Effective use of a "learning narrative" assignment in a gen ed science course This spring I will be teaching a physics course that is new at our school. Titled "Relativity for Poets," it's a nonmathematical freshman gen ed course on Einstein's theory of relativity, and cosmology. There is no lab, and there will be only a tiny amount of traditional-style problem-solving. I'm looking for things I can have my students do that will (a) give them some practice wrestling with the (difficult) concepts, and (b) give me something other than just exams on which to base their grades.

A possibility that I've thought of is something I'll refer to as a "learning narrative." I'm sure I'm not the first person to come up with this. The idea is that the student is assigned to write a 1-2 page paper on a topic that they initially had trouble with. They describe the topic, what they didn't understand, why (in hindsight) they didn't understand it, and how they overcame the difficulty. This should be written in such a way that a future student could read it and benefit from it.

Have others done anything similar to this? Was it successful? Any tips for implementing it effectively?

When I TA'ed a survey neuroscience course, we had a similar type of assignment where we asked students to select a topic from the course that was challenging for them personally and put together a (short) PowerPoint presentation on that topic as if they were going to teach it to next year's class.

Overall, I thought the assignment was a good one, and the course reviews at the end of the semester generally indicated that the students felt the same way. Many of the reviews commented on the fact that the process of thinking about how to teach the topic to someone helped solidify or clarify things for themselves. Others mentioned that it helped them learn how to learn on their own by searching the web, looking things up at the library, et cetera. Establishing and building upon this skill is key no matter what you end up doing, so I consider this the biggest positive of the assignment.

The downside seemed to be that many students struggled with the "why they didn't understand it" part. It can be frustrating to not understand something, and especially when the student doesn't plan on pursuing further study in the area (which is probably the case in a class like "Relativity for Poets"), there can be a certain lack of motivation to break through conceptual or other barriers to understanding. You might need to offer some guidance in this particular area of the assignment.

Looking back, one possible improvement might have been to assign these "learning narratives" multiple times throughout the semester. I noticed that a lot of students chose the exact same topic, which might have been because it was truly the hardest topic or because it was the easiest to make a PowerPoint on. We might have gotten more diversity in responses if we split the assignment into two (or more) parts that were due at uniform points across the semester. Plus, we might have been able to reinforce the "learning to learn" aspect of it through repetition. Of course, that's just speculation on my part.


How can I prove that I did a review for a journal? About two years ago, I did a review for a journal (Engineering Failure Analysis, which is published by Elsevier). At that time my affiliation was different from today and I used my institutional email at that time to register as a reviewer in the Elsevier website. But right now that email is deleted and I don't have access to that email. I need to show somewhere that I did a review for this journal and they need some evidence. Despite, I have access to my account in Elsevier (The email is deleted but the account in Elsevier website remained unchanged and I have access to it), I can't find their acknowledgment email for my review. I asked their editorial office and their editor-in-chief 3 times and still after about 1 month I didn't get any answer yet. So, basically I want to know is it enough to take screen capture and show that I did the review to proof or not? Cause in some websites like Publons, it needs to send the confirmation email to their email server to be able to put it in your webpage and count it as a review, but I don't have that confirmation email and I don't think I could get that due to they're ignoring my emails. Any idea, suggestion, and recommendation is appreciated.

Also if somebody knows some sort of customer service or front desk information for Elsevier, I will appreciate if he/she could give it to me cause maybe it could be helpful to contact them directly. I searched a lot in their website but I didn't find anything about how to contact them.

Ask the editorial office. You write that you've already asked them, but send them a reminder. Tell explicitly what you're looking for. In my experience for example, a letter saying you performed a review, on official Elsevier letterhead paper & with the desk editor's signature, suffices. This really should be something the journal office can do quickly. If they haven't responded my guess is that they're waiting for the editor-in-chief to respond, which is unnecessary.


GRE Math Subject Test Overkill for Statistics MS? I got a degree in Applied Mathematics, but while I aced my Statistics courses, my performance in my math courses was weak. I have retaken some of the courses but will not be able to retake them all. Is the Math Subject GRE, though difficult, worth the effort of preparing and doing, hopefully, well on it?

If the Math GRE is "strongly encouraged" and you're concerned that your performance in mathematics courses will negatively affect your application, then yes, you should take it. It doesn't matter so much that it's only for a Master's degree, because the GRE is only useful as a predictor for courses, which is Master's-level work.


Masters in education during physics PhD How feasible would it be for a PhD student in physics (who is interested in teaching high school after their PhD) to receive a masters in education from the university they are receiving their PhD from?

I would think that at least during the first 2 years of a PhD program, before qualifying exams when you are taking courses and being a TA, this is in no way feasible.

What about if you had permission from your PhD research advisor to do so during the later years of your PhD, when you are only doing research and have less (or none if you're funded) TA duties?

How competitive would getting into the school's masters in education program be? I would think that being a PhD student there would help.

Would being a current PhD student help in receiving scholarships to alleviate the costs of the masters in education?

Seems to me like a long shot. There are a lot of obstacles. But first, few secondary schools require a doctorate to teach. So, what is your real goal? The doctorate? Secondary teaching?

Next, you won't have much of a life if you try it. Think 80 hour weeks for a couple of years. A doctorate doesn't often get easier after you pass comps.

Just the scheduling will be an issue. If you are taking courses in two departments, they won't coordinate class times to make it easy for you.

But, perhaps, the biggest obstacle is fining an advisor who thinks it is a good idea. "Where is your commitment?"

As for being competitive for admission, I think it might be a minus. Again "Where is your commitment?"

Costs might be an issue or not. A doctoral student in the US normally has funding sufficient to live, but it normally comes with duties that take time. Tuition is normally waived. But it might not be for the other program.

But, it may be possible (just) if you want to completely set aside all other concerns for a couple of years. Hard, though.

Most secondary teachers with degrees in field, get their education credits over time through continuing education. It is the normal practice in the US. Finding time for a course or two in field-related pedagogy is a more modest goal, and more feasible. But still not essential, as few people actually do that in the US.


What research expenses to request for early career fellowship? I'm applying for an early career fellowship in the UK. The fellowship has a budget of up to £6k per year for research expenses to further the fellow's research activities, which must be requested upfront. Other than travel to conferences, small equipment, and perhaps organising a workshop, does anyone have any good ideas about what this money might be spent on?

The following list is very subject dependent, but some items you might want to include are:

High Performance Computing time (e.g. comp-sci, physics, maths, chemistry etc)
Lab or equipment hire costs
Research technician time (i.e someone who might help acquire data or do some other more routine tasks)
The all-encompassing "computer-consumables" (that covers quite a lot)


How to cite indirect sources in CSE/CBE (name–year) system? I’m writing my first review paper and I don’t know much about the CSE system. I couldn’t find the indirect citation rule for CSE (but for others). So how do I cite indirectly in this style?

If you mean by "indirect citation" citing a source cited in another document (which you, most likely, cannot access for some reason) then your citation would be for example:

  (Rawls 1971, cited in Brown 2008)

See the CSE style guide for more information.
Anyway, I would strongly encourage you to find the original source and to avoid indirect, secondary citations as you do not know whether the citation is correct.


What to do if I have a good proposal for experiment but don't have an ability to fully conduct it? I've recently began working on machine learning, and I was a mathematician before then. Despite such background, as ML is a fast moving area, since I have studied the recent progress considerably and numerous papers, I'm confident in my knowledge. However, I'm neither good at nor fast at implementing my ideas to algorithms. I have no problem with writing pseudocodes, adding details and designing experiments, but it takes bit more time to implement algorithms in Tensorflow and PyTorch for my designed neural network not too slowly. I'm not used to debugging such codes either, since it's much harder than simple, fast algorithms I had to learn before. Therefore, it takes an incredibly long time to conduct an experiment by myself.

An interesting paper was published 3 days ago, and the author does neither understand its full implication nor have an access to enough computation resources. I can attempt a very interesting experiment, and if successful (which is likely), it would be a great deal for both the author and me. However, due to my incredible slowness, I probably have no chance for it, since others will probably publish before I will. I need someone with machine learning knowledge who is not too bad at coding.

I have three choices: grad students in my university, the aforementioned author and well-known experts in the field. I've never met the people in last two options, but both are familiar with the topic. The author doesn't possess a good coding skill either and failed at coding one thing I'm trying to do, since he is a mere student.

I'm not sure whether I can trust either of them. If I will propose my ideas and coauthoring a paper, since I lack coding experience and it bothers them, there's no guarantee that, even if they don't even know the paper (for experts' case) or my idea yet, they can just claim to have the idea already or just ignore my email, and they can publish the paper based on my idea before I do. Grad students probably can help me, but I'm not sure whether they will show an interest in or familiarity with the topic.

I believe this situation can be generalized. In such cases, what is the best choice? Any advice? By the way, as far as I know, it's uncommon to just upload to Arxiv a non-theoretical paper with proposal of experiments and generalization of an existing algorithm. Even if I do, it will not give me much credits, since if it does, then proposal papers would have abounded.

If I were you, I'd look for a friend who is a postdoc/professor and he, or someone in his research team is good at coding. If they are interested in the problem, I could start with them.

Alternatively, I would ask my friends to put me into contact with someone in machine learning who can also code and might be interested in the idea.

Once you start working, you could contact the original author for questions, and in the likely event he's interested in what you do, you could ask him to help you with the work in exchange for co-authorship.


How do I refer to myself in a postdoc application research proposal? I'm writing up a STEM postdoc application and the major component is a lengthy research proposal. I'd like to speak to my specific strengths in the area and provide examples (some of which may not have associated publications), but I'm not sure about language choice. I'm aware of this SE question, but that's more for journal publications. It's easy to say "we" in a journal article, even if I did all the work, because my PI's name is always last author.

Some proposals I've seen have included language like "the applicant's expertise in..." or "this researcher's previous investigation into..." but that seems inelegant and forced. What's the best way to do this?

You don't mention the formality of the application - for example is this an application to a specific PI or program, or an application for a fellowship to a nonprofit or government institution?

I'd say the safest bet is to rely on extreme formality and refer to yourself as "the applicant." I see this all the time in proposals and use it myself when discussing prior work in grant applications. So I wouldn't characterize it as "forced," (inelegant might be a matter of opinion).

However, if it's not very formal (i.e. submitting to an individual professor, or department/working group) then simply using first-person "my" or "I", etc., might be fine and suit your personal style better.


How can I up my confidence level in my technical skills? Let me paint a picture of my background in brief. I did my undergraduate degree in mechanical engineering. I was a good student (almost all A's) till my high school. However, I struggled a lot in my first two years of engineering. I failed 3 subjects and had to retake them. I did fairly well in my last two years and managed a GPA of 3.7. But, my early failure played a heavy toll on my self confidence. I always felt and still feel like I am not worthy for my grades or getting a job.

I was interested in research, so went to a better school for master's degree. Again, though I had very good grades there, I struggled a lot during my job interviews. I always felt inadequate and unconfident about my ability to sustain in that job. As a result I did not get selected in those companies. I got offer in a small company which hired me only looking at my grades. My professors also said that I deserve better workplace but I didn't get it only because of my lack of self confidence and technical speaking skills.

I figured that, since I loved doing research, I should go for a PhD. I worked hard during the last five years. I tried coming out of my comfort zone, try different things, work on challenging projects. I started feeling confident midway through my PhD. However, now I am in my last year and towards the end of writing my thesis. And I am feeling the same anxiety of technical inadequacy and unworthiness.

I am again getting the feeling that I am upto no good and I can't get a decent job or postdoc position with my skillset. Only issue is that I am 29 years old and I will have to get a proper job soon to support my family. I don't know if I am capable of doing that.

My question is, assuming that I suffer from severe case of imposter syndrome, what's my remedy? How can I improve my confidence levels during an interview? I want to feel alive during job search and interviews. I don't want to feel all hopeless and inadequate during any future opportunities.

Are there any suggestions?

My advice is to focus less on the abstract unknowable questions "how good am I?", or "am I technically skilled?" - and instead focus on the concrete things which you've actually done. Focus on the achievements you made in your education. If you like, make a list of all the problems you solved and things you did in your PhD. When you get asked questions in your interviews, don't think about whether you are "good", just think about all the things you did and (metaphorically) give the interviewer that list, and let them judge for themselves if you are a good fit. The other clear solution to having nerves during interviews is simply to do a lot of interviews. Try to schedule some "easy" ones early, so that when you get an interview with a company you really want to work with, you have a bit of practice under your belt. You can also of course have mock practices with your colleagues and friends.


How should LinkedIn summary look like for a person seeking PhD positions? There are many intros, how-to's and guides about writing professional summaries for LinkedIn accounts over the net; however I can not find a good guide to write a summary for academics.

I also tried to write one for myself but I think that this is so vague. Because in the profile we list most of our previous activities such information about our education, career experience, skills, voluntary activities, etc.

If we have detailed information and our CV listed in the profile, what information should explicitly be written in the summary part? Should we summarize the profile in a format like "I have a huge number of publications and thousands of years work experience!"? How brief this part should be? Or is it a bad idea to leave it blank?

What's the purpose of a summary part in a LinkedIn profile for an academic person?

Also, should we mention that we are looking for a PhD position or not? Something like the objectives part in the normal CVs?

Look up some of the professors you are applying to. Unless they work in fields that have strong connections with industry, they will probably not have a profile at all; and if they don't have a profile, they won't even think of looking you up on it.

Even if they do, your application has a lot more information about you, and structured in a way that is more familiar to them (since everybody that applies has an application, but mostly do not have a linkedin account), so it is quicker to look up the information they may interested in.


What to do when majority of the students do not bother to do peer grading assignment? I'm trying a new type of essay in the community college class that I teach. Once a week the students write a 700 word analysis of a topic I choose. It's worth a regular essay (a measly 10 points) but I've been trying a new grading method.

Turn in the paper (1 points)

Peer analysis x 3 (3 points each)

In the peer analysis, students dissect three of their classmate's essays and give them between 0 and 3 points. On average, I find that students give a higher grade than I would.

The main issue I'm facing is that 19 of my 30 students aren't even bothering to do the peer review. By default, they are giving their peers F's on their assignments. This is vastly dropping my class's average score, and as a relatively new teacher, I'm somewhat concerned that I'll be penalized for their inability to do their work. In my opinion, bumping up everyone's grades would be immoral.

You seem to have the grading scheme mis-targeted.

When you make peer review part of your grading scheme you grade the review not the paper reviewed. Failure to do the review should be reflected in the reviewer's grade not in the author's grade.

The criteria I use for grading reviews are along the lines of

Does the review correctly identify strengths and weakness of the submitted material?
Does it communicate problems clearly and helpfully to the author?
Are the criticisms couched in constructive language? (I know, this is not actually necessary or honored in the real world, but I want my classroom to be a comfortable learning environment so I insist.)
Does the review identify what parts of the paper are the source of particular complaints. ("Section 3.2 is unclear because..." as opposed to "Some parts of the paper are unclear").

Note that this means I have to read and review the paper myself and then read and grade the reviews. It's painfully time-consuming.

The positive aspects of this kind of assignment is that it engages the students at the "evaluation" tier of Bloom's taxonomy, and exposes them to a range of different quality of work so they get a chance to understand for themselves that some writing is just plain better than other samples.

The negative aspects include the amount of time used, the somewhat subjective nature of the grading criteria, and a tendency for students to tell each other how very well they are all doing (it requires a certain expertise to do a good—and especially a critical—job of evaluating the work of others; if your students aren't at that level yet they won't set high standards for their peers).

Addendum

Over the weekend I saw a talk on a system called calibrated peer review, which provides a framework for using peer review as part of the grading scheme for student essays. I have no personal experience with the system.

The whole system is mediated over the internet. Assignments proceed in several phases.

Student receive the prompt, do any necessary research, then write and submit their response.
Students then receive a rubric for assessing responses to the same assignment and apply it to three sample responses provided by the instructor (designed to mimic poor, adequate and good student responses).

Success in this stage is defined by having a rating close to that assigned by the instructor. They are allowed a second chance on any where they deviate excessively.

The weight of a students review in the third stage is determined by their performance in this stage (students whose use of the rubric does not match the instructor's will have less impact then student whose application of the rubric matches the instructor's).
Students then read and rate three anonymous responses from their peers (and possibly from the instructor who can provide a 'student' response as well as the three used for calibration). These responses are factored into the author's grade on the assignment using the weights established in stage 2.

Finally, students read and rate their own response. Success here defined by matching the consensus.

Disputes and special cases are resolved by the instructor.

Clearly there is a lot going on there. The anonymity, the use of the calibration stage, and the weighting of student evaluations by their success in rating the calibration responses all work to prevent the worst failure modes of just asking students to grade each other's work directly. Even so, you need that rule that the instructor can overrule the system in exceptional case.

When all is said and done a student's grade on the assignment can be based more on their rating (of samples, of their peers's responses, and of their own submission) than on their own writing. The speaker showed a grading scheme he used in which the essay itself was only worth 20% of the assignment grade with the rest coming from various parts of the review sequence.

This is a lengthy process and is used more on short writing assignment than on substantial papers. It also requires considerable prep, as the instructor must provide the prompt, the rubric, three calibration responses and possibly a fake 'student' response.


Managing relationships with uninvolved supervisors I'm currently a visiting research student at a university in another country for a year as I finish my PhD project. My host supervisor/contact here has been very attentive in terms of writing administrative letters so that I can be affiliated with the university and have permission to access the library, use a shared office space, etc., and has even included me in her monthly catch-up meetings with her official advisees. However, besides briefly meeting with her individually every 2 or 3 months or so to provide a recap of what I'm doing, she's largely uninvolved in my research which is at best tangentially related to her field. My research funding also comes from an outside source.

The problem starts here: I recently told her that I published an article alone. This solo article was based on work that I had discussed once in a meeting and which is a major part of my dissertation. She's now become distant and has stated that she will provisionally renew my university affiliation only after I write a report which shows that I can provide more products/deliverables this semester.

(In addition to doing my independent field work for my diss, which requires a lot of traveling, during the time that I've been here I have presented two papers at two separate conferences, with the latter paper undergoing preparation for a peer-reviewed journal. I have listed her as a second author on all of these - she read them and provided some brief comments.)

I have operated on the understanding that it is often expected of the student to publish at least one paper without her advisor. (And this person is not really my advisor.) This is supposed to help differentiate between the advisor's work and what the PhD student has done on her own. Furthermore, this is the general philosophy of my home university.

I ultimately believe there might be a misunderstanding taking place - PhD students here tend to publish with their advisors, and she might be holding me to the same standards, even when I fall into a different category. But I'm admittedly a bit annoyed for her insinuating that I'm unproductive, when I'm not. We also continue to do these side projects where I do 99% of the work, which seem to make our relationship worthwhile and at little cost from her end.

The main problem from your side that I see here, is that you published the article without even telling her in advance. (Which might be based on you seeing her so rarely.)

Had you asked in advance, and maybe told her that this is how things work at your home university, she would probably have given her consent. That way she might feel backstabbed.

So the immediate action for you should be an appology from your side, telling her, like you told us, that this is what you thought you were supposed to do. (But don't make it a pure explanation, but make it an honest appology, the phrase "I am sorry" should appear at least once.)

I never had a publication without my advisor during my PhD, and (since we did alphabetical order) he was first author of all the papers. But than again, I met him on a weekly basis, so he was far more involved. I assume that by now, things have gone wrong for too long to change without you havily interfering (by requesting more frequent meetings and more involvment from her side). However, if you want this, I would tell her in a seperate discussion.

Thus, from this short description, I see the main flaws in your relationship on her side, but the main need for a concrete appology on yours.


Reviewers Conflict of interest: failing manuscript to possibly keep dominance A biomedical research area is led worldwide by a certain research group in a particular famous university. They are very productive and advanced, with numerous postgraduate students worldwide, with whom they keep cooperating after their PhDs are finished. They also cooperate with other important universities that have entered their research area. They were basically the pioneers in their area, and put in the public domain some data that is a reference in the field.

Anyone submitting a paper in the same research area will:

Use their vast data set (public domain).
Have reviewers assigned that belong to, or have belonged to this group.

I accuse these reviewers of systematically rejecting the manuscripts they review, in order to:

Bulldoze other groups' advances in the field, thus keeping their dominance.
Get their own postgrads working on the ideas of the papers they are reviewing, where a strategy of taking too long to review (and reject) the papers fits well.

What can I do, in order to overcome this predicament?

Of course most of the magazines allow for the authors to list a set of people they would prefer not having as reviewers, but in this case this group contains many researchers, scattered around the world, and there seems to exist a great level of cooperative work and well established alliances.

The vast majority of scientists are ethical people. To claim that every single one in that group is unethical to the point that they gratuitously reject other people's papers does not comport with my view on my fellow scientists.

My approach to getting papers rejected is to make an honest assessment of why the paper was criticized, and then to set out to write better papers. Statistically, journals reject about 2/3 of all papers, so having a world view of "My paper was just not well enough written" is at least not incompatible with empirical evidence, and I find that a far easier perspective on life than to have to assume that all of my colleagues are unethical people.

All of this isn't to say that it never happens that someone behaves unethically -- it almost certainly does -- but that the assumption that everyone does is probably wrong and, moreover, that it's not productive to think that way because there is nothing you could do about your fate if that were so. A growth mindset in which you take setbacks as an opportunity to learn and do better -- regardless of the reasons for the setback -- is, in the long run, a more productive approach.


Whether to use the author name with numeric references when describing a particular study I am a little bit confused regarding the best way to attribute a research paper in my thesis.
Example:

" The work in [1] proposed a new method for ..."
" John et al.[1] proposed a new method for ..."

Also, when I have the following context:

" our method results outperforms the results in [1] ... "
" our method results outperforms the results provided by John et al.
[1]"

Sometimes, due to space limitation, I can not mention the names of the authors every time which pushes me to use the paper only (like examples 1 and 3). Also, I think it is unnecessary redundancy to mention the authors every time.

My question is, is that OK? should I mention the authors of the work every time?
Are examples 1 and 3 accepted or weak?

There may be slight differences between fields (I am in the chem-phys-mat. sci triangle), but the short answer is no, you do not need to explicitly name the authors.

Stylistically, the "the work in [1] proposed" sounds rather forced and exactly as long as "Smith et al.[1] proposed". Note I am not a native speaker, so I have no clue what I am talking about. On the other hand I would definitely would leave the name out if I am talking about the same work over and over. Also, if you structure your statements like "This problem has been approached using this [1] and this methods [2]", giving the name is actually more awkward than leaving out.

I think it also improves readability. Compare "our method outperforms the name-of-the-method method [1]" with your examples (name-of-the-method: you explicitly name what is the main difference). Assuming that the reader do not know the reference list by heart, this kind of reference is more explicit and more informative than the other two.


How to approach potential PhD advisors What is the correct way for a new PhD student to approach an interested faculty member to discuss becoming their student?

Is it better to come with a few thesis project ideas prepared to pitch? Or is it better to come in expecting to have the faculty member to pitch them to the student?

Typically, the student has a year or two after joining a group to formulate an actual research proposal - but at the beginning of the program, when approaching potential advisers, there is only limited time, and limited knowledge of the lab's current focus and planned future projects.

Of course, the answer depends very much on the actual faculty member in question. But in what ways does it depend? Are there any aspects to the decision that remain invariant?

I am in the physical sciences (biology) but to make the question useful to more users, perhaps it may be better if we could have answers covering the peculiarities and commonalities of this question for different fields.

(This is for Computer Science and Medical Informatics, I suspect that most STEM fields are similar.)

  Is it better to come with a few thesis project ideas prepared to pitch? Or is it better to come in expecting to have the faculty member to pitch them to the student?

In my experience, if a faculty member is looking for a PhD student, they already have one or more projects in mind.

I think one reason for this is funding, and what faculty need to do to get it: The process of coming up with a grant proposal, submitting it, and getting a response takes months, and some grants can only be applied for once a year. That means that when you, the student, are joining the lab, there already is funding for you from a grant, and some general research goals are outlined in the grant proposal that your research needs to fall within. Some grants are more general than others, and there are also "training grants" out there the goal of which is to train you in a field (almost no constraints on the research topic).

The other reason is that faculty also have research interests.

I seriously doubt that you will need to pitch an idea out of the blue. It's possible that the faculty member will give you a general idea of what the direction of the research will be, since it would be under the constraints of their own interests and under the constraints of whatever grant is funding you, and then you would need to propose something more specific within those constraints. It's also possible that they will have something much more specific in mind and it will just be a matter of saying whether you're willing to do that research.

  [A]t the beginning of the program, when approaching potential advisers, there is only limited time, and limited knowledge of the lab's current focus and planned future projects.

That's why you need to read up on the potential advisor's interests, look at their publications, look at the publications coming out of the lab, and figure out what the research focus and direction of the lab seems to be.


Is it possible to get a PhD position with only a Bachelor's degree? I have done a Bachelor's (4 years) and my GPA is quite low. But I have research experiences (more than 3 years) and few publications in some good journals. I want to do a Ph.D. in biology or a related field. Is it possible to get a position (e.g. in the USA or Europe) when research experience is the only strong point? Or should I go for a Master's first?

It's certainly possible -- in fact, in the USA it's more common to start a PhD directly after a Bachelor's than after a Master's. In Europe, having a Master's first is a more typical requirement, but I have known some people to start PhDs straight after their Bachelor's (in physics, in the UK). Having significant research experience and published papers will certainly help your application a lot.

Why not apply for PhD and Master's positions at the same time? That way, you may get accepted to a PhD, in which case great, if not then you will likely have the Master's to fall back on.


Bad experiences with the production of an accepted manuscript The long and erroneous publishing process after a recently accepted  (Open Access) paper has led me to ask this question. I'll explain its context briefly.
We submitted a journal paper (a LaTeX manuscript including supplemental material) which after, in my domain (Computer Science) somewhat reasonable, 7 to 8 months time got accepted subject to minor revision. The journal has a very good reputation, the reviewers unanimously liked the manuscript and gave very helpful and detailed feedback. I handed in the revision not quite a month later. About 4 months from then I got the final acceptance notification. Although I felt already that took quite long, what followed seems like an Odyssey to me: after more than two months I got the first online proof which had numerous (100s of) typos, type setting and conversion errors introduced, tables wrongly formatted, cross-references lost, etc. I had to invest considerable time to point out all the errors, and after several more weeks (about two months in the meanwhile) and two proof revisions, I'm still stuck with waiting for another iteration of the proof. The editorial office has politely and helpfully handled the corrections with the production team, however, my requests/concerns also got a bit lost in translation. Overall, we are about to reach 9 months after acceptance with minor corrections and, after a couple of emails with the editorial office, I have no idea how long it will still take to at least see something like an official online-first version, not talking of the journal issue the article will possibly be included.
I believe that journal's procedure seems inappropriate inasmuch as I opted for full Open Access according to the funding policies and my Uni accepted (by a default waiver for that publisher) to pay a decent amount of article processing charges (I believe from their library budget). This inappropriateness stems from the long production time and that the conversion of the LaTeX manuscript caused so many further issues and required several proof iterations. Maybe strange, but again, I would have expected a more accurate production process than for a non-OA publication. But OA might not play a role here.
Just for comparison: a year earlier, we had a non-OA article accepted with minor for another (even higher ranked) journal where it took them about six weeks from this acceptance to complete publication, no typos introduced, and those six weeks even included our time to submit the minor revisions.
That whole thing made me wonder what expectations one ought to have on the paid portion of work done in the production process, other than reviewing and editing which in the majority of cases is purely voluntary in my field? How could one improve this situation? E.g. would a notification of my Uni (maybe our library) be exaggerated, so they can consider blocking future APC waivers for that journal/publisher?
I believe my concerns go beyond this interesting question about long review processes.

It doesn't matter whether you paid an APC or whether the publisher is getting money from subscribers for seeing your article.
There are journals that have very significant production backlogs, so that accepted papers are not produced for months or even years.  A long production backlog is not really cause for serious complaint, though undoubtedly both you and the editors of the journal are not happy about it.  Note that frequently the only way to fix a production backlog is to stop accepting papers (or accept very few papers) for some period of time.  (In particular, back when people mostly read papers by going to their physical library, there was no reason for the production backlog to be any better than the publication backlog, and some publishers still think this way.)
However, the number of errors in the production process and the amount of time and number of iterations it has so far required to fix them is completely unheard of in my experience.  I have had some production issues twice in 20+ papers (both times with the same publisher but different journals), but they were nowhere near what you are describing.
At this point, you should let the editors know what has happened and ask them to complain strongly on your behalf.  (Of course, you should be nice and understanding about it, since it's not their fault in any way.  But they have leverage that you don't.)  They are on your side.  They can see you have been treated badly, and they know that incidents like this are very bad for their journal.  This should be a serious issue, to the extent that, if these kinds of production issues are a common occurrence, the editorial board might try to switch publishers (if they own the name of the journal) or resign.  (You don't know if your case is a one-off or common, so you can't very well ask them to do this, but they should want to know and should take this seriously.)
Finally, I think you are well within your rights to not submit to a journal run by this publisher until you have some indication they have improved their processes, and you should quietly let anyone who asks you for journal advice know about what you have gone through.  (If someone reads this question, figures out who you are, and e-mails you, you should let them know who this publisher is.)


Academic publishing: advanced questions about figure/table positioning I am writing a textbook and am in the process of making final adjustments, such as the positioning of figures and tables.
I know the basics: figures and tables need to be at the top or bottom of the page. However, I'm concerned about fine-tuning. I have three questions:

figures are always at the top, which makes sense because captions are below the figure and captions are very close to the text. However, does this mean that tables should be at the bottom? The captions are above the tables and if you put the tables at the bottom, the captions are closer to the text.

what is the best styling in the situation where you have two unrelated figures on the same page? From a contextual perspective, one should be at the top and the other at the bottom because they are unrelated. But from a caption perspective, they should both be on top, since the caption is closer to the text in this case.

what is the best styling when the page is divided by a new section and the figure belongs to the new section? From the contextual perspective, the figure should be at the bottom because it belongs to the bottom section. However, from the caption perspective, the figure should be at the top because the caption is closer to the text in this case.

Do you have any ideas for this situation?

The simple answer is that it doesn't really matter, as long as you're consistent about how you do it.
If you stick with the LaTeX defaults, the figure will always go to the top of each page, and that's a perfectly reasonable convention. If you shift to placing things "nearest", that's fine as well, but will take more care on your part, since it's easy to end up with unexpected shifts caused by distant upstream changes.


What are good tips/ways to improve my writing on chalkboards? Recently, I have started to regularly write on chalkboards. I have also found out that I am quite terrible at it, although my handwriting is quite good.

Any tips or strategies for a beginner are welcomed.

This is going to sound stupid, but I've seen it work. Try dividing the blackboard with vertical lines to create narrower "pages." This will make it easier to write in a straight line and will discourage you from writing too large. Of course, the "pages" need to be large enough that you don't write too small.


How to restore trust in a toxic lab environment? A friend of mine started working in a biology research lab where several research groups share space and lab equipment.

Recently the environment has become quite toxic as the people started to mistrust each other.

It started with people not talking to each other and instead preferring to email everyone about "How to use Equipment X". Then later "To the person who used Equipment Y before me, please ask your supervisors how to use it properly". Now everyone watches each other to guard the equipment. In spite of this chemicals and samples started to disappear from the stock and tools get contaminated over night.

As my friend is "the new guy" he is often the target of accusations.
His colleagues from his research group are trying to protect him but still something needs to be done.

Now what to do? How to get back the trust? Should the institute heads get involved?

Institute heads seems like overkill at this point.  How about the group leaders for starters?

Your friend might find it helpful to schedule his lab time when his groupmates will be present.


Is it a good strategy to reproduce figures from related articles in NSF proposal? I am starting a tenure-track position soon and writing a NSF CAREER proposal for the first time. I have no preliminary data on this topic; therefore I am using a number of figures from related papers to illustrate my idea.

Without preliminary results, is it a good strategy to use others' figures at this stage (this is a bit philosophical question, but I am little worried about the impression I make with the reviewers)?

I would strongly advise against doing this. Instead, create your own original work that illustrates the main points.

Sometimes I see figures reproduced from a journal article in a grant application. Usually, the figure doesn't work well in that setting. When the grant writer copies the image into the proposal, they typically shrink the image to save space, which makes the image hard to read and understand. Journal article figures are often very complex, making points that are not necessarily relevant to the proposal. It's usually best to create your own figure that says what YOU want to say - to make a point about the science you want to do. Also, I worry that reviewers may regard this as plagiarism.


How to evaluate a software implementation for master thesis I have developed a software to meet a specific requirement in a research field. There is only one such software developed so far, mine is second.

In the thesis, I explain the implementation of the software. However, I feel like I also need a "Results" chapter. Most of the master theseses I have gone through from various disciplines have such a chapter. Looks like it is a must.

My software generates tangible models, storing a specific information, to be manufactured with various methods, such as CNC or 3D printing.

Output of the software should be considered as results. However, I don't want to conduct a cheesy case study with a bunch of people and publish it as a scientific result. An extensive, thorough study is takes more than 6 months and neither I have that much time nor the the knowledge/experience to conduct such a case study.

For example a friend of my implemented a software for twitter clustering and analyzing. The results are quite straightforward with his software. Run the tool, get the results and interpret them. Done.

I am not sure how to evaluate the results. Models are manufactured successfully, whereas that does not look like a result to me.

How would you approach this question for a possible solution? What my alternatives can be?

The goal of your thesis was to create a tool that meets certain requirements. Consequently, your evaluation should show that your tool satisfies these requirements.

One way to organize your thesis is to have a section called "Requirements", where you walk through all requirements detailedly. For example, you could have following requirement with sub-requirements:

R1: Generate 3D cat models: the tool can generate 3D models from 2D cat images

R1.1: Brown cats: the model generation works for brown cats
R1.2: Black cats: the model generation works for black cats
R1.3: Checkered cats: the model generation works for checkered cats

Then you have another section called "Validation" where you walk through the requirements a second time, this time discussing for each requirement how you satisfied it.

R1: The cat model generation was implemented in the catgen component of the tool that uses the XYZ algorithm to build the cat models.

R1.1: for 4 sample cats, the tool was able to produce a model (see Fig. 1)
R1.2: for 5 sample cats, the tool was able to produce a model (see Fig. 2)
R1.3: for 3 sample cats, the tool was able to produce a model (see Fig. 3)


Can I copy my own work within the same class? I've seriously never encountered what I just have, nor have I had to ever ponder this before. I am taking an international business class where we have to write six papers and six journals. I am currently writing my third paper and am now stuck here. One of the criteria for the last paper I wrote was to explain the cultural components in international business. Further breaking down the components, I had to write about learning language in international business, so I did about three paragraphs on that. Now I am writing a completely new paper and one of the criteria is to do what I just said I did in the last one regarding language. I'm sitting here thinking: do I seriously repeat myself? Can I even? In this case, what exactly is expected of me when the same thing is being requested to be written essentially back-to-back?

I just want to make sure it is clarified, this is the same course. This is not about re-using content from one paper in one course and asking to use it in another.

There are two issues to consider, self-plagiarism and meeting the course requirements.

The existing answer deals effectively with the self-plagiarism issue. If you quote and attribute just as you would for something written by someone else, you are not plagiarizing.

Even so, your paper might get a poor grade for not meeting course requirements. It would be unusual to set two exercises such that quoting the first one is sufficient for the second. For example, you may be expected to go into more depth.

Consulting the professor is the best solution to that issue.


Data sets of academic conference budgets I am looking for data sets of academic conference budgets. I am mostly interested in the expenditure/revenue breakdown. Ideally, other information such as as number of attendees and location would be useful as well.

I am principally interested in the field of computer science (natural language processing and machine learning), and English-speaking venues.

Based on my experience as a conference organizer, there are only two sets of organizations likely to have this information:

Professional societies, such as IEEE and ACM, which require their sponsored conferences to make budget reports as a condition of sponsorship.
Funding agencies, such as the US National Science Foundation (NSF), which have explicit programs for sponsoring meetings, and which therefore require reporting on how those funds are expended.

No other organization is in a position to compel systematic reporting (not even universities, unless they are managing the conference accounts), and thus conference organizers will not in general report it anywhere else.

Neither funding agencies nor professional societies are likely to give this financial information out willingly, since it is financial---though you never know what you might get if you ask the right people nicely enough.  Government agencies like the NSF, however, have public reporting requirements and may be susceptible to data gathering via requests for records release, under FOIA in the US or its equivalents in certain other countries.


How should I fix the problem of two part surname taken as middle name by google scholar? I recently published my first paper in a conference proceedings (CogSci2020). Before submitting I was struggling how to give my name. My name is:

First: [Alireza]
Last: [Mahmoudi Kamelabad]

The two words for the last name are both my last name. First I was thinking to get rid of Mahmoudi and publish with Alireza Kamelabad since Kamelabad is pretty rare and except my uncle and a relative who publish there are no Kamelabads in the world. But I thought maybe it is better to give my full name. So I did and now that the paper is appeared in Google Scholar it considers Mahmoudi as a middle name and for citation makes it AM Kamelabad instead of A Mahmoudi Kamelabad.
I have set up my Google Scholar account and tried to fix my name by there but it does not happen. Also the citation that Google Scholar shows is wrong in general in terms of format.
My question is how can I fix that? Is there any way I could specify in google scholar that [Mahmoudi Kamleabad] is a chunk and not separable?
Thank you.

Google crawled your data from somewhere, I suspect that source gave Google the wrong data. E.g., perhaps a bibtex listing is wrong. So, to fix the problem, you could fix the source.
Taking Mahmoudi as the middle name in Alireza Mahmoudi Kamelabad is a standard reading. To avoid that reading, you could use Alireza Mahmoudi-Kamelabad in the future.


How should I approach the issue of students not writing their name and student number on an exam? I am a teaching assistant (TA) in a second-year undergraduate course and have just received the results of my students' multiple choice midterm exam, which were marked by an optical marking ("Scantron") machine. The students are required to print their name in pencil, and are also asked to fill in a clearly-marked set of bubbles with their student number so that the Scantron machine can create an overview printout with each individual student's mark for me (as well as statistics related to the test, i.e. class average, percentage of students who selected the correct answer, etc.). These forms are standardized across our university, and all of my students have used them before. There are 4 students who did not fill in their student numbers, even though they are explicitly directed to do so before the start of the exam.

We check photo ID at the door of the exam to ensure that students are on our class list, and the course instructor may still have the list of highlighted names of students that attended. This means that I very likely can identify which four students these no-name exams belong to. The bigger issue in my mind is that we require students to fill in their student number so the scanner will be able to identify them, but also as an extra measure to ensure that students are writing a test in their own name, and not impersonating another student. Even if I can go back and look at the students' individual bubble sheets, I still need them to understand the importance of filling in their testing sheet correctly. Other instructors or TA's are not necessarily so understanding.

How can I address this issue with these students? It feels very unfair to say, "Sorry, you didn't write your student number, so you get a zero," but I also need to ensure that we aren't allowing students to cheat because we are being lenient in verifying student identity. Is this something I should just say at the beginning of the next lecture, or do I need to approach these students individually and remind them of the requirement?

Y'all have never proctored or taken SATs?

Give only the answer sheets out first, and have students complete the important information before they even get the questions.

If you don't give the questions until students have filled out the relevant information on the answer sheet, they won't be able to ignore the answer sheets, in lieu of answering questions.

It may require a bit of a rethink as to the time available for the test (i.e. take five minutes away from testing and put it onto "administrivia"), but this might just be time well spent.

You could even incentivize students to arrive early to complete this task quickly by saying that the question packs will be given out as soon as all students have filled out their information; any student who shows up to class (up to five minutes) early will be given their answer sheet to fill out.  If all students have their answer sheets filled out by the time "##:##", the tests will be handed out then.  Anyone who shows up late will have to complete their information on the answer sheet at the front of the room before being given the questions.

Or, have part of the ID process be that students have to show you their IDs AND a completed information section on their answer sheet before they get the questions (or, maybe before they take their seats).

If it's an important step in the process, make sure it has a defined step in the process.

To forestall the comments I know are coming: Yeah, I know: Young adults should be able to follow directions.  OTOH, negative reinforcement doesn't have the learning results you think it does. Don't penalize students for a bad process.


what exactly does a research supervisor pay for PhD student funding? Why do supervisors normally tell potential PhD students that they don't have funding, hence they can't accept students? does that mean the stipend? I thought stipend is paid through the department?

could someone clarify for me.

Depending on your country, there may be different kinds of funding, including positions where you're an employee of the university/state/country. Such positions are usually owned by an individual professor. This is different from other funding sources that are not owned by individual professors, like stipends.

So, when you ask a professor if you can be her PhD student, without specifying a funding source, she may assume you're asking if she has a funded position readily available. In this situation, the answer is often no.

In addition, "no funding available" can also be a polite way of declining, if there are actually other reasons for saying no.


What are examples of appropriate journals to publish new mathematical conjectures? The paper I want to publish is just a conjecture.

There are several ways in which conjectures propagate, and each has its own method for publishing.

As future work/further direction on a set of theorems you proved. In this case, you submit the paper based on the set of theorems, and the conjecture is just a bonus. Your primary contribution is the original theorems.
As a reasonable technical lemma to use to prove a difficult theorem. One again, submit as you would a paper proving any other theorem. Your primary contributions is the interesting/non-obvious consequence.
As a consequence or expected result based on a novel model. In this case the empirical model is usualy motivated by some sort of science, attempt to publish in the relevant scientific or applied math journals. Your primary contribution is evidence in the reasonable model.
As a synthesis of connections between many different areas of math that your conjecture brings together. Publish this as a survey that unifies the areas of interest. Your primary contribution is the connections between fields.

If your paper does not have any results apart from the conjecture, then such are usually disseminated informally. Tell your friends, colleagues, publish a blog post, ask for a proof on MO. This is a great way to find someone to work with in helping you turn your conjecture into a theorem.


Professor wrote me a recommendation; I need another one with short notice but he hasn't replied About a month ago I asked a professor for a letter of recommendation with 2 weeks notice, he agreed and wrote it. I found out about another opportunity but the deadline is tomorrow; I sent him an email Tuesday night asking if he could write me a letter of recommendation again but he hasn't replied. Could he possibly not be willing to write me another recommendation?

He doesn't have office hours until tomorrow at 2:00 which seems really late to be bringing it up to him. But, I don't want to bother him by sending him another email in case he's ignoring my request on purpose.

Speaking as a professor who writes a few dozen letters of recommendation a month (it seems like that, anyways), I would suggest that he is not ignoring you; he might be behind on his e-mail or simply preoccupied with other matters.

I would recommend sending another polite follow-up e-mail, and barring that, drop by his office hours.

Usually, the first letter of recommendation is the most work. Sending a second one is a lot easier, as your professor should hopefully just be able to make a few minor alterations and send it off to this opportunity.


Applying for Masters when Family Member is Associated with Department I intend to apply for a masters program in the coming months. A parent is a professor in the same field at a nearby institution and is also an adjunct in the department I am applying to.

Do I have any ethical obligation to "disclose" (or, for that matter, to avoid) this fact in my application? If I do not address it, could it be seen as trying to hide a conflict of interest? If I do address it, will it be seen as inappropriate name-dropping? If I must mention it, what is the proper way to do this?

I have an uncommon last name which will probably be recognized, and some members of the faculty already know that I am the child of their colleague.

I think you should say nothing.  If your name is uncommon and your parent also teaches in the same department, it seems certain the admissions committee will twig to the connection.  If they do that on their own, human nature being what is, you'll probably inherit a slight glow.  But if you make any mention, I think that will sound like name-dropping.


Asking for recommendation letters for math PhD applications Fall 2018 application cycle has started and I have a couple of (hopefully not too specific) questions regarding recommendation letters. I am applying for a PhD position in pure mathematics in the USA, with lots of top schools included.

(1)  Does the status of the letter writer matter greatly to admission committees? For example, I have done research with a full professor, an assistant professor and a lecturer in my department. The latter two got their PhDs in 2011. If the three of them write me a letter, does that automatically put me at a disadvantage because two of them are not full professors or one of them is a lecturer? I have heard that, in principle, letters from people that are known in their field are looked upon more favorably by committees, particularly because they might be familiar with the letter-writer and can 'read between the lines' and get more information out of the letter.

(2) Should I bother asking for a letter from professors that only know me through classes? I have a potential fourth person in mind for a letter - he is a professor I took two classes with and did well in both. In my understanding, "so-and-so was a good student in my X and Y class" will probably impress no-one, even if it comes from an established professor. All programs require 3 recommendation letters, so would you think it is worth the effort to have an extra letter if it comes from such a professor?

Thanks in advance for any responses.

Many, if not most, successful PhD applicants in mathematics have no research experience, and even when an applicant does have "undergraduate research experience, " it's usually not worth much as an indication of talent. If the first three letters are from the same project, it's probably better to skip one of them and go with the course professor instead. Rank, or at least reputation, of the recommender does matter, but what's most important is what they have to say about you.


What is the preferable way to share data? Suppose there is data that you as an author of a journal article wants to share with the readership of the article (e.g. raw experimental data, code, gold standard / ground truth data).

What would be the best way to do this? Possibilities include:

Add a footnote that data is available upon request by e-mail.
Make the data available for download on an institutional webpage.
Make the data available for download on your personal webpage.
Make the data available through the article's publisher.
Something else...

The most common and sustainable thing to do is to deposit the data in a research data repository. Depending on which one you choose, the data will get a persistent identifier, e.g. a DOI, can be cited properly in publications, might be reused by other researchers, ...

You can find a list of available data repositories at re3data, the registry of research data repositories. The number of repositories is still growing. Even your institution/university might offer an institutional data repository.


How to deal with GPA-related questions in standardized job application forms, if you have no GPA for graduate studies I recently finished my PhD and am currently applying for several positions both within academia and in industry. Some companies I'm looking at have standardized job portal where you can leave your info and do a "general application" (e.g. IBM).

In the education section they ask for GPA for each entry, including PhD which appears to be a mandatory field. Here's the problem none of our grad courses are graded, you pass or fail. Thus no GPA. I tried to write N/A, but that wasn't accepted by the system.

Anyone with experience on how to deal with this situation?

As noted in the comments, the first thing to do is to contact the company HR department.

If you don't get a rapid response, however, then I would recommend filling in the form with as obvious a nonsense number as it will let you (e.g., -1, 9000), or if it won't let you do that, then fill in whatever it thinks is a perfect GPA (you passed all your classes, right?).  Then explain the form problem and your true situation in text.  The best place to do this is, in order of preference:

A free-text "Comments" or "Other Information" field on the application form, since that will typically be seen at the same time a person is seeing the GPA.
Your cover letter
Your resume

Note, however, that you are not very likely to get a positive response in any case from this type of completely generic application form, since it is likely getting filled to the brim with pseudo-spam from a vast number of recent graduates worldwide.  HR departments often put such a "catch-all" form out in order to satisfy formal requirements, rather than because they expect to actually do much hiring in this manner.


How to manage lot of random yet potential ideas for research and startup? I am a graduate student and planning to pursue a PhD. For one year, in search for a research idea, I have been reading random research articles and papers in many dimensions of Computer Science.

Suddenly, I have been blasting my advisor with various ideas. The ideas as per my advisor are possibly a new paradigm but do have great potential. Also, he says the complete idea may or may not be doable by a single PhD student. I also see those ideas converting into good startup ideas as well. (I was an entrepreneur before pursuing research in search of some challenging work).Most of the ideas are not very much related to each other but still concentrated to my specific field of study (Computer Vision).

I am concerned that pondering of so many ideas may prolong my research without results. My questions are:

How can I manage so many wavy ideas in a streamlined way ?
How feasible is it to focus the research so that the outcome may be a startup (since making it commercially viable would require some amount of research in other areas of Computer Science such as Data Mining, Large Scale Search etc. ) ?

For your first question, here is the workflow I follow:

Write them down (as @JeffE mentioned)
Organize them in order of viability/ease
Take the most viable idea and do a (very) quick prototype
If prototype is successful, develop it. If not, iterate.

From the prototype you probably have a better idea of how much work it would take to fully develop the research idea. If it seems like you won't be able to handle it in the amount of time you have, or if the outcome is not worth the effort, I usually archive that idea for later. For a  prototype I usually try to do the bare minimum to produce the simplest result possible. A common trap is to start from the complex before you've mastered the simple.

The second question depends a lot on your personality, so don't take the following advice much too serious. Personally, I have a very hard time focusing on two things at the same time. What I would do is focus on my PhD. You'll surely get many more ideas as your work progresses. For every problem you solve, you'll generate 10 new ones. Be sure to write things down so that you don't forget them later on.

This is a very personal question and you have to see what works for you.


IRB-questionable research from places that does not require IRB process: How publishable/contributing? Some entities, when carrying out research, do not strictly require Institutional review board (IRB) approval (or may be doing the whole thing in a place where IRB does not exist).
If we believe that a piece of contribution has ethical concerns that may fail an IRB inspection but see no IRB requirements on both where they are from (where they work) and where they are going to (where they publish),

Is it OK

to endorse this work?
to use this work in another research (without ethical concerns)?
to use this work in another research that requires IRB approval?

What should we do?

It is (or should be) a principle that any research involving human (and some animal) subjects should be subject to prior independent ethics review, such as is done by IRB structures. If you are reviewing for a reputable journal, I would expect (or at least hope) that the journal has such a requirement on anything they would consider publishing.
Whether they have such a requirement or not, you would be wise to note the lack of a statement of ethical review in anything that you examine. Let the editor know that there is a missing, ethically required, piece.
If you seem sure that no review was ever done, rather than just a missing statement, then you would probably also be advised not to review the paper further. Ethical constraints on such research isn't something that can be patched up after the fact. People have died. People have died horrible deaths after long illnesses. Doing such research without independent prior review is not ok.
Note, of course, that there are some kinds of research that don't require IRB approval. But it is usually an ethical board that makes that determination. See this for example.


Explaining inconsistencies in literature in thesis and/or supporting information of journal article I've found a model which explains my results excellently. However, the actual equation and parameters of the model have been interpreted and treated differently by different authors, sometimes leading to vague and/or inconsistent interpretations and parameters resulting from a fit of the model to the data.

Additionally, the original article which derived the equation did not capture a scaling with the equation that was obviously there experimentally. This scaling is very important for the interpretation of my results.

Unfortunately, these inconsistencies haven't been pointed out by any authors, and I am probably the only person who has studied this model well enough to have realized them.

My thesis and a journal article I am preparing hinge on correcting these inconsistencies, but doing so may create some controversy with the reviewers of the article and will definitely take up a good 20 pages of my thesis  and maybe more in the SI of the article.

Any advice for how to deal with this in a thesis and article-efficient way would be highly appreciated.

With regard to your thesis, you should be as explicit and verbose as possible. It's your thesis, and you will likely never have another chance to explain this issue as clearly as you will now. Avoid being accusatory, but show all the various interpretations of the model in the literature that are relevant and explain your insights thoroughly. Use as many pages as you need, it's not like they charge by the page :)

For the journal article, I would describe as clearly as possible your interpretation of the model and the application to your data, beginning with the best reference available, and adding or clarifying only what is necessary for the results you are describing in the article. There is no need to explore all of the other interpretations. If a reviewer raises concerns, deal with it through the editorial reply process. You could send a concerned reviewer a draft of that section of your thesis, if necessary.

FWIW, I was in a similar position and followed this plan, and I did not get pushback from journal reviewers on this point.


Is it OK to do a grad school interview if I was already accepted informally by another program? I recently got accepted to my first choice graduate program, but then my second choice school emailed asking for an interview.

I feel like since I applied, I should at least do the interview, but I am worried that my first choice school will find out and revoke my acceptance. (it was an informal, unofficial acceptance directly from my faculty advisor)

Am I just being crazy? Do professors from different schools talk about their PhD applicants? Should I still do the interview?

I would advise that, until you have a formal, firm offer letter, you keep following the steps of the rest of applications you submitted. Even after making you an admission offer, you will have some time to consider any other option and decide (many people get accepted in multiple programs and it is fully alright and understood). Now, once you accept an offer (not only receive it), it is very recommended that you contact the other programs that have made you an offer, and tell them that you will not be attending there because you already accepted an offer somewhere else. They will all understand, of course. But, most important, if you tell them as soon as you have decided, then they will have some time to make an offer to another candidate.


How to reconnect a relationship with a professor Today

I'm currently in my final MSc year, and I have finished working for my thesis. I am under supervision of professor X, which I find myself at ease and actually enjoy what I do. My field is Chemical Engineering.

Background

Before starting my thesis, during the "thesis choice" period, I was contacted by professor Y, which I was in very good relations (we did some external projects before the thesis, with good results). One of the major aspects of working with Y was the possibility to go abroad, as he sent out his students quite often for thesis work. The drawback was the lack of direct supervision. Professor X on the other hand contacted me, but he was not in favour of the abroad experience, since he only works as a direct supervisor with thesis students.

Issue (first mistake)

I had two initial proposals from both professors. At first Y's proposal was way more interesting than X. I got a week to confirm Y, but after the third day, Y's initial proposal was changed (in a uninteresting project).

I thus contacted X, and after a week arranged for a thesis meeting. X's offer was also changed, but now very being intriguing, and Y remaining proposals were not as interesting as X. I said yes to prof. X and went personally to Y's office to tell my decision.

When I entered Y's office (without notice, as MSc students - per Y rule - are free to pass by his office freely), he welcomed me with a project that "was sure I would love", and there were also external profs and industry reps (for which I had not been notified) and quickly explained to me the thesis, all taking like I was in from the start. This "meeting" with me was not programmed, as I expected only Y being in his office.

Right after this meeting I made a big mistake. From all that was said in the meeting, and the confusion that was created, I said (verbally) yes to Y.

Issue's Aftermath (second mistake)

I continued working with X, and received NO news or advices or any message from Y. My suspect is that Y's project came to nothing, but seeing that no messages came from Y, I made the second mistake as I continued working with X not alerting Y. I know that a single e-mail could have resolved the issue, but since that period was also characterized by a grave family issue, that e-mail was never sent.

Question

As the months passed and considering my today situation, and (fortunately) all the personal issues have subsided, what could be the best course of action of regaining contact with Y? After all, he did nothing wrong to me and I know I made some terrible mistakes, I want to apologize such to not truncate our 4 year relationship.

I think you have gotten yourself into a pretty deep mess if it is really as bad as you suggest and not just a sense you have of the situation. But, the only way to proceed is to go visit the professor in person and steel yourself for whatever occurs. I'd make an appointment first, to give the other person a chance to think about their own response.

You may well owe an apology, so prepare to give it. But, as long as the prof isn't a monster, it may well turn out better than you fear. But it may also take a while to completely dispel any bad feelings if they exist so a single meeting may not turn things around like flipping a switch. But a face to face meeting will give both of you a sense whether a continued professional relationship is possible and desirable.

It may be the professor was disappointed when you left, but also possible that he/she is so busy generally that it didn't register too much.

The past is what it is and can't be changed. The future is up you you. But expect that the transition may be uncomfortable.


Is it appropriate to ask a prospective PhD advisor whether working for them would be good for my career? Summary Between my Ph.D. offers, I narrowed down my choices to two. Right now, my decision is mostly dependent on a few factors I didn't discuss with either advisor. I want to ask about these issues directly, but am worried about alienating either or both advisors.

My two options

Option 1:

Advisor is a veteran of the field and some of his recent graduates have landed excellent postdoc positions
Institute is well-established in the field and widely recognized as one of the bests in the world

Option 2:

Advisor is much younger, though so far very successful. His first advisees will graduate this year (so can't yet gauge their success).
Institute is very young and its PhD program has had too few alumni so far to give a good image of how successful they are in landing jobs in academia. That being said, institute X has been able to attract excellent faculties and postdocs from top universities (top 10 of the world) and some of their more experienced faculties left tenured positions at those top universities to join X. They also invite world-class faculties and postdocs from the best institutions from all around the world for their weekly colloquium. They're not still as successful in attracting PhD applicants though (perhaps because, as I saw during their interview event, those other offerees that also hold offers from more prestigious universities have the same concern as I do).
Good program structure and flexibility
Good resources and opportunities
Tempting financial offer.

My concern: I like option 2, but I want a job in academia. If I choose option 2, the name of the institute I'll have done my PhD at may not carry enough weight to help me get into excellent postdoc positions and eventually land a tenure-track job in a decent university.

Question: Is it inappropriate to share this concern very frankly with the advisor at institute 2 (who himself has graduated from an incredibly prestigious university)? Could asking that question upset the advisor and negatively influence my chances for later becoming a postdoc in their group? I was thinking of describing the situation as I described above (with a little more details) and ask for Prof. Q's opinion fully honestly. If that's inappropriate, is there a more appropriate way of doing that?

Could asking that question upset the advisor...

You have a legitimate concern. If advisor 2 is angry that you brought up a legitimate, important concern, you're probably better off working with advisor 1.

  ...and negatively influence my chances for later becoming a postdoc in their group?

It is far too early to start worrying about specific post-doc options.


Faculty job in France VS US In September I got a (permanent) junior faculty position in France. The academic year is about to finish and I am taking stock of the year to see if that is really the right place for me to be. Before moving onto this position, I was doing a postdoc in the US and confess that I accepted this position in France mostly because was permanent. Now, if I look back over the year, the main thing I did not enjoy was the teaching load I was given, it was absolutely unsuitable for someone that is starting as a junior professor, but this is the way it is in France and it is not going to get any better. So I was thinking whether I should try to look for other opportunities back in the US and wondered perhaps someone with a wider view could provide me with some tips on that.

I lived through this same situation myself: I had only really known the US system when I accepted a MCF position in France, and was pretty overwhelmed during my first years. For example, my first year I had to prepare several cours magistraux, and I didn't know enough to refuse. At one point I explored returning to the US, in fact for two years I moved back to Boston, but in the end I found a better return on investment making the French system work for me.

Here are some take-aways.

If you are ambitious and your research record is good then you should very seriously consider applying for a position as research scientist at a national institute: CNRS, INRA, Inria, Inserm provide working conditions superior to the best research universities. You can still teach undergraduates if you want to. In my case I went MCF to DR, but MCF to CR is more typical.
Faculty in the US have a lot of administrative responsibilities and committee work that aren't counted towards their teaching load. In most French schools you will get a décharge from your service for this work and you can negotiate that. In the end of my time as an MCF some 40% of my service de 192 was counted this way.
Taking on Masters students early is important for getting ahead, and while the hours counted towards your service don't completely represent the work that is involved, they can be far more rewarding. Especially if you have ambitions.
As a tenured French civil servant you are free from the precariousness that junior faculty face in the US.
In France, advancement is almost entirely based on research output; taking on administrative responsibilities is a necessary evil but will not in itself get you promoted. Don't get suckered into responsibilities early; do enough to show you are a team player but try to save your non-teaching time for research projects.
The US research system is very individualistic, in my experience junior and senior faculty are pretty much expected to go it alone, and hire students to work with. The French system is very team oriented and perhaps half of a team's members will be permanent faculty or staff. Find a good team.


How to politely respond to a PhD offer follow-up email from potential supervisor? I received an official PhD offer from University A on Jan 30 (15 days ago).

In an interview with the faculty from University A, they asked me where A stands among my applications. I honestly replied that A was among the top 3 universities and said that I need to hear from the other two schools before making any decision. I also expressed that it would be hard for me to make the decision before hearing from the other two schools from my top 3 shortlist. The offer from A arrived soon after the interview (obviously).

Today a professor from University A sent me a very short email asking if I had questions or I was close to making decisions.

Is he implying that I should hurry up?

I have not sent them any email since the offer as I had nothing to update. The offer follows the rule of April 15, but the school would offer me a small amount of fellowship (which I don't care) if I accept before late February. The other two schools just interviewed me several days ago and I would expect to hear from them soon.

How should I politely respond?

Thanks!

I don't think the professor is necessarily implying that you should hurry up, they are simply putting pressure on you and hoping that you accept their offer, keeping open a channel for communication if you have questions (like a salesperson asking if you need any help as you are browsing a store), and trying to politely test whether you may have accepted another offer.

If you choose to go elsewhere, they likely want to know as soon as possible so they can extend an offer to another candidate.

I would say it is sufficient to respond with a brief, polite note that you decided before applying to wait for all offers before making a decision, and that you promise to inform them immediately once you have made a decision.

  Dr. Professor,

  I appreciate the email, I will certainly ask you if any questions come up. My plan when applying was to wait until I hear back from all institutions I interviewed at before making a decision.

  I will inform Impatient University immediately once I have made a decision, either way.

  Best,

  Prospective Student

Your responsibility is to inform them as quickly as is reasonable once you have made a decision, but you shouldn't be pressured to respond more quickly than you are ready.

You mention "the school would offer me a small amount of fellowship (which I don't care) if I accept before late February" - this is certainly against the spirit of the April 15 Resolution, though I don't know enough about the specifics of the agreement to definitively say it's disallowed. The whole point of the resolution is to not make financial offers of any sort contingent on making a hasty decision, to keep a level playing field across institutions and in the best interest of the students. That said, I wouldn't suggest bringing this up at all or making an issue of it, unless it makes you uncomfortable in which case you could certainly consider it in your decision-making process.


Is it considered plagiarism when you modify your professor's proof when solving a problem in a homework assignment? I have a homework wherein a problem is eerily similar to a theorem we have proven and discussed before in class. Since we have a policy that the only concepts and theorems that we can apply to our homeworks and quizzes are those discussed in class, I figured that if I slightly modify a set defined in the proof of a previously discussed theorem, I would be able to prove my homework (I managed to prove it following the proof of the previous theorem).
Can I do this? Is this considered plagiarism?

No, this bears no resemblance whatsoever to the concept of plagiarism. The goal of homework is to get you to review what you learned in class and demonstrate that you can apply it. That is exactly what you are doing.
Moreover, the purists who will wag their fingers at you and tell you to “cite” the earlier proof are part of why we have a generation of students who have no common sense understanding of what plagiarism is or what it means to plagiarize, and instead view the avoidance of plagiarism in terms of adherence to some mechanical set of algorithmic rules whose meaning they don’t understand (and I mean no offense to you personally, it isn’t your fault that you are being led astray in such a way by well-meaning but misguided — in my opinion — educators). The professor knows what they did in class, and know that you know it. There is no need to cite anything, just write a correct proof of the result you were asked to prove. If you want to mention that the proof is a variation of something that was done in class, that may be a nice way of showing a good level of understanding of the material, but it’s not required as some kind of plagiarism-avoidance algorithm.


Is it inappropriate to decline presenting paper on behalf of someone else (outside my expertise)? I have been requested to present a complex paper outside of my own expertise at an upcoming conference. I have rejected this invitation on two occasions stating reasons such as:

Not my expertise
My first Conference
I'm not an author on the paper
I don't understand the paper
and so on...

Apparently people present other people papers in Computer Science all of the time at conferences, but surely these people are knowledgable on this subject? Would it be inappropriate for someone to present a paper, for the reasons listed above? I'm not feeling like a team player right now.

First of all, I think that in your particular case, it was a right course of action to reject the "invitation".

To answer the general question

  Would it be inappropriate for someone to present a paper, for the reasons listed above?

let's look at the single reasons one by one:

  Not my expertise

A somewhat valid point. You probably shouldn't be talking about something way outside of your area of expertise. However, if the topic is at least marginally connected to yours, it could also be argued that you should not enclose yourself in your personal bubble, but try to get somewhat acquainted with as many other topics as possible. In general, despite researching specific questions, an educated person should have some wide knowledge, and maybe knowing about such another topic even provides you with opportunities for expanding your own research into unforeseen directions.

  My first Conference

This. In my opinion, this is the strongest point in this list. You don't have any conference experience yet, not only giving talks, but also listening to how conference talks work at all. As so often, it is advisable to start out somewhat simple, and presenting a paper you are not fully knowledgeable about yourself is probably not a good way.

  I'm not an author on the paper

That is not a valid reason. As you said, people present on behalf of others all the time, and there are various reasons why the actual authors might not make it to a conference personally1.

  I don't understand the paper

Acutely, that is a severe issue, though it could be said (also referring to the first point) that in that case, you just need to spend some more time trying to figure it out (and having the original authors help you understand it!). So, it is a somewhat valid reason, but given a little more time, it is an issue that can be mitigated.

A word on your statement

  surely these people are knowledgable on this subject?

No. Sometimes, not at all, which is unfortunate, as like that, the Q&A session degrades into nothing but: "Next question, please." - "... ?" - "Sorry, I didn't write the paper." However, if the presenter is at least partially knowledgeable, in a way that they prepared the presentation well (together with the original authors!), it is fully acceptable if the presenter cannot provide an answer for every very specific question, as long as they can sufficiently describe the gist of the research.

1: Scheduling conflicts, visa issues, illness, or restrictive travel funds come to mind.


Should I provide my transcripts for all years or only the last year? I am applying for a a PhD in the UK, and they ask for my bachelor transcript. Should I only include the third year transcripts or full three years ? Since I am translating it from another language it is better for me to only include the last year

This may vary by university, but a transcript is a full academic record of your time at an institution. As such, they will expect information on every course that you took, all three years. A partial transcript is obviously acceptable for degrees which have not yet been completed, but omitting completed courses may look like you have something to hide.

There will likely be a firm requirement to provide a full original transcript, and if not in English, an authorised translation, before your place is confirmed, regardless of whether a partial transcript is acceptable for an offer to be given.


What is the benefit of submitting to a special conference session instead of the regular track? Assuming that I want to submit a paper related to the topic X to conference Y in CS, and there is a special session in that conference which covers the topic X; in that case, is the best choice to submit the paper to the special session?

Well, as far as I know, the special sessions have a small pool of submitted papers around similar themes, from which they need 5-6 papers to accept. So I was wondering if I would lower down my chances by submitting to a SS as the pool becomes more competitive for me?

It depends on the conference. Sometimes, "Special Sessions" are organized by an individual to "fill the program" and the organizer will try to find people willing to submit to this session. In those cases, you might even be asked to submit your work for the session and review might not be overly tough.

In other cases, it might happen that the special session is overcrowded - in such cases you might have a hard time.

Nonetheless, a good paper chair will move your paper to the session which is most appropriate - so it might happen that you submit to the special session and end up in a common track, or vice versa.

One good thing about special sessions is, that they draw the audience interested in the field, and they are a good opportunity for networking and exchanging ideas. Therefore, I would recommend selecting the special session.


Is source code provided in the appendix of a thesis copyrighted? [US] I'm contemplating including source code in the appendix of my thesis. Although, I will not be strictly required to, I think this would be something that my committee would like to see.

Will I run into any copyright issue for this? Will the university own the rights to the code if I include it? The project was not funded so the university didn't pay me to write the code and no one else has contributed to it or even seen it.

Also, if the university is to own the right to my code, another concern of mine would be that I have used various open-source libraries and I would worry about running into license issues for using those as well.

In general, US law says that you are the one who owns the copyright to your work, and you own that copyright automatically from the moment you set your work down in tangible form. US law has a concept of "work for hire," but traditionally work done in academia is not considered work for hire. More about that here: Copyright for lectures, slides and textbook: university or professor? So you own the copyright, not the school.

It actually doesn't even matter if the school has some policy on this matter, because the law says that work for hire is determined based on certain legal criteria, not based on the employer's policy. Even if you signed a piece of paper saying it was a work for hire, that wouldn't necessarily make it a work for hire unless it met the relevant legal tests.

Brian Borchers asks in a comment:

  What is your institution's policy on the ownership of copyright of the thesis? Are you allowed to keep the copyright or must you transfer copyright to the university?

He has also pointed out in a comment that there are some schools, such as MIT, that claim in their policies that they are entitled to claim the copyright on a thesis. For the reasons described above, I suspect that this is not actually something they can legally do, but in any case it has no effect on the answer to your question.

  Also, if the university is to own the right to my code, another concern of mine would be that I have used various open-source libraries and I would worry about running into license issues for using those as well.

This is a non-issue. If those libraries are under the GPL (or some other "viral" license), what would violate those licenses would be if you linked them to your code and then redistributed the binary, and your code was not under GPL. That's because linking your code to the libraries creates what's known in copyright law as a "derivative work." This has nothing to do with printing out your code and putting it in your thesis. The thesis is a derivative work of your code, but the thesis is not a derivative work of the libraries, because the libraries aren't in it.


My advisor said that I should be more modest, and we should meet more often. Should I tell him about my impostor syndrome? If yes, mail or personal? I am a PhD student in Europe, currently in my second year, and I have some attitude problems concerning my work.  I really want to work on my problem, that's fine, but what bothers me is the following. I struggle with "impostor syndrome", so I always think that I know nothing. This leads me to the thought that it's not worth meeting with my advisor, because I am afraid of saying stupid things (which happens!), asking stupid questions (which has led, after all, to the solution of many important problems!), not knowing things which I should know (but if I don't ask, it will be even harder for me to learn these things), and am just afraid of wasting my advisor's time.

You see that I know that I know that my thoughts are completely irrational, but they just won't go out of my head.

Now my advisor (currently abroad for several weeks) sent me an e-mail that he thinks that I should be more modest and that we should meet more often. While I agree with the fact that we should meet more often, I disagree with the statement that I should be more modest. Not being modest means for me (in this context) thinking that I don't need my advisor because I can do everything on my own (correct me if I misunderstand his statement). But the opposite is the case.

Should I tell my advisor about my thoughts about not being good enough, as described above? If yes, should I respond to him via e-mail (note that he's abroad for some time), or should I prefer to talk to him in person about these issues?

My advisor sent me an e-mail that he thinks that I should be more modest and that we should meet more often.

Your prompt answer:

  Sounds good!

Nothing is gained by getting defensive.

(Do you know what meeting rhythm your advisor has in mind?  What often works well is a standing, weekly meeting.  If you have no progress to report, that's okay -- it can be helpful to establish a habit of meeting regularly, rain or shine.)