text:
How to cite sources written in a different language than English?
Assume one wants to cite a paper written in a different language than the article citing said paper (e.g., ones own article is written in English, but the source is French).
How to properly handle citation in such a case?
Do I cite the original (French) title or a translated title? If I use a translated title, people might have a hard time to find the source; if the original (French) title is cited, people might have a hard time understanding it.

You cite the original title, for the very reason you gave: to enable readers to find the original title. If your work is subject to guidelines, you should also check those.
Usually, there is no point in giving a translation of the title as it does not contain any relevant information for the reader. Many citation styles do not mention the title of papers at all. I see two exceptions though:

If a translation of the cited work into English exists (but you worked with the French original), you can mention it in addition to the French title, e.g. with:

[actual citation] (translated into English under the title [translated title])

If the title allows the reader to estimate what the source contains and whether they want to read it at all. In this case, you should arguably change your text such that it states in what way the citation is relevant for your work.

It actually depends on the citation style. It is particularly well documented in the APA Style (see Citing Translated Sources in APA Style):

For example, here’s how you would cite the original French edition of
  a work by Piaget (note that an English translation of the title is
  included in brackets):
Piaget, J. (1966). La psychologie de l’enfant [The psychology of
       the child]. Paris, France: Presses Universitaires de France.

and:

Here’s another example, from a German journal. Again, brackets contain
  an English translation of the work’s title (the article, not the
  journal).
Janzen, G., & Hawlik, M. (2005). Orientierung im Raum: Befunde zu
       Entscheidungspunkten [Orientation in space: Findings about
       decision points]. Zeitschrift für Psychologie, 213(4),
       179–186. doi:10.1026/0044-3409.213.4.179

If the reference uses a foreign alphabet, be sure to also check the transliteration requirements.

Much better answer, since it gives a concrete example of how to do this.

It is common to either use a combination of the original title and a translated title. The exact form for punctuation has to be adapted to the specific journal. I use an example from "my" journal (Instructions for Authors):

Author name(s), year. Title in original language (if possible) [Title translated into English]. Publication name in original language (if possible) [Publication name translated into English]. Volume/issue/page information (according to type of publication). [In ‘language’]

Example:

Krenke, A.N. and Khodakov, V.G., 1966. O svyasi povercknostnogo tayaniya lednikov s temperaturoy vozdukha [On the relationship between melt of glaciers and air temperature]. Materialy Glyatsiologicheskikh Issledovaniy [Data of Glaciological Studies], 12. 153–163. [In Russian]

If the original is in a language written with different characters such as Russian, Chinese or Japanese to mention a few then one can also use a shorter form such as (again using the example above:

Krenke, A.N. and Khodakov, V.G., 1966. On the relationship between melt of glaciers and air temperature. Data of Glaciological Studies, 12. 153–163. [In Russian]

In the Russian case there sometimes exist a transcription with Latin letters but not always.
I will add that many journals in my field do not translate titles in for major languages such as Spanish, French and German since it is assumed that everyone has some grasp of languages. This is of course a notion of the past since the "western focus" is, and has not been for long, a useful perspective.

For references in other languages (non-English), I use titles translated into English if the translation by the author is given in the paper (usually together with an English abstract). In such a case, a remark should be put at the end in brackets, eg. (in French). The use of translated titles should also be recommended for papers written in non-Latin scripts, eg. Chinese.


text:
Does a PhD student need a co-supervisor?
I am a few months into my PhD and my supervisor and co-supervisor are close friends.
Unfortunately, I find that my co-supervisor is not useful – he doesn’t provide any help or input into my project. Additionally, he has given me a hard time on more than one occasion, e.g. making a derogatory comment about the source of my PhD funding, not including me in discussions with his other PhD candidates (although I was physically present), and asking me to buy items for another PhD candidate using my budget.
I would like to stop being supervised by my co-supervisor, but I have not yet built a relationship with another academic that I could ask to take the role.
Do I need a co-supervisor? Can anyone recommend ways I deal with this situation?

Does your department require PhD students to have co-supervisors?  If so, you have your answer.  If not, you have your answer.

Since your supervisor and co-supervisor are close friends, if you decide to go without a co-supervisor, be careful how you raise the issue with your supervisor. Rather than criticising the co-supervisor outright, it may be better to say something like "we just don't click. Our personalities are too different."

The direct answer is not a PhD students does not need a co-advisor. The problem here is to think about the role of co-advisors. I am sure the view on this varies so my view is coloured by situations with which I am familiar, which is the US and Sweden. Co-advisors may be involved because they have specific expertise that may be relevant to part of the work, for example specific investigations, lab work ec. Co-advisors may also be there to provide overall scientific expertise and provide feedback on written articles or the final thesis or both. Hence a co-advisor may not be very active when you start your PhD. At the same time by signing up as a co-advisor, I would expect the co-advisor to be open for discussion during your time as a student but it may fall on you to initiate such contacts when you need it. The main advisor is, after all, the one responsible for the direction of your work within your thesis topic.
So while one does not need a co-advisor, there are many instances where such support is necessary or at least very useful.

Normally, a co-supervisor is not needed. However, there are some circumstances where it can be extremely useful. One such instance (with which I have some experience) is related to supervising students between departments. At some institutes, candidates admitted to department X can work with a primary advisor in department Y (and vice versa) if they have a co-advisor in department X.
Beyond that, though, there aren't many places I know where a co-supervisor is required. If you have concerns with how your co-advisor is treating you, the first thing to do is to speak to both of your advisors. If the behavior continues, then you may also want to consider talking to the faculty member in charge of graduate affairs within your department.

I'm studying in The Netherlands where cases of scientific fraud among psychology professors have been surfacing lately, and one of the conclusions was that students should be co-supervised as a safety measure. Another potential reason is to have a clear idea what will happen with the student if the main supervisor would at some point become unavailable for supervision. This is the case in the institute where I am, and so far the co-supervision on my project is on paper only, and will remain that way.

A co-supervisor must be useful. It is not fair to take a role of "useless supervisor" who can later be added as a co-author with relatively little input to the published works.
This of course depends somewhat on the status of the co-supervisor. Some professors already do not spend much time on experimental research, focusing on lectures or department-level supervision instead. In such case the department may have several intermediate supervisors, each having small own research group. In such case, without co-supervisor, you stay alone and may not even be able to get equipment and reagents you need for work.
However situation when some freshly baked post-doc starts "teaching" a good PhD student without use is also common. The goals may be to get into co-authors or even to take over the promising research topic. Sometimes such co-supervisor may be even obviously less competent than his student, so why to piggy-back him?
In case a co-supervisor is not useful, talk to professor and ask to remove co-supervisor out of your head. Simply say you do not think you benefit from additional supervision, explaining that the problems you are supposed to solve with ones help you can solve no worse or maybe even better yourself. Some cases / examples would be good.

Generally, the co-supervisor is somebody to guide you when your primary supervisor is not available. A good co-supervisor can boost your research power as he/she can share alternative viewpoint about research information. This supposes to encourage your research/work to become more rounded and more suitable for larger group of people.
Nevertheless, my suggestion is based on my experience in Australian system that heavily relies on the guidance of the supervisors. To deal with this situation, I suggest you seek for the person with the higher power as he/she can make a change or comments on your co-supervisor.  One of the options is the primary supervisor usually holds more power than the co-supervisor.  Also, he may know who is more proper than that guy, if they aren't friends. A more safe option is to consult with the head of the postgraduate office who has more power as the person has to take care of everyone in the school. So, he/ she should be able to regulate the inappropriate conduct or move him from your supervision panel.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

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

sort: votes


text:
MPhil vs. MSc. in the UK?
I'm currently finishing a B.Sc. Honours in Canada, and I'm applying to Edinburgh (among other places) to do a Masters. They have two research-based degrees, and I was wondering if people with experience in academics and CS could help me distinguish between the two. I'm not overly familiar with the British Education system.
The M.Sc. is a one-year degree of independent research, with very little to no classes. The MPhil is a two-year degree, where classes are taken in addition to independent research.
In particular, I'm wondering:

Which is considered "more academic" or "more prestigious?"
Which would be better for getting into a PhD program?
Since there aren't classes in the MSc, are you expected to have a higher level of knowledge coming in?

In the UK it's relatively unusual to apply for an MPhil - MSc and MRes are much more common. MPhils really exist to cover failed PhD candidates. When you apply to study for a PhD in the UK, for the first 12-18 months you are placed on "probation" (even if you alread hold an MSc/MRes). After this time, a review (and mini-viva) of both your progress and quality of research is conducted and you are either "confirmed" as being a PhD candidate or are relegated to MPhil.

The practice varies from university to university though. At some places (including Manchester, where I did an MPhil) PhD candidates are registered as MPhil and then either continue to the second year of a PhD or hand in an MPhil thesis (or fail altogether). Some people choose to leave so it is not necessarily a 'relegation' or bad thing to get an MPhil. It's also possible to get an MPhil if your thesis at the end of three years isn't good enough fro a PhD.

I don't think this is really true. My impression is that different universities choose the names of their master's degrees according to their own traditions and that there's no overall national pattern. As a specific example, Oxford seems to use MPhil for master's courses that are designed as one way into a PhD (which Oxford calls DPhil) programme and MSc for those that aren't. Cambridge has 13 pages of master's courses, most of which are MPhils: these definitely aren't semi-failed PhDs.

Such a wrong and offensive answer. How can you be a "failed PhD candidate" if you never started a PhD in the first place? What if someone is a successful MPhil and don't wish to pursue a PhD? Is he also a failed PhD candidate? Come on...

Looking at the courses there appears to be a one-year taught MSc and a one-year MSc by research. The two-year MPhil while described as a research degree, has a one-year taught component. It seems to me that the MPhil is just the two MSc courses combined. The programme description says:

The first year of MPhil studies is probationary.

suggesting to me that if you do not do well enough on the taught component that you cannot progress to the research part.
I would say that taking classes is less "academic" than doing research and therefore the MPhil is less "academic". I would also think that the MSc by research has the highest admission standards and therefore is more prestigious
For getting into a PhD program you need to prove you can do research. Graduate level course work often helps in doing research. If you already have the fundamental skills that you would be learning in the taught components, there is no big benefit to taking more courses. Similar with research experience. If you are lacking both the MPhil might be the way to, but if you are lacking only one chose the appropriate MSc.
As for entry requirements, it is probably best to contact the department and ask them. As I said above, my guess would be that the MSc by research has the highest entry requirements.

Generally in the UK, the MPhil is seen as a senior level research qualification just above the MRes and below the PhD - at least in computer science. I do not agree that an MPhil is necessarily a failed PhD as there can be many reasons why a candidate cannot produce a full PhD thesis ranging from company support, time and funding to personal circumstances. A PhD fail to me is someone who has done a PhD thesis and failed the PhD viva and failed to get at least major corrections or a recommendation for resubmission in 12 months.
This was true in my case that I was transferred from PhD to MPhil, albeit my situation was rather difficult; I was in a PhD route for 3.5 years full time at Lancaster University and the sponsor company (a major water utility company) stopped communicating with me and my supervisor. As a result, my prototype was left untested in a real world scenario which was necessary for my PhD work as there is a requirement in producing innovative and original work. After a year of starting my PhD, I had a supervisor change resulting in a research area change resulting in a late panel 2 years down the line which didn't help either. The panel is a useful tool to know if you are being guided in the correct path and to know if you are getting along well with your supervisor as well as to see if you are producing work that is up to PhD/MPhil standard. If your work is not up to MPhil standard, they can altogether cancel your registration and you are out.
I can't stress this enough; you should have your panel early in your PhD and never late. In my case, it was given late due to a supervisor change and that "I fell through the cracks of the system" and nothing could be done other than to make a formal complaint which I have already.
The panel concluded that I had enough work to do a PhD and decided to change my route from PhD to MPhil on the premise that I was running out of time and no funding available for me (I only had 6 months left of funding, but due to other circumstances, this went well beyond my defence and upto summer 2017 surviving on a TA salary which was less than £5000 pa). This was compounded with fears that I might leave with nothing. They did say that if got the MPhil, then perhaps I could use this as a stepping stone to a PhD and upgrade my work.
It took me 5 years to complete my "over bloated" MPhil and I decided not to pursue the PhD in my area due to difficulties with my current supervision - it is another long story. I feel I do have enough research skills to carry out research in other areas which are of interest to me.
To clarify whether the MPhil has any classes: no, it doesn't. It is purely research unless you are doing a professional Doctorate which have taught components with research. The MPhil is research work done at the same quality and academic rigour of a PhD, albeit shorter in length - hence why the MPhil is seen as a higher degree than an MSc by Research. The MPhil used to be the gold standard during the 60's and 70's for lectureships until requirements increased to have a PhD under your belt.
Which is considered "more academic" or "more prestigious?"
From the Masters degrees, the MPhil as it is the highest Masters qualification that you can get before embarking on a PhD. I know people in my area who haven't got a PhD but have an MEng and produced academic output equivalent to that of a Professor with a PhD. Having research output and published by top ranking publishers is more prestigious in my opinion.
"Which one is better for a PhD?"
It depends on which subject you are studying; in computer science, you only need a BSc honours with a first class honours to enter the PhD route directly without requiring an MSc. Having an MRes or even better, an MPhil in a related area, would considerably boost your chances in succeeding. Other subjects like psychology would require an MRes to enter the PhD route depending on research areas.

This could be a helpful answer if the question were about MPhils at Lancaster, but as David Richerby rightly observes in a comment on the accepted answer the meaning of MPhil varies between British universities. As such, absolute statements like "It is purely research" are misleading.

As I quote from a book written by E.Phillips, "How to get a PhD" p29,30.
"A candidate for an MPhil must undertake an investigation but, compared to the PhD, the work may be limited in scope and the degree of originality...
...In a high quality MPhil, evidence is required of the ability to test ideas; understand appropriate techniques; make use of published work and source material; and show familiarity with different theories and empirical studies.".
Therefore I do not see why my statement is misleading as a high quality MPhil is "purely by research".

That quote claims that all MPhils involve research, which may be true, but does not say that they are purely research. David Richerby's comment links to some counterexamples at a prestigious UK university.

It depends on the context of the degree being awarded and this opens a new discussion, i.e. Which one is more prestigious, the academic PhD or a professional PhD?
The difference is due to articles being published in trade or non academic peer review journal and the title awarded (DPsych, EdD, DProf). Thus, the qualification is seen as a watered down version of the PhD by certain groups. I would not expect a taught MPhil offered to students who would want an academic career.
https://www.timeshighereducation.com/unijobs/article/phd-v-professional-doctorate-which-is-better/

Mphil is an interphase between MSc and PhD. I.e above MSc but below PhD. Masters program pose more importance to thesis. Mphil is usaully research based and that case higher than MSc.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Academic affiliation: which to choose?
I am actually working for two different universities in my country, and the problem is that they do not give too much support to academic research. I mean for paying the costs of tickets, travel expenses or accommodation when one paper get accepted for a conference.
I usually work as an independent researcher, but the problem that I have is that if I put my author affiliation as Independent researcher maybe I will be not be considered "serious" enough for the reviewing program committee of the conferences that I plan to submit my work.
Now what should I do? should I put the name of one of the universities that I am working at random, and at the end change my affiliation and put the name of the university that will give me the funds for the travelling expenses of the presentation?
What would we the best way to act in this way? I remember that for one paper that I was submitting, the Dean of my past faculty told me that he could give me the money, but if I put him like a co-author. Actually it was his way to get publications to his name without working on them. Of course, I did not accept that.
Any suggestion would be of great help
Thanks

Layla, you better associate yourself with a lab or research centre and then use the fund you get form the lab for publications..etc. I went through the same situation before

Affiliations go into affiliations, and it is regardless whether they provide any funding; or I am wrong?

My immediate reaction is to put them both on; It is not unusual to have two affiliations. I then mean to state "A and B" to show a shared affiliation. That way both departments could benefit from your publication. The question is then how to get the different departments to losen up their purses. In my system no such funding is typically given out by departments/university, one has to apply for money from different sources oneself. I could possibly convince my head to provide the money if the reason was particularly well deserving. So I cannot comment on how such support would be provided.
I would suggest communicationg with both univesities stating that you will publish the paper with them as an affiliation to see if anyone would provide funding. I would obviously put any funding source as my first affiliation afte the fact.
Finally, to get a request to put an extra name on the paper in order to get money sounds terrible, in fact unethical. It is of course easy to say that when you are not facing the situation so thumbs up for standing up to that behaviour.

I was thinking of suggesting the same thing. Add both locations as your affiliation.

In fact, I think you must list both affiliations.  In alphabetical order.


text:
How to bring one's PhD research to another university?
I was talking about a probable research topic that I got in mind for following a Phd in Computer Science to one of my past Lecturers. This professor told me that I should make a research proposal and see what happens with the evaluating committee. The research proposal was made and it got finally accepted. Now the issue is that this university, in which they accepted my proposal is not so well known worldwide. So I would like to apply to another more renewed university with the same topic, I think that could help me better in my academic career. What should I do? It is unethically to move to another university with my research idea? maybe my past professor could feel like betrayed?
Thanks

It is not so important, how well-known your university is, it is important whether you can do good research there (and have funding for travelling, etc.). It might be good to have some supporters. But of course, if the university is regarded as low-quality (BTW: never trust rankings!), I understand your intentions to leave.

You are free to take your idea wherever you would like. You cannot take your professor's project proposal to another university without her permission.
The professor at your school seeing this as a "betrayal" is a separate issue. A good advisor will of course want a good student to stick around. A good mentor will want what's best for the student—regardless of what's in the mentor's best interests as a potential advisor.
So, my advice is just to talk to the professor and let him know that you'd like to apply at other universities as well. (It's your right to do so, of course.) Ask if the professor would be willing to write letters supporting you. If the professor isn't supportive of this, you'll have your answer. (And if the professor is not supportive, then do not get letters of recommendation from that professor!)


text:
is it possible to have different research topics for the MSc and PhD?
Here is my case, before I studied my master´s degree I managed to write a research paper jointly with a Professor (not from my university) on databases. After that I pursue my master´s degree in CS, but on neural networks rather than databases. The thing is that I would like to do my PhD in databases with the professor I wrote the research paper with. Do you think that I can have problems with the admission committee? I would not like to go to study a PhD without any financial support at all.

I don't see why there should be any problem with this whatsoever. It is quite common for students to move around topics, particularly if you are switching between programs or universities. If everybody agrees that you are a good candidate for the position in question, then it shouldn't really matter too much that the topic is not an exact match.

I agree. Switching fields between MS and PhD is actually quite common in CS. And given that you actually have a paper in databases, it'll probably be easier to get into a PhD program to study databases than to stick with neural networks.

It is possible. As long as your professor agrees. You have to work 4 years+ on the topic so it should be something that you are passionate about.


text:
Academic freedom and unpopular or offensive views
Academia values academic freedom. However, there may be some practical limitations on academic freedom. What repercussions might an academic face for voicing unpopular or offensive views in the name of academic freedom?
For example, how might a professor's academic reputation be impacted by publicly expressing views that support dictatorships (and other type of politicians) and their established crimes and violation of human rights?

Thank you Ben Norris for the editing. @Daniel E. Shub: I think a more common scenario is personal views expressed in public outside the academia (e.g. in a newspaper or a TV show--this is exactly what I meant), but could also include academic/research views but this may complicate the question.

Thanks to the whole Academia crew for taking care of this question, from start to finish. You guys rock!

Note that (a) the term "Academic freedom" refers to a number of ideas (teaching, research directions, acceptance of ideologies), and (b) in practice, the freedom isn't that broad at all.

As an example, you could read about the Ward Churchill affair.

@Orion Are you interested in scientific research on sensitive topics (e.g. "A meta-study showed that green-eyed people are significantly less intelligent than people of other eye colour.") or personal opinions and unsupported claims (e.g. "Green-eyed people are inferior. It's obvious.") or political statements encouraging undertaking action (e.g. "We should get rid of green-eyed people in the government!")? Depending on point, the answer may vary.

@Piotr Migdal: originally, my the question was clearly related to the second example: encouraging undertaking crimes and violation of human rights. But after being edited, the problem in question is probably perceived more as happening in academic context (your first example).

All three answers were downvoted, with no comment below them. Maybe the people who voted them down could explain their reason, so the posts can be improved?

@Orion it seems like the edited question does get exactly at what you are asking. Further, there seems to be a little confusion about what is being asked. Please consider further editing the question.

You have currently the case of Prof. Salaita as another proof that you may be punished for expressing personal views on a delicate topic outside academia.

First, academic freedom as it is commonly understood does not refer to one's views and publicly stated opinions, but to the freedom in which they conduct teaching in the classroom. The reference in US is the 1940 Statement of Principles on Academic Freedom and Tenure stating that

Teachers are entitled to freedom in the classroom in discussing their subject

But as a rule, academics do not get special treatment outside of the classroom with regards to freedom of speech. It's certainly not the case in the US, and I am not aware of any other country where it might be the case.
Now, regarding the impact of unpopular or offensive views on reputation, it will heavily depend on your colleagues! I personally find that, while freedom of speech is highly valued in academic circles in general, Academia as a system is a rather conservative institution and I suspect you would not find much more sympathy for extreme views than in any other workplace.

NB: Academic freedom is also used to refer to a US jurisprudence applying to universities and colleges; in that sense, it is unrelated to rights and duties of an individual teacher.

I think your answer is suitable for the modified question (but not so for the original one which is not restricted to political views in an academic/research context but in the public media--where Paul's answer may be more relevant). Anyway, kindly let me undo the answer acceptance and wait for what others may say.

@Orion of course, no problem… regarding public media, see the second part of my answer: academics will take flak for extreme views, including negative job perspectives, but probably neither more nor less than in any other job

For propagating unpopular view (which can be considered offensive) a professor may lose a position (see e.g. James Watson's case). And in general, sensitive topics (e.g. like gender and ethnicity) may be risky, regardless of the scientific value of a statement one is making.
Moreover, sometimes there is a particular ban on some ideologies (e.g. propagation of Nazism in many European countries). However, it this case it is (usually) not a limitation on academic research, but only on political activity. (Similarly, "encouraging or assisting crime" is an offence and it does limit what one can say.)
As a side note, a humoristic slide from a presentation Beauty and the beast at the 2nd Offtopicarium:

What about the current case of Prof. Salaita and his dismissal from the University of Illinois for tweeting his condemnation over Israeli actions on the people of Gaza?

In addition to getting flak from your colleagues, some views might also get you fired or forced out of your position. For example, if you publicly state that the best solution for Africa is to drop a few nukes, the university might force you to resign.
I think what is important is that you can provide rational arguments for your opinion, as science is based on facts (and the interpretation of those facts).


text:
In which type of schools can I have better research experience in Biology, liberal arts college or large research university?
I'm struggling with deciding to which type of school to go in order to gain a better research experience. Basically, the research experience is the most important factor for me to decide my college, since I want to be a strong applicant in PhD admission. Most reputable, research universities are far larger than LACs (liberal arts colleges), and they (except for top schools like HYPSM) are not so friendly places for those who want to conduct their own research and engage in research from Sophomore or even Freshman. To get rich research experience, I want to be involved with research as early as possible and not only during the summer but also throughout a year. Just for example, Reed College has mandatory Senior thesis like Princeton, and profs are eager to help even Sophomores to do their research. However, in research universities, I can take graduate-level courses and touch with cutting-edge research as a research assistant. So, I can gain more advanced knowledge than those in LACs.
Could you tell me your recommendation both for me and those who have the same aspiration?
*If my question is too vague, please just compare UC Berkeley/University of Michigan vs. Reed College/Carleton College. I'm sure this will be a good comparison, since the quality of the students are almost equal.

My main focus is in PhD admission, which, I believe, is one of the main focuses of this website. So, I asked how to gain the best research experience in order to perform well in the admission.

Undergraduate research is on-topic: http://meta.academia.stackexchange.com/questions/666/undergrad-research-is-on-topic/668

Undergraduate research is on topic, as is graduate admissions (in many fields undergraduate research is an important factor in the admissions decision).

I went to a small liberal arts college and worked at a large university lab, that had undergraduate interns. From both experiences I agree that it is the lab and not the school that matters. However, there are conditions that you will be more or less likely to find, depending on the type of school. In general liberal arts colleges will give you more personal attention and large universities will have more resources. Funding at liberal arts colleges is focused on undergraduate education and funding at larger universities is focused on research.
Personal Attention:
Liberal arts: A lab is led by a principal investigator or PI. Liberal arts colleges often do not have graduate students or have few graduate programs. So, at a small liberal arts college you will work closely with your PI and get to know them well. I left my college with great letters of rec that helped me overcome a poor GPA (due to a medical problem in my first two years) and get into grad school.
University: The undergrads were trained by PhDs and post docs and had little contact with the faculty. Post docs and PhDs can often be great teachers, though, since they either are students or were students recently and might be able to anticipate the student's perspective. At a university, they will normally write your letters of recommendation and the faculty will sign them.
Independence:
Liberal Arts: All of our grants were training grants, so the emphasis was on teaching, as opposed to producing results. This means you will get to do more independent work. I got first hand experience with the equipment (EEG) and techniques (analysis of FMRI and EEG data) that few undergraduates get to use. Additionally, I know of at least two of my friends who published, as first authors, in major research journals. This is not uncommon in my school.
University: The undergrads had to learn a program that is no longer used by most labs in the field. There was little room for mistakes (all of the labs grants were research grants), so the undergrads were given the task of modifying previous work and really did not develop any understanding of how the program actually works. However, this lab was an older lab. I also believe students at an older lab at my undergraduate school had a similar experience, where the methodology they were taught was not consistent with current standards in the field.
Connections:
They are pretty equal in this area. Liberal arts college professors often collaborate with people at larger institutions and can connect you with other labs. I have friends who got summer jobs at Stanford and CalTech this way. At the large university, one of our undergrads got to go to Oxford for the summer, because of the professor's connections to a lab there.
Equipment and Resouces:
Liberal arts: We did not have access to some of the most expensive equipment (an MRI, for example). However, one of my professors also worked at a local university that had access to an MRI and we got to use it there. Ideally, you should get some lab experience at a major research university, so you are exposed to techniques that require more expensive equipment. You can do this during summer internships. Getting more experience at different labs will look good on your application.
On that note, a liberal arts college is more likely to have grants that will help students study at other institutions. My college had several such grants for student research grants. Additionally, all senior thesis was funded by the department. The senior thesis funding and one of the summer fellowships both require students to focus on their own original ideas. In most fields the first author is the person who had the idea for the project. This is how undergraduate students were able to become first authors.
University: Universities will have the best equipment, but they are less likely to have funding for student research. The institution I worked at had grants for students, but they were only for work at that university. They also had no specific grants that would allow students to propose their own projects, based on their own ideas.

Your comment made me realize how LACs' focus on funding on their undergrad students is beneficial for the students who are really dedicated to research. There seems further more opportunities in LACs, so I will go to Carleton rather than UCB, even if I will be accepted to both. Although I thought publishing in research journal is almost impossible for undergrad students, it seems quite possible in LAC.

My observations are based on my own experience, which did not include Carleton or UCB. In high school, I decided to apply to a bunch of LACs, because I believed that, in general, LACs had more resources for undergraduates. However, each school will differ.
I would keep an open mind and check with the departments and schools. Have undergraduates ever published with faculty? Do they have an undergraduate capstone or thesis project? Are labs normally open to projects proposed by undergraduates? Do fellowships and internships for undergraduates allow for off campus mentors?

I spent vast amount of time for collecting such information from my favorite LACs. They basically have mandatory Senior thesis requirements and programs which encourage dedicated students from Freshman to Senior to conduct their own research. They have strong biology courses, and some of the LACs are known for their academics which are the most rigorous in the nation. Fellowships and internships for undergrads allow for off campus mentors. I know that Reed and Carleton have produced many students who succeeded in publishing their thesis, but I'm not sure about others.

I wouldn't say that any university "type" is universally better or worse for gaining undergraduate research experience. The culture with respect to undergrad research varies so much, even within one school.
My advice is to look up the Biology faculty in the schools you are considering, and identify those you would be interested in working with. Do your homework  - don't just spam the entire department. Then email them:
Dear Professor {X},
I am {applying to, accepted into} the B.S. program in Biology at {University}. I am interested in pursuing a PhD in {specific area related to X's research} when I graduate, and am hoping to start doing research early in my B.S.
I am very interested in your ongoing research on {subject area}. {Say something intelligent about subject area that demonstrates your ability to contribute.} Do you take on undergraduate research students?
(I highly recommend reading the tips here for contacting a prospective research advisor: http://www.cs.virginia.edu/~evans/advice/prospective.html)
By doing this, you'll get a good sense for where you're most likely to have undergraduate research opportunities, and a head start on finding a potential research advisor.


text:
Transitive copying - plagiarism?
I am writing a paper with a co-author. I need to explain some terms in the preliminaries section. I am copying the definitions from my co-authors previous paper. Afterwards, I want to include the paper into my thesis. If I use the same definitions word for word in my thesis, would that be considered plagiarism?

You are usually permitted to copy stuff from publications into your thesis. See this question on sandwich theses. http://academia.stackexchange.com/questions/149/what-is-a-sandwich-thesis

I understand that, but in the end, the original material, that was in my co-authors work (which was done without me) will end up in my thesis (which of course has only one author - me). That's the problem

Your question sounds like you're asking about a math paper.  Definitions in mathematics are a bit of a strange corner case for plagiarism issues because they're not supposed to be "in your own words."  My understanding of normal behavior is that you would never put a definition in quotes (unless you're writing about history), that you can nonetheless reuse definitions verbatim, but that you need to either cite the original source or say that they are standard definitions.  A typical way to do this would be by saying "We recall some key definitions from X."

Computer science actually. The definitions are not as solid as in case of some math terms.

You need to clearly reference the definitions.
For example, Definition 1 [paper_reference]:  or Definition 1 ( as in [paper_reference] ) :
By this, it is clearly your are copying the definition of the other paper..

If you are going to use their definitions verbatim, then use quotes, or otherwise make it very clear that the words are not your own.
In any case, cite the sources.

If you use other peoples' words in your thesis, without making it very clear that they are other peoples' words, then yes, you would be committing plagiarism.
Granted, this case would not be extreme, compared with say, including a chapter from someone else's thesis in your own, but it does meet the definition. Given that many universities have adopted draconian anti-plagiarism policies in recent years, you should be very careful to avoid even minor infractions.

You could take two approaches:

Modify the text slightly, rewording, to make it different.
or, easier, just refer to the other paper, i.e. "I use the definitions of Doe (2011), which for convienience I repeat:".

In that way it is not plagiarism.

I fail students all the time for this behavior. If you edit something to get around a literal quote, you are still taking someone else's idea. If you use someone else's work, cite it (and citing definitions is quite common...'according to websters...').


text:
How important are the grades compared to the cover letter when applying for a Ph.D?
Some months ago I finished my MSc. I immediately started to send several applications for Ph.D vacancies.
So far I've spent a lot of time in doing this, but there is only one place that did not reject me. This place was actually the least interesting for me in terms of the job, therefore I was not keen from it at all.
I believe almost no one applied for the place I was not rejected by...
As for all other applications, I'm seriously thinking the problem is my final MSc mark.
To tell the truth with my mark I can access to most of the Ph.D programs (it's a UK "merit").
However if I know there are almost no chances for me to do what I would like to do then I resort to something else and avoid waisting my time in writing cover letters that no one bothers.

Welcome to academia.SE. From your writing it seems like English might not be your first language. While a merit is not a great mark for an MSc degree, it likely won't get your application thrown out. Did you have someone else read your cover letter?

This issue has come up before and been addressed. This question http://academia.stackexchange.com/questions/324/how-do-you-get-a-bad-transcript-past-ph-d-admissions and this question http://academia.stackexchange.com/questions/7753/what-should-someone-who-has-been-rejected-from-all-phd-programs-do-to-improve-th and this one http://academia.stackexchange.com/questions/977/what-to-do-when-graduate-admissions-havent-gone-well and this one http://academia.stackexchange.com/questions/582/how-can-a-graduate-school-applicant-improve-his-application-for-next-years-seas.

This question is not exactly a duplicate of those others, but your answer may already exist. I added the [tag:graduate-admissions] tag to your question. Browse through the questions with that tag. There are some good answers to similar (or broader) questions.

@BenNorris I will probably post a new question based on the links you suggested.

What's a "cover letter"?  Is that another name for the "statement of purpose"?

@JeffE Are you American? If you are then I know why you don't know what a cover letter is. In Europe a Ph.D is not something a student proposes, rather it's a project directly issued by the university. This means that the phd is just a job whose purpose is to do research on the topic required by the university. The cover letter is just the application letter, where you say "Dear  Sir/Madam, I received the announcement of the vacancy X on... I would be interested in the job because...". Of course in Europe a student has fewer "freedom" than in America...

So, yes, it is what Americans call a "statement of purpose" or "application statement".  You should include this information (or at least the phrase "in Europe") in the question for the benefit of us Yankee readers.

@JeffE in Europe a "statement of interest" is a short (1 page) phd proposal. This is why I didn't know what you meant

When I look at an application there are four aspects that count:

grades
cover letter
earlier written work (BS/MS thesis)
Recommendation letters

Out of these, I focus most of my attention on the latter two: if the thesis is well-written, has received a good grade, and the letters of recommendation support the candidate in terms of ability to do research (from reading up on the field to writing everything up) and independence (how much (or little) support the candidate needed.
The cover letter would not make the application, but could break it if it is unfocussed and does not show any skills in expressing the interest in a structured way while avoiding irrelevant information. The grades would, in most cases, be the least interesting since they primarily show one's ability to read and understand, not necessarily reasoning and deduction. The exception is the grade for the thesis.
So, to answer the question, I am not sure which might be more important but anything that supports your ability to do research is of prime interest to anyone evaluating an application.
EDIT: To follow up on Gerrit's suggestion, my personal ranking list would be (in falling order):

Earlier written work
Recommendation letters
Cover letter
Grades (although the grade on the written work is included in 1)

But, all parts are useful and in the end some mix of all will be used. I would also add that 1 and 2 will "make" the application while 3 and 4 will mainly help to "break" the application.

The quality of the writing in the cover letter and thesis can also damage one's chances, if they are not well-written.

Perhaps you can rank them by importance?

@PeterJansson Thanks a lot, with your advice you just told me to give up. I think what blocks my applications are exactly the most important points, ie the grade of my MSc thesis and possibly the references.

@PeterJannson what if I added in my CV I have started a Ph.D but I'm probably quitting it because I don't like the topic? may it be a good reference like eg a discrete MSc thesis grade?

@ragnar I am sorry to hear that. To be persistent is, however, a very good personal trait for a researcher so your efforts should not be thrown away. I think you need to try to assess where your interests are and then also try to contact some to find out the reasons for the rejections. There are many unknownsthat once charted may provide you with a better overview of your situation.

@ragnar In response to your second comment. To start a program and then drop it might come across as not having drive or direction. What you certainly can do is to to list that you were offered the PhD position, after all, that is a merit. But you then also need to explain why you did not go for it in a way that does not seem undecisive.

@PeterJansson to tell the truth I know what my interests are and most of the times I also had my cover letters reviewed by a friend of mine who works as a senior scientist at my former university: he always said my cover letters are OK, there is not so much to discuss about. Therefore I can easily conclude I must either retake the master or resort to other possibilities. In this case however I would have no chances in my country: I'd move out to work only for something really rewarding, which is not the case...

@PeterJansson that's exactly what I'm trying to figure out. Frankly saying, I've clearly found out a research jobs requires a great motivation, especially when you're doing it abroad or far away from the place where you've always lived. This is my situation. Maybe I would have the motivation to do the same job in my town, surely not in the place where I am now. I'm currently working as a PhD student, I can actually carry out the job my boss tells me to do, but I find no interest in the topic. What would you do if you had to mention this on the CV?


text:
Disabilities in the Classroom
Are there any special provisions provided for students who have schizophrenia (for example)? Is there an "adjustment" to grading? Or perhaps there is no adjustment to the grading process per se, but only to the due dates? Is there anyone here who has been in this type of situation?

Depends on the relevance of the disability to academic performance, on the severity with which the person suffers from the disability, the kind of assignment, the policies of the given school, and the laws of the country the school is located in (just to name a few things). Though I don't have the ability to vote myself, I advocate for closing the question as overly broad.

This question is not too broad on the "entire book can be written on the subject" scale(although I can imagine chapters in books). There are some chatty elements to the question, but it has a nice short answer: consult the institutional office for disability services, as Anonymous suggests.

Every university I have been affiliated with (in the U.S.) has had an office of disability services, tasked with evaluating individual cases and making (binding) recommendations to instructors.
If your university has such an office, then you should refer this case to them and avoid judgement calls of the type you ask about.

Often the policy is also to inform the instructor of any special needs that may be pertinent to grading. Usually, as a matter of fairness, the specific disability isn't given. Regardless, that informs the instructor that that student may need certain provisions (ex: taking the exam in room with services, etc.)

This answer is totally right. Those offices are trained in the relevant practical and legal issues, while individual professors are not.

I love that these offices exist for the very reason @NoahSnyder suggests. I am not trained on how physical, mental, and psychological disorders impact learning, nor do I know what the legal requirements are. The folks in my Disability Support Services office do. And if my students do not have the waiver from said office, I am not permitted to make any concessions.


text:
Are there any specific teaching techniques to handle "virtual" classroom sessions?
In the past, I have attended a few "virtual" classroom sessions as a trainee and I always found it a little boring.  I could notice the sincere effort that the trainer has put through but I couldn't control the feeling of boredom.
Are there any techniques specific to teaching in a "virtual environment" that can improve the pedagogical experience and keep students motivated?  I do have a list for a normal environment but it is of little help in this new medium!
Thanks for helping.

This question is purely pedagogical, which is off-topic for this forum.

I beg to differ.  In the FAQ section, it has been mentioned that this forum is applicable for university professors. Conducting sessions in a virtual environment is becoming more frequent and I think this question will help me and my likes.  I could see questions in similar context asked about conferences in this forum.  (from a audience point of view).
Ex: How can I get the most out of conferences?  (it is from you actually)

@eykanal, I think the issue is with framing. I would recommend that the question be rephrased: "Are there teaching techniques that are specific to 'virtual' classrooms?" This would satisfy the mission scope as well as the questioner's needs.

Thanks @aeismail.  I agree.  I have rephrased it as you suggested.  Thank you very much.

I've changed the body of the question as well. There is no need for mentioning the specific of your virtual environment. The fact that you're conducting a training seminar for software isn't really relevant here.

@eykanal: Questions about pedagogy are not automatically off-topic.

@JeffE - Ha, and I was the one who had written that. Thanks for reminding me.

@aeismail I think the specific type of virtual environment is important to mention. I have been involved with one that runs like a forum: I post a topic or question and the students post discussion or answers. I have been on the receiving end of one that was run like an interactive webinar, i.e the class still 'met' at specific times, the instructor was present, and the class interacted in real-time. In this case, it doesn't matter whether the instructor uses Second Life or Eluminate, but such a course is vastly different than a forum discussion course, and I would teach the two differently.

@BenNorris: I understand what you mean—but I think you need to make the description generic, rather than specific. Don't ask about specific platform X, but the nature of the category (online forum, web-based video lectures, etc.).

When I read this question, I immediately thought of this TED talk.
In it, Peter Norvig, who taught a huge online course on AI, shares what he learned about teaching to a large virtual audience.
His main points:

Mimic a one-on-one teaching style by positioning the camera overhead as you write and speaking as if it is a single student.
Alternately, use a livescribe pen (I've had experience with this for a math class; loved it)
Make short, <10 minute videos to retain attention
Ask questions to check understanding (they will pause+answer) and then go over them
Have due dates for watching the videos; students need motivation to watch them in a timely manner
Encourage online forums because peers are great tutors they "remember what it's like to not understand"

take them down after a week? What about repetition? Do you expect people to remember everything? Do you realize that you penalize less technical people since more technicall ones will be able to save them.

take them down after a week — I think you misspelled "Leave them up forever, so that students can review them later as needed."

Snark, snark! I believe, not that I'm rewatching the video again, that he mentioned having due dates and some sort of limit. I know the videos are kept up for posterity, but he emphasized making sure current students got to them during the class. I will edit.

Yes, agree completely with this approach.  Nothing more boring than an online class where the instructor just drones on and on.  I stopped teaching online because the Uni I was working for had a system that only supported this approach and I was spending more time un-teaching in the chat rooms what I had "taught" in the pre-recorded lecture.

"Make short, <10 minute videos to retain attention" I suggest 3 minutes is more appropriate for normal students.


text:
What are issues to consider when making your code for an experimental paradigm, which was conceived by someone else, publicly available?
General background
In the cognitive sciences, it is often necessary to program/script experimental paradigms to conduct your studies. Basically, these programs present stimuli and collect responses, such as in the Eriksen Flanker task. However, programming capacities are typically limited in my field because it is rarely taught during graduate education (at least in my country). Also, it seems there is a somewhat reluctant culture of sharing this software unless there is some sort of scientific cooperation.
Consequently, when designing a study the decision for one of several paradigms used to measure a given construct can, among other things, be motivated by availability of the software or the effort necessary to implement it. With respect to sound science (choosing the most appropriate rather than available paradigm, software bugs, etc.), reproducibility (incomplete descriptions of methods, lack of programming skills, etc.), speed of scientific development, and, more generally, open science this is less than optimal.
The situation at hand
For a current study, I have started to implement three paradigms from scratch for different reasons:

One paradigm is publicly available from the authors but implemented in a commercial development environment for which I don't have a license (I, therefore, can't run it).
Another paradigm, to my knowledge, is not available from the authors at all. I contacted the authors for a copy of the software but got no reply.
The third paradigm is commercially available but is also closed source and only grants access to a limited set of the response data. For my analyses, I'd like to have access to richer data.

Given my prior general considerations, I think about releasing my implementations of the paradigms under an open source license, once they are finished. Now my question is:

What are issues to consider when I release my software to collect data in an experimental paradigm, which was conceived by another scientist, under an open source license?

Here are some of the things I'm wondering about:

Are there legal issues, such as copyright infringement, to be considered for commercially or non-commercially available software? Note, I created all of the code and  all images based on low resolution prints in publications. I'm merely copying the concept.
Would such a release conflict with common etiquette in the case where the software is simply not available from the original authors (remember, I asked but got no reply)? Is it necessary to ask each author before releasing my code?
Can I be held responsible morally if the software is used and turns out to be faulty? I'm less concerned about legal responsibility because the license I intend to use does not provide warranty. More importantly, I certainly intend for the software to work since I'll use it my self but you never know.
If my study ends up being published and points to the availability of the software, can this benefit the citation count of the publication?

I'm sure there are more things to consider that I haven't thought of. But that's why I'm asking the question. ;)

Related questions: What are the disadvantages of opening the source of your own science tools and How can we change things so more researchers are willing to share their source code?

Also see Why don't research papers that mention custom software release the source code?

Are there legal issues, such as copyright infringement, to be considered for commercially or non-commercially available software? Note, I created all of the code and all images based on low resolution prints in publications. I'm merely copying the concept.

Unless their method is patented, no. Software is covered by copyright which protects a given implementation, not the general idea. Just as you are allowed to write an own novel on a topic that is covered by existing novels already.

Would such a release conflict with common etiquette in the case where the software is simply not available from the original authors (remember, I asked but got no reply)?

No.

Is it necessary to ask each author before releasing my code?

You need to get permission from all copyright holders. Depending on the actual settings, that means: for each author who contributed to "your" code the acutal holder of the copyright (could be the author or the author's employer).
The authors of the "original" software are not involved at all.

Can I be held responsible morally if the software is used and turns out to be faulty? I'm less concerned about legal responsibility because the license I intend to use does not provide warranty. More importantly, I certainly intend for the software to work since I'll use it my self but you never know.

moral responsibility: just like you will be held responsible for any other scientific publication.
legal responsibility: while no liability clauses are common for FOSS licenses, completely excluding liability is not possible in all legislations (e.g. in Germany a general no liability at all clause is/can be invalid).

If my study ends up being published and points to the availability of the software, can this benefit the citation count of the publication?

Definitively, yes

I'd give you another +1 for the legal advise for Germany if I could. Thanks a ton.


text:
Should one research multiple independent topics while pursuing a PhD?
While pursuing a PhD in an experimental field, one usually researches a given topic and conducts experiments that are rather closely related to this topic and one another. I imagine this specialization can be beneficial as one attains expertise in the research field and can work in a timely and focused manner.
However, I can also imagine that this specialization may make changing your area of research more difficult when applying for positions as a post-doc. Therefore, I am wondering about the advantages and disadvantages of researching scientific questions one is interested in, but that are irrelevant to ones PhD thesis on the side.

In more theoretical areas, the answer is "Obviously!"  But since you're asking specifically about experimental fields, I hesitate to write that as an answer.

Even in experimental fields, you still need to branch out and explore different experimental paradigms/approaches/methods. Because, as a researcher, at some point, you will have to design new experiments or change/improve the current experimental paradigms/approaches/methods, and then you really need not just depth but also breadth.

The main downside is that it takes a significant amount of effort to gain enough specialization in a given topic to be proficient enough to perform useful experimentation. Given that a a graduate student you're spending almost all your time familiarizing yourself with the topic you're actually performing research on, it would be very difficult to become an expert in an area unrelated to your work.
That being said, many research topics are very conducive to multi-disciplinary research. To use myself as an example, I usually tell people that I'm a cross between a neuroscientist, behavioral psychologist, signal processing engineer, and statistician. A colleague of mine started his research examining how to use the lungs as a power source for an implantable device, and ended up publishing a significant paper in the field of organic chemistry, fairly unrelated to his intended research. Becoming an expert in your own field enables you to research some pretty interesting and diverse topics.

The main downside is the opportunity cost of time spent being "unfocused".
Accordingly, I think the relative merit of pursuing ancillary research topics hinges on how much time you want to spend on your PhD. The road to tenure is long and so there are strong arguments for starting on it early. A PhD is just the beginning. However, later on, I do not think one can drop a side-project with as few consequences as during graduate school.
You should also distinguish between the same research that goes by different labels. Different fields call the same thing different names, which can make it seem as if someone has more varied interests than they do.

However, later on, I do not think one can drop a side-project with as few consequences as during graduate school. — Really?  Why not?  (I'm assuming that once a project attracts enough money to employs RAs, it's no longer a "side project".)  How could faculty explore new research areas without doing exploratory side projects?

I see your point that my use of 'side-project' has a shifting definition. Perhaps its better to say that there is a bigger loss if you sink money, RAs, etc into a project that doesn't pan out as opposed to if you as a grad student wasted a lot of hours on something. Then, my comment just the time of someone with more experience can be worth more.

@JeffE - Because later on, instead of just having time to play around doing research, you're writing grants, teaching courses, performing departmental administrative duties, and mentoring grad student & postdocs. Compare this to being a grad student, when your responsibilities include (1) showing up and (2) doing research.

@eykanal — Right.  But playing around with half-baked crazy ideas that may not pan out is a prerequisite for writing good grant proposals, which is how we get grants, without which we have neither students nor  postdocs.  Side projects aren't a distraction for research faculty; they're a requirement. Departmental administrative duties, on the other hand...

TLDR: You will probably become a better problem solver if you do it, but there is a chance that it won't count into the formal requirements for graduation!

In general I would say it is not a good idea to research multiple independent topics when you are a PhD candidate, especially if your PhD is supposed to be really narrow. The risk is that you will become distracted from the main focus of your project. Your main focus will then suffer and even if you actually do find results in the topics too far away from the project you are part of those are likely to be judged to not fit the project. Those results may impress other people for example in various industries and maybe academics too, but maybe they will not help you pass the formal requirements for graduation!

( Everything I've written is assuming you value graduation above all else, of course. )

I can see pros and cons to this. The pros are obvious and are just like you state: you will be gaining specific expertise, you'll be doing truly independent research , you'll be pioneering.
I would point out one major con though: if you do work that none of your professors are "in charge" of there is a good chance they will act like little babies and discredit, ignore, or openly assault your work! It happened to me.
I had my master's thesis in Scientific Visualization, which was an already funded idea hosted by my advisor. Unfortunately it wasn't a very popular idea so a) it wasn't that interesting, and b) I couldn't get much attention from my advisor. But then my friend, who was doing research in Computational Biology came up with a really great idea for a collaborative visualization project and I started working on that in parallel. It turned out to be really cool, I got a poster accepted to a major conference, and my friend actually benefitted from the output.
My advisor, however, was just pissed off. He didn't give a shit that I was doing my own creative work. He just saw that I wasn't playing his game. I actually got in trouble for this. I tried to appeal to my team of 3 professors who were my secondary advisors but they reamed me too. One of them said "well none of us know if your work is actually quality. Anyone can get a poster published." Mind you out of the entire group of 12 students who submitted work to the conference only 3 posters were chosen and two of them were mine.
So the short of it is: academics are like little boys tied to their mother's apron strings. Don't expect them to support you in being truly creative. If you follow this path then make sure you either convince a professor that it was his

Don't walk.  Run.  (We profs aren't all spoiled brats.  Honest!)

Seems like a required primary goal was replaced by an optional, personal secondary goal, for whatever reason. But the question is about keeping primary as primary itself, a disciplined approach. +1 to @JeffE

Boy reading this after a few years and man did I have a charge! @JeffE, a few years will cool ones head off a bit, I trust that all professors aren't that bad. Noble, I actually completed both projects, though to be fair my focus was mostly on the secondary project.

Not to mention the irony that I'm exploding in rage as I call other people babies! Oh man...

I did several unrelated projects during my PhD. Here are my thoughts:
You need to publish in order to graduate and find good postdoc opportunities. So if you have three unrelated projects/collaborations, but all close to publication stage, then just plan your time wisely and go for it.
Otherwise, if you have several unrelated projects, that are super cool, but you have different PIs guiding it, and it's all in the troubleshooting/design stage, you have set yourself for a 7+ PhD gig. You will need to report to each PI, show good progress, all while switching rapidly between projects. All doable and rewarding, but in the end, you will need to publish them, and its gonna be hard.
Another detail to consider is if your committee will require your dissertation chapters to form one cohesive story. Some departments require it, in which case you can end up with a lot of data you cannot use in your thesis.
So in retrospect, I wish my "eyes were not bigger than my stomach", but I did have fun doing the other projects, and I found what I want to do for my postdoc through trying different things. I am finishing in my 5th year with 3 publications, but so burned out :(.


text:
Asking for the second/third recommendation letter, should I tell the referee he is writing the third letter?
Many have suggested me to include a sentence like this while asking for recommendations:
"Do you feel that you are able to give me a strong reference?"
I am afraid that my third referee, who was only a professor of one my courses, knows me but not well enough to give a "strong reference". So if I asked him this way, he might ignore my request.
I could also tell him that this is the third letter, so he does not have to exhaustively write about my every strengths. But telling him that he is only the "third” might be considered impolite? Because, emotionally, everyone wants to be regarded as an important person.
What shall I do?

This answer basically echoes the comment of Andreas Blass.
I agree that calling it the "third letter" may offend the professor, so I wouldn't use that phrasing.  But the general idea of acknowledging that the scope of the letter will be limited, and that you have other letters as well, seems fine.

Dear Professor A,
I am applying to grad schools, and I wondered if you would be willing to write me a letter of recommendation.  I know that the only course I took with you was BASK 301, and so I understand that your letter would only really be able to discuss my work in that course.  But if you feel you would be able to write a strong letter on that basis, I would greatly appreciate it.
I am also requesting letters from Professors B and C, who will be able to write about my [other coursework / research / internship / relevant skills / etc], so I feel that between the three of you, a committee will be able to get a broad sense of my record.
If you are willing, the letters would be needed starting on [date].
Many thanks!
Sincerely, etc.

If the course involved particular elements that you think would be helpful to discuss in the letter (e.g. a project on which you thought you did noteworthy work), then you can mention those specifically.

No, do not do this. It is an immediate insult, and done so from a point both of need and of ignorance. At best, the person would (as a good grandfather or grandmother) understand your militantly naive foolishness, and lack of intent of insult, but... Don't
Also, most application systems do not "rank" letters, so all your letters of recommendation will be taken with equal weight... depending on the degree of acquaintance the writers claim to have with you.

I agree with this answer, but I think it would be OK to mention something along the lines of "I realize that I took only one course from you, but I think your letter would nevertheless be useful. I'll have another letter from a professor from whom I've taken several courses." (Assuming of course that the last sentence is true. If it's still true with "other letters from professors" in place of "another letter from a professor", then you could say that.

To clarify my previous comment: If you asked me for a letter after taking only one course from me, I wouldn't immediately say no, but I'd probably suggest that it would be better to get letters from people who taught you in more than one course. If you're getting one or two such letters in addition to mine, then I'd feel more comfortable about the situation.

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


text:
What is importance of author listings when resumé/CV differs from actual publication?
In examining published papers of employment applicants, I am noticing that authorship position shown on the resumé/CV (first, second, third authors, etc.) do not match those shown in the published papers. Is this significant? The field is cognitive neuroscience. My applicants are often shown as First Author on their CV, but not on the published papers. Is this significant in any way?

Is this industry or academia?  I think it makes a difference, although I expect disagreement.

In general, I think it is inappropriate to rearange author positions. But would make a difference between middle authors (for N authors, this are the ones from position 2 to N-1) and first and last author because they imply a special role. So if someone claims to be the first author but isn't, it's kind of a misstatement for me, while claiming to be author 2 instead of author N-1 wouldn't bother me much.

That's imo sufficient reason to immediately trash the application. If it's a young student, write him a note explaining how inappropriate it is to take credit for other people's work.

In fields where "first author" means something, promoting oneself to first author on one's CV is dishonest. In fields like mine, where authors are almost always ordered alphabetically, putting one's own name first seems pointless but also harmless.

In general, author position must be the same on a CV as it is in the official publication. Changing author position on the CV is generally deceptive. In particular, first authorship often conveys a greater role on a publication. So this may suggest the applicant is trying to indicate that they had a greater role in the publication than they did.
That said, it seems like a rather strange thing for an applicant to do. If someone is going for an academic job, it is common that the employer would have a look at a few publications. Thus, it would quickly become evident that CV and publication differ in author-order. And this would typically be perceived poorly by the employer.
A common and better strategy is to bold or star your own name in the CV (and perhaps the names of students you have supervised). This makes it easier for a reader of a CV to scan author position.

Strike "should", insert "must". It's definitively fraudulent, and if the journal has alphabetic ordering of author names, also insulting to the reader. Another thing is omitting a half-dozen other "middle" authors names.


text:
Is there any (known) way to have Arxiv waive the endorsement requirement?
I’m trying to submit a preprint of my paper to the Arxiv as an independent researcher. My academic background is in theoretical physics; I have a PhD in physics, did a postdoc, published several papers in Physical Review and PRL before taking a job in industry. I’ve been working in industry ever since, so I do not currently have an affiliation (i.e. an .edu email). I’ve spent the past few years working on my research project independently, and I’d like to submit to the Arxiv and have the community review my results.
I’m currently stuck at the “not endorsed” step. I’ve reached out to qualified endorsers in my subject per the Arxiv’s endorsement process but got no replies. I then contacted the moderation to appeal, but they rejected with what seems like a template reply (“We insist submitters be affiliated...”)
Given my situation, I am wondering if there is any known way to make the Arxiv waive the requirement of endorsement? For example, does the Arxiv make an exception for former academic researchers who have previous publications in peer-reviewed journals?

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

Just to check, your first request for endorsement emails were hopefully to your thesis advisor/postdoc advisor. If they haven't gotten back to you, either you definitely haven't waited long enough or there may be some other issue (they don't want you to submit to arxiv without them looking at it first?).
Worth looking to see if there are other ways to get a .edu address. If you are a researcher in a relevant industry, you could potentially get some degree of honorary affiliation with a local university just by asking the right people. However, this is probably much harder than getting an endorser! You should also look into your PhD and undergraduate school's policies: many offer "alumni" email addresses that are .edu - but I'm not sure if this is sufficient for arxiv's purposes.

I would suggest that you reach out to several more qualified endorsers – perhaps waiting a few days before contacting the next. There are many reasons why the one endorser you contacted already may not have replied. Maybe they're busy, sick, or on holiday. Do you know any old supervisors or collaborators that are endorsers? They might be much more likely to help out!
There is no officially documented way to circumvent the endorsement process, though I would argue that you do have the right to have your work endorsed within a reasonable period of time. Otherwise, clearly the endorsement process is broken. Endorsers should not be endorsers if they don't have the time to endorse!
If you have no success after contacting at least several more endorsers, you could try contacting the moderation team.

"Endorsers should not be endorsers if they don't have the time to endorse!" I disagree. Being an endorser means having submitted a large enough number of papers on the arXiv in the last 5 years. That does not make you have any greater obligation to respond quickly to endorsement requests.

@TobiasKildetoft "Being an endorser means having submitted a large enough number of papers on the arXiv in the last 5 years." I disagree: The latter (i.e. "having submitted a large enough number of papers on the arXiv in the last 5 years.") means that submitter has been actively submitting papers to arXiv. The former (i.e. "Being an endorser") means, by definition, someone who can/could/would/will endorse a quality paper. I absolutely disagree with you stating the former "means" the latter.

I agree with @Moriarty; arXiv should only mark authors as "qualified endorser" IFF they are actually willing to expend time endorsing. Otherwise, it's a complete waste of time for all parties. Also, it's completely misleading for the submitter to think that contacting said "endorser" has even a possible chance of getting an endorsement from him/her.

@TobiasKildetoft "That does not make you have any greater obligation to respond quickly to endorsement requests."
This discussion/answer is not about "responding quickly"; it's about responding at all.

@TobiasKildetoft I was unaware that the status of "endorser" is an automatic thing based on your number of submissions. This is likely why it's difficult to get a reply – you can be sending endorsement requests to people who are not going to read them. Clearly, this is not an optimal situation...

I agree that it might be more optimal with a system in which one could more easily find people who had actively chosen to be endorsers rather than just having submitted papers (probably a lot of people are endorsers without being aware that this is even a thing).


text:
What to do when I’m not affiliated with an academic institution and submitting a manuscript?
I am seeking to re-establish my research career after a 7-year career break. The first step involves submitting a paper to a peer reviewed journal which reports a study that was conducted 7 years ago. In the cover letter to editors that I have prepared, I point out that the topic remains timely, and I provide relevant references to illustrate this (which have also been used to update the paper).
Because I am not currently affiliated with an academic institution, I don’t have a university address to provide in the contact information section during the manuscript submission process. Any thoughts on whether this will affect my acceptance chances? Should I provide my current home address instead?

And for the other half of your question (on acceptance chances), see https://academia.stackexchange.com/questions/385/

Just list your affiliation as "independent researcher" and use a valid email address that you expect to maintain. You should be fine. Scholarship isn't for employed academics only. It is the quality of the work that matters most.
The only block I could see is if your research requires Ethics Board (such as IRB in the US) prior approval.
For the submission process any physical address will probably do if it is required. But for final versions to be published I would seek advice from the editor. Perhaps a post box would be preferred to a residence.


text:
Professor asking me about my financial condition
For masters degree, I have contacted one of the professor of university of Tokyo. He told me in his 1st email reply that he would not like to have students only for 2 years. He wanted a student for 5 years(MS+Phd). Then I emailed him saying that I am ready to study for longer time. He replied for the 2nd time writing that, he is very happy to hear it, that I want to pursue both MS+Phd. But next he asked me if I have a concrete plan for my financial support as there is no salary paid by the PI or University.
In my first email, I didn't mention about any scholarship.
What should I write to him now? How should I ask him for University recommend MEXT scholarship?

What should I write to him now? If you just want information on the MEXT scholarship, then you probably needn't contact him (in the first instance), you can contact whoever is responsible for the scholarships. (You might like to respond to his question, mentioning that you are looking into a scholarship.)

@user2768, your comment is probably better as an answer.

@Buffy It remains somewhat unclear to me what the OP wants to achieve, so I don't know whether my comment answer's the OP's question

Please read through this forum if it is a good idea to work as a phd student without getting money and then decide if you want to do this.

A Japanese university professor's view. People sometimes contact me and tell how they want to join my lab and so on. In the past I used to involve myself into lengthy conversations just to realize they will do it only on condition of winning a competitive MEXT scholarship. So now I quickly ask about their financial situation, too, just to save my time. If you want to have your application supported, put this topic forward as soon as possible. What's the point of discussing your future research activities if the chances of them to come true aren't high?

Dear Professor X,
Thanks for your email.  Regarding your question about financial support, I am planning to apply for a MEXT scholarship.  If I receive this scholarship, it will provide me with [explain the terms of the scholarship].  Would you be willing to support my application for this scholarship?  If so, I would need [explain what you would need from him].
If I do not receive the MEXT scholarship, I would plan to finance my graduate education by [explain your backup plan].
If you are aware of other funding opportunities, I would be glad to hear about them.
Sincerely,
[your name]

If the professor does not already understand MEXT scholarships very well, I would guess they are not a good supervisor.  I believe MEXT is the main funding agency in Japan.

@AnonymousPhysicist Even so, showing that the student understands the aspects of any funding is good.

What’s wrong with just reply describing your situation:
Dear Sir, In regards to your question on financial support I do not have access to funding now,
OR
Dear Sir, In regards to your question on financial support I already have access to funding for the next xxx years.


text:
Who is an Academic Associate?
I've recently shifted my career to teaching at University, and I am quite not familiar with the post I am assigned, from the answers what I have read for entry-level Assitant Professor and Associate Professor.
I am not familiar with what entry-level means. I have completed my Masters and I am going to enroll in Ph.D. next year.
I am also unfamiliar with the term Academic Associate, I know my roles and responsibilities, but what is the difference between an Academic Associate and Assistant Professor?

I've never heard this title; it may be specific to a particular country or university system.  Can you state where you are located?

Probably salary, expectations and the possibility of getting this position permanently.

@NateEldredge India

The term Academic Associate may be specific to India or it may be generic. But a reasonable definition might be: Academic Associate. It seems to be something like a post-doc, though not actually requiring a doctorate. But, according to that definition, it isn't really a faculty position, but one for an assistant to a professor. I suggest that if you want a career you want to look beyond that.
Entry level probably means different things in different places. I would hope that it always means entry into an actual career and not just a dead-end job. Thus Assistant Professor (in the US) is entry level, in my view, but adjunct instructor is not, since the latter has little future. An assistant professorship normally requires a doctorate, though there are some exceptions at smaller institutions. But an assistant professor is a regular faculty position with normal faculty requirements: teaching, research, service.
An associate professor nearly always requires a doctorate and a period of probation to earn, normally seven years as an assistant professor if in the US. At the end of the seven years you either get promoted to associate professor or are required to leave. The necessary activities of a probationary faculty member are dependent on the nature of the college or university. For most it is heavily research oriented, but in teaching college the research requirement may be only nominal rather than fundamental. (Again, this is a US perspective and some of it may apply to India, or not.)
But for a career, even as an educator rather than a researcher, you are well advised to earn a doctorate. It will take time and effort, but it gives you options that you won't have otherwise.

Thank you, Buffy, for your answer it helped me to understand the true nature of my job.


text:
Academic tassel at convocation: left or right for dual undergraduate/post graduate students?
Apologies if the question I ask is not suited for this SE.
At convocation, it is usually the culture for undergrads to wear the tassel on right and switch to left after being given the degree. For postgraduates, the tassel is supposed to be on the left.
My question has two parts:
a) What about people who are straight away getting their post graduate degree (in case of students who have opted for a dual degree program or integrated course)? Do they wear the tassel on the right (as they have never been given a degree before)?
b) When exactly should the turning of the tassel happen (for undergrads)? On the stage itself when receiving the degree?
Many thanks for any answers in advance!

For (b), someone will likely announce when it's time to move them.

At my institution (in the United States), students always wear the tassel on the right, even if they've earned a prior degree.  At Commencement, the President tells the students when to switch.  (In our case, that's everyone at once, after diplomas (really, diploma covers) have been presented.)


text:
Is it formal to inform readers that a point will be discussed later in the chapter?
I mentioned an important idea in a section without developing it.
Is it formal to inform readers that the point will be discussed later in the chapter?
For example:
This idea will be discussed in detail in a subsequent section.
If yes, should it be presented just like any sentence, maybe next to the idea? Or Does it require special treatment?
Thank you

If your sections are numbered, include the actual number of the section with the discussion.

There is nothing wrong with doing so. if you would not, the reader might start wondering. In cases where no other alternatives apply then signalling to the reader that more details will follow allows the reader to continue concentrating on the details at hand. If you end up with a situation like this, you should of course make sure that following such a structure is the best way forward. If it is not then restructuring the text is necessary. After all the goal of writing is to provide the reader with the easiest way to understand your writing (the way you want them to). If you find yourself using this form of signalling often, you should probably take a critical look at your writing and ask yourself why this happens. It might be that you are not structuring the text in a good way.

"If you find yourself using this form of signalling often, you should probably take a critical look at your writing" This. I usually tell my students that this sentence has sort of a bad smell. It may not be bad by itself, but if you end up using it all the time you are explaining stuff in the wrong order.

Thanks that is exactly what I tried to say but in more general terms.

@xLeitix I only partially agree. In developing a conceptual structure that is new to the reader this construction should designed around for exactly the reason you identify, but when writing for experts about yet-another-application-of-[something they are familiar with] it often helps to shorten a lengthy argument and reduce the effort of reading. As always it is about the audience you are writing for.


text:
Would successive rejections of different papers by the same journal lower the probability of acceptance of the next submission to the same journal?
I have tried to submit some of my papers on unrelated topics to a journal and gotten rejected, either desk rejection or rejection after peer review, by the journal. Recently I worked out a new paper and would like to submit it to this journal again.
The reasons for rejections have never been elementary ones, say "poor English" or "of poor quality" or something like these (I know all these reasons from my peers). For most of the time parlance such as "the results are not significant enough to warrant publication in ..." is the reason.
Then I would like to know: Does my records in that journal significantly affect the viewpoints of the editors on my current submission?

My guess about the situation is that your prior rejections will not significantly affect the editors' opinions on your new submission.
However, the fact of your prior repeated rejections is evidence that you are misjudging the suitability of your papers for that journal, either the aptness of the topic(s), or the level and quality. Thus, if I had to wager, I'd bet that you'll be rejected again... not because you were rejected before, but because the factors in play that led to your prior rejections will most likely manifest themselves in the present case.
So, really, you should get more-specific advice from an advisor or mentor about appropriate venue(s) for your papers, as well as possibly critiques of the writing style.

Thanks; that reminds me of the important information. If possible, please be referred to the edited question.

@Chou Your edited question suggests that this answer is relevant in your case.

@JessicaB: Yes, I just would like to inform the kind answerers of updates :)

Well, some evidence.  By coincidence, I just received the following email from an eminent senior mathematician just now in response to my somewhat plaintive request for advice on where to submit a paper proving a result I had written to tell him about: "But these days it's seems to be quite random, because the good journals are getting so many excellent papers. [My colleague Professor X] said something like (he's an editor for [Very Good But Not Top Journal Y]) 'I've been rejecting papers that I have no right to reject.'"

The answer lies in why they have been rejected. Papers can be rejected because they are unsuitable for the journal, are of low quality either technically or scientifically or both. You should have received some words of why the rejections came about. There is of course a chance that an editor will tire from seeing papers to be rejected from the same author time and again and that this will lead to preconceived ideas that all output from that author is of the same quality.
So key for a successful submission is to find out why rejection has occurred. Try to avoid any mistakes that can be the grounds for the rejection. Supply the manuscript in exactly the way any Instructions for Authors dictate. Provide a good accompanying letter for the submission that details the importance of the research and the conclusions you have reached as well as why the journal appears to be suitable for your point of view.

Thanks; that reminds me of the important information. If possible, please be referred to the edited question.


text:
International master programm in Physic at university of Rostock
I am a physic student from Jordan, few days ago i got an admission to do my master in physics at university of Rostock, Germany.
Am I able to get a PhD position from other university when I finish my master study, i.e., will other German universities recognize my Master degree from Rostock university?

A master's degree from a German Universität (University) or Technische Hochschule (Institute of Technology) is directly recognized by other universities in Germany (and usually by most other universities around the world). The same cannot be said for a Fachhochschule (FH). Rostock is officially a university, so that shouldn't be a major concern.


text:
What is the difference between Article File and Related Manuscript File in Nature?
They ask to submit those both files.
What is the difference between the two?

The text in Nature states

Submission to Nature [...] is taken to imply that there is no significant overlap between the submitted manuscript and any other papers from the same authors under consideration or in press elsewhere. (Abstracts or unrefereed web preprints do not compromise novelty). The authors must include copies of all related manuscripts with any overlap in authorship that are under consideration or in press elsewhere. If a related manuscript is submitted elsewhere while the manuscript is under consideration at Nature Communications, a copy of the related manuscript must be sent to the editor.

In other words, related manuscript files means any other manuscript that overlaps with the one submitted to Nature and hence runs the risk of duplicating the Nature paper in some sense. Nature assesses such papers to see where and how the overlap occurs and, probably, rejects the submitted manuscript is the overlap is deemed significant to that it may be considered duplication. This is likely to safeguard the uniqueness of the Nature paper when (and if) it becomes published.