Can I justify my PhD if I have mostly adapted existing code instead of writing it myself? My PhD in computational mechanics (field is materials science) involves writing Fortran subroutines for implementing new constitutive equations. More specifically, my research involves continuum mechanics, finite-element analysis and other numerical methods. Though theoretically I have a decent understanding of the subjects, I find it impossible to implement them in code.
I have published a paper on implementing a modified model through a subroutine. But the truth is that I have not written the code from scratch. More than 80% of the code was written by someone else. Here's the original code. I just modified the hardening law to suit my purpose. I did not change the integration method or the structure of the code. I have cited their paper of course.
Truth is, I would not have been able to write the code from scratch even if I had been given five years to do that. I just can think of how to implement theory to code.
Now, I am about to defend my PhD, which is based on this code.
I feel like a charlatan and that I can’t justify my PhD. My advisor doesn’t know this. I am not suited for a career in computational mechanics or materials science. How can I reconcile this?

You weren’t earning a PhD in FORTRAN Coding (gasp – I shudder to think of it). You were working in continuum mechanics. That is where your contribution was, and is.
If I read it correctly, you took an existing tool and adapted it for a new purpose. I can’t find anything wrong with that, especially as you cited the creators of the original version. If you keep it up and continue to make contributions to continuum mechanics you will do fine. You didn’t screw up. You did what any sensible person should do. FORTRAN was my first computing language. I doubt that I would even recognize it anymore.
Relax, have a culturally appropriate beverage and celebrate your success.


Answering the "why do you want to do a PhD?" question This question is ubiquitous when applying for PhD studies, and it's one I don't understand. On the surface it's a simple question, but I found it to be frustratingly complex.

I tend to think in economic terms. My calculations indicated that PhD studies are not worth it, especially in a world of exponential growth. The details aren't that important, but briefly, I calculated that if I stay in industry and invest most of my salary into the stock market, I can expect to greatly outperform someone who spends 4+ years in a PhD program unless he or she commands a very high starting salary, which is usually not the case. This doesn't take into account the fact that 49% of PhD students are depressed
 and half of them don't complete.

So since the economic argument is a failure, when I wrote my PhD applications, I put in all the other reasons I had to do it, such as:

I felt I'm in a dead-end job where my skills aren't appreciated. A much less-trained person can do what I'm doing, and while I believe I do a better job, I do so in ways that management does not track.
I wanted to swap careers. To do that I needed a new set of skills, and further study would not only let me pick that up, it would let me back up my skills with a paper qualification. Since I already had a Masters degree a PhD is the next obvious thing to do.
I choose this field because it provides transferable skills to the careers I want to move to, and because I'm sufficiently interested in it to want to keep up to date with its most recent developments (even though I probably won't stay in it as a researcher, per the fact that the odds of finding an academic job are very low).
I did well in my Masters (which was in the same field), including the research component, so I believe I can also do well in a PhD.
I can afford it. I hadn't been in the workforce for long, but I'm extremely conservative with money and we've been in a bull market for the past several years. Of course I would rather not self-fund, but if I have to, I can.

When I showed these reasons to my professors, they responded with "you are telling them why they shouldn't admit you!" Following their advice I rewrote my statement of purpose to what I'll call half-truths, which got me admitted.

I don't understand why my original reasons to do PhD studies weren't valid. I'm happy doing what I'm doing right now, and my supervisor has said I'm progressing well. That seems to be indicating that my original reasons aren't inappropriate. I further don't understand why PhD programs care about the reasons why the student is doing a PhD. It seems much more natural to worry about whether the student is capable of doing it. Certainly the latter question was the focus of all my non-academic job interviews. Finally it seems admission committees like candidates who are passionate about the field and want to become researchers themselves. However I also see plenty of complaints by academics about academic life (e.g. the funding lottery, the nomadic lifestyle). If academics are trying to convince students that they shouldn't try to be researchers, why are they turning around and looking for people who want to be researchers? It feels like they prefer the ignorant and starry-eyed over those who're aware what they're going into.

Can someone explain?

Let's consider why "you are telling [professors that] they shouldn't admit you!":

I felt I'm in a dead-end job...

That doesn't show motivation for doing a PhD.

I wanted to swap careers...

You don't need a PhD to swap careers.

I choose this field because...

...it provides transferable skills to the careers I want to move to...

This requires more detail to be relevant.

...because I'm sufficiently interested in it to want to keep up to date with its most recent developments...

You can do that without a PhD

...(even though I probably won't stay in it as a researcher, per the
fact that the odds of finding an academic job are very low).

This doesn't show motivation for doing a PhD.

I did well in my Masters (which was in the same field)...

Many "do well" in their Masters, PhD students do better.

...including the research component, so I believe I can also do well in a PhD.

This requires more detail to be relevant.

I can afford it.

This doesn't distinguish you.


Should we ask ambiguous questions on an exam? I'm TAing an undergraduate course at a university in the US, and had a disagreement with the professor teaching the course about a question in an exam. Here's an abstract version of the relevant part:

Select the single most appropriate method, out of the list {A, B, C, ...}, to solve problem X.

Both A and B are appropriate to solve X, and objectively superior to any other method on the list. Weak arguments can be made for either of them being more appropriate than the other. After a debate with the professor, we agreed that the question is ambiguous.
My opinion is that we should not be asking such a question. I think students might waste a lot of time trying to find their presumed mistake, since the question asks for a single most appropriate method, and there isn't one. Therefore, I think we should either remove it, remove one of the two methods, or rephrase it to

Select a single appropriate method...

The professor argues that the ambiguity is not an error on our part. They suggest we'll give full credit to either choice of A or B, and say that students shouldn't obsess over this minor detail at the expense of other parts of the exam.
I feel like this is problematic in terms of ethics (because of the possibility of misleading students) and pedagogy (since I would like students to distinguish strong and weak arguments for a method being superior to another). I would like to know others' position and arguments on this issue.
I'm also very interested in references that address the pedagogical aspect, based on either research or experience. The only such reference I could find is this blogpost (in Hebrew), written by a teacher, that defines "what's in my pocket" questions to avoid as teachers.
Edit
I might have overdone the abstraction, and made the example trivial. Consider the question

Select the single most appropriate method, out of the list {A, B, C, ...}, to solve each problem in the list {X, Y, Z, ...}.

{A, B, C, ...} are standard methods, all taught in class. Each other problem, {Y, Z, ...}, has a unique method most appropriate for solving it, and the ambiguity rises only for X.

I think the focus on ethics is a bit misguided. If your professor genuinely believes that asking ambiguous, "what's in my pocket"-type questions (a closely related concept is that of a "gotcha" question) on an exam is an appropriate testing strategy and serves a useful pedagogical purpose, then I cannot say that they are behaving unethically.
So the problem as I see it is not that the professor is behaving unethically, but simply that if they believe such a thing then they are wrong. I can't support this with any scientific argument based on research; but just based on my own experience with teaching, one major reason why I'm pretty sure this plan will not work  as your professor expects is that students in the US (and other countries I'm familiar with) have been conditioned to expect, over their many years in the educational system, that all exam questions, in STEM and related technical subjects at least, have a single, unambiguously correct, answer (unless explicitly stated otherwise).
Now, a professor might be of the view that this is poor preparation for real life, where situations are typically much more vague and nuanced, and a suboptimal way to develop critical thinking skills. So it's tempting to think "why don't I design an exam that simulates real life more closely, and this way test for more of the things that really matter and encourage students to really think". This is well-intentioned, and perhaps even correct in an idealistic sense of being closer to the Socratic method. If you were gathered together with a small group of students on an island somewhere and had all the time in the world to develop their intellect, and no earthly concerns about schedules, tuition, the need to test and grade hundreds of students in X amount of time with Y resources with no easy chance for a do-over if something goes wrong, etc., then asking such questions would be a wonderful method to stimulate their thinking.
On the other hand, here in the real world, the conditioning I mentioned is so powerful, and the conditions under which students are tested so stressful and unforgiving, that asking questions with more than one correct answer (without stating that explicitly in the question) is a very clear recipe for trouble. A lot of students are already so stressed out and anxious taking tests that it's difficult to them to think creatively or be resourceful in an exam setting. What I expect will happen is that many of the students will obssess over whether A or B is really the correct answer (despite your professor saying they "shouldn't obsess over this minor detail"), will get confused and spend unreasonable amounts of time on this issue, will end up not having enough time for other questions they are perfectly capable of solving, and will end up frustrated and hurt and feeling that they have been treated unfairly over this testing strategy. And of course, they could complain, leading to a nasty headache of a problem for you and the professor to have to explain to the undergraduate program chair.
Here's a final thought to consider: it's hard enough -- by which I mean essentially impossible -- to get students to believe you're treating them fairly when you're bending over backwards not to create problems of this type and "just" giving honest, error-free, clear exam questions each of which tests one unambiguous snippet of knowledge. Even then, some students will still manage to come up with explanations for why they did poorly that somehow put the blame on you and your teaching/testing/grading practices and not on themselves for not studying hard enough. So the way I see it, things being hard enough already, why make them intentionally even harder still? This particular headache is easily avoidable. Let the professor try out their creative teaching ideas during the semester and not in the high-stakes, pressure-cooker environment of an exam. For the exam, my advice would be to stick with standard principles for designing exam questions that follow the same conventions everyone else uses and that students are used to. Anyway, that's my unscientific two cents.


Where to put the interpretative mathematical derivations in my research paper? In my research, I've got some new data and there should be some mathematical derivations to interpret the results of previous work. Is it appropriate to put this part of content in the Discussion section or in the Result section or even a new single section?

I suppose the results of your mathematical derivations matter for your paper's conclusions, not the way you derived them.
The results will probably have a natural place where they belong in your paper. If the derivations are short, you can present them there.
But if the derivations occupy significant space (and aren't part of your core content), presenting them in-place would mean a detour for the reader. Then I'd recomment to place them into some appendix, and include a link to this appendix there where you present the results.
P.S. At my time as a student, professors often used phrases like "as you can easily see ..." to avoid lengthy detours into less relevant mathematical derivations. But for completeness' sake, the derivations should be accessible to the interested reader.


How to treat papers or other work from dyslexic students? I know that as a student with dyslexia you get all kinds of benefits such as extra time for work, exams, access or licenses to spell checkers, etc. (Never used or been offered any, not that I needed it.) However, I cam imagine that by the time you graduate you would be expected to have a competence level of at least a certain degree. I myself am currently graduating for a bachelor's degree in Business IT. While the focus here mainly lies in IT, I have been told that my use of language is seriously sub-par for the degree despite knowing of my dyslexia.

Now, I have been told that my work is well above average (average of 8/10) but that due to my use of language, the grade doesn't reflect the work. Having teachers fail me fully based on language has become quite common for me. In particular my use of the Dutch language; I should note English is my second language.

Just to clarify, the spelling is not the problem, the way I build up my sentences is (think of starwars-yoda). While the text can be understood, it's not something you can breeze through with a martini like some other papers.

So as the final question here: How should students with dyslexia be handled? How would one get them to improve on their language? Should we even need to help them improve their language? Other than just redirecting them to some dyslexia institute. And, how should their work be looked at?

Edit:
To clarify, I'm interested into how both students and teachers alike could approach this. Not just myself personally.

The disabilities office at my Univ (large state univ in the U.S.) strongly advises that instructors not attempt to improvise accommodations for students with disabilities, whether self-declared or documented through the disabilities office. Their point is that we (outside the disabilities office) are not at all experts in such things, in the first place. Rather, the disabilities office will discuss with faculty the possible sensible accommodations, and in effect negotiate something. Faculty should not "get creative" and take initiative.

A significant point is that, although the circumstances or environment or timing or... for exams can accommodate, there is apparently never any notion that the grading rubrics should accommodate. That is, it's absolutely not that lower standards are applied to the output, but that the situation in which the output is produced can be modified. Indeed, it is not that we expect less in such cases, after all!


How do SJR and Web of Science journal rankings and quartiles differ? I want to know about how journal quartiles  (i.e., Q1 to Q4) calculations differ.

Web of Science (WoS) uses Journal Impact Factor Quartile the journal’s rank in category (X) is based on where the journal stands relative to the total number in the category. InCites (WoS)  displays the best quartile for journals that appear in multiple Web of Science Research Areas. When a research area is specified, the quartile for that particular journal and research area is displayed.

I've recently submitted an article in a ISI journal.
This journal (urban design international) is ranked 36 out of 40 journals in the "urban studies" category; when I searched it in the Scopus, it was showed as a Q2 journal. But according to the web of science calculation, it is Q4 (36/40 = 0.9, Q4>0.75 ~ 0.9 = Q4)

So my questions are:

How  are SJR journal quartiles calculated?
How can SJR and WoS journal quartiles differ so much (e.g., Q2 in SJR and Q4 in web of science)?
Which ranking (SJR or WoS) is more important or valid?
When someone asks about journal quartiles, which system is more commonly used?

Presumably, when you say SJR quartiles, you mean the rankings presented by Scimago. I previously posted details about how journal ranks and quartiles are estimated on scimago.

There are several key differences between WoS and Scimago that lead to different journal ranks (and quartiles):

Database of journals: WoS rankings uses web of science indexed journals and I think Scimago uses Scopus ISI indexed journals. Scopus is much more inclusive than WoS and also provides better coverage in some disciplines (e.g., social sciences) than WoS. In some disciplines, simply being listed in WoS suggests that the journal is at least a reasonably strong one in the discipline.
Source of citations: Indexing different databases mean that the citations used to evaluate journals are also based on different databases of articles. WoS has a more exclusive set of journals and the coverage is not as balanced across the sciences. The consequence is that metrics based on citations per year per article (e.g., impact factor, citescore) will be higher when using Scopus, and this difference will be amplified for social sciences and other disciplines with less WoS coverage. However, although journal metrics based on citations per year will be lower in WoS, this in itself wont necessarily affect journal rankings within disciplines, because in many cases all journals within a discipline will be broadly influenced.
Definition of an article: I believe that Scopus/Scimago and WoS define articles differently. In particular, I believe that Scimago categorises some items as articles that WoS does not. In general, most citation metrics have a formula that divides citations in a given period by number of articles. I believe this scopus approach reduces citations per year indicators for some journals that include a lot of non-standard article types (e.g., Nature and Science).
Metric: Irrespective of the database of citations used and definitions of what is an article, impact factor and SJR are different citation metrics. See my previous answer about how SJR works. In short, SJR is based on a 3 year window, and impact factor is based on a 2 year window. SJR also has a bunch of corrections to reduce discipline-specific differences in citation practices and a way of weighting certain citations more highly (based on the prestige/impact of source). While I think SJR is much better than impact factor, this might not change within discipline rankings too much because most of these differences between metrics address discipline-level differences.

So, why is it that a journal can be Q2 in Scimago and Q4 in WoS? I think this is most likely due to the database of journals used. WoS is more exclusive and particularly deficient in certain disciplines. So for example, a journal may have a reasonable reputation (e.g., ranked 35 out of 100 in Scimago), but only ranked 35 out of 40 in WoS, because there are a whole pile of journals in Scimago that aren't even listed in WoS.

Which indicator of journal quartile is more valid?
First, I think that SJR as a metric of impact and the more inclusive journal database are better and make the sicmago metrics of journal impact more valid. Of course, at some point, you need to ask about what it means to speak about the rank or quartile of a journal. What should the criteria for membership in the population of journals from which a rank is obtained? The WoS criteria is quite high. Most people would agree that predatory journals with no legitimate peer review should not be included.
I think an argument could be made that Scopus / ISI is sometimes too inclusive (e.g., it includes some journals that have questionable peer review). But I think the stronger argument is that WoS is too exclusive. So perhaps  the Scimago/Scopus interpretation aligns more naturally to what we might think of as a rank or quartile. I.e., of the legitimate journals (or at least, reasonably legitimate) in a discipline that are published, where does a given journal sit.

What quartile is typically used? It's difficult to say how people will interpret a statement like "this journal is Q1" without you specifying the source. It's a bit like when you say "this article has 50 citations", but you don't say which database this citation count is based on (e.g., WoS, Scopus, Google Scholar).

In contexts where it matters, you should clarify which source you are relying on. That said, my impression is that the Scimago quartiles are becoming more popular. For example, at my university we are encouraged to mainly publish in Q1 journals, where quartiles are based on Scimago.

As a minor practical point, access to WoS citation metrics is by subscription only and the user interface is terrible. In contrast, the interface for scimago is public and quite user friendly.


What counts as an outcome of a grant? When one goes from one grant to another, there are a few papers that are in the pipeline during the process. I have one such paper that was in submission when I switched grants. Submitted on the first grant, and then revised and resubmitted on the second and with additional changes on the second. This paper was then accepted. I acknowledged both grants in the final transcript as work was done to the paper on both grants.

The second grant agency asks for updates of research outcomes and consequences during the grant in a very black and white way of listing publications that are a product of the research. Is this paper considered a research outcome to the second grant?

This is in mathematics, if that helps, and there was some math to be done to fix the referee's complaint(s).

The rule of thumb that I generally use is that if any portion of a work has been supported by a particular grant, then it counts as part of the outcomes of that grant.

Typically, in reporting on outcomes, one is asked not just for names of papers, but also for some sort of narrative of the work, in which it is simple to state what work was done, much as you just did.  If for some odd reason the funding agency only wants you to list papers and nothing else, then I would think that it is incumbent upon them to understand that they may not be the sole source of support for some of the items listed.


Why do editors sometimes reject manuscripts for being out of scope even though they cite references from the same journal? I wonder why editors sometimes do reject  submitted manuscripts for being out of the journal's scopes while the authors have utilized published papers from the same journals.

Is it just a polite way of rejection?

Cape Code has given a good answer, but it's not the only possibility for such a rejection.  Suppose you publish a paper in, say, "Topology and Its Applications", in which you prove some topological result using (among other things) a set-theoretic lemma. And suppose I later prove some result in algebra using (among other things) your lemma.  Of course, I would cite your paper, but that doesn't put my algebra paper into the scope of "Topology and Its Applications".


What should I do if I found a citation error in a published paper? I've found a mistake in a published paper, and am unsure what to do now.

I was looking at all cited articles from a paper over 10 years old, and found one that is citing the paper in error.

A variant of a certain protein and a fusion protein made of 2  proteins have been confused, that is the citation points to a paper on a protein which shares an abbreviation but is entirely different - this is a pretty big mistake and suggests they haven't actually read the paper they referenced!

The Elsevier journal published this in 2013 and I don't know how to report it, or what the etiquette is here. I can't see contacting the authors to be of much use as it is already printed, and they could very easily delete my email and forget about the error, whereas an editor or some such person would surely be able to take reasonable steps to address it.

For the record I'm an undergrad and have no professional link/competition/other conflict of interest with this researcher or department!

Small errors that do not affect the results or conclusions of the paper are normally handled through publication of a correction (or erratum). This is handled by the journal editor, who will be in contact with the authors for confirmation that they agree as to it being an error, and provide for the exact correction to be published.
The journal that published paper should have a policy on corrections, check it out! Physical Review Letters’s editorial policies and practices state, for example:

Errata.— The Errata section contains notices regarding errors or omissions in papers previously published. Besides the standard Erratum, several special categories of documents may appear in this section. In the online journal, each of these documents involve bidirectional links between the original article and the document in the Errata section. The category of the corrective document is indicated in its title and in the link from the original article.
The standard Erratum is a statement by the authors of the original paper that briefly describes the correction(s) and, where appropriate, any effects on the conclusions of the paper.

Thus, what you should do is:

Make double sure it is actually an error.

Then ask someone else to double check it again. Preferably someone more senior, i.e. with some experience of academic publication.

Write to the corresponding author, pointing out the error. Be nice, and make real sure not to assume to worst.
You say “this is a pretty big mistake and suggests they haven't actually read the paper they referenced”: depending on context, it could actually be something minor like a copy-paste mistake (pasting the wrong reference, when they meant another paper)

If you do not obtain a response, or they respond but don't intend to correct the error, then consider contacting the editor.

I can understand why, as an undergrad, you would consider contacting the editor directly without writing to the authors first. However, as long as you remain professional in your correspondence with them, I think it's best to contact the authors first. It's more polite, and they may actually be able to provide you with some explanation you haven't thought of. Contacting the editor before the authors is somewhat overdoing it…


Do I need to tell my rec letter provider that I have language disorder? This might be a weird question. But here we go.

I'm applying for business/data-related master programs.

I'm a stutter with a certified moderate language disorder.

Do I need to tell my professors (who provides recommendation letters) the fact of my disorder?

I'm afraid that the recommendation letter or the questions asked by the master programs require my professors to evaluate my oral English level. If they don't know this fact, they may attribute my stutter to my English (I'm an international student btw).

Added: is it common that the professors are required by master programs to evaluate the students' oral English skills in RL.

No, nobody needs to know. Your letter writers need to attest to your academic abilities, whereas your medical history is not something they need to know nor do they have any business telling anyone else about it.

As a matter of fact, all that ought to matter are your academic abilities. The fact that you're applying for graduate school implies to me that you must have been reasonably good in school/college -- in other words, that your disability has no implications for your academic performance. That's all the admissions committee wants to know: that you'll excel academically, and they will be able to see that from your transcripts and what your letter writers describe in their letters.


How to write a postdoc research proposal in mathematics? I have to write a research proposal for some (post doctoral) fellowship (for Mathematics/Mathematical Physics). The authority wants me to submit a short research proposal (preferably in two pages which includes bibliography). Can someone suggest what one should consider while writing such a proposal with a length restriction? I believe, I just have to highlight the main points of the the research and give a bibliography with it, but I may be wrong. The idea in my mind contains several steps. Should I give a time frame as well to finish each one? Please help.

Reconsidering once again, can someone tell me how to write good research proposals in areas like pure mathematics (I mean, like Non-commutative geometry, K-Homology etc. where, unlike some other subjects, number of papers, an average researcher can produce at the time of graduation, is less).

I think this might be useful as complementary to the questions mentioned by Suresh. I heard for the first time about Heilmeier Catechism in one of the grant writing workshops. Since then I always think to Heilmeier questions while writing a proposal or paper.

I copy Heilmeier questions from DARPA website, however another version is available from Wikipedia.

What are you trying to do? Articulate your objectives using absolutely no jargon. What is the problem?  Why is it hard?
How is it done today, and what are the limits of current practice?
What's new in your approach and why do you think it will be successful?
Who cares?
If you're successful, what difference will it make?   What impact will success have?  How will it be measured?
What are the risks and the payoffs?
How much will it cost?
How long will it take?
What are the midterm and final "exams" to check for success?  How will progress be measured?


Do authors normally check their own papers for plagiarism? I was recently asked to review a paper (for a very reputable journal). In the cover letter, it says

"This paper has been checked with turnitin to ensure there is no similarity to other papers."

I haven't seen this before (although I have limited reviewing experience). Is this normal? Or does this indicate something strange about the author?
I've never checked any of my own papers for plagiarism. Should I?
EDIT: Also, why would you mention this in the cover letter?

I've never put such an assertion in one of my own cover letters, and would find it very strange to do so.

It's assumed that I should be behaving honestly and avoiding both plagiarism and self-plagiarism.  Saying: "really, I'm not plagiarizing!" just makes me wonder why the person felt they needed to say anything.
If I'm not behaving honestly, why wouldn't I lie about the results of plagiarism-checking too?

If I saw this as a reviewer, I would think it reflected an odd but almost certainly irrelevant thing about the authors, and then proceed to ignore it.


Can a PhD thesis consist of "exploratory research"? I am a physics graduate student at the stage where I need to come up with a PhD thesis proposal.

I have an idea for a thesis project that I think is very interesting and has not been explored in the literature. Specifically, the idea is to take a powerful new numerical technique that was developed in a completely different field and try to apply it to problems in my own field. If it works, it could greatly impact the field by drastically reducing the computational cost of calculations, which is one of the biggest limitations of current research.

The problem I face is that this research would be exploratory in nature. By this I mean that I do not have a well-defined problem to solve beyond "attempt to adapt it to my field and establish how well it works on some basic problems". In contrast, every thesis I have read has consisted of applying known techniques to new problems. My approach would be to do the opposite: apply a new technique to known problems to establish whether it could be feasible as a new tool in my field.

So my question is: can exploratory studies such as this one constitute a PhD thesis? In my experience, I have never seen a thesis of this type, and I am worried that this is because it is a bad idea.

Yes.  A PhD thesis that introduces new methods to old problems can be an excellent thesis if:

The new methods are in some way better than old methods.
The new methods are widely adopted.

Some of the most successful physicists work in this way.


Is it ethical to host ads on an institute provided homepage? I am affiliated to an institute and they provide each student an opportunity to make their own homepage, which they can put up as www.[institute-webpage]/[username]. Now, this webpage is not reviewed by the institute. I made my homepage recently and I am wondering if it is ethical to put ads on it.

On one hand, it is my own website, while on the other hand, it is hosted on their server and I don't have to pay anything to get this.

It may depend on the rules of your institute, but I'd bet that putting ads on your homepage is not allowed.  You should certainly not put up ads without verifying that you have official permission to do so.

If you work at a public university or other governmental institute, then putting up ads could be considered using government property for personal gain.  That's probably not just unethical, but illegal (but you'd have to look into the appropriate laws in your jurisdiction to be sure).

If you work at a private university or institute, then it may not be illegal, but there are still probably institute rules against using institute property in this way.  I'd be surprised if any big organization didn't have such rules.


My advisor escalated things after not getting a coauthorship he did not deserve I am a 3rd year PhD Student (Computer Science, India). I have two advisors, one internal and one external.

The internal advisor has no knowledge of my area and he doesn’t care what I am doing. He has no contribution to my research so far, but he keeps forcing me to make him co-author (2nd author) of my papers. I am a part-time PhD student (full time faculty in my college) in my college and he is my colleague. He has contributed nothing, did not even know title of my paper.

The external advisor is the one who actually helps me with my research. He wants all authorship to be based on contribution. He is external to my college and lives in a different city.

Recently I refused to make my internal advisor second author of a paper. Due to this, he got upset and he wrote in my progress report that I have attitude problem and I don’t obey my advisor. Now I have to stand in front of the dean, head of department and the entire committee (my advisor will also be there in the meeting with me).

Should I tell the monitoring committee about how my internal advisor unethically tried to manipulate me? Can it worsen the situation in future?

How are 'attitude problem' and not obeying your adviser a 'crime'?  In my university, there is a 'co-authorship policy', which clearly states that any co-authors must have made significant intellectual contributions.  If such a policy exists at your university, I would bring it to support your case.

If you're fronting the committee because of supposedly poor progress, then I would gather as much evidence as possible to support your case. For example, your communication with your external adviser, papers published, etc.

I suggest you change the supervisor. The situation will definitely get worst because it looks like the internal adviser is unethical.  He/she will 'burn you alive'.


Cultural Differences in the Hard Sciences I saw this question, and I got interested.

Besides a culture or country having a lower level of technology or research ability due to wealth, access, etc, is there any difference in how cultures study and research hard sciences (think physics, chemistry, etc) differently from one another? E.g. does an Eastern European scientist think about or conduct scientific research differently than a scientist from the United States, Australia, Africa, or any other country or culture? I don't need an exhaustive list, if there are strong differences, but some examples would help in my investigation. I am trying to decide if I want to pursue a graduate program in physics/materials science abroad, or just stick to my own culture, for now, since it is what I am used to.

It's not impossible that there is some effect, but figuring it out would be a complex task. A researcher would also need to guard against making value judgements that would, in the end, be treated as racist.

However, if you look at other fields, you see some differences, but I would attribute a lot of it to language more than culture, and some to history. In literature, the South Americans in general have produced some amazing stuff in Spanish and Portuguese that is quite different from literature elsewhere yet shares some characteistics. Art is another field in which different cultures have produced qualitatively different things, say China and Europe.

As humans we use language to express ourselves and the language both captures and guides thought patterns. If your language structure helps you think in a certain way that may effect how you think about, for example, mathematical problems and what insights you have naturally.

Likewise history (and the accidents of history) play a role. If one region of the world generally does something different than others, it may just be the accident that some person started a line of thought in a place and it was picked up by others.

On the other hand, the academic community is pretty much a world-wide phenomenon now, with a long history of students and teachers moving about. The effect you suggest is likely dampened, if it exists at all, by this world wide exchange of ideas and the consequent sharing of thought patterns.


What is the best PhD choice for gauge-gravity duality research? I am a mathematician but want to do a PhD in mathematical physics focusing on gauge-gravity duality and more generally quantum gravity, what is the most appropriate PhD choice to do research in this field, is it an astrophysics (cosmology) PhD or a particle physics one?
I am looking for a program that I can take a lot of relevant abstract mathematics courses like topological quantum field theory, functorial quantum field theory, algebraic geometry and topology, while at the same time I can get a good understanding of physics concepts about quantum gravity.

At least in the US, your first question should be whether to do a mathematics or a physics PhD.  It's possible to work as a physicist with a mathematics PhD and vice versa (and I know people who do it), but it's hard enough to find an academic job (which is the only kind of job that will pay you for theoretical research of the kind you seem to be interested in) as it is, and having background and teaching experience in the "wrong" field makes it much harder.
It's important to understand that physics and mathematics are different fields with different ideas of what it means for a statement to be true.  In mathematics, a statement is true if and only if someone has given a valid mathematical proof for it.  In physics - well I'm a mathematician who is ignorant of physics, so I think it's best to let physicists speak for themselves - but it's not what I just wrote for mathematics.  Their definition (in the mathematical sense of definition) of truth is different.  Which definition of truth do you want to work with?
Also important - would you rather teach introductory physics or calculus?
In either case, you want to be at a university where the mathematics and physics departments have a good relationship with each other.  (For this purpose unlike many others, having no relationship does not count as having a good relationship.)


Feeling incompetent about a written exam scheduled for today. Should I skip it? I have a written exam scheduled today evening in 2 hours for a research scientist position at a major British company. They want to check competency in theory and programming for a position.

My PhD thesis has been broadly on the topic they have advertised. So, I applied for the position as I was interested in the job description. However, the outline of written exam scheduled today demands heavy mathematical and programming expertise. The written exam was scheduled within a week of resume submission. There's no sample questions or preparation materials available on the internet.

To be honest, my research was not mathematically or computationally intensive as what's expected from me. Now I am dreading to appear for the written exam. I am afraid that I will not be able to answer anything.

What should I do? Should I skip it? Doing poorly will create a bad reputation. I am afraid that would affect my future chances of working with the company.

In general, blowing off an agreed-upon meeting is strictly worse than not performing well in that meeting; the only exception being a temporary issue, such as a scheduling conflict or illness. In either case you would need to contact them immediately, explain the temporary and serious issue, and ask to reschedule.

In your case, this does not seem to have anything to do with a temporary issue, its just that you don't feel you'll do well in general.

My advise is to prepare to the extent you can, such as by trying to brush up on basic facts if you can find any that seem related to the interview. So if it includes programming, for instance, remind yourself of basic data structures and algorithms (at a high-level), the general syntax of any specific language mentioned, etc. If there are a few basic facts you can review on the math, such as if they mention stats you can brush up on your definitions of standard terms (regression, deviation, distributions, etc.).

Then go in and give 'em hell, i.e. do your best. Remember, you have no idea what is actually expected in terms of performance. This could be like the Putnam, were anything better than miserably failing every single question is considered a fantastic result. It could be an interview that is mostly about testing you with overly hard things and seeing how you react - can you calmly reason through hard problems, break them down, point out assumptions, clarify, suggest potential approaches? Are you affable and interesting to talk to, or do you break down the first time you encounter something you don't know?

If you don't perform well, oh well - at least try to do it with a good sense of humor and a bit of grace. If you don't know, you don't know. This attitude can make the conclusion "this job isn't a good fit for this person's background", which could be true, in which case now you both know, and this would not usually prevent you from re-applying to the company later. You are generally welcome to re-apply later, and you can then know to emphasis the highly related experience you picked up in the mean time.

But since you don't actually know what's on the test in terms of actual questions, and you don't know what their real expectation of performance is, I can't really think of a worse strategy than admitting total defeat and giving up before even trying. If you applied to a job that seemed like it would be a good fit for you, and they agreed enough that they want to interview you, it seems like a good time to give it your all and learn as much as you can from the process regardless of result.


Should results of a journal paper always be reproducible? This question might seem silly at first read. But in my research, first I have done mathematical analysis and simulation and provided the results in section I. Later, in section II, based on Sec. I, I did simulation in which nodes are distributed over 2D plane and some parameter is calculated over the mobile-nodes (parameter is "transmission rate" to be precise).

Now, since every run of simulation will distribute node on a different location (as in a real-world environment where mobile-users can be located anywhere), hence I will get a different result in each simulation run.

How can I present this result in my paper now?

It is important to run multiple indepemdent replications and statistically analyze the results rather than simply running the simulation once and reporting that result.
It is also important to save the random number seeds that were used so that the simulation results can be replicated.


PhD duration in the USA I am trying to find out what the average duration of PhD studies are in the USA. Here in Spain it used to be 4 years, but it seems that Europe is moving towards a 3-year scheme since students are expected to do their MSc before they start. What is it like in the USA? Is some kind of shortening also occurring?

This varies so widely by discipline that asking for an average across all disciplines is unlikely to be very helpful.  Most individual disciplines do keep careful records of this statistic, and it should be easy to search for them on (e.g.) google.

However, I would say with some confidence that no American PhD program requires or even expects its students to complete a PhD in less than four years.  In some programs the "party line" is that it is desirable to complete the degree in four years, but in my experience this means that you start to feel the squeeze of increased teaching and/or decreased funding after four years, not that you get ejected from the program or forced to graduate.

I work in a discipline, mathematics, with a high entry cost but for which, once you acquire the necessary background and skills (with which a small minority of students do enter the program), there is no specific reason why you couldn't do all the work for a great thesis and write it up in a rather short amount of time, say on the order of a semester.  Nevertheless I have met very few people who have completed a math PhD in fewer than four years.  When we get to the upper echelons of talent, preparation and work ethic, this surely must mean that the culture of a PhD program strongly encourages students to stay for this amount of time.

To answer your final question: yes, many programs are trying to shorten their average time to degree as funding is being cut.  In my own PhD program (mathematics at UGA) I was involved in an initiative to do just this: up until recently we guaranteed six years of funding to incoming PhD students without master's degrees and five for students with an incoming master's.  We now guarantee five years to all students.  Note that this does not mean that we do not have funded sixth year students: we certainly do.  But it means that students will, throughout their time in the program, have to keep their eye on the five-year mark, which is something that our former arrangement was not doing: even very strong students would often stick around for six years for no especially good reason.

Finally let me also note that we changed (with my involvement) all our requirements to be independent of whether students arrive with master's degrees.  We have found that the difference in the level of preparedness of such students is not significant enough to justify more stringent time-to-degree requirements.


What is the Minimum GPA for admission in a graduate school in a respectable science university in the US? I am thinking about applying to graduate studies in physics related Phd or master degree in the US, but my GPA is very low, 2.4/4.0 to be specific.
I wonder if there are respectable universities in the US that can accept such low average?
Notes:
-I have some experience in research from my undergrad.
-I had my Undergraduate degree in physics from a respectable Canadian university.

Thanks in advance!

(In the US) in Physics, some programs will weight things like the physics subject GRE and research experience, especially publications, ahead of the GPA. However, some schools do have a GPA cut-off around 3.0, so it's possible some schools wouldn't get far enough into your application to read it.

If you want to apply to prestigious or highly-selective programs right now, I think you would need:

To have scored very well on the general and physics-subject GREs.
Very good letters of recommendation that speak directly to your ability to succeed in a graduate program.
An "explanation" for your GPA in your application. Was it because you worked a lot? Was it because you spent a lot of time doing research? Do your last couple semesters show a better GPA than your overall GPA? If so, you could make an argument that you addressed the issues that led to your lower GPA during the course of your undergraduate career, and these issues will not continue to impact your graduate performance.

If you don't fee you have documented supplementary support like that, you still have options:

Take a year off and gain experience
You can also take a year or two off and work a research/physics-related job or internship, and/or take a couple extra classes. Taking one class at a time while working a job or internship can push up your overall GPA that they will consider (and can go a long way to making your graduate career easier), and if you spend a year or so doing something else, there will be more focus on what else you were doing. If you can get a publication during that time, that's an excellent way to display that you do have the skills to succeed in a graduate program.

Apply to "Bridge" programs
Several universities have Bridge programs, meant to help students build a competitive background for graduate study. Often, these Bridge programs also grant your access to that institution's graduate program, if you finish 1-2 years of the bridge program in good standing. One example is The University of Chicago's Physics Bridge program. This is not a masters.

Apply to Masters programs
Many universities have Masters programs, which may include the opportunity of transferring into the university's graduate program, or to another university's graduate program.


Appropriateness of a second-authored article in external review file for tenure I am wondering what others thought of including a second-authored article being included in an external reviewer file for tenure review in the health sciences. This is my second tenure review, since I transferred institutions, and my tenure did not transfer from my original institution where I was granted tenure.

I can include five articles in my external review application. For one of my main areas of research, my collaborator and I provide equal leadership, so we generally switch between first and second authors. The article from our work that I would like to include has me as the second author, not first. Do others believe that it would be strange for a reviewer to see a second-authors publication included in a file?

It sounds reasonable to me, especially if explained as you did above.


Professorship without PhD in the United States In the discussion made in comments to this question, it has been stated that in France, it is possible (though improbable) to become a professor without having PhD. It made me curious if there is such possibility in the United States. I know that in 1970s there were leading professors in the US university who had only MSc. However, I think the main focus was on knowledge in the past, but now formalities are much more important.

Anyway, I am curious if the current regulations in the US universities allows this at all? For promotion to full professor, one needs to be assistant/associate professor. In the past, having a PhD was privilege, but it is now mandatory for holding any assistant/associate/full professor.

Does the current regulations allow a professor without PhD to teach PhD students?

This question is about impossibility vs. improbability.

At most US institutions, you need the terminal degree in your field. For many fields this is a PhD, but in some it might be an EdD, a DMA, a DPH, a ThD, etc. However, all of these degrees are considered to one level or another to be research doctorates. Presumably faculty positions at a medical school require an MD or equivalent. Likewise for other professional schools. Positions in the visual arts, theater, dance, creative writing, cinematography, etc., may only require the MFA (Master of Fine Arts) degree, as it is considered to be the terminal degree in those fields.

"Regulations" about the requirements to hold certain academic ranks and perform certain academic duties (like mentor graduate students) are made at the institutional level.


Where does the money earned by universities in the USA from sports activities go? In the USA, professional sports is big at many universities. Many, if not all, get a lot of money from such events (e.g., broadcasting rights to ESPN, or from different sportsware/equipment companies for brand endorsements, etc.). Does any of this money go to educational and research activities of the university? Or only sports department of the university utilizes it, e.g., in paying the coach and other staff?

Edit: I know that the above question is related to this question: American universities - where does all the money go? in some sense but mine is narrower.

Revised answer:  At my university, where football is big, the athletics department supports itself, and that some of the money goes back to the university, but the only specific instances I know of are donations to the art museum and history of science collection.
That said, I am sure most of revenue generated stays within athletics.

For instance, this article talks about the most profitable football programs, and out of Alabama's $110 million revenue in 2013, $6.5 million (5.9%) went back to "academic programming."  However, the details of how that money got used, and how much actually went back athletics (via athletic scholarships) is unclear.  In any case, this is a small amount of the university operating budget.  Florida that year gave the most back to academic programming $7.2 million, but the general and educational expenses were $524 million.

However, most universities lose money on athletics (see, e.g., this and this).  These universities make up for this by doing things like charging students fees for the athletics program and cutting funds to other programs/units.  Even some of the ones which are termed profitable get large subsidies (e.g., student fees)--only 7/230 Division I athletics programs did not take subsidies last year .  These articles say that even the donations athletics help generate goes back to athletics and that a relatively small amount of the athletics costs (about 16%) goes to student aid.


Can I patent part of my work presented that in my own research paper? I recently published a paper in which I proposed a new transmission design relevant to wireless communication (skipping the details here).

Now I am thinking to file a patent but I am not sure if the work already published can be patented? Can the community kindly suggest me if I can patent this work either fully or part of it?

There are caveats to the grace period but the U.S. you have a one year grace period to file.
35 U.S.C. 102 Conditions for patentability; novelty.

(a) NOVELTY; PRIOR ART.—A person shall be entitled to a patent unless—
    (1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention; or
    (2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
(b) EXCEPTIONS.—
    (1) DISCLOSURES MADE 1 YEAR OR LESS BEFORE THE EFFECTIVE FILING DATE OF THE CLAIMED INVENTION.—A disclosure made 1 year or less before the effective filing date of a claimed invention shall not be prior art to the claimed invention under subsection (a)(1) if—
        (A) the disclosure was made by the inventor or joint inventor or by another who obtained the subject matter disclosed directly or indirectly from the inventor or a joint inventor; or

For most all of the rest of the world, the day something is published it is no longer patentable, at least to the extent of what was disclosed. Nor is anything patentable that is obvious from what was published.


What are the requisites for Scopus to index the proceedings of a conference? I have seen that some conferences in the CS field are indexed by Scopus, I mean their conference proceedings. I have found some information about the requisites a journal should have to be indexed in Scopus, but I did not find any information about conference proceedings. Are those requirements the same?

Thanks

Scopus's website on content policy and selection gives a good idea of what you need. The book policy is probably the relevant one, since conference proceedings are "edited volumes", but if you're trying to index individual papers then look at the conference papers selection criteria at the bottom of the page.


Electronic recommendation letter tips Is it possible the recommendation letter be sent directly to the recruiter by the person who writes it?

Also, does the letter needs to be signed by hand? Maybe is enough to see that the letter comes directly from the sender, but is not signed.

Thanks

As a letter writer, I either email the PDF directly to the hiring department or I use a letter service such as Interfolio. I never give it directly to the student.

I also insert both a scanned image of my signature as well as a digital cryptographic signature embedded into the PDF, with a note that the digital signature can be authenticated through Adobe Reader.


Do two rounds of major revision lead to a better chance of getting the paper accepted? I submitted a paper to a prominent journal in my field. The reviewers all indicated that the paper would make a positive contrition to the field in the first round of review and asked me to make a major revision. I revised the manuscript according to their review and all reviewers indicated that they like my revision. However, one of the reviewers kept raising new issues and asked me to undertake another round of "major revision." Personally, I really feel that the new issues are not too difficult to address. However, I am wondering whether it is fair to keep raising new  (major) issues in each round of review. And, what is my chance of getting the paper accepted in the scenario described above (two rounds of major revision)? Thanks very much for your insight.

I think of requests for revision as falling into three basic categories, sorted in order of importance:

New technical results (e.g., additional experiments, more theorems)
Large-scale text improvement (e.g., reorganizing text, dealing with pervasive language issues)
Localized text improvement (e.g., improving explanations, adding references)

Of these, only a request for new results should be of concern as a possible road to rejection: for the other two, if you want the paper published, if one cares to one can typically always put in sufficient work to address reviewer comments.  It may be hard, unpleasant, and unrewarding (depending on the particulars), but this is an area where any request for revision almost always has a clear path to publication, and of a stronger paper than you started with.

Requests for new technical results, on the other hand, might or might not be something that you cannot reasonable address.  If you can address them, then it's still a clear road to publication of a stronger paper.  If you can't, however, then it's a question of scope and may be worth discussing with the handling editor to see whether they are a sine qua non for publication.

In general, however, my feeling about requests for revision, even major revision, is that they're generally good news.  Once a paper hits at least a major revision, it's highly likely to be eventually accepted if the authors just keep answering the requests for improvement, and will likely be the stronger for it.  There are exceptions (I just had one rejected by a journal for the rather unusual reason that "they only allow one revision,"), but in my experience these most frequently reflect an author who has chosen to fight the reviewers rather than to improve the paper.


Finding reproducible articles My idea is learning new methods/fields by reproducing someone else results, and I would like to pick nice/good papers to learn from.
If we define reproducibility as starting from the same samples/data, use the same methods, get the same results I would like to know papers which has already been reproduced.

Is there any project/web-service/method that tracks reproducibility?

Of course, some people citing an article might have (partially) replicate it, but that wouldn't help me as I don't have access to new samples/data.

I am interested in bioinformatics field.

I would suggest graduate level textbooks for that. They often leave proofs or part of it to the reader and some of them even have exercises, allowing you to learn the new topic by actually working on it. Furthermore, they made sure that what they left open is solvable in an appropriate amount of time.
Another nice point is that they often discuss the most important theories and concepts in a field, where on the other hand a paper might be focused on a very tiny topic.

There are textbooks for many different levels (starting at undergraduate and going as far as to being interesting to a professor who wants to extend his knowledge to a new field), depending on how much you already know.


How to quickly understand the main idea when reading a paper? I have problems in reading papers, specifically papers where the subject is not so new to me and I am familiar with the problem which the writer wants to solve.

How to find the those parts which talk about the main idea?

When I go to their suggested work to understand the main idea, I have to have first read their previous sections, because they define some notations and definition which they use them on their suggested work. When I go to read those parts to understand the notation. I am not sure if my reading method is good. because after reading the notations and definitions , I have to start their suggested method section. This one has its own challenges too.

My advisor said you should understand the main idea of a paper in one hour, or at maximum in two hours. But I need at least 5 hours.

(Maybe help: I am reading a paper in the field of computer networks.)

How to efficiently read a paper is not something that can be taught over the internet in broad generalities.  It seems pretty futile to try to teach it "in general" in general (!!), by which I mean that if you're trying to teach someone how to read a paper, you had better have at least one actual paper in hand.  You can try to draw broader morals, but whatever lessons are there to be learned should be grounded in the reading of that particular paper.  Thus for instance

  How to find the those parts which talk about the main idea?

would be silly to address without seeing the paper.

I find more promise here:

  My advisor said you should understand the main idea of a paper in one hour, or at maximum in two hours. But I need at least 5 hours.

Your advisor knows me?!?  Sorry, just kidding.  Anyway, that's exactly whom you should be talking to.  But even with your advisor you are stuck on a way too general discussion.  Go to her with with paper you are trying to read now, and learn how the advice applies to that paper.

Let me also say that I am a bit skeptical of the hard limits your advisor is imposing, or more precisely with the way you are construing whatever your advisor told you.  Obviously 1-2 hours cannot be the amount of time needed to understand the main idea of every paper: some papers are just significantly longer, more difficult and/or more obscure than others.  Speaking for myself: after some years of experience for reading for the main idea, depending on the paper, sometimes I can now grasp the main idea just as soon as I run my eyes over the first page; sometimes it takes me an hour or two; sometimes it takes me a full day's work; sometimes at the end of a full day's work I find that I don't understand the main idea.

Where is this 1-2 hour figure coming from, and what does "should" mean here?  Maybe she means "Come back if you've spent more than two hours on it and I'll give you more help."  Or maybe she means that's an upper bound for how long it would take her to read the paper.  But she's not a student, she's supervising one.  If there's one matter in which students should be skeptical of their advisors, it's in their advisors' estimations of how long it will (or "should") take a student to do something.  It's not a matter of arguing with your advisor but rather letting her in to understand your process.  If it's taking you so much more time than she expects, show her what you're doing and see what she has to say.

Let me also say that a longer time spent on something isn't inherently problematic.  If you are reading in a language different from your own native one, it will take you longer -- and skimming will take you much longer.  Most academics eventually realize that the people who can complete tasks more quickly are often but far from always the ones who can do the best work on those tasks.  Real breakthroughs are things that people chew on and work through for weeks, months or years.  Some speed freak types simply don't have the patience or focus to linger on something for much longer than it takes for others to see how quick they are.  So if you are eventually understanding what you're reading quite well and you're not lagging far behind in other tasks: ask yourself whether you really have a problem or just a certain skill that you'd like to optimize when you get the chance.


Mid-stage PhD student lost motivation I'm a PhD student in literature who is nearly half way through my third year.

Recently (last month or two) I feel like I've lost all motivation to work on my thesis. Instead of treating it like a normal 9-5 workday I now go in late most days and procrastinate for a few hours before starting any actual work.

I'm not up to where I wanted to be in terms of chapter drafts at this stage of my program, but instead of this motivating me to work harder I just feel disheartened and like I will never catch up so why try. These defeatist thoughts make me feel even less like working so i end up in a vicious spiral of not working, guilt about not working, no motivation to work, more not working.

I feel overwhelmed by the amount of material I feel I still need to read to be 'across' my field and don't have a good sense of how im going to tie my various chapters into an coherent piece of work connected by an overarching argument and theoretical framework.

I have been managing an anxiety disorder throughout my PhD, and have in the past suffered from depression. I struggle to know if these feelings mean my overall mental health is deteriorating and that's what's causing the negative feelings about the PhD, or if it is the fact that I spend most of my time doing/thinking about PhD and so if I feel good about it then I feel good most of the time, and if I feel the research is going bad I feel bad most of the time. I've been sleeping to avoid going to the office and feel down about the thesis but this doesn't carry over to other aspects of my life - which leads me to think it's more phd-caused than mental health but who knows.

My supervisor is unaware of the underlying mental health issues. I struggled early on in first year which lead to me telling her I felt overwhelmed and she instructed me to take a week off, but I didn't outright disclose the anxiety. I've tried to flag recently with my supervisor that I feel a bit lost and behind, but she didn't seem overly concerned and I think I downplayed the extent to which this is impacting on my day to day work on the thesis. I wonder if I need to be more overt about how much I'm struggling, or disclose the underlying mental health issues. We have a very good r/ship which often feels more like a friendship than a supervision - which has it's upsides as well as downsides when it comes to something like this as I don't want to let her down or for her to be disappointed in me by disclosing how much work I'm not doing, but also don't want to ruin the friendly vibe by getting all serious with how I'm feeling re: thesis. I'm worried that even though she seems happy with where I'm at draft wise, she thinks I've read much more than I have because she doesn't know how much time I'm spending avoiding the thesis.

Part of me feels I should just 'get on with it' and if it is mental health as the underlying cause this is not something my supervisor should have to manage anyway so why bring it up. Another part of me feels I should be more honest with her about how much I feel I'm struggling with the thesis and not worry about seeming needy or incapable.

I feel like the time toward completion draws ever closer and yet the amount of work I need to do to finish doesn't progress at the same rate. I feel like I don't work hard enough at the moment to finish on time, and this feels both terrifying and paralyzing. I've read lots of blogs about procrastination tips and such but struggle to put them into action. I've also read lost about mid phd slump/doldrums so logically know this isn't uncommon, but at the same time I've lost some of self-confidence to think I'll be able get through this phase like others have.

Gamification of your time-management method maybe an answer. Gamification is the latest trend in the Internet that involves putting game elements to motivate users to engage more in a website's activity. First of all, you can set experience points to each task, and exp requirement for each leveling up, badges for completion of tasks. Be sure to take care of your health while you do this.

About anxiety, procrastination and other symptoms, there are a number of reasons:
(1) The slow monster
(2) The not-believe-in-future monster
(3) The exhaustion-of-thoughts monster
(4) Nightmare and risk monster
(5) Anger monster
(6) Crying monster
(7) Self-restriction/limiting monster

So, these are the monsters that you need to fight in your adventure. If you can fight off them, high chance you will be able to finish your thesis. Good luck!


Is there any value in self-publishing a book as an academic? Recently, I contacted a publisher about the draft of a book that I wrote about a year ago. I found their advertisement over the net. This is a scientific book that I have worked on for about two or three years and have revised it more than four times.

The publisher proposed that if I pay a certain amount of money that they can publish my book in a month or two.

Does this kind of pay-to-publish or self-publishing of books confer any reputation in academia? What are the advantages and disadvantages to doing so?

I would recommend that you ask yourself a question: why do I want this book "officially" published?  You could, after all, just make the material free online via arXiv or as a webpage or an archival technical report of various types depending on its contents and your situation.

Prestige of having a published book?  A pay-to-publish press will generally give you negative credibility, since there are so many publishers that will publish your book without making you pay (including lots of dodgy low-quality ones that will publish pretty much anything).  Pay-to-publish smells like desperation or resume-padding.
Money from sales/royalties?  If they thought it was going to make money, they would be paying you, not the other way around.
Higher visibility?  A pay-to-publish press will generally not be any good at promoting your work.  They're not going to invest any real money in promotion if they aren't expecting to make significant money from sales.

Serious and reputable academic publishing houses are always looking for good books to publish.  The right ones for your field will generally have booths at the major conferences in the field, with representatives that you can talk to.


What happens if you use the wrong reference? I recently submitted an assignment but realised a week later that one of the sources I have used in the essay and bibliography was wrong. I'm not sure how it happened I'm guessing some mix up with the citation software I used but I'm really scared that my professor will be able to tell. Does anybody know how thoroughly lecturers check the references used?

It's a mistake in good faith. You are a student, so you're supposed to learn. It's great that you found it yourself. Just send the lecturer an email explaining what happened. He probably won't really mind, but if the bibliography is included in the grade (e.g. if this is an Academic Writing course or so) he might deduct some point.


How to decline answering details about my thesis? I am a graduate student studying Education. I am currently working on my thesis, am about half-done with this and I expect to finish in one year. For the research, I am visiting classrooms at various public schools.

Recently, one such public school asked that, in exchange for letting me visit, I share my advice about teaching. Since they welcomed me their classroom, I did not see much of a problem with this and did not think that would present any problems. I prepared an outline for a 90-minute discussion covering some areas, drawing somewhat on my findings related to my research. After sending this off to them before the lecture, I found they are quite disappointed and want far more from me, essentially they want the very core of my thesis.

Is it acceptable practice for graduate students to be guarding of their work? Is this common enough that I can cite it as a reason for wanting to avoid sharing the details?

The one valid point I can see here(*) for not sharing the state of the thesis:

  For the research, I am visiting classrooms at various public schools.

You should not share the preliminary details of your thesis if this could affect the outcome of your study.
As I understood the question, the school (or some teachers or students) may be the subjects you study, so they should be as little influenced by you as possible (that is, don't tell them that they are in the placebo group).

(*) things would be different e.g. if you were in an engineering field and working towards a patent


Can my co-advisor be from another institution? I started my PhD program and have finished qualifiers already. I had a discussion about topics with my research advisor. However, my advisor admitted he does not know so much about the topic of my PhD.

Thus I had the following questions:

Can my co-advisor be from another institution?
If so, will this impact my thesis committee?

Yes, it's common in the institutions that I know. Where I graduated, at least one member of the committee even had to be an 'external'.
That doesn't mean the same applies to your institution. Read your local examination rules and check with your first supervisor if external (co)supervision is possible in your institution and what the implications are.


How do you find interdisciplinary collaborators for your research? I would like to know if someone knows whether there are IT solutions (websites etc) that help with meeting interdisciplinary researchers from local academic institutions (socal).

If you really want them local, the best social network is actually being social.

You can either attend conferences and university events in your city, attend seminars at other departments (some are announced in their webpages), or just send a series of polite emails to researchers working in thins you want. Just list the departments that may be doing something you like, browse their personnel, and skim their last publications to see if your research interests may be aligned.


How to quote in the title of a thesis in APA style? I am writing my bachelor thesis (in psychology) and I am planning to use a quote from the series Game of Thrones as my title. More specifically, my title is:

  ‘The lone wolf dies but the pack survives’: The influence of perceived social consensus on the fear of death

Now, I am really unsure how to quote this. According to APA Style, I would have to write the producer, director and the year in brackets but it doesn’t make much sense to this for the title (it looks stupid).

Is there any possibility to quote in the title using footnotes?

I'm not sure that you would need to provide a full citation for a quote that's used that way.

It's not uncommon to use a small quote at the beginning of an article to provide some "flavor text," as in the picture below. In cases like this, some attribution is given, but the quote source isn't included in the APA Reference list.

I would think that if you provided the full Game of Thrones passage as a "flavor text" quote at the very beginning of the article (including an informal attribution), that would be enough to get the job done. It's not too different from articles that use a quote from an interview in a title and then to provide the full context of that quote later in the article (e.g., http://dx.doi.org/10.1080/09518398.2010.495091).


A question about reviewer's comment I have recieved a comment from a reviewer as
'You had less than 100 cases per division in Table 3, so you should only report with less than three significant " .
I could not understand what she/he wanted me to correct in Table

The reviewer is probably talking about https://en.m.wikipedia.org/wiki/Significant_figures

If you are reporting numbers like 3.23436, you likely have far too many significant figures: you are reporting precision that just isn't relevant. Report something like 3.2 instead.

In your table you have percentages. Round numbers like 40.6% to 41% throughout. And be consistent either with number of decimals (round to nearest 1%) or sig digits (12% and 3.5% both have 2 significant digits).


What is a "normal" teaching load for a Lecturer in a UK pre-'92 University? What is a normal teaching load for a Lecturer on a teaching and research contract (equal split) in a physical science field in a UK pre-'92 University? Is there such a thing as "normal", or is the variation huge? In this case, what is the range in "normal"?

I can only answer for biological sciences:

Universities will have something along the lines of a "Workload Allocation Model" system for dividing up work. Under our departments accounting you get 3 hours prep time for every formal teaching session you give, plus 20 minutes for every exam script you mark. Tutorials don't count as "formal teaching sessions" and so get no prep time.

For for example a 10 credit module, with 18 lectures,  and 2x 3 hour practicals for 50 students would get you an allocation of 100.5 hours.

A full time contract is ~1600 hours, so a 50% teaching load would be 800 allocated hours. However:

50% teaching load would be unusual - the normal split is 40:40:20 teaching:research:admin
There is generally an (informal) recognition that prep takes longer for new hires than for old hands.

A common load for a lecturer would be very little in the first year, perhaps one module in the second, rising to around 30-40 contact hours a year once you pass probation (about 4 times the above, if you had the same mix of lectures, practicals and tutorials), and then rising again to a "full" load of around 120 contact hours as you become more senior/part of the furniture.

There is obviously a massive variation in this. If your research goes really well you might never rise above the ~40 hour category, while some of us can teach things the department desperately needs, but no one else can teach, and so have to do more.

For example, I was on a full load of 120 hours within three years of arriving (which was unusually large). My experience of this sort of load is that if you do the teaching well, then you are basically a full time teacher during term time. This makes securing the grant you'll need to pass probation difficult to say the least. While semester is in full swing I only really have time to meet each of my mentees once a week (note that supervising postgrad students counts as research not teaching) and run my lab meeting and journal club on top of my teaching and admin duty. I then concentrate on pushing my various research projects along properly during the vacations.


Advantages of taking the Subject GRE exam in April Background (skip this if you want): I'll obtain my master's degree in about June/2018 or so (if everything goes smoothly), and I intend to pursue a phd in the US. Thing is, I'm from a country in the south hemisphere and the academic term here is different than in the north hemisphere, and so I'm a bit paranoid with deadlines for graduate applications. Looking around at questions such as here and here, and around in some universities' sites, I understood that graduate applications are usually open from October through December, and the academic term would start around September.

Question: is there any reason why someone would want to take the GRE in April, other than if he or she were actually retaking the test trying to get a better score? I know that they keep the scores for five years. The bottom line is: I'm unsure whether I should take the GRE in April or in September. April seems too soon, the fee is expensive and I'd like to do it only once, preferably being well-prepared. I'm sorry if I'm missing something obvious or common sense, but I'd rather ask than remain ignorant. Thanks!

Your approximate dates for start of term and for graduate application availability are correct.  Some are open through January and some even as late as February, although most PhD applications do close in December AFAIK.

If you're not finishing until 2018 then the only real advantage is that taking the GRE in April will allow you to take it again in September if you need to improve your score.

Of course you could also take the October one if it's offered in your area, but you won't get September's scores back until after the October registration deadline.  And the October test's approximate score reporting date of December 9 may be too late for some applications.  IIRC, some applications close on or very close to December 1, but TBH it's been a long time and maybe that's not right.

On the plus side, there's a new rule in place ("new" relative to 2006ish) where you can submit only the score(s) you want to the schools.  In the past you had to submit everything on your score report, good or bad.

Sources:

https://www.ets.org/gre/subject/register/centers_dates
https://www.ets.org/gre/subject/scores/send/asr

My recommendations:

If you really feel like you're fully prepared for the April test, then take the April test.  If you don't do as well as you wanted then you'll have time before the September test, and you'll have time to earn extra money to help pay for it.  Tutoring is always an option, and if you tutor subjects that are on the GRE then that's a double bonus.
If you aren't confident you can be fully prepared for the April test, don't take the April test.


Can I add a baby as a co-author of a scientific paper, to protest against co-authors who haven't made any contribution? Can I put the name of my baby as one of the co-authors of a scientific paper?

I know it sounds disturbing, but it's a way of mine to protest against co-authors that haven't made any contribution (they haven't even read it or are part of the research area) to a paper, but they are part of the research group.

What are the legal / ethic concerns?

So technically I was writing the paper with my baby in my hand and the baby was talking with me in its own language. The baby even wrote a few characters in the paper when it managed to get near the keyboard while I was holding it.

There was a similar case in 1975, when an American mathematician and physicist, Professor Jack H. Hetherington of Michigan State University, added his cat as a co-author. Apparently, a collegaue who had reviewed his manuscript, had pointed out that he had used "we" and "us" throughout the manuscript, but this was incorrect as he was the sole author. so, instead of typing out the entire document once again (those were the days before Ctrl H), he decided to speed up the process and added the name of Chester, his pet cat as a co-author. However, to disguise the fact, he put "FDC Willard" as the name, with FD standing for "felix domesticus" and the C for "Chester." And Willard was the name of Chester's father.

However, these days, with so many regulations in place, I'm not sure if it would be ethical to include your baby's name. If however, you choose to do so, I would suggest you inform the editor and mention this in a disclaimer somewhere within the title page, so that readers are not misled about your intent.

Another well known case is the paper "In a fully H-2 incompatible chimera, T cells of donor origin can respond to minor histocompatibility antigens in association with either donor or host H-2 type." by Polly Matzinger and Galadriel Mirkwood in The Journal of Experimental Medicine, 1978.
As Ted Anton described it in his book Bold Science, "Refusing to write in the usual scientific passive voice ('steps were taken') and too insecure to write in the first person ('I took the steps'), she instead invented a coauthor": her Afghan Hound, Galadriel Mirkwood. Once discovered, papers on which she was a major author were then barred from the journal until the editor died and was replaced by another.


My application is declined because of covid - true or false? I am looking for an master's internship in Berlin in biology. (background in short: I am a student in another city's university, but because the lectures are online and I have a relative here, I moved to Berlin.)
I am cold-emailing professors and ask them if I could do an internship at their lab. Some don't answer, some simply decline my application with that because of corona restrictions, they can't accept students.
Can it be possible or is it just a nice excuse? As far as I know, people can go to work in Berlin. Also, this would be an laboratory internship, so I would have to attend in person.

I suspect it's true. I mean, why lie? In the past, when I've decided I don't have the time or energy for summer interns, I've just replied "Sorry, I am not taking any summer students this year". They are not under any obligations to take students, so there is no reason to lie.
Most labs currently have strict occupancy and distancing limits. Many researchers are only attending labs under restrictive timetables or on a shift-work basis. Even where there is enough space for those employed at the lab, there may not be space for additional people. Even where there is, teaching people in the lab requires close contact and that might be hard with 2m rules in place. And even if all those problems can be surmounted, an extra person in a room always increases the risk. Why increase the risk for those you are responsible for?
Add into this that many academics are far busier this year than normal, may have extra child care responsibilities, or are trying to catch up with things missed during the pandemic. For example, my postdoc was out of the lab for 6 months. Normally they would look after a summer intern, but they don't have time for that this year as they have 6 months (out of their 3 year contract) to catch up on.


How important are citations when applying for jobs or promotions? How important is citation count for fresh doctorates? Is this number more important for joining the academia than the industry?
What is the importance of citations for someone seeking tenure? Does this depend on the field, as papers in an esoteric area can be expected to have few citations?

In my experience, citation counts are considerably less important than recommendation letters, but they still matter, especially for tenure.  For fresh PhDs, high citation counts are definitely helpful, but they're not a hiring requirement for most fields in CS.  But for tenure, it's really hard to build a successful case without at least one high-impact (post-thesis) publication.

Smart committees know to gather citation counts, publication counts, acceptance rates, impact factors, h-indices, and other quasi-objective numerical data from reasonable sources and to compare them with peers in the applicant's field.  (For my promotion cases, for example, my citation counts were mined from Google Scholar, not ISI, and I was compared against other theoretical computer scientists, not other computational-geometers-who-play-with-surface-graphs.)  Alas, not every committee is smart.


What exactly should I add in an extended and revised version of my research paper? My original paper has already been published in the conference proceedings. Now, the body organizing the conference has invited me to submit an extended and revised version of my paper to be included in a new book.

In my experience, extended versions most typically contain three classes of new information:

More extensive prose and examples to explain, discuss, and otherwise clarify the material presented in the original paper.  Conference papers are sometimes rather haiku'ed due to page limits.
Important details omitted from the original paper due to length.  For example, a discussion of the key points of an algorithm may become a full presentation of its details, and a proof sketch may become a proof.
Extension work, either enhancing evaluation or extending the set of material studied, as suggested by the original paper's future work, feedback from the reviewers, questions raised in the conference talk, etc.

Some combination of these is almost certainly the right sort of material for your extended paper, but which combination exactly is something that only you, your collaborators, and your advisors are in a good position to determine.


When is it most appropriate to post a preprint? I am a student who is very enthusiastic about open access and sharing research. When I worked with my former supervisor, we would write a paper and then post it to a preprint server (e.g., arXiv) at the same time as submitting it to a venue. My current supervisor, however, is of the mindset that we should post a preprint after receiving confirmation that the paper was accepted to some venue.

Is there a generally-accepted time to post a preprint?

It makes the most sense to put it on arXiv when the preprint is complete (i.e. when xou submit it to a journal). (Some people even post to arXiv, wait a few days to maybe get interesting comments from other people (comments which improve the paper), and then submit it to a journal.) So the community can use your results before formal publication.

However, if for some reason or another, your supervisor does not want to do this, then their opinion trumps this argument.


Are professors paid during sabbatical? Are professors paid during sabbatical? I'm mainly concerned about schools in the US. Answers about other countries are also welcome.

The short answer is: yes.

Sabbatical is not a vacation but is rather a leave of teaching to focus on research and publication. At many schools it is not automatic but must be applied for and is granted at the provost's discretion.

Some schools will only provide six months of funding, but will release a full year of teaching, making the faculty member responsible for getting grants for the remainder, or effectively working at half salary.


How is a new department born? I can think of two possible ways in which a new department is born: one, the university decides to start teaching a certain subject, and in the other, an existing department splits into two (e.g. department of physics and astronomy -> department of physics + department of astronomy). If the answer in these two are different, please say so and I will split this question into two.

Clearly the initiative must come from a senior university administrator. Who though - the chancellor? The vice chancellor? The dean of the faculty?
Starting a new department is presumably very expensive. Where does the university find the money? Do new departments usually only start when there is a sudden source of funding (e.g. ___ big new discovery leading to a massive surge in student interest + external funding in the field)? Or do universities spend years saving money before starting a department?
Once the decision is made to go ahead, how does the university go about it? Do they hire a new professor who works in the field, provide her with a budget, and let her hire everyone else? Or do they decide on every individual hire by committee, which is not always made up of people expert in the field or affiliated withe the university?

In all of the cases I have heard of, existing departments split. Sometimes not one, but sometimes faculty from several existing departments split to form a new one. For example, faculty from mechanical engineering, physics, chemistry, and maybe math may form a new department of materials sciences.  Or faculty from math, statistics, computer science, biology, and a variety of engineering departments may form a department of computational science. Oftentimes, such departments are born after there is already a graduate or undergraduate degree that exists in this area and to which the involved faculty members have previously contributed.

In the cases I know of, the initiative has always come from the bottom, not the top. Typically, this has to do with faculty members feeling that there is a critical mass of faculty in a variety of departments to create a new degree program, and they later realize that they may as well build a department around it. The other reason is that the members of such a group may feel that the department they are in does not value their work -- this is, for example, how many statistics and applied math departments started as forks of mathematics departments dominated by pure math faculty who did not appreciate the work or style of the stat or applied math researchers.

In all of these cases, new departments consist of existing faculty. So at least as far as faculty salaries are concerned, this is often not substantially more expensive than the existing structure. Where things get more expensive is that departments typically duplicate support structures as well, such as staff, web site maintenance, etc. But it is not necessarily true that this is "very expensive" as you state.