in most disciplines the way to obtain deep results is quite painful.
But, as long as you obtain reasonably deep results in your topics of interest, you should be fine. Then, it shows that you are willing to learn new things, able to tackle problems that you don't know for a long time etc.
However, bear in mind that the boundary between the 1st case (no deep results) and the 2nd case can be very thin, and different people may consider it differently. For the sake of a Masters or a PhD, I think that each of them should be quite narrowly focused. On the other hand, it does not harm at all if you have a thesis on your primary field that contains good results, and at the same time you publish something in a secondary field.
Last, but not least, you have to remember one more thing: Who is funding you? Does he mind that he spends his project money on you and you work on something else? Your supervisor should be aware of the fact that you work on something else and should, at least to some extent, approve it.

You may work on different topics but you still at need to specialize on some topic, and there should preferably be some relationships between the various topics.
You basically need a main topic for your M.Sc and a main topic for your Ph.d and you can have another topic after that, but it need to be related.
I will give you an example. I did a master degree related to e-learning and cognitive modelling. During my Ph.D., I still did the same topic but slowly changed to data mining in e-learning. During post-doc, I did pure data mining.  And then, now I do mostly data mining and some applications of data mining. As you can see, I have changed topics over time, but there is always some overlap.
It is important that the topics are related because you will probably want to apply for some grants/scholarships and so on, and it may be easier to get grants/scholarships if you keep working on the same topic.
You may also have a few side-projects with other collaborators during your studies (that is what I did), but you should still focus on a specific topic for your main research.
Lastly, I ever saw some senior researcher working on two very diferent topics. For example, a researcher was publishing fundamental papers in Physics and in Computer Science. Although, this is possible, this is an exception.

Having a good knowledge of other subject areas can allow you to think about a project in different ways; for example by making you more aware of some confounding factors or being more able to come up with an explanation of something because of a link to some other area.
However, a PhD is really an in depth study of a fairly narrow research question over a few years. If you go into the application process looking like you want your PhD to be broad but shallow, you will likely look like you don't really know what a PhD involves and probably wouldn't enjoy doing one. It is also good to look like you have a particular passion that you would like to follow.
I think it would be good to say something which amounts to:
"My interests in Computer Science are broad, and I have enjoyed thinking about a range of subjects from A to Z and the links between them. This has allowed me to make a more informed decision about the subjects I would like to continue working on; and I have decided that an in depth study of either A or B would suit my interests."
Ideally A or B are things which are covered by the research interests of the person or institute you are applying to. If the CS department has a wide range of research interests you could also say that you would enjoy being in a place where you can still hear about a range of topics through seminars etc.
Finally, cross-subject and collaborative projects which span research groups are also possible. I assume there are opportunities for this in CS, but I don't have the knowledge to comment on that.

Most in academia say that it is the freedom in research that is the only attractive part to come to academia. Then you enter academia and realize that you are 'supposed' to work on a specific research topic or two, you are allowed to change topics only if they are related to each other, either funding agency or establishments (in the US, read: tenured committees) or both govern your research choices. What's the point of being in academia having low salary and not much (after choosing your first research topic, that is) freedom in research?
I suggest you follow your heart and work on whatever you like. Of course, you have to demonstrate your research by publishing in respected journals in those areas. It is your university and thesis adviser who will decide (and guide at various step during the ph.d. of course)  if they want to give you a ph.d. Once you have a ph.d. from a genuine university, what others think about 'depth' or 'shallowness' of your thesis etc. are just opinions. If the establishment doesn't support interdisciplinary research, and don't give you a job - well, you have a computer science degree, and you will be easily absorbed in the industry. At least you will have died hard by then without bowing down to anyone. If you find a permanent job in academia, then do support such academic freedom as much as you can.

Adding to the excellent answer written by @yo', I will point out that when you submit a CV as part of an application for something specific, you don't have to include everything you've ever done.  It's generally a good idea to have a master CV that has everything in it, including the dry cleaning store you worked at when you were 16, but when you're preparing an application for something that requires submitting a CV, do some pruning so that the version you submit fits what you think they are looking for.
What might help you keep your focus narrow enough to complete your graduate study in a reasonable amount of time, would be to keep a special file or notebook where you jot down areas, projects, and ideas that intrigue you for future use.  I believe creative writers do this, to help them finish a book they've started, before wandering off into another project.
It's nice to see you excited about several strands, which may even feed each other at some point.  Just remember, you still have many years ahead of you.


text:
How should I deal with my groupmate's unprofessional behavior as a TA?
I have a colleague in my group who became TA for a course which we took together, which is taught by our mutual advisor. It is almost a policy that a student can't become TA unless he scores an A in the course, but he was chosen because he asked "first" and the professor is "nice", even though I was the highest scoring student, which usually gets the teaching assistantship. He also knew that I wanted to TA that course, yet he still asked.
Many students come to him for questions or help. He usually tells them to copy the homework (!) or to ask me or a colleague of mine for help because "he doesn't know and [me and my colleague] know the material much better!"
How do I deal with such a person? I mean, my colleague and I try to answer all the questions the students have, but the annoying thing is that we can't be doing half the job while he gets all the money. We spend our time trying to help others where he should do that. We are very busy people and we don't have time for this when we don't have to officially do it.
Should I talk to my advisor about this? I don't want to sound as if I'm envious.

I don't want to sound like the envious person here Well, you do. Get over the frustration and stop working for free if you think it doesn't benefit you at all.

This sounds much more like a rant than a question.

This is not a full-fledged answer but simply a suggestion that you should definitely talk to your advisor about this for the following reason: if your colleague was given this position because your advisor is "nice", it leads one to wonder what other unwarranted advantages others might get at your expense because your advisor is "nice".

If you don't have the time to help others, don't do it! Tell them there is a TA paid to help and if he can't THEY should complain about that fact. If a lot of people go to the professor for help because the TA is of no use, he will get the picture! (And he will help them if he really is "nice")

Some of your colleague's behavior is rude, but "He also knew that I wanted to TA that course, yet he still asked" isn't. Whether within academia and outside, if you want things in life you should be prepared to ask for them and to explain why you deserve them.

Being nice is nice, but you also need to set your own priorities. You are not the TA for that course, so you are not obliged to answer any questions. If you happen to have time and feel like answering a question (notice the singular), then fine, answer it. When not, just politely say you don't have time and that they should go see the TA. Also, you are not responsible for (bad) advice given by that TA. Instead I would focus on getting your own research done, or do the TAing of some other course.

I would go further and say that you could actually be doing more long-term damage by helping these students. You should refuse to help on the grounds that you're not the TA. If a student is upset, let them know that they should take up issues about their TA with their professor, not with you. If you and your labmates keep picking up this guy's slack, the professor might get the idea that everything's going fine, and might continue to hire sub-par TAs to be "nice" in the future. However, if he gets a bunch of complaints from the students he'll know that he needs to hire a better TA next year.

@DaoWen So if a customer asks his waiter for a refill and the waiter tells the customer to ask the busboy, the busboy should say to the customer "no, that's not my job, go ask the server again" rather than the busboy informing the manager like a professional? ie the student's job is to learn - why is the onus being put on them to solve the behind-the-scenes academic drama? This person sees a problem that can be easily addressed with the professor and the answer is self-evident, he/she just doesn't want to confront it.

@coburne - Analogies only work so far as the analogy actually holds. In this case, I'd say a more accurate analogy would be that the waiter tells the customer to ask the guy running the burger stand on the corner about the refill. The key distinction here is that the OP is not in any way involved with the course in question, so why would it be his responsibility to deal with problems between the students and the TA? The professor should be the one dealing with that.

@DaoWen If your analogy is more accurate, then the usage of the word "colleagues" doesn't apply.

The students don't know what kind of arrangement these guys may have.  The questioner on the other hand knows the situation and he knows all the parties involved.  So he's 100% capable of addressing the issue and working towards resolution.  But your answer here is "its not your problem, pass the buck".  Don't you remember the lesson from the beginning of the Spiderman movie?  Spiderman could've stopped that criminal, but he didn't and his Uncle Ben died because of his inaction.  Why do you hate Uncle Ben?

@coburne: As I explain in my answer, identifying problems that are not yours, and assigning them a lower priority than those that are, is a vital skill for success in academia.  Frankly, I find your analogies inapt (graduate students are neither busboys nor Spider-Men) and your tone needlessly argumentative.

@coburne - "colleagues" does apply because the OP and the TA are grad students at the same university, and even have the same advisor—but that still doesn't mean he's involved with the course in question. A big part of the issue here is that the OP really isn't in a position to fix the problem. It would be bad for him to go to their mutual advisor and say "the guy you decided to hire instead of me is lazy, so you should fire him and give me the job now." He wouldn't say that—but no matter what he says, that's how it'll seem. This is why it's on the students to take care of this.

@coburne Think of it from the students' perspective.  They go to their TA and ask a question.  The TA responds "I don't know".  What does the student do?  Sit around hoping the situation resolves itself?  I would hope the student would elevate the issue to the professor.  "Hey prof, I asked the TA but they don't know the answer...can you give me an answer for xyz?"  If the professor receives lots of these kinds of e-mails, they might take the hint themselves..."Hmm, my TA isn't good at their job..."

@coburne, both the asker and the OP are simple students, but the TA is not - he's part of the teaching personnel. Is HIS duty to answer that questions. The OP is just another student that HAPPENS to be groupmate with the TA. So, using you bar analogy, is like asking the guy next table to get your refill and not the waiter.

@coburne what you wrote isn't quite clear to me, but if it's what I think it is it sounds grotesquely inconsiderate and malicious. You wrote that instead of the busboy telling the person to ask the TA, he should "inform.. the manager like a professional?"  That is a very sly way of complaining that the TA isn't doing his job,so what you want happens, the TA loses his job so u can get it. My memory being a student was when a TA wasn't good it got reported(at least one student will want to report him),it happened twice, different TAs different classes.But not by another TA trying to get the job!

@barlop Its not that he's not doing is job, just more shock at the apparently widely-accepted disregard of the importance in upholding some sort of code of ethics in seeing to the students' proper education.  There's clearly a problem that's preventing a proper learning environment and everybody's jumping over each other to make sure it's clear that it's not his problem and he shouldn't do anything.  Don't you guys have some sort Declaration of Geneva equivalent? I guess the answer to that has already been given in the replies above.

All the analogies confuse me more than it helps me to understand your points. As I understand the situation: there is a TA that does not work well, and the course suffers. What should someone who is not involved with that course and is not in any position of authority do about it? He should not "hide" the problem by covering for the bad TA. In the long run that is in the best interest of the students. The current students suffer and that is too bad. You cannot solve all problems, and if you try you will solve no problem at all.

He could say to the TA  that he got an A and he got the highest score, he loves the course and he is very disappointed that he didn't get to be TA.  I think that's ok particularly given that the other guy asked when he didn't really deserve it. But to say the other guy isn't good that's bad, and not your job particularly bad since you are saying it partly to get his job.  That's up to students to decide of their own volition. Or go over the head of the TA if that fails.. as u got the highest score and if that's a firmly kept rule then it's very unfair.

I agree that this is unprofessional behavior on the part of the other TA (let's call him X).
I understand your instinct is to try to help the students when they come to you, and that's certainly generous of you.  Unfortunately, this sort of thing represents a very common pitfall for young academics.  Working with students is very rewarding, in the short term: it feels like something where you can make an immediate difference in someone's life.  This is especially true in contrast to research, where work is often solitary and progress is slow and difficult to discern.  So spending extra time with students, while helpful in itself, has the potential to become a serious distraction in the long run.  Balancing one's time between teaching, research, and other activities can be one of the hardest thing for an academic to do (it certainly is for me).
So I think this is a good opportunity for you to practice "protecting your time".  Helping X's students, even if you enjoy it or feel the students really need it, is not something that can take priority over other tasks that are specifically your responsibilities (e.g. your research).
I would suggest having a talk with X and tell him that you're not going to be able to help out his students, and to please not send them to you.  If you feel you need a justification for this, you can just say it's distracting you from your research or studies or something similar.  If X's students keep coming to you anyway, you can politely tell them "I'm sorry, but I'm not the right person to help you with this.  I'd suggest that you ask the professor during her office hours."  You don't need to get involved any further; if lots of students start coming to the professor and complaining that X can't answer their questions (and in my experience, believe me, they will), or even that X sent them to you, who couldn't help: she will figure out that something is amiss.
I agree with the other posts that you should not explicitly try to play this to your advantage as far as getting the TA position.  That seems to have the potential to backfire.  It may work out for you in the long run, but stay at arm's length while things run their course.
On a side note, you mentioned that you've overheard X encouraging students to "copy their homework".  I'm not quite sure what that means out of context, but if you mean X is telling them to do something dishonest like copy from each other without attribution, then this is a much more serious matter that I think obliges you to step in - it puts X over the line from unprofessional to unethical.  If you feel you have enough of a relationship with X to speak frankly, tell him that's a bad idea: it's likely to get students in serious trouble, and also him if they tell the professor he told them to do it.  Otherwise, or if X doesn't seem to take you seriously, alert the professor.

+1 and I think you need to elaborate on the first few paragraphs in an answer to this question

This is very sound advice, probably the least likely to backfire.

+1 for "talk with X and tell him that you're not going to be able to help out his students, and to please not send them to you", and if the students keep coming, say "ask the professor during her office hours."

The biggest issue, I feel, is how you're handling the situation where your friend asks you for help. Whereas other people have addressed your bounds, I feel like we have to address how you are treating those bounds.
I'm going to say a statement that, up until a year ago, felt very alien.
"My needs are as important or more important than the needs of others."
Say that a couple of times in your head. It sounds selfish or wrong to say such a thing. And that's what I felt as well when I was told this statement initially.
But is it really wrong? Of course not. When we evaluate the greater good, we sometimes devalue our personal selves, even though we have a vested interest in it, in an attempt to remain unbiased. This works well in standalone situations, but not in this one.
Consider the scenario you've presented.
Your friend, knowing full well you wanted the spot, took it from you. Then he comes to you to ask you to help his students. And you've gone ahead and helped him and now you're complaining about why you have to do that.
You've, in short, placed his needs above your own needs. You don't get anything out of this relationship. You may have heard of this type of relation: a toxic one. It wastes your time and returns you nothing and gives him all the credit when his students succeed.
You're never going to get the TA job you want if he's in it. And you're helping him stay in it!
You may feel like you're doing people a service, but you're not. If this TA is bad, he should be removed. Your helping him will keep him there and impact the learning capabilities of other students, and waste your time for little to no benefit.
If you really want to help these students, you should be doing this on your own time when you feel like it, not because your friend asks you to help him do something he should be doing by himself. Instead, you're helping carrying your friend's responsibility for him when he accepted a role that traditionally bears all the responsibility alone.
You need to be willing to say no to this person.

Voted down, because it's pseudo-psychological gibberish, not actual advice.

There are two separate issues here that you should mentally separate:

Your friend got a job you wanted.
Your friend is not doing that job well.

As for the first point, not much can be done after the fact. Perhaps make your interest in the course known to the professor who will teach that course next time.
As for the second point, you are well within your bounds to refuse to help students since you're not associated with that course. You can tell your friends that you're too busy with research and other TA duties to help his/her students. This dissociates the prior TA-assignment incident with the actual matter at hand.

It strikes me that the underlying cause of your unhappiness is not the professionalism or otherwise of the person that got the TA position, or the impact of  his behaviour on you, but the fact that he got the position you wanted and that seems unfair to you. Here's a lesson that will serve you well I think: life is not fair. The world of work is not fair. Career progression, in particular, is not fair. Good things do not automatically go to the most deserving. If you want something, do not sit back and wait for it to fall into your lap because you think you deserve it for working hard or whatever.
Rather than focusing your anger on him, you should ask yourself: who or what is responsible for this state of affairs? Some helpful information would be to know whether you made your desire to be TA known to the advisor - if you didn't then you must have been hoping the advisor would simply offer it to you. Your colleague meanwhile made his desires to be TA known. Why shouldn't he? Did you really think that he should not pursue his ambitions out of some sort of deference to you because you have better scores? If he (or you or anyone else) adopted that policy they would never get anywhere in life. If you think he should not have been made TA and you should AND the advisor knew of your desire, then the responsible party is the advisor for picking someone else. If the advisor did not know of your desire then either you are responsible for not making your wishes clear, or your advisor is responsible for not asking you whether you wanted it before giving it to someone else. In either scenario, your colleague is not responsible for "depriving" you of the TA position.
So, if you feel something is amiss with him being made TA, talk to the advisor.
With the day-to-day behaviour of the TA it's a different matter - if you are not happy having work pushed over to you in this way then talk first to the TA about it, and if that has no effect talk to the advisor about it. Sitting there complaining and making accusations behind someone's back isn't particularly professional either. If you want things to change, start asking for what you want.

I would try to quantify the manifestations which are objectively problematic. How often are you interrupted by students? How many tell you (in so many words) that your so-called friend could not or would not help them? What other tasks suffer because of this, and by how much?
Collect data, black on white, until either (a) you can convince your professor that something is wrong, even if not to the point where you can get things your way; or (b) you convince yourself that it may not be worth your time and effort after all -- I know it seems preposterous now, but my experience is that sometimes that's what happens when time passes.
Don't wait too long to make that decision. Sounds to me like maybe you should give it a week, maximum.
You might not need your data, but it's a good starting point for objectively assessing the situation, and if somebody should ask you for numbers or other proof, you know you are prepared.
Strive to remain professional. Try to reason about what's beneficial for the students, the department, the collective, in the long run; not yourself or the problematic TA. Still, if you are doing unpaid work, I would consider bringing up the topic of fair compensation.

Honestly, your question could be (and probably should be) shortened to:

I'm really good at subject X, and students keep coming to me for help on subject X.  How should I respond, given that I don't have time for this?

I'd advise the following response:
"I really wish I could help, but I don't have time.  You really should ask your teacher, or teacher's assistant if you have one."
And you're done.  There is no need to be concerned about how they came to know of your skills, or become involved in petty politics or whether someone is getting a free ride or passing the buck.
If the student indicates that they've already tried those resources, you might remind them that they are paying students, and if their teacher or TA aren't meeting their needs, they may have to have a discussion with them, or bring it up with their guidance counselors. Also suggest that they might want to form study groups with others in their class.
Lastly, if you enjoy teaching them, offer tutoring services.  This will give you the ability to receive pay for your work, without all the overhead the TA has to deal with, and you're already receiving free advertising.
Regardless, there is no need to carry bitterness and acrimony into these situations. Treat it as though you hadn't been hurt, and as though the TA and teacher are both acting in the student's best interests, and then decide how to act from that point.  The answer should be obvious once you ignore your personal baggage.

If you have to answer most of questions from students, it seems to me that the TA does not prepare enough the material he suppose to teach and this is a totally unprofessional.
Answering students is not helping them, since you can answer particular questions (about a particular homework,...) but you have no time to teach how to have a global understanding on the material. In this situation, you should speak to your advisor. If you want to make it smooth and keep a friendly relation with the TA, you may warn him first that you cannot continue to answer the students questions and that he has to prepare thoroughly the material.
Of course, noone has a perfect knowledge of everything, so you probably should keep yourself available to answer theoritical questions from the TA, not homeworks questions from the students. The TA validated this course, so he knows well part of the material. By ponctually answering the question of the TA, you help him to master it completely and to answer himself to students questions.