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Can I reuse parts of a chapter from a text book in my thesis?
This question is related to this one. Only this time it's not about a journal paper but a chapter in a text book.
I am first author of the chapter in the text book that was published by a renowned publisher. I would like to reuse parts of the chapter for my PhD thesis (including a citation, of course).
Is this acceptable? Is there anything different with respect to the situation with a "normal" paper? Is there anything I need to pay special attention to?
EDIT: The publisher allows reusing my own work in my thesis.

Q: Can I do this in my thesis?  A: Ask your advisor.

@GEdgar, thanks! Before I do that I would first like to know, if there are general concern in the academic community regarding this topic.

There are two sides to this, copyright and academic integrity.
On the copyright side you presumably made some agreement with the publisher when you published the book granting them some form of exclusive rights. You need to check whether re-using part of the content in your thesis is in conflict with said agreement and if-so whether the publisher is prepared to grant an exception.
On the academic integrity side you need to find out what your unversity's policies are. My understanding is that "original" in the context of a thesis usually means "written by the author and not submitted for assessment as part of another qualification", so you are probably ok but it pays to check. Putting a citation is always good practice.
Also you need to make sure that the work is actually yours. If substantial portions were written by other authors of the book you should probably re-write those parts or at least clearly mark them as not your own work.

You need to make it extremely clear that you are re-using material in your thesis. And yes, make sure the publisher is happy with this, because even if "nobody reads it", there might be a data miner looking for plagiarism that does look.
But shouldn't your thesis be original material? If you have already published three chapters on the topic, it is not original anymore. You need to check the rules at your institution, and make it very, very clear which bits are new and which are recycled.

I did this in my thesis - my introduction was going cover a lot of information overlapping 3 textbook chapters I'd written, and I really didn't want to write it all again!
I did check with the publisher first, however (just an email asking for their consent), and added an acknowledgement to them in my acknowledgements page. I'm sure this was probably over-zealous, but it felt better to err on that side of things.

After reading your edit, it looks perfectly fine to use small parts of your chapter while citing your previous work carefully.
There should not be any problem at all. People often do it.


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What to do after receiving poor academic recommendation(s)
I was recently applying for a number of PhD programmes, and I asked a number of my previous professors for recommendation letters.
However, after the results of these applications were released, it was found that one of the professors has written a clearly negative recommendation (in comparison to the others), despite the fact that I felt that the academic relationship was good and on comparable levels to the other professors, and that he specifically agreed to write me a strong recommendation letter.
I even noted in the request letter that "If you feel that you would not be able to write me a strong letter of recommendation, you should feel free to decline to write a recommendation". As other questions on this site have shown, it is not generally considered good form to write a negative recommendation, whatever the reasons.
I came to know about this, because the said professor submitted a number of recommendations late, and one of the interview requests from one of these universities was withdrawn, with the admissions department stating that it has been withdrawn after "reviewing recently submitted recommendations".
Furthermore, after speaking with some of my other recommenders regarding my other interviews and asking for advice regarding further steps, they mentioned that they received calls from admissions departments regarding "inconsistent recommendations".
As someone who would like to understand what went wrong during the process, what would be a good course of action in this situation? Should I approach the said professor and ask what went wrong, or would that not be a socially acceptable action?
I believe any answers should probably be relevant across all fields, but I am personally applying for a PhD in the US in the biosciences field.

Note: some people aren't good at writing letters of recommendation and they don't realize it.

Your professor either wrote the good recommendation they promised, in which case they are probably as shocked as you are, and happy to discuss what might have happened, and what to do now; or they lied to your face, in which case I wouldn't worry if talking to them is "socially acceptable." I don't know what would be the best course of action if the second is the case, but my first step would be to talk to them in person - just don't assume beforehand that it's one or the other, to make the meeting productive.
As two comments pointed out, there's also a (small?) chance that the professor meant to write a good recommendation, but failed at it. If that's even remotely a possibility, as well as probably in the first case above, it might help if they contact friendly faculty (should there be some) at one of the universities applied to, to better understand where the bottleneck is (within what is possible, considering the confidentiality of the process). Given that a letter-writer usually has some interest in the student they write a letter for succeeding, I wouldn't dismiss the idea before bringing it up with them, if appropriate.

To elaborate on @shane's comment.  I've seen letters of recommendation that were so poorly written (in terms of poor English or just complete misunderstanding of what kind of program the student was applying for) that the letters hurt the student's chance of acceptance.

@Brian: that's just wow. :) Then it sounds as if, maybe, this was actually the case here, which could be good news if followed up on.

In addition to competence at writing, there may just be a cultural disconnect. Recommendation letters in Europe, for example, tend to be much less effusive than American letters, to the point where moderately-positive rec letters would read as "negative." See, e.g.: https://chroniclevitae.com/news/795-only-positive-recommendations-please

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Which quantitative metrics are there of the quality and prestige of journals, and how do they compare?
I have seen several different metrics that are applied for ranking journals: Impact Factor, SJR, and H-index.  Which of these is the most useful and robust for comparisons with respect to the quality and prestige of journals?

This question is not answerable as such. What does "reliable" mean to you? What is SJR? And I am not even sure whether the h-index is actually used to measure journal quality.

h-index is normally an author metric, but I could also see how you could make it into a journal article (e.g., a journal has an h-index of 50 if it publishes 50 papers in the last x years, each of which has acquired 50 citations).

What I meant by reliable is the most robust, comparative and indicative of the quality, prestige of the journal.
Thank you for your comments.

@Ahed You should add these clarifications to the question, and possibly expand on why you are asking (evaluation of publication profiles, choosing journal to publish in, etc?). Readers of the question shouldn't have to go through all the comments to understand your question.

I have clarified the question to match answers (addressing the "unclear what you're asking" closure reason), and nominated to reopen.

In short:

Impact factor is the traditional measure of mean citations per year shortly after publication.  It can refer to either the official Thomson-Reuters computation (which has lots of problems), or other competing similar computations.
SJR attempts to improve on impact factor by using an algorithm like PageRank to more heavily weight citations from "better" publication venues.
H-index for journals is just the same as for people, essentially looking for the volume of consistently good work.  The only large place I know of that applies this to journals is Google Scholar metrics.

All of these are subject to manipulation and gaming, all are highly field-dependent, and none are very good actual ratings of quality.  Still, they can be used to get a rough sense of the significance of a venue that you are unfamiliar with.

Thank you for your brief, useful answer. I've benefited from this answer.

Can you expand on the 'lots of problems' in Thomson Reuters IF?

@CapeCode Among other problems, it has atrocious coverage of computer science venues, the limited time window penalizes journals with slow review and publication processes, and disproportionately rewards "hot" work, even if it has no lasting impact.

@CapeCode Also, the IF figures that ThompsonReuters reports are not consistent with their reported algorithm run on their reported citation data.

One difference between the traditional Impact Factor (JIF) (the official Thomson-Reuters score) and the SJR score (SCImago Journal Rank) is that the former is based on the ISI Web of Science database and the latter on the Scopus database. Depending on the field you are in this can translate to differences in coverage, which can affect the relative rank of journals. The SJR score is also a weighted score, which takes journal prestige into account, and this is not the case for the Impact factor.
The H-index is strongly influenced by the number of papers published by a journal, since this translates into the number of "attempts" of a journal to obtain highly cited papers. This is the main reason why journal rankings based on the H-index usually deviates quite alot from ranking based on avarage-based metrics (such as the Impact factor and SJR). When using the H-index to rank journals a small top-journal within a field (based on article impact) can be surpassed by large journals. As an example, journals from the publisher "Annual reviews" generally come out much lower on H-index rankings compared to IF or SJR-rankings. Personally, I find the H-index a poor proxy for journal prestige, but it might be somewhat useful to determine overall influence on a field (as in number of relatively highly-cited papers). Overall, I think that the H-index is much better for evaluating individual scientists than to compare journals. Why Google Scholar chose it as the only score to present when comparing journals is beyond me.
However, there also exists many other indicies of journal performance, influence and prestige. Hocking (2013) provides a comparison between 11 different journal metrics, using ecology journals as a case study. This study show that while all indicies are positively correlated, they form 3 relatively distinct clusters. The traditional impact factor is closely related to SJR as well as to Article influence (AI) and Source Normalized Impact per Paper (SNIP), while the H-index and the Eigenfactor are part of other clusters. This means that journal rankings based on e.g. JIF, SJR, SNIP will be very similar, while rankings based on the H-index or Eigenfactor will emphasize other aspects of journal performance.
References
Hocking. 2013. Comparing the influence of ecology journals using citation-based indices: making sense of a multitude of metrics. Ideas in Ecology and Evolution 6(1).

Among widely-available indicators, SJR and the Article Influence Score (AIS) are best for characterizing journals. An important property of those two indicators is that they weigh citations with the relevance of the citing journal, whereas in computing the impact factor (IF) or the h-index all citations are considered equally, regardless of the relevance of the citing publication. While all these metrics are typically highly correlated, taking into consideration the relevance of the citation sources can matter especially when trying to assess journals that are not among the top ones. For example, in the case of a journal that would artificially inflate the IF through self-citations or by participating in a citation ring within a publisher, or in the case of a journal hosting publications of a relatively isolated field, the SJR and AIS would remain relatively low if citations would come from low-quality sources. Another advantage is that the typical values of SJR and AIS vary less among different fields than the values of the IF and h-index. There are established methods for field-normalizing the IF (see, e.g., the SNIP indicator), however is more difficult to field-normalize the h-index.

SJR and AI do not include a measure of "relevance", if you by this mean the relevance of specific citations to the paper or the scientific field. Both indicators include a concept of journal "prestige" in their weighting of citations, but this is simply a single measure for each journal and does not equate to "relevance" (whatever that is).

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Postdoc with full-time appointment while doing business part-time
I understand that postdocs can be too busy to even sleep, but if we put this aside - would US school allow a postdoc (full time appointment) having his/her own business in spare time? If so, what kind of regulation is applied here? Also, would the mentor be annoyed/alerted by this kind of planning?
I guess the field of the business also matters. For example, if the business is related with research the postdoc is doing, it is probably highly restricted; while being a landlord is something completely different.
Any thought? Thank you in advance.

You need to give at least your country. For example, in Germany the respective rules can be found under "Nebeneinkünfte" and can be pretty complicated (but, as far as I know, do not incorporate the type of buisiness).

Thanks @Dirk . I'm asking for US situations, but I do agree that the situations can be complicated and should be avoided if possible.

I know in my university (in the US) there is pretty strict rules on what you can do outside work as a university employee. You should really consult with your department chair or ethics office (or something like that) for more info.

We try not to give legal advice on this forum, so the legal question of whether or not (and if so how) you can have a business on the side is one that you probably need to ask a potential employer.
But I do want to comment on a separate point. As you point out, being a postdoc is a tiring phase of your life. In essence, people who want to be postdocs do so because they aspire to getting faculty positions in their next career step. I suspect that that is the same for you.
The reason why being a postdoc is so tiring is because you're competing with others for these few faculty positions: it's not necessarily that your job description requires you to work 60 hours a week, but that you feel like you need to because you see all of these other postdocs crank out 3 or 4 papers a year, and these other postdocs are your competition. So, if you are thinking of running a business on the side, then you need to be aware of the fact that that curtails your productivity compared to other postdocs, and that that in itself curtails your chances to get a faculty positions because you will have less to show on your CV.
If you know that your chances of getting a faculty position will be significantly diminished, and you still keep your side business, then you ought to ask yourself why you want to become a postdoc.

While possibly true, this seems like an extremely unhealthy atmosphere. If I thought I had several years ahead of me doing 60 hours a week and pretending it's my own idea when it's actually just the unannounced standard of the field, I wouldn't want to become a postdoc. I also wouldn't advise anyone else to be a postdoc ever. At least in my view, what your answer boils down to is "Don't be a postdoc." I also suspect it is field-specific, isn't it?

I don't know. I think it's just fine to want to be a postdoc if you are driven and motivated and want to compete with the best in your field. It all comes down to what you value in your life: if the competition and being among the best in your field is important to you, then this can be a very rewarding career choice. The same is the case if you aspire to eventually be in upper management of a company. If your overarching goal is to have a work-life balance, then maybe postdoc is not for you (though of course compromises can be made).

Thank you @WolfgangBangerth and thisismynamenow for the kind answer and comments. I almost unexpectedly got a grant that support me to be a postdoc for two years, while I was originally already settled to concentrate on my business. I will need sometime to make a decision. Thank you.

A postdoc who is looking into the decision of business vs. academia may not have the same pressure to compete as someone who knows they want a professorship. That is, for what I've seen so far, the competition is less about the postdoc positions than about becoming group leader or professor.

@cbeleites -- by why look into the decision between business vs. academia when you start by hamstringing yourself regarding at least one of the two choices? What if you find that you like academia but spent too much time on the business side? If your competition goes all in, you have no choice doing the same.

@WolfgangBangerth: a) OP already considers a (side) business. Thus, even not pursuing this option is a decision between business and academia. b) Personally, I found small side-business + full-time postdoc very beneficial. The side business made me basically insensitive to the drawbacks of fixed term contracts, IMHO a decided advantage in academic contract negotiations. But I like research and therefore don't want career in academia  - and I see harsh competition (and even nepotism) about permanent contracts and professorships in my field, postdoc positions are much easier.

I take issue with the idea a postdoc has to work 60+ hours to be successful. I actually think that is ridiculous.  Spending hour upon hour in the lab doesn't mean your experiments will work or you will find something publishable.  Doing the "right" experiment is what matters, not just spending tons of hours doing experiments.  Have a life, have a family, start a company.  When you sit down to do your postdoc work, think very carefully about your question, think through your experiments, make sure you picked the most efficient and feasible method and then go for it.

There is more to any academic position than "spending hour upon hour in the lab". Few academics (successful ones anyway) get away with a time-boxed schedule. It is a profession, not a job.

I just don't agree. That is the culture, so we think it is required, but it isn't. This is a throw back from the time only old dudes had this job and house wives raised the family. I did grad school with two kids and postdoc with three. I don't work weekends, nights or holidays. I love science and I am good at it, but IT IS NOT MY LIFE. Success doesn't come from living for science, it's about focusing on the lab when you are there. Step one to having more women in science is to throw the "science or personal life" idea in the trash.

Typically, in the US, a postdoc's employment contract specifies that the postdoc must get permission to have additional employment.

But this doesn't answer what happens if the OP has her own business, i.e., isn't an employee.

Someone who operates their own business has additional employment.  It is no different.  Another way to put is "outside work."

Formally, we have a similar rule (ask employer for permission) here in Germany. However, legally the employer is allowed to refuse the permission only in rather specific circumstances.

Answer for Germany, based on my experience:

Legal: employees need to inform the employer, but the employer must grant permission unless they have specific grounds to restrict a side business.
An obvious rule that you cannot start competition with your employer. However, as most universities and at least basic research institutes do not offer their services on the market, this is often unproblematic even if your side business is related to your research. Applied research institutes who offer industry services would be different - but then they may be interested in having a spin off, see below.
When I formally asked for permission at my (Leibniz) research institute, they just pointed out that I need to take care not to violate the maximum working hour laws and that it stays small enough side business to not hamper my performance working for them.
Whether a university/research institute is happy or annoyed with this depends on circumstances.

They may be very happy if your research leads to a spin-off. There are even funding programs to help with founding university spin-offs. They'd sell this as a huge success, even better than a bunch of patents, and worth many papers.
In my experience, they are often less happy if your business is totally unrelated to the research, say, you're computer scientist running a grocery store side business (they cannot list that as achievement as they'd try to with, say, a software spin-off).
I'd expect "landlord" to be relatively neutral.

You'll have to be careful about IP rights. E.g. over here an employment contract usually means that whatever software you write, as long as it would be useful for your employer they automatically get the commercial rights.
So you may need to negotiate changes in your employment contract.

Thank you @cbeleites for the reply. Very helpful insights, especially where you mentioned institutes can be welcoming to a spin-off. I will look into that. Appreciate it.

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Publishing poor research at advisor's request
I'm currently in the first year of my PhD. Some time ago I published a paper at a very small, accessible venue because I was required to do so by my advisor. It was my first publication, and I wasn't even involved in the PhD program back then. It was rushed (I did it all in a week or two) and I knew nothing about the field. Now I know that the paper is totally worthless. With what I learned over this period, I know that some basic knowledge and a reasonable amount of effort are enough to do something way better.
The problem is that now my advisor wants to submit pretty much the same thing to a journal, in order to meet academic requirements. I insisted that it was worthless, and that I could do something much better, but she just wanted to get something done with minimal effort. If I had other ideas we could publish, then that means we could have even more publications.
My worries are related to both the effect this could have on my record and ethics, of course. I was not too happy with the first publication when I realized that it was worthless, but I guess that anyone would understand the poor quality of an unimportant paper by a master's student, especially if it's the odd one out in the list (which I hope it will eventually become). Now, however, I'm starting to have contacts with other researchers in the field, and I'm worried that more publications of this nature in my CV might stain my reputation among them, since there are almost no other publications to judge my abilities from. I also worry that this could have an impact on my chances when I try to apply for a postdoc position further down the line, even if I manage to publish a couple of good things by the time I finish my thesis. Also, while I understand that
institutions put strong requirements on their researchers and sometimes one has to publish not-so-great work in order to keep going, I think that is completely different from publishing something you know to be worthless sh*t. I've also suggested removing my name from the list of authors to no avail.
My advisor has NO knowledge of the field. She basically caught wind that it is a hot one and assembled a team of grads and undergrads in the hope that they would start producing publications pretty much right away. Of course, it took me about a year and a half of really, really hard work almost completely on my own to start feeling slightly confident about my (still very limited) knowledge, and to come up with something that I consider worthy of publication in a reputable venue. I would like to concentrate on these findings, but I'm required to devote effort to those questionable publications instead (as well as other duties that I don't want to discuss here). Sometimes I get the feeling that I'll complete my thesis in spite of my advisor, rather than thanks to her.
So my questions are the following:

How likely are these publications to mar my reputation/CV in the future? Will people just understand that everyone has had to undergo a similar situation some time in the past and disregard them in favor of better publications? Does everyone have a couple of stains in their record?
Is this common in academia? Are PhD students often pressured to publish no matter what just so that the advisor or the group can score one? How strongly should I consider searching for a position elsewhere? The main reason I'm staying is because I'm financially comfortable here, and I now feel that I am making a lot of progress by myself and I'll be able to complete the program with a decent contribution, even though I have little scientific support. Also, moving elsewhere would be a considerable personal sacrifice, so if I take the step it must be totally worth it. I know I could perhaps learn more with a knowledgeable advisor, but I'm positive I'll learn a lot on my own anyway (perhaps with occasional inputs from other professors from my institution who are active in the field), so it's not like I'm wasting my time completely.

About my worries for my reputation, it's not that I want to become a celebrity or that I'm planning to make a breakthrough in the field. It's just that I devote a lot of effort to becoming competent in the field and I am very thorough in making sure that the work I do is proper, so I would like at least to be recognized for this by my peers.

There are many inconsistencies in your post. "My advisor has NO knowledge of the field." Then why are you doing a PhD with her in this field? "my advisor wants to submit the same thing to a journal". If it is in CS (or any other field where conferences matter for publishing), you cannot submit the same thing without a 30% enhancement. And if you do those 30% enhancements, your paper might become a decent (not top) publication.

She engaged me as a Master's student, and when it was time to start the PhD program I just went on with her. I felt comfortable financially and I had the feeling I was making progress. Also, I was planning to have another professor (a true expert) as a co-advisor, although because of some disgraceful faculty politics that's proving more difficult than expected.

There were some additions, although hardly a 30% improvement. I did propose other, more significant changes, but she rejected them, as she wanted to devote minimal effort to get the thing done.

you cannot submit the same thing without a 30% enhancement — Within CS, that fraction varies significantly by subfield and by publisher; in some subfields (like my own), for all practical purposes, the required fraction of new material is zero.

I think you should fire your advisor.

Yeah, that'd feel good. Not an option, though.

Without going into details, I suspect I have met PhD students/postdocs/researchers who were once in a similar position. I'm not sure I can answer Q2 without knowing more about the field you work in (CS/maths/life sciences/social sciences/whatever) but as for Q1: I think that writing enough good papers offsets the "mark" on the CV left by a poor paper, which people will acknowledge may have been done under someone's orders/directions

That said, if the earlier paper contains actual errors then you should definitely fight to have your name taken off it. My comment was based on the understanding that the paper merely lacks worth compared to what you can now do.

Thanks, @YemonChoi. It's not so much that it contained errors, but rather that the proposed method was very poor. It was a naive approach and it did not actually solve any of the problems that arise when addressing the matter. However, is it possible to remove one's name without retracting the paper completely? That would leave the other authors in a very bad position, wouldn't it? Also, I don't see any editor keeping a paper that one of the authors decided not to stand behind anymore.

It's difficult to advise without knowing further particulars, which I understand that you probably don't want to give here. I would tentatively suggest that you just let the paper appear with your name on, but concentrate on getting better things done and published during the rest of your PhD.

This is a complex situation, and to even attempt a truly thorough answer one would need to know more details than you have provided (though your reticence is understandable).  I would begin by saying that in my opinion the main problem is not what you think it is.

My advisor has NO knowledge of the field.

This is the main problem.  You're just starting a PhD with someone whom you feel has much less knowledge than you and accordingly is pushing you into professionally dubious situations.  You say the situation is that she needs publications and is thus making you do the work...without enough understanding that the work you're doing is not mature.
I think you have one of the worst kinds of advisors.  It would be less pleasant to have an advisor who is overly intense / unfriendly / borderline abusive, but such an unpleasant advisor would still impart knowledge and experience.  I encourage you to very seriously consider transferring to a different PhD program.  You describe the non-academic aspects of your situation as  comfortable enough: that makes it harder to pull the trigger, but it does not make it less of a good idea.

I know I could perhaps learn more with a knowledgeable advisor, but I'm positive I'll learn a lot on my own anyway (perhaps with occasional inputs from other professors from my institution who are active in the field), so it's not like I'm wasting my time completely.

You can remove the word "perhaps."  The main thing that makes one PhD program much better than another -- not necessarily in the sense of rankings, but really "better" for any given student there -- is the level of knowledge and expertise of the advisors, and their ability to impart their knowledge and skills to their students.  I went to one of the top three programs in my field, and every faculty there is a world leader.  My former PhD advisor is, truly, one of the world's great living mathematicians, and being guided by him for four years was really priceless.  You mention that you are skilled at learning on your own, and I believe you, based on your ability to, at such an early stage of your career, gain expertise in a field beyond that of a faculty member.  Learning on your own is also a very important and valuable skill, and I did a lot of that as a student.  But you know what?  If I had it over again, I would talk to my advisor more: there were times when I spent whole months doggedly figuring something out on my own which one conversation with my advisor would have cleared up.  (I now see this happening with my own students sometimes.)  Learning on your own and learning from the real luminaries are  the two great tastes which taste great together.  You're right: you are not wasting your time completely, you're only wasting it relative to what you could be doing.  You sound like quite a good student: I think you deserve a better experience.
Let me now address the top-billed question:

How likely are these publications to mar my reputation/CV in the future?

Most academics I know worry about their reputation and standing to a degree that would make most fraternity guys / sorority gals envious.  There are very few single events that outright ruin an academic's reputation: these mostly center around academic dishonesty or non-academic crimes (e.g. being truly abusive to a student).  If you have published a paper that is subpar, then the way to bounce back is to publish more good papers.  And by the way that is what you should do even if you haven't published a subpar paper!  If the subpar papers are the first ones published, most people will understand that you wrote them as a young student before you really knew what you are doing.
To my mind, the key worry is not whether your paper is worthless, it's whether it is wrong.  Publishing a paper that you know to be critically flawed in a manner that you don't call attention to is a form of academic dishonesty; some would view this as even worse than plagiarism.  I would try to avoid publishing such a paper at virtually any cost.

Will people just understand that everyone has had to undergo a similar situation some time in the past and disregard them in favor of better publications? Does everyone have a couple of stains in their record?

It depends on the people, I suppose.  I have never been pressured to publish a paper by anyone, but I work in a field (mathematics) with somewhat distinctive cultural norms.  But if you're asking whether every academic in your field has been put in your situation: almost certainly not.

One quibble: "The main thing that makes one PhD program much better than another . . . is the level of knowledge and expertise of the advisors." While you do need knowledgeable advisors, you also need advisors who are good communicators and mentors. A genius who can't impart his knowledge to others does not improve graduate education in a department by very much.

I have seen a case where a good mathematician's publication record began with some very poor papers.  Fortunately, they were joint papers with his adviser, who was known for publishing junk.  Once he escaped from his adviser's influence, he did some very respectable work. (I had to explain that as an outside reviewer when he was up for a promotion.)

@aeismail: Yes, I agree, and I have edited the answer.  Of course, if you have little or no knowledge to communicate, your communication skills don't come into play.  I think we all know examples of incomprehensible geniuses, but in my experience this phenomenon is relatively rare (perhaps because it is hard to tell someone is a genius if their communication skills are truly poor).

Thanks for such a thorough answer. I am now a little bit more convinced of the importance of having a knowledgeable advisor. However, the problem that @aeismail points out is an important one. I could land a position with a very good scientist, but if they do not devote time to their students it might end up not making much of a difference. Also, as I said in another comment, I was planning to involve another professor in the program, but I'm not sure that's going to happen. I'll certainly look for positions elsewhere and give it a serious thought.

@lost: Of course you want to avoid bad communicators and mentors as well.  In terms of busy advisors: I think you would be better served by an advisor that is knowledgeable enough to put you on the right path even if they have little time to devote to you.  In my answer I indicated how much I learned from my advisor.  I did so while meeting with him on average of perhaps an hour a month.  That was enough to keep me in the right direction and clear up my mistakes.  But yes, try to find an advisor who is good overall!  If you can switch advisors within your own department, try that first.


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Is is possible to keep working on MBE, particle accelerators after in-body metal implants?
I am about to undergo surgery after which I will end up with small titanium rods in my body. I wanted to ask if i would be able to continue working in my chosen field (which involves MBE (molecular beam epitaxy) and working with other devices with strong magnets). Wondering if I should switch my research field to a non-magnetic environment.
I have asked my doctor who says that it's a big no for pacemakers, but it should be okay if i don't spend too much time near those machines.
Wanted to ask if any one knows of cases, or has experienced anything like this?

Ask your doctor what "too much" time means. Not strangers on the Internet who don't know your medical history.

This isn't enough for an answer (it's not precisely relevant, and kind of a side-answer), but I had some titanium plates and screws put inside me which were later removed once the bone was sufficiently healed as to be able to withstand daily movement without them. It took about 1.5 years. This isn't ideal, but at least it's an option, although it may take some time and be dependent upon your recovery.

@ff524 edited to remove that ambiguity. I was only asking for experience. The question about time was rhetorical. Sorry abt that.

@lafemmecosmique thanks for sharing. this thing is going to become a part of me, will be inside forever.

You shouldn't be allowed to work in a magnet lab if you don't know the answer to this question.

@Wrzlprmft I would like to point out that it is concerned with switching topics due to health issues!

Also, titanium is not ferromagnetic, so you should even be able to go into an MRI.

@AnonymousPhysicist I'm starting next year. That's why wanted to if somebody in this community has any experience with this

1) “Does anybody have experience with this?” is a poll and not a good question for any Stack Exchange. 2) Right now, it is unclear what this is: Changing fields, working in a magnetic environment with titanium implants or something else entirely. 3) @AnonymousPhysicist was remarking on the fact that there should not be a problem in the first place.

@Wrzlprmft This is a yes/no question with a correct answer.  It's not a poll.

"titanium is not ferromagnetic, so you should even be able to go into an MR"  Paramagnetic materials also experience magnetic forces.  This is dangerous advice.  Also, it might be an alloy.

@AnonymousPhysicist: Titanium is used to make surgical instruments for MRI operating rooms. Patients with titanium implants can go into MRIs. Yes, there are fringe cases such as if your implant acts as a coil or is ferromagnetic due to being an alloy, hence “should”. However, in the vast majority of cases falling under the asker’s description (“small titanium rods in my body”), there should not be a problem. Should the asker fall under these fringe cases, there is no way to answer this without knowing further details (and the question would be off-topic anyway).

@AnonymousPhysicist: There is only one way I can think of interpreting “Wanted to ask if any one knows of cases, or has experienced anything like this?” as a yes/no question and in that case the answer is the maximally unhelpful: “Yes, somebody knows of such cases and somebody has experienced something like this.”

I'm voting to close this question as off-topic because it is a request for specific medical advice in a health-critical situation, which should be directed to medical and physics professionals with full knowledge of the individual case.

If you have a paramagnetic body implant, you must never enter a strong magnetic field.  You should consult with your institution's safety department about establishing appropriate controls, procedures, and permissible exposures.  Probably you can continue to work in a magnet lab, but only when the magnet is off.  An appropriate interlock should be used.
Magnet injuries


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Good idea to start PhD with a potentially obstructive medical condition?
[EDIT] I have a medical condition, diagnosed after I received and accepted my PhD offer. I am wondering if i should defer or have the surgery in the middle of my program. [/EDIT]
The condition makes it difficult  for me to stand for long periods of time (due to vertebra slippage). I'm still able to function on my desk job. Taking classes should not be an issue. However, working in the lab (somewhat unavoidable in my field) might be challenging.
There is surgery to fix this issue, by fixing the vertebra. But that is not the first line of treatment and is used only if the problem gets worse.
I'm unsure if I should start the program and then take a quarter off for the surgery or wait for the surgery and then start my program. Your comments/ideas/advice on evaluating my situation are welcome.
P.S. It might be relevant, I am an international student accepted at a US university.

So would you be applying for a PhD in a (sub)field that would require you to stand for long periods of time (as opposed to most fields of research, which don't)?

I should have pointed out, I already have an offer, diagnosis of the condition came after the offer.

Since you already have an offer, you should ask your advisor which option would be less disruptive for you. He/she knows the details and timeline of the program, we don't.

Fair point. advisers are chosen after the first quarter, and my program has not started yet - almost all potential advisers work on lab heavy topics.

Contact the person responsible for students in the first quarter, then. Same deal: He/she knows the details and timeline of the program, we don't.

Part way through my PhD I was diagnosed with ovarian cancer, requiring major surgery followed by chemotherapy. I went to one course unit for a quarter, so that I kept my connection to the department and parking pass, but was not expected to do much work.
I don't know whether the school where you will be doing your PhD will allow that sort of option.
I agree with the advice in comments to discuss with whichever professor is responsible for first quarter students.

Thanks for sharing your story and how you managed the academic aspect. I will ask my point of contact about handling complications arising from this.


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Conflict of interest: My research reflects badly on my PhD supervisor
Post Q2 2016
I am in the final stages of writing-up my thesis. Unfortunately, my findings don't seem to reflect well on my supervisor. I have just had a key chapter returned with many comments like "rubbish", "full of mistakes", etc. I don't think they are justified.
I am reporting on the quality control of a trial for which she was PI. There is clear evidence of QC problems and it seems to me that there is a conflict of interest which is preventing objectivity in the feedback I'm getting. I feel that I'm being pressurized into coming to conclusions in my thesis that I don't agree with - i.e. the trial didn't have any significant QC problems.
My relationship with my supervisor was amicable enough before I sent her this chapter. In order to complete my conclusion I need to reach some sort of agreement, but after her recent outburst I feel this will be difficult.
My University doesn't seem to have any policy about this type of conflict of interest, yet it must be common enough. What should I do?
UPDATE (June 2017):
The good news is that I submitted my thesis and it was accepted with minor changes at my viva. My examiners were kind and described it as a 'tour-de-force', though after five hours of argument I suspect they just wanted me to go home ;-) Therefore I have my PhD.
The bad news is that the papers derived from two of my PhD chapters which detail the quality failings in the trial have yet to be published. This is despite significant support from my examiners who both felt it was very important for the information to be published. At present there is a big row going-on at the highest levels of the University with good scholarship being pitted against the medical school's desire to avoid reputational damage and potential loss of future grant income.
I sincerely hope that no other PhD student is going through this sort of debacle, but just in case I give the following advice:

Don't give-up. Just keep on writing the best thesis you can. Let the pages become chapters and the chapters become a finished thesis. Save worrying about your viva until after its been submitted.
Don't keep quiet about problems with your supervisor. Stand-up for yourself and keep in the light. In my case I made sure senior management knew was going on and also that I was documenting everything. This wasn't something that they could easily sweep under the carpet. In the end it became very much in everyone's interests that I got my PhD.
Try to maintain a relationship with your supervisor and keep the arguments on a professional than a personal level. You want your supervisor to congratulate you on getting your PhD and write-off the arguments over your thesis as healthy academic disagreement.

I must thank the >1,000 people who have viewed my original posting. Good luck to all PhD students and remember that careers are built on results not methods ;-)
UPDATE (March 2018):
My main paper was accepted by the key journal in the field in August 2017 and finally appeared in print, March 2018. I'm still working on getting the second paper accepted.

Why do you not ask her politely ?

It's not really about being polite, though I have been very polite in my dealings with her. It is about her not wanting to accept my results and the obvious conclusions that must be drawn from them. This arises from a conflict of interest - i.e. duty as my supervisor vs. preserving her own reputation. It's tricky situation and should have been addressed at a much earlier stage. My other supervisor did read the chapter and thought it was fine. I don't think either of us thought it would evoke the response it did.

Wait - your PhD dissertation is about quality controlling the research of your advisor? That sounds like a phenomenally bad idea :(

Like I say, it's tricky situation and should have been addressed at a much earlier stage. The problem is that my supervisor thought I would report that the QC was excellent - her previous student did. However, I discovered that half the results from a part of the trial were bad - even my supervisor accepts that. I probably should have given-up doing my PhD at that point. Where do I go from here?

@Innocent "I probably should have given-up doing my PhD at that point. Where do I go from here?" - woebegone! You are talking about conflict of interest here - when you put yourself in a position where you have only the choice between harming yourself or your supervisor (not that they may not have brought it upon themselves, but does it have to be you to find that out?).

You probably need a new adviser.  The first place to go, though, would be the appropriate administrator in your department. (In my department, that would be the chair of the doctoral committee or the associate chair for graduate studies; in a smaller department, it might be the department chair.) You mention another supervisor who thought the relevant material was OK; perhaps that other supervisor can give you good advice tailored to your department's specific culture.

@AndreasBlass Sounds like an answer. Can you post it as one?

I've just had a very interesting conversation with my supervisor's boss. Apparently, I am wrong. The trial was excellent because by the standards of what is current practice in medicine there is no problem with 50% of the results being classified as ok when they're not. Furthermore because I'm not a medic, I cannot criticize this.

By the way, my supervisor has just been promote to run the entire institute so I have no place to go. I suspect this thread will soon be terminated, so thanks for the input. Much appreciated.

ANSWER: From my supervisor's boss: There is no conflict of interest because the trial was a complete success. Therefore I just need to change my conclusions to reflect this reality. The Rev Dodgson would be so pleased!

@Innocent I think "you can't criticize this because you are not a MD" is a very lame excuse. Either your assessment is wrong, due to lack of expertise, and they can point out where, or it is correct. Can you discuss this in detail with a trusted, non involved, expert?

@Davidmh Read between the lines.

Re your last comments: This is insane... I can't believe it.

There is no conflict of interest because the trial was a complete success. — And this is where I write Don't walk.  Run.

I suggest that the Updates be made into an answer, instead of edits to the question.

I had interesting situations during the final stages of my PhD career, and I found that my dissertation committee was an incredible resource. If you are in the final stages of writing your thesis, that means you have a dissertation committee (or have otherwise established a collegiate network of professional academics that support your PhD training). Now is the time to use this resource. Ask to speak to them in person about the problem. Specifically, you should approach your committee chair (who should be different than your supervisor). If your chair is your supervisor, then just speak to the most senior person in your committee.
The way that I understand the power dynamics / vested interests of the whole PhD situation is that your supervisor has inherent conflicts of interest - they want you to do research that supports them. Thus, they 1) are better off keeping you as long as possible (but not too long) and 2) want your research to support their research. Your committee chair, on the other hand, wants to see you graduate. Your department chair also wants to see you graduate. Your supervisor wants to see you graduate, sure, but as I mentioned, they have other motives.
Ultimately the goal is to keep everyone happy, and especially your supervisor. Having your PhD supervisor on your side is key to a successful career in Academia (or at least makes getting recommendation letters are lot easier).
Use this situation as a learning experience (one of the many tangential learning experiences associated with a PhD) for how to navigate the people problem of science. So in conclusion-
1.) Give your supervisor the benefit of the doubt. Try to understand their points and try to actually discuss it with them - IN PERSON. Abandon email for this interaction - you need the full spectrum of our human communication abilities.
2.) If #1 fails, engage your dissertation committee. This exact situation is a fine example of why dissertation committees exist.
3.) If #2 fails (or you're in a program that doesn't have dissertation committees), engage another trusted senior investigator if you've created relationships with other investigators.
4.) If you get to here, go to the department.

You could actually roll past 4 even though. Your supervisor could be the department head...

"If you are in the final stages of writing your thesis, that means you have a dissertation committee."
You are assuming that the OP is in the US, I think. This varies a lot depending on where the student is.

@ Significance , interesting. Yes, I guess my answer is US-centric. I included a broader term that hopefully communicates the sentiment.

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


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How to disagree about author order when my advisor has been dismissive of such concerns in the past?
I'm being asked by my advisor to perform a specific scientific experiment that she conceived from start to finish  on our apparatus over the next two months (which could easily become 3-4 months or even longer).  There is a senior graduate student, but he is writing his dissertation.  The advisor has asked me to run the lab 45 hours per week to take data on this experiment.  The advisor has told me that the senior graduate student will provide some guidance and we will work together on a conceptual level, but that I will do all of the day-to-day setup and data taking.  So far, the senior graduate student has only acted as a buffer of communication between the advisor and myself, and he has simply passed on parameters for me to test that were suggested by the advisor.
The advisor has indicated that she wants the senior graduate student be the first author.  I believe that this is only because the senior graduate student has not published a satisfactory number of papers and must graduate this semester (he is a 7th year graduate student).
In the past when I've questioned the ethics of authorship on papers, particularly pertaining to this exact scenario, my questions have been brushed off and I've been told that this is how it has been done in the past in our research group: a junior graduate student will take a lot of experimental data for the senior graduate student.  To call myself a junior graduate student may be misleading, I am in the fifth year my PhD program and I have not yet started my independent research in the lab because I have been taking data for the previous graduate student for several years now.  I fully have the expertise to run this new experiment without any input from the senior graduate student.
It seems to me that, simply questioning my advisor's ethics with regard to how she assigns responsibility and authorship in the lab, has run into a brick wall.  It has made things awkward and has not changed anything.
I want to consult other professors but I fear that their conception of authorship is just as corrupt.  I would also like to speak to our dean but I fear that word will get out and it could come  back to hurt me a later point in time.
How have people dealt with this in past?  It seems that there are no definite guides for how to determine authorship in such specific cases, and I feel that my advisor is abusing the undefinitive nature of authorship ethics!

@Alexandros, there's a difference between not being able to do something, and having to follow the orders of an overbearing boss who pays your salary and controls your chances of graduating. If it's the case that Mike could be fired for not doing what his supervisor demands, then I think your comment is way off base. I would suggest toning down your criticism if you don't understand Mike's situation.

@BillBarth The OP never said he disagreed to do those experiments. In fact, he wants to be first author on the publication that comes out of them. I do not think that having a supervisor that suggests so great experiments that all his graduate students a) are certain that those results will be published b) want to be first authors on the subsequent publications, is the definition of an overbearing boss.

@Alexandros Thanks for your remarks. To address your concerns, I do disagree with the path forward, I can do something similar myself.  I could be fired for not doing what the advisor demands because I do work for her.  My issue is less with the advisor herself than her wanting to put the other graduate student first if I'm doing all of the research.

I wonder why this question was downvoted. It seems perfectly reasonable to me, and is well-phrased and measured in tone, which is commendable when dealing with what must be a difficult situation.

Just a quick moral perspective: While yes, there are rules determining authorship, there are also other morals and ethics. For one, the senior student might have had a bigger part in coming up with the idea and setup in the first place as they seem knowledgeable enough to be selected to guide you. And then, what would you like others to do when one first author paper is all that is between you and graduation? When you have fought to be first author on another paper where you felt you deserved it but failed? It happens all the time. Caring supervisors try to help as much as possible.

Depending on your field, it may be possible to submit your paper to a journal which allows for "co-equal first authors": that is, both the first and second are treated equally as first authors within the journal. You could then mention this in your CV. That way, I don't think there's much harm done; this would represent the path of least resistance.
Otherwise, you're going to have to be willing to involve someone to deal with this issue—whether it's your advisor, the dean, or other professors in the department. There's no way to resolve this issue without it. (I presume you mean the chair of your department, or other similar official, when you use the term "dean.") But the first step should be to talk with your advisor, before the paper is written. You may be able to clarify things at that stage. I'd involve the other members of your thesis committee (if you have one), and then finally work with the dean.


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Is it a good idea to go to a university just because of its high international ranking?
I'm an international student and I'm currently studying pure mathematics in undergraduate level with a relatively low GPA (~3.5/4.0). I've recently read so many positive reviews about the universities in Singapore. I checked the "National University of Singapore (NUS)" on the internet for its international ranking and it was ranked 9th in mathematics!
How much do you think the ranking of a university positively affects my future career? For example, one of my dreams is that I can study in some Ivy-league university in the USA or some grand ecole university in France like Paris Sud 11 in the future, but because of my low GPA I'm afraid that that will never happen for me. Do you think that going to the NUS can help me to get accepted into world top universities in the future?

You should select a school because its program is interesting, not its rank is high.

@scaaahu: Yes, that is correct, but if the ranking of the university can greatly impact my future admission opportunities, why not?

@some1.new4u: "Why not" is the same reason you were already given: because you should choose a program you're interested in instead.  If you have two programs you're interested in, and one has a higer rank, that might come into play, but you should consider interest first and rank only if and when choosing between places that interest you.

if 3.5/4 is a low GPA.. Then what is 3/4

I've spent some time at the centre for quantum technologies at NUS and it was a blast. Their quantum information/computing program is great, so if you are going into that then I would recommend it. I don't know much about the mathematics department though. However, as so many advised, rank is not the end-all-be-all.

Is it a good idea to go to “National University of Singapore”

It may be. I have recently visited NUS, and talked to a lot of smart faculty and some truly outstanding students. Personally, I can only recommend both NUS and NTU Singapore. Singaporean universities are well-funded and offer a reasonable research environment. Singapore itself is also a nice place to live, with a quite interesting mixture of different cultures, lots of food, high standard of living, etc.

just because of its high international ranking?

Oh god no.
If you want to go to NUS, then because of the reasons stated above. It think convincing the world that university-level rankings are a good thing is the largest disservice that the US has done to research. Let me make this clear - if you graduate from NUS and do uninteresting research, nobody will hire you. If you graduate from another reasonable university and do good research, you will find a post.

Do you think that going to the NUS can help me to get accepted into world top universities in the future?

Only for the reasons stated above - NUS has an environment that certainly enables you to do world-class research. For this reason, NUS may certainly help you get into a top university, but it does not make you accepted. The hard part (being a good researcher) will still be required from you.

@scaaahu I was not aware of that. I clarified this bit. However, from context I think it should be pretty evident that I was talking about Nanyang Technological University in Singapore

Rank is not an absolute index, it's relative. University X may have rank 9 this year, 15 next year. University Y may be ranked 16 this year and then rises to 10 next year. Different ranking agencies have different ways to rank universities.
I see those rankings as references. It's a factor. I would put more attention on the programs/faculty when selecting a school I want to attend.
I will not choose a school just because I want to increase my chance getting into Ivy-league universities. One reason for that is, I might have even lower GPA in a high ranking school. Of course, we can argue that better schools may have better professors so I can learn more. The bottom line is still, how hard do you study? In particular, you don't need expensive labs in order to study math. So, ranking may be important, but not a decisive one.

Indeed, and moreover, it might be worthwhile to question if such a ranking is reliable. For instance, is it a ranking made up by outsiders or one that is recognized by many serious mathematicians?

In my opinion, it is more important who you will be working with, than what university you will be at.  There exist productive scientists who are great at supervising PhDs, while working at medium-ranked universities.  Likewise, there exist tenured scientists at highly ranked universities, who are far past the peak of their career and lukewarm about PhD students.
After your PhD, what matters most, is your publications and possibly reference letters.  If you have great publications and superb reference letters from famous scientists in the field, I don't think you will miss out on this or that post-doc because whoever reads your letter doesn't immediately know the university where you got your PhD.
This is my opinion, based on quite limited experience — having recently finished my PhD at a university that is not top-ranked, proceeding to do a post-doc at a university that is.  I don't think the name of the university where I did my PhD is a handicap.  In fact, I've always been better at doing research than at writing exams, so if the place where I'll be going for my post-doc would accept PhD candidates purely based on GPA, I'd never have gotten in.

It might be enlightening for you to carefully study how these rankings were formulated. Some of them are based entirely on reputation and subjective opinions. Some of them are based on a suite of detailed metrics – factors which may or may not be of much interest to the typical graduate student. Seldom, if ever, are they formulated by a team that visits university classrooms to evaluate lecturers, or interviews graduate students to accurately determine overall satisfaction with their programs. These rankings don't come close to telling the whole story.
Some schools have meteoric rises in the rankings just because their institutional research department is able to collect all the right data and send it back to the organization doing the rankings.
I'm not saying that most of the highly-ranked schools are not good schools, or that they are undeserving of their good reputations and high rankings. However, you can get a very good education an unranked school, and you can get a below-average education at a very highly-ranked school. There are several factors that determine how well someone does in graduate school and beyond, and school ranking is probably not a very big factor in the overall scheme of things.

authors: მამუკა ჯიბლაძე


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Etiquette or useful guidelines while making video lectures
I'm in the midst of creating a series of videos to teach statistics online. Do any of you have a list of common do's and don'ts that can make a big difference?
Also, how does one assess how much to explain a topic, since you do not get instant feedback by looking at facial reactions to a given concept?
In real classroom scenario, it's quite easy to course correct if someone didn't understand the original thought, but in video, you have just one shot. The student either gets it or he doesn't.
Any way to minimize this?

Do's:

Do your best to pretend there are students in the classroom. Obviously, don't ask questions to the void, but scan the room, move about as you might in a real classroom (but don't go off camera), and take "normal" pauses if you're writing on a board.  This is an example from a short video I made for some of my pre-algebra students, and there weren't any students in the classroom at the time:  http://www.youtube.com/watch?v=est2X6-BVkw
Write big enough and clearly enough so the video picks it up. In the video I linked to, I realized that the pen I was using was pretty crappy, so I switched to a better pen (although I probably should have redone the entire clip). Even better is the way Khan Academy does it, with a digital board that he writes on during the lecture.
Make sure you have a good microphone, preferably one that is wireless that you put on your shirt/lapel. There is nothing worse than trying to watch/listen to a video that has poor sound.

Don'ts:

Don't block the board!
Don't be afraid to make a few mistakes that remain on tape. You can spend too much time re-doing videos for simple mistakes. If you make a mistake and recognize it immediately, fix it as you would in a real classroom. If you find a mistake in post-processing, feel free to overlay the video with a text box that fixes the error -- no one will care. Obviously, you can re-record if you wish, but keep in mind what your time is worth.

How does one assess how much to explain a topic?

This is one of those times you have to do the best you can and try to elicit feedback from the students after they watch the video. The reason I posted the video I linked above is because I realized that a number of students didn't get it when I first taught the topic.

In real classroom scenario, it's quite easy to course correct if someone didn't understand the original thought, but in video, you have just one shot. The student either gets it or he doesn't.

Well, that's one difference between face-to-face instruction and online video instruction. This is what email correspondence with the professor is for. You can also consider posting response videos to frequent questions you've been asked via email.

Good list… though looking at your video, I would add: make sure the whiteboard is readable, avoiding direct reflexion of the lights

Yeah, good point -- that was a big problem in that classroom!

Wow, I am on the same boat! Way to go!! Anyway, I'm slowly experimenting as well and am happy to share what I know.
Synchronous or asynchronous, or both?
Foremost, you'll need to decide if your online module is going to be synchronous or asynchronous.
Synchronous module involves real-time interaction. For example, online conference where students can type in comments into a twitter-like platform or directly ask you through microphone. The pros about this format are that you can clarify any problem instantly and the format mimics class-room interaction; the cons are that one technical error can throw the whole class into chaos, and multi-tasking in talking, reading, typing, and clicking through slides require some skill. It'd be better to have a teaching assistant to comb through the incoming messages and give you a synopsis of students' question.
The number of enrollment matters very much as well. If there are a few students only, you can afford to tune up the interactivity (e.g. more discussion, Q&A, etc.) If the enrollment is high (from my experience, more than 20 or so,) then the format may have to be less spontaneously interactive: perhaps a relatively longer lecture, coupled with break-out group discussion, and a big wrap up as a whole group.
Asynchronous module is a bit more like learning anything online. For example, online presentations/workshops through which students can learn the materials at their own pace. Comments and evaluation are usually done through blog post, e-mail, or forums. The pros of this formats are that students have a lot of flexibility, and the lecturer usually has to devote one large fixed chunk of time to set up the workshop, and it can run itself (more or less.) The cons are that the preparation is extremely intensive and assessments have to be carefully chosen and planted here and there to make sure the course is working.
Hybrid or fully online?
Some online course would mix in-class lecture and online together. For example, students may meet at a classroom for the first two weeks to learn about the requirement and format of the class plus some fundamental background lectures. And then they'll go back home and switch to online. Some other hybrid model may involve coming to class every alternate week, etc. The pros are quite apparent as the lecturer can establish a real presence, and it also provides some opportunities for networking between students, which is a crucial component especially in graduate schools.
Another sub-genre of hybrid online teaching is called "flipped classroom," through which students will watch the lecture in advance, complete the assignments, and come to class for more challenging group exercises, case studies, or journal critique. I am actually planning two classes using this format and hopefully I can get a real sense of what a difference it may make.
You may also conduct your course fully online... that way no one have to travel, leading this format to have probably the lowest carbon footprints, if limiting such is part of your aspirations.
Microlectures
For video lectures, length matters. I'd suggest breaking up your lecture into one-idea, one-bite chunks. Formats like microlecture will be a good place to start. For me, I usually try to explain an idea within 10 slides in 20 minutes, which is usually the attentions span for someone sitting in front of a computer. Never make hourly videos; they are a pain to download and very tedious to sit through. Pausing and coming back later is possible, but it's better to capitalize on the online features and make learning (esp. technical subjects like statistics) more modular.
One good way is to incorporate some Interspersed exercises. For instance, after the microlecture on normal distribution, build in some exercises asking the students to check the z-score table, or answer some online quizzes about application. What exercises to put in there depends on your class objectives and competencies to be taught.
You also mention that:

In real classroom scenario, it's quite easy to course correct if
  someone didn't understand the original thought, but in video, you have
  just one shot. The student either gets it or he doesn't.

which is not totally true. As long as your script is clear and correct, students can always replay the video to listen again. They can also try the exercises to evaluate themselves. From the exercises you can detect problems and misunderstanding to some extend, and provide feedback accordingly. I would like to emphasize that this is a pretty different generation we are looking at, gen Y and after are actually much better as a communicator online than in person. In the tool paragraph I'll talk about some ways to let student provide feedback or ask question about the video.
Combine self evaluation + formal evaluation
As mentioned above, build in plenty of self evaluations within and between students: online quiz, blog post, comments for others' post, exercises, etc. Let the students know in advance that how they will be formally evaluated for grades.
Be present and don't be always present
One "curse" of being an online teacher is that students think you're as convenient as the materials you put online. This can be bad cause you may get an e-mail at 3:30 am and you happened to have forgotten to mute the phone that night. Be very upfront about your availability and honor the promised office hour. You can use online communication such as Skype, Google Chat, etc. to communicate with students. Also, make sure to give them an expected time for your response (I have been using one office day, which seems doable.)
Use the right tools
Looking for the right tools has been the biggest deal for me by far. I broke my class into three major components:

Lecture: I use a few ways and they all have their own advantages. MS Powerpoint with voice recording is amazingly easy. Users can also correct and re-record on each single slide if you're not happy about it. Adobe Presentation has been wonderful, you may even edit the soundtrack and record over with the corrected script. Both are quite friendly to multimedia such as embedding videos. Invest in a good microphone, for recording lecture on screen, a headphone with built-in microphone (around $30) and a quiet room will work fine. For recording real lecture, have some school IT unit hook you up to a wireless microphone. Video lecture + speech submerged in echo + difficult subject = withdrawal.
Software demonstration: I use a software called Snagit to take screenshot video of all software demonstration. The software allows users to export it as movie files, which can be linked to the lectures.
Other materials: I use a wiki platform to host all materials. I also authorized all student as editor so that they can maintain a project page in the wiki and collaborate.

Some teachers start going online by videotaping the lecture and upload that online. I feel slightly negative about this approach because it does not exploit the pluses of going online. However, if someone so wants to do that, I'd suggest investing some time to identify a software that allows picture-in-picture. One camera can focus on the lecture, one zoom onto the board or show the slides. Having said that, I have to admit that in most of the "online" lectures I have watched, the board writing is mostly illegible. I haven't incorporate writing into my work, but if I have to, I'll consider to:

Use a 3-D project to show my writing onto the board. There you can use thicker pen or play with the zooming to make sure all space on the white screen is used. An added benefit is that projecting on screen does not cause glaring on the video, while a white board may show glaring that obstructs the text.
Use a drawing pad and a very simple drawing software (even MS Paint) as your writing tool.

For students' feedback, I have been having some luck with online forum and tweeter-like bill such as Todaysmeet. Todaysmeet allows your to open a chat thread in which student can post questions or comments. You may even archive them if you wish to. Most online meeting software (such as Adobe Connect) also builds in some "raise hand" button; users can click that to initiate a question.
As for video, look for some video markup tools so that student can bookmark a certain section of your video, generate a link and send it to your with related questions. They can, of course, mention the video link and time stamp as well. E.g. "I have a question about a point at 12:45 of the video on [link to the mp4, etc.]."
Provide ONE and ONLY ONE official announcement site where students can get the most up to date announcement. Because online teaching involves a lot of software and different forms of communication, it's easy to fall through the schedule not knowing some is due or a new lecture has been released. Make sure all announcement can reach the students' official e-mail address.
Lastly, I cannot stress enough i) pilot run, pilot run, pilot run!! Try all modules and make sure they work on at least Mac and PC. You may want to check the course shows up correctly on iPad and Android pad as well. For a very similar reason, don't use any Adobe Flash to make animation. ii) have a plan B, plan C... plan K: Isolate your critical control points and prepare a second plan if the control point falls through. For example, if you decide to use Skype for an online talk, but Skype's server goes down, think 1) how to contact the students? 2) Where to re-establish the meeting? etc.
Study guide
Because you're not there to guide them in person. It's crucial to have a very protocol-based syllabus. I adopted the idea from Smith's Conquering the Content. For every single session, list:

Learning goals and outcomes: After the session, what will the student know and learn to do?
Learning resources: List all resources including the required and optional reading, supplementary websites, journal articles etc.
Learning activities: Describe the flow of learning, provide due date or schedule.
Self assessment: Lay out how the students can assess their learning.
Formal evaluation: Lay out how you'd assess their learning.

I like this approach very much. Smith particularly emphasizes not to put time-sensitive information in your video, instead, put them on this learning guide. For instance, in the video you can say "refer to the suggested journal article" instead of saying the exact title. That way, you can just update your learning guide without the need of re-recording your video, saving some time to renew your lecture every year.
Closing remark
Sorry for this really long post. I still have a lot to say but I guess I have long passed the socially acceptable length of SE responses. Teaching online is a fun challenge, and all I have described here are just a fraction of this domain. There are online interaction, engagement, etc. which are other cans of worm. If I were to do it again, I'd start simple by switching 2-3 classes to online as an experiment, and build from there. It's dangerous to go online in a semester, I'll invest a good 6-month period to be familiar with all the tools. I'd also suggest planning the whole course before putting anything online, because that helped me eliminate a lot of irregulars, and make the format a lot more uniform.
Hope these comments would help, and have fun!


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Is it considered okay to mention all the correction in an accepted article which is typeset by the press
Let's say that I got a paper accepted to a nice journal (feels so good!), in fact of a very reputed publisher. Then, the press / editorial office asks me to submit all the source files for preparing the proof for publication and I have submitted all the source materials (in word / .tex format).

Here it is worthy to mention that the accepted manuscript is already respecting the journal's format (closely). But of course, the press will completely change the article's looks to match the journal's own proprietary style(s) etc.

A few weeks later, I receive the proof (in the native journal format) and much to my surprise, I see that the original mathematical equations in the manuscript got vandalized (in terms of alignment, even missing some equations etc.), subfigures (in a whole figure environment being named as a, b, c, d, ...) getting copy pasted (even including the subcaptions etc.), texts running across the borders, tables being sloppily copy pasted as images and even what not the mathematical symbols in bibliography are typeset as images!...
If that is the case, could you advise, whether I can mention each and every mistake that is present in the proof that is sent to me?

Honorable mention: I deeply feel bad for my paper, because, even after giving all the source files for compiling the proof, the typeset is being subpar given the journal / publishers standards (IMO).
Update: Today,

I got an email from the publisher that the corrected proof is available online --> which accoring to their definition means ready for  production.

Upon seeing the so-called corrected proof I found that it was an exact replica of the one they sent before.

I thank all of you for your suggestions :)

Yes, in decent journals which are not math-specialised, I have had to go through every single mistake. They were not bad journals, just not really well equipped to handle math. Be prepared to have to do so.

I'd report all the mistakes that I found.  I'd also provide (if I didn't already) the pdf version of the paper produced from my source file, so that I can show them how it's supposed to look.

If there are so many issues, I would suggest to not mention every last one of them but instead write a short email to the editor.
Don't go blaming people, ask if there is something you can do, maybe you sent your sources in the wrong format, maybe there was a misunderstanding.
If this journal frequently publishes mathematical papers, they should have proper ways to do things and what happened here is most likely not a small typo that can be mentioned while reading the proof, but a deeper problem that should be solved before doing the final proofreading.
(If, on the other hand, they only use MSWord 2003 and just copied stuff from your .tex-file or PDF, then maybe you need to reconsider your choice of journal...)

Because this publisher, as I noticied, in general, outsource the typesetting and it is not done in house. As a matter of fact, they also use Latex for compilation. Since, I used their own class files for typesetting the manuscript (up till acceptance), I am pretty confident about the source files. So, I am not sure yet. (Nevertheless, +1 for dont go blaming people)

+1 and I'll add that you should not write to the journal's editors (the ones that handled peer review), but the person who sent you the proofs. This is their job.

I generally agree, but if you actually have a list of errors, you might as well provide them. It will make the number of cycles of return and repair smaller, hopefully. Don't expect their first fix to necessarily correct all issues.

@Buffy I think your comment with the aforementioned answer gives a collective answer.


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How to properly claim credit for peer review?
I acted as a reviewer for a paper this year and would like to mention this in my CV. However, I would like the authors not to know that I was the reviewer before some time.
At the moment, I have remained intentionally vague in my CV, mentioning only the journal name and the topic of the article. Is there a way to do better, namely:

Is it possible to make this review work verifiable? (perhaps by giving the email of the editor?)
Is it ethical to point to the full published paper in a CV that I don’t intend to distribute widely?

Usually, in a CV, you simply list the journals for which you acted as a reviewer, not the individual papers you reviewed. And if a committee wants to verify that you really reviewed anything for those journals, they can simply contact the editors.

How is mentioning the paper name vague? Or did you mean the journal name?

You have no control over the distribution information in your CV, unless you never send it to anyone. If it gets into the hands of anybody who has an issue with that particular paper, or that topic, do you want to send out a message like "AllthePineTrees must have thought it was good (even though I think it's just plain wrong) since he/she reviewed it and it got published"? Don't kid yourself - people talk to each other, and stuff gets around, even if it takes years to do so.

Regarding documentation, I started using Publons recently: "Publons is a website and free service for academics to track, verify and showcase their peer review and editorial contributions for academic journals."

@rafa11111 yes indeed. I mean mentioning the journal name, not the paper name. I edited the question accordingly. Thank you very much.

What would the benefit be of specifically referencing one article that you reviewed?

The standard information to give is the journal's name and only this. As far as I recall I have never seen a CV that gives more details than that (mostly I know academic CVs of mathematicians).
I would not go as far as saying that it would be unethical to include more information, but it would seem unusual and the advantage is not very clear.
If you are concerned about the claim not being credible, I'd not worry too much about this. However, some journals and publishers offer certificates for reviewers. See for example this information about reviewer recognition at Elsevier
There may be exceptions to this if you happen to be involved in some very high profile reviewing endeavor, but if you reviewed a normal paper I'd just give the journal's name.

I've seen some people (again in math) also mention the year(s) and/or the number of times they've refereed for a given journal.  I personally prefer not to give out such detailed information for multiple reasons (one of these is: you don't need to keep updating your CV).  I just say something like "Referee, various journals."

@Kimball Exactly. If they want he specifics, they'll ask for them during the interview.

Even listing the journals already seems rare, at least in my field. Only editor positions are usually listed.

@MarcGlisse in mathematics, especially for early career researchers, it's quite common. It's not an important point though. As the career progresses one might drop it or address it in more general terms. It might be that reviewing a paper takes (on average) relatively more time in mathematics than in some other disciplines.

I would recommend against doing this unless the journal editor or conference chair tells you it is ok. I assume the review was blind or the question wouldn't arise. But blind reviews are intended to remain blind.
But I wonder what your motivation is here. Why not just state in your CV that you have been a reviewer for [journal name] or [conference name year]? Reviewing is intended to be a service to the community, not a way to associate yourself with someone else's work.
My own reaction to seeing a specific claim on a CV would not be favorable, I think.
It may be, in some cases that an author will want to thank the reviewers for helpful comments, but even then, it is very rare that names are used, or even known.
If you want to change the reviewing process, on the other hand, removing the "blind" aspect of it, I'd suggest that you do it directly and openly, not by just doing it. There are venues with open reviews.
But ask the editor.

I have recently started using this service called Publons (https://publons.com/about/home/) by Clarivate Analytics. They request that you forward peer-review acknowledgements to a certain email address, and they show up on your personal profile page after verification with sensitive details anonymized. It might help to just link to your profile on your CV or use the list they provide.

I have also started using the same. It is a good aggregation platform. Not sure how much they will be recognized in the long run.

+1 to this advice. Publons also has arrangements with some publishers so you just press a button when you submit the review and it appears in your Publons list. In my CV, I simply list the journals I have reviewed for in the last two years or so, but I use Publons to actually do the tracking so I can remember, and it also provides a report that you can use if you need more detail.

I would leave off reviewing entirely from your CV.
Not used to seeing reviewing on CVs, even by journal.*  Let alone specific papers.
Why not accumulate some bigger things to list.  Your own papers, being a subeditor, running a conference, etc.?  But reviewing papers???
*This doesn't even make sense to me.  Does one paper reviewed for a journal make you "their reviewer"?  If you are a part of the scientific community, you will just occasionally get requests to review or not.  From various journals.  Or not.  But it's not like a "position".

This is really bad advice, especially if you don't know where the OP is applying. Apart that is not uncommon to list reviewer's duties in a CV, being asked to review means that at least someone thinks that you have enough expertise to review a paper. Moreover, maybe it doesn't count much in the overall evaluation of a candidate, but why leaving this small advantage to the competitors?

This is actually decent advice once you’re senior enough.

The only reason to omit this information on a CV is if you have some sort of page limit; otherwise, it simply gets relegated to somewhere below all of the shiny achievements you mention.


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PhD with no prior research experience, how?
I am an IT post graduate (with no thesis but project) from IT industry and I have practical experience of about 10 years in the industry. I want to carry a PhD research in a subject related to IT field. Practically and theoretically, I know the subject very well, but I don’t have any prior real research experience or any publications. But I have studied some theoretical subjects on research methodologies, statistics etc. during my university learning. But I found that most the universities have “research experience” as prerequisite or requirements to start or to be eligible for PhD research.
So, what can I do to fulfill that? (Off-course other than doing another research just to be eligible). Any ideas or suggestions?
Is there any chance of getting accepted without prior research experience? Should I keep on trying(esp in US and Australia)?
I have seen some doing PhD after their undergrad. I have master degree and I am confident that I will be able to manage things with in those 3-4 years as it’s not that I don’t research at all. It’s just that I don’t have something to show now.
Any suggestions?

Yes, In the UK, you can get accepted to a Ph.D. based on Bs.c. or Msc diploma, with no publication records.
I can answer this, because computer science is my field, and saw many people like you doing research here in the UK.
Background Work
Ok so you want to do a Ph.D. with a postgraduate degree which is on the practical side of things. That is totally fine; however you need to do some work before finding a supervisor. In essence there are three types of supervisors in the field of computer science:
Know it All: There are number of impressive supervisors, that know both the theoretical and practical side of computer science. These supervisors publications on both theory and practice (e.g., code generation, language design). This is the best kind of supervisors to have because they can bridge between theory and practice; and can navigate you through both theory and practice.
Theory-Oriented: They use Latex to create their papers/journals/books. They have no idea what so ever about the practical stuff. God forbid you ask them about JVM internals. They can still be useful, because you are covered the practical stuff; and they can help you through theory. However, they have no appreciation about how hard it is to make something work in practice. Also, they might not the best people to link between theory and practice.
Practical-Oriented: There are much fewer number of supervisors, that for example transferred from electronic engineering into computer science. They know very practical stuff (e.g., embedded system programming, active on developing Erlang application for telecommunication purposes); however for you these are the worst choice. Because, you have the practical background (so don't supervision on practical stuff), but because you need to introduce theory into your research they can't do much in helping you. So you end up wasting number of years just because for example your supervisor don't know game theory.
So overall look for their publications and the track record. How much open-source software they produce. How much theory-oriented paper they publish. These are the things that you will curse yourself later on during Ph.D. if you didn't think it through.

Thank you. Was really helpful and I agree. Have started looking for my “Know it All” superior. Hope everything goes fine. Yes when I was trying to post this one another post with answer “it’s allowed in UK” popped up so I added “Australia and US” in the question. By the way,in addition to experience, academically my results have been very good in university (top 0.5% in class), may be can I ask for some exception based on that? If things doesn’t go right personally I feel maybe I can start with MRes and upgrade it to PHD proving my caliber. But it will make things bit uncertain.

"Theory-Oriented: They use Latex to create their papers/journals/books." I disagree with the generalization you imply here! LaTeX is actually incredibly practical, and absolutely does not solely belong to the domain of the fuddy-duddies. I would be much more circumspect about supervisors that use Microsoft Word to write a paper...

@Moriarty I get the impression that Dave meant that LaTeX is the full extent of their coding skills, not that LaTeX is bad.

This is quite common in the U.S. Most programs would ask you take some introductory courses in research areas to build up your research skills.
When I started my doctorate program, I had no real research skills and learned everything I need to learn in the program.

Take a broad approach to what you define as "research experience". You can probably find a way of spinning/describing some facets of your "practical experience" in terms that demonstrate your suitability for a research programme. When talking about such experience in interview, reflect on how some of the work you have done constitutes a form of research, what you learned from it, and how it could have been developed in research terms if you had had the time (maybe, there is something which still has research potential). Finally, although peer-reviewed academic publications generally command the most esteem within the academy, there are other types of output (including "practical" outputs) that can embody and/or form the basis of serious academic research.
Be positive about how your experience will equip you for a research programme, irrespective of whether it constitutes a so-called "traditional" background for a researcher in your field. Turn any weakness into a strength, by explaining that you are keen to acquire the new skills that a research programme has to offer.

This is also possible in the US as well, but it varies from school to school. It is fairly common for people to be accepted into a PhD program without research experience, provided that their previous academics were exceptional. Don't get too discouraged and keep looking.


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Using first person in literature recommendations in a masters thesis?
I am currently writing my masters thesis in computer science. I've heard that one should avoid writing "I".
In cases where one describes what was done and it doesn't matter who did it, I understand why writing "I" should be avoided. I, however, wonder if it is ok in the following case:
In the following, it is assumed that the reader knows XYZ. In case
the reader needs a refresher on any of those topics, I recommend ...

It is a subjective statement which is not necessary, but might help students who might in future read it. I should probably point out that a CS master thesis is expected to have about 80 pages, hence length-wise it doesn't really matter. It should be clear that it is subjective; if I changed it to the passive (it is recommended...) then it sounds as if there is a consensus in the community.
Some people recommend writing "the author". It, however, sounds strange and it is absolutely clear that "I" is "the author". Hence I don't see an advantage in doing so except for beating automatic tools / grading sheets.

Personally, if length (and time) is no issue, then I would write my own summary of XYZ. That way the thesis remains nicely self-contained.

Unless there is some reason to specifically avoid it (e.g., your have an advisor who absolutely won't tolerate it), feel free to use the first person and "I" statements in lieu of traditional academic language like "the author" or a strict adherence to the passive voice. Your readers presumably already know you are the author. Anything you can do to improve their comprehension of your work is worth doing. Plus, as this editorial in Nature suggests, "Personal language builds a connection to the reader and helps, ultimately, to persuade".
As for the literature suggestions, a separate section for providing some brief background explanations may be helpful. You can use such a section to include context along with references to the further reading.

+1 for "Your readers presumably already know you are the author."

It is generally easy to rephrase it to avoid the issue altogether. Doing so is often more readable, since the sentence will be about the literature rather than your recommendation.
"For a thorough survey of topic X, refer to Blah."

Good point.  And this could be supplemented by pointing out that if the culture in your department goes against the use of "I," then you might as well rewrite the sentence to avoid the first person.  This would not be a big deal.

@aparente001I'm not even concerned about culture, but rather readability. Is the sentence about your recommendation (e.g., "I recommend...") or is it about the literature (e.g., "For a review of topic blah..."). Updated my answer to reflect that point.