Can I perform and publish studies on patented chemical compounds? If a set of chemical compounds is patented by somebody else, am I allowed to perform studies (e.g. Pharmacophore, structure-activity relationship or QSAR analysis) on these patented compounds and publish the studies ? Provided that I'll cite the patent (as citing articles) but without having any type of permission.

Thanks

Patent law varies around the world, but in general doesn't prohibit study and discussion. Lots of things that are covered by patent are regularly discussed in popular and scientific literature. You don't need Apple's permission to analyze an iPhone, for example.

One of the reasons behind patent law, in fact is to make the essence of the thing known to the world. The patent application has to reveal everything essential on which the patent claim lies.

Patent is intended to prohibit you from reproducing the thing for most purposes, but you aren't doing that.


How to best present a PhD application when moving from professional work without a masters or honours degree? I have been invited by a potential supervisor to apply for a PhD scholarship based on some research I have done in a professional role. I have a history of presenting this kind of work at mixed academic/professional conferences in the past, and have written some of my research up for professional associations and as whitepapers.

In my opinion, the work that I have done may well revolutionise my particular field and there is a lot of interesting applications I have been able to articulate, but I feel having it as part of a doctoral thesis will help push these ideas into the mainstream.

However, I am concerned, as when I did my Bachelors degree I kind of messed around for my first few years and haven't got a strong background in actual academia. While I did clean up my act and finished with a high enough average grade to continue onto an honours year, I chose to work instead.

The application says:

  Minimum admission requirements to the PhD program at [University name redacted]: a relevant Bachelors degree with at least upper second-class honours, or a Masters degree with a significant research component, or equivalent.

Given my ordinary academic history, how can I best demonstrate my ability to perform research and give the best chance to be successful?

Your next step is quite clear. Discuss this with your potential supervisor. That person will be aware of university policies and practices, and could perhaps set up another meeting with the relevant staff.

Be proactive.


Find out author’s name in foreign writing system (Chinese, etc.) I have some literature written by Chinese authors who I would like to attribute in my bibliography with their names in Chinese characters (汉字). The problem is that, as the literature itself is not in Chinese, their names appear only in their romanized form (Pīnyīn or Wade–Giles).

What resources can I use to find out the correct characters for their names, e. g. library catalogues with both forms given, author lists, etc.?

I am not only looking for Chinese names but Japanese ones as well.

UPDATE:

Examples include:

Pao, Erh-li / Ying Cheng (1982): Wörterbuch der chinesischen Redensarten. Chinesisch–deutsch; Tetragramme des modernen Chinesisch [= 漢語成語]. Berlin, New York: de Gruyter.
Huang, Yankai (1964): A dictionary of Chinese idiomatic phrases. Hong Kong: Eton Press.
Hisa, Michitaro (1896): Some Japanized Chinese Proverbs. In: The Journal of American Folklore 9, 33, pp. 132–138.

I don't know much about other languages. I'll answer the question in Chinese case since I am a native Chinese speaker.

The literature you have is not in Chinese. The best way is to contact the authors. They will give you the correct answer.

As far as I know, there is no such reliable resources at the moment. There is no unique and consistent way of translation between English name and Chinese name. As you already know, Pīnyīn and  Wade–Giles are two of them. I don't think there is one-to-one correspondence relation. There are other issues, such as traditional Chinese character and simplified character. You won't know the correct answer unless the author tells you.

If you have no way to contact them, try their collegues or others who might know. Don't use the Chniese name unless you are sure. Use whatever the name appears in the literature if you are not sure.


PhD interview: Why in particular us? I have applied to a very well-known institution for PhD in Europe. They evaluate students first and then match them with advisors, so this is not a position with a specific supervisor; an admission committee will decide, not a single supervisor.
I am thinking about an interview that one will have with them. This university has almost the best group in my field and is extremely famous for it. It’s obvious that many students, who are interested in this field, want to study there. I was thinking about the following question in their interview, and how I should answer?
“Why did you decide to apply to this institution/Why in particular this university?”
I am having a hard time in preparing an honest while strong answer to this question. The problem is that, as I said, it’s obvious they’re good and I think they aren’t interested in hearing this from an applicant. At the same time, that’s basically my reason for applying there: since there are great professors there, very talented students, etc. On the other hand, their research is very specific and I believe they do not expect from a candidate to show off with “knowing” their research in “detail”. I know what they are doing, I believe it is important and valuable, and it matches with my interest as my background shows. However, I cannot prove to them by examples or other ways I know in details what they are doing since that’s not right. My question is this:
What is your suggestion to me? Should I start reading their research in detail to be able to make specific examples to support my reasons for applying to their group? I am a bit puzzle about this.
Please if you think more information is needed leave a comment before writing an answer. Thanks a lot!

Don't overthink this. Tell the truth! "Your group is the best!" (... and I want to be with the best)...
Yes, if you can make some incidental remarks about how/why you know that their group is "the best"... and in what field, precisely... that would be good. Not just "gee whiz! Gosh!", but something a bit substantive.
I'd think departments/groups would want to hear from prospects that those prospects appreciate the expertise of the group/department/whatever. Otherwise it's really silly cold-calling. (When I (in the U.S., in math) get cold-call emails from people who're manifestly using a uniform template about "Dear Sir, I've studied and admire your research", with no details pertaining to me (either in the form-of-address or anything else) it's easy to hit "delete".


What are acceptable criteria to select publications for a (systematic) review? I'm in the very beginning of my scientific career, so I don't yet know the standards for (systematic) reviews very well. I feel I don't have so much experience that I could publish my own research in good journals (I have now just two conference papers), so I'm considering to pay close attention for 6-12 months in other peoples' works.

I have a clear research question, but given the massive amount of related papers it's difficult to choose which ones to pick. Of course, I will select papers related to my research question as the first criteria. However, could I narrow the range of included papers more by

publication date (e.g. only take papers published during the past five years),
impact factor or citation count,
type of publication (conference, journal),
sample size (e.g. number of subjects)?

Or, if not these, what criteria are commonly used? I guess the answer is different for reviews and systematic reviews, so please cover both if possible. thank you!

EDIT: I'm considering this so that it would be possible to try publish my results.

I do not find any of these points very relevant. The publication date couldbe useful if your topic is such that older references are indeeed obsolete.

To write a review you want to collect papers that describe your topic as well as possible. A review is usually a good point for others to see the depth and breadth of a subject so being complete is usually a sign of quality.

Given that you have a topic, you need to consider how you should organize your information. Is there any new that can come out of the way you organize your review? A review is not just a collection of older results, you need to provide a synthesis. Often the outcome is to made limitations in older work visible or to identify gaps in knowledge or point at directions for new development. Depending on what the purpose will be you may end up chosing papers differently. However, often you do not know the structure until you have read enough and come to realize how the knowledge in th earea is distributed.

So for me there is no real difference between review and systematic review. A review is simply a way to orgnaize and sort older information in a new way so that new patterns emerge and hint at directions for further research or other forms of new ideas.


How To Cope With The Stigma of Quitting a Second PhD for a Third one? As per the title, I quit my second Ph.D. after 10 months, having quit my first after one year.

My first supervisor was narcissistic and a sociopath. (Nonetheless, I received prizes for my research.) After one year I left.

I took a lab position, in an isolated country, whilst seeking a second PhD program. The lab took advantage of my situation (low salary, humiliation, harsh work conditions). After 5 months, I was about to commit suicide, until I started a second Ph.D. I thought this was the salvation.

I didn't know my second supervisor. They seemed nice. Ultimately, I took the position out of desperation. However, after several months, I found myself stuck with a supervisor who was always jealous, in a constant fighting mode, moody, angry like infant. The final straw came when I was nominated for an prestigious award, which I was to collect at a conference, which waived the usual conference fee: My supervisor refused to support my travel, even though it was only around 500 Euro. They weren't constructive at all. Perhaps more importantly, the lack of dataset from our collaborators, sketchy understanding about my research which leads to lack of feedback,  this was a wrong match in all levels.

I've found another lab in a different country. They are interested in my work and I've joined their
group.

My question: I feel so much stigma about the situation and I feel sometimes insecure about what happened. In my current position, they know my situation, but they did not know all the story.

Now, I have to move by the end of the month. But, I am torn. I feel a failure because this situation doesn't sound good. Even though I asked many wise people and having a discussion for hours to split the emotion and facts about my situation that my decision to leave is right, I am stuck somehow emotionally about all experience, I saw a psychoanalyst, but not so much helpful, how can I get out of this stigma, I am afraid this would jeopardize my academic career? How I can remove this past?

First things first, if you have suicidal thought, then you need help. The fact that you tried one psychoanalyst, and that did not work for you, does not mean that the entire mental healthcare system is useless for you. Finding a therapist and a therapy that works for you can be long process of trial and error. Don't give up.

As to your question: You can't remove the past, all you can do is focus on making a better future.

If you want to reflect on your past experience to try to learn from it: I notice that you externalize the blame a lot. In the way you present your story there are three person: you are a top-student who wins prices, while the two others (the advisors) are narcissistic sociopaths or jealous and childish. That is probably not the whole story, and sticking to it will probably prevent you from learning from your experiences. However, now may not be the right time to process this. The only advise I can give you is: find a therapist that works for you and discuss this with her or him.

If you worry about how to present your story to others, then it is this black and white presentation that raises lots of red flags with me, not the fact that this is your third attempt.


Sending mail to the Professor for PhD, after seeing his tweet A professor tweeted that he has a PhD position in his lab. I am trying to write a mail regarding that. How should I express that where did I find the advertisement?

Is it right to start mail like this:

Dear Prof. ZZZ,

I am writing to apply for the PhD position which was posted on your twitter.

Or should I write something else?

That is perfectly fine.  The professor chose to use twitter as a medium of announcing the position.  They are expecting responses to that advertisement.  It's always a good idea to explain how you heard about the position.  Your email does all of those things.


Despite excellent grades, does having no rapport with any member of the faculty preclude my getting LoRs? I am a decently good student (3.8 gpa, 4th year undergraduate). I have gotten A and A- in all major courses (except a B- right as I transferred), but I have a concern. I have Asperger Syndrome and dislike social encounters and crowds; therefore, I have always done my work in solitude and avoided interaction with peers or faculty whenever possible. I am sure that I am a good student, so I was convinced on this basis that I'd be a good candidate for a PhD program. Now I am finding out, however, that 3 letters of recommendation are expected to accompany an application to a US PhD program (in philosophy).

None of the professors whose classes I've taken, despite my above average work (including a handful of A+ essays), know who I am or what I've done or what I'm capable of, etc. Therefore I feel very hesitant to ask for a letter of recommendation, as I expect it cannot contain more than a restatement of my transcript in some way. [Even if I explain that I had good reason not to interact with others, that doesn't retroactively cause anyone to know me better.]

If I were to ask my professors/lecturers (past and current) for a letter of recommendation, am I correct in concluding I will likely get none, or at least none that are good? Additionally, is it true that one cannot apply to a PhD program in the US with no recommendations? Finally, if I secure 3 mediocre letters of recommendation, should I apply just in case I'm accepted?

Thanks.

Yes, you can ask for recommendations from people you don't know well; send an email with one to three of your best papers attached, as well as an unofficial transcript; in the body of the email, remind the professor which course(s) you've taken with that person.  Include a sentence or a paragraph about what draws you to the idea of grad school, that is, show your spark.
Yes, you can apply for grad school with mediocre letters; you may or may not get in.  (I do not know whether the letters you would harvest at this point would be mediocre or not.)  You are right that this might not be the optimal way of proceeding.
Now I'll address what you asked in a comment.

"What does being more involved look like?"  In other words, as a student with Asperger's, who is not naturally outgoing or extroverted, how can I get to know my professors better, with the goal of garnering more effective letters of recommendation?

I'm glad you asked this well in advance of application season, because this gives you time to get to know potential letter writers before you really need the letters.

Ask questions and contribute to class discussions.
(You've done this -- check!)

Visit office hours to start to build an academic relationship.
You don't have to need help with a project in order to visit office hours.  If you are not sure how to structure a conversation in office hours, you could send an email requesting an appointment (so that the professor isn't thrown off thinking you're just coming in for five minutes to, for example, request clarification of an assignment); if I were in your shoes I would say, quite clearly,

"I would like to go to grad school and am hoping to get to know you better, so that I can comfortably ask you to write a letter of recommendation.  However, I have Asperger's and am not accustomed to visiting office hours, but I would like to try; I may need some help getting started with having a productive conversation." (You can use this as is or modify it to make it your own.)

You can also start a conversation through email.  Some individuals are more comfortable with email than in-person visits.  If you're not sure which would work better for you, you might want to try both approaches.
In office hours and in email correspondence, in order to break the ice sometimes it is helpful to share a list of universities you are thinking about applying to, and ask for help in narrowing down the list, or adding to it (depending on the length of your list!).  In other words, you can ostensibly be asking one thing, as a way of getting the ball rolling.

Note that you can ask your university's office of students with disabilities for assistance if you want to.  There is no guarantee that they will help, but they might, and as long as you don't put all your hope in that external assistance, there's no harm in trying.  (Some of these offices are great, some less so.)

You might find it helpful to have a grad-application buddy.  Sort of a partner in crime.  Someone who's going through the same process as you, and you support each other through the process.  In fact, your application buddy might go with you to the first couple of office hours visits for moral support.


Is it possibly considered weakness in my statement of purpose if I mention that I would like specific people to advise my PhD programme? I'm writing a statement of purpose for my PhD applications and in some cases I'd be very happy if any person from a certain group (say the Algebra Group) would take me as his/her student. Could this be considered a weakness in my application? How should I handle this?

I've been researching people and groups for over 4 months and I know (as much as I can right now) what I want to do and who does it. It's just that some universities and programs have some amazing faculty.

I would include which certain aspects of the faculty would support your intentions and why, especially if you can include meaningful references to their previously published work.

For example

"I believe that University X would be a great place to undertake my research into topic Y because it has a great reputation in this field. For example books A and B published by person C are well known texts in the field and I believe the research of person D in the area of E would compliment mine."


Can someone continue her education in Germany if the first university degree is not recognized? My sister is living in Saudi Arabia in a city that has very few limited education options for her. She has to stay there for certain circumstances and she can't leave for a different country. She has now been enrolled in an architecture program at a private University there for a year so far. Yesterday, she found out that her degree is only recognized throughout the middle east and not world-wide and we don't know why. So, her university is only recognized in Saudi Arabia and other middle-eastern countries.

I live in Germany and once I start working, I can afford to sponsor her and bring her here. She has the dream of continuing her education here in Germany. Now the problem is that we don't know what to do in that case at all.

I recall when I got my master admission in Germany, that they told me that although they didn't find my home university in their universities catalogue, yet the admission commission decided to give me the admission because I had good grades and good recommendation letters.

My question is:

Considering her situation, can she still continue her education in Germany after finishing her degree in Saudi Arabia?

Even if she has to re-do some courses. We are wondering if there is a possibility to get an admission from a German university regardless if they ask to redo a lot of courses or not,  we just want to know that there is a hope for her to continue her education in Germany.

If her high school degree is not recognized, then there is the possibility to apply to a Studienkolleg. They generally offer one- or two-year programs that teach German and enough other subjects to be accepted as an Abitur or Fachabitur. Then she can start a bachelor's program. Most universities have a quota for taking in students from foreign countries, this is generally 5 % of the places to study. But enrollments are down in Germany at the moment, so there are good chances of getting a position. Check the enrollment dates: usually July 15 for the winter term, January 15 for the summer term.


Is it ethical for a CS profesor to assign development of real world systems? I am a CS major, currently enrolled (about to finish) in a Software Engineering (II) course. My teacher told us at the beginning of the the first course (SE I) that the main objective of the class is to develop real world systems, as such she asked us to search for an NGO who was in need of an information system and go develop it for them during the length of the course. It is supposed that it is a way for the university to socially  project itself (and supposedly us). To be fair to her it was assigned as a group activity but I decided to work by myself.

I went to an NGO and asked if they were in need of a system and told me that they were, but that if I were to develop anything for them I couldn't just go and install it, I would merely be presenting it to the local authorities and they decided it was good they would propose it to a higher authorities. So the implementation of the system was (obviously) not guaranteed, and that was a requirement (the system must be implemented).

My teacher said she wouldn't consider any systems that were not guaranteed to be implemented. I feel that is an overstretch considering we were (are) not certified professionals (yet), and the NGOs were not asking for the software. Other majors are (for the most part) not required to participate in real world activities (e.g. a civil engineering major is not required to go look for a real world construction and WORK on it, to ask for some information maybe, but not to go do actual real work).

To be clear this was not a research assignment, she asked us to look for a real world system that needed to be developed and just go do it.

The justification for this is that we would gain experience by doing it (both in systems analysis and working in teams) but she never really taught us any of that (no git, no unit testing, no UI testing, no integration tests, no nothing). To emphasize how she didn't even teach us how to work in groups: I told her that I had created a repository to host my project and show all the changes that occur, and suggested her to tell the others (who were working in groups) to do the same and make sharing code easier and she basically told me that passing the projects around in flash drives and making full copies of the different versions was a better way to do things.

The few lectures we had were about types of software and software lifecycle without which were really shallow in nature (merely definitions of concepts).

She would ask us to show her our progress weekly, and she didn't care of under the hood changes, if it was not visible on screen, she would say we had done nothing (with is something she even taught us: changes are not always visible).

In the end everyone had a horrible time with that class (specially me as I was working by myself) and had to relive it for the next class. I saw how my classmates were doing disastrous jobs with their software (dbs with no passwords, no sanitizing SQL queries, every client was making a direct connection to the dbs instead of through an API, etc...) and she really didn't care at all, indeed she suggested some of those things, she really just cared about the UI looking nice.

So the question is: Is it ethical for this teacher to require us to go work (unsupervised) on an unsolicited real world system (which was not backed, required nor supervised by university authorities), without being paid for it, and requiring that whoever accepted our work would have to guarantee that they would implement our software, and if they didn't we would fail the course?

I think it is unethical, and a potential legal problem for her, the university and us the students, given the high potential of these systems malfunctioning or being insecure, considering these are sort of high profile organizations. But still I want to hear what is the general opinion on this matter and could I do about it.

BTW since we had so few lectures we didn't even had a final test, instead we would have to prove that our systems were implemented to pass.

Implementation is ethical. It is ethical for your teacher to require implementation of a system for real-world deployment. Albeit, it would be better if the word prototype were included.

Deployment is unethical. It is unethical for your teacher to claim that any such implementation is suitable for deployment.

Side note. Your teacher cannot expect any NGO to deploy implementations.

Additional remark. It is abysmal to teach students that
"passing [source code] around in flash drives and making full copies of the different versions was a better way to do things [compared to using a repository]."


How to Reference to Online Articles What is the right method to follow when referencing an article published on a website?

For example, I want to include the below sentence from this article.

  A mere 81.7 seconds later, a chunk of insulating foam tore free from the orange external tank and smashed into the leading edge of the orbiter's left wing at a relative velocity of at least 400 miles per hour (640 kph), but Columbia continued to climb toward orbit.

Is the below a correct way to do so?

"A mere 81.7 seconds later, a chunk of insulating foam tore free from the orange external tank and smashed into the leading edge of the orbiter's left wing at a relative velocity of at least 400 miles per hour (640 kph), but Columbia continued to climb toward orbit."

Under References:

Hutchinson, L, 2016. 'The audacious rescue plan that might have saved space shuttle Columbia, USA, ARS Technicia

Thank you,

Since the web isn't a permanent repository, either reference something that is, or give the date on which you access the web article as part of the reference. And in your example, give the URL at which you found the article, not just the title of the website. So, more like this:

  Hutchinson, L, 2016. 'The audacious rescue plan that might have saved space shuttle Columbia, USA, ARS Technicia: https://arstechnica.com/science/2016/02/the-audacious-rescue-plan-that-might-have-saved-space-shuttle-columbia/, accessed April 1, 2020.

The Internet Archive and its Wayback Machine is permanent, but the date will be required for resources that change.


Applying for graduate programs, will missing classes count against me? I'm working on some graduate school applications, and I've been wondering...
If I'm missing some classes these schools require(this is more relevant in different states)will my application be less desirable to that particular school, because I will have to take some extra classes in order to start that program.

It's probably inappropriate to say it always "count against you," but it is fair to say that it will be taken into consideration.

For instance, some schools may not admit you officially to the master's or doctoral program in a field if you are missing classes normally expected of students in a given program (for instance, if you're missing analytical chemistry and applying for a chemistry master's). In still other cases, you may be admitted to a program, but with no allowances actually made for the courses missing—that is, you'd be expected to pass the graduate-level courses just like everybody else enrolled in the program.

On the other hand, if you are missing too many "core" classes, then you will probably find yourself struggling to gain admission, since the admissions committee may (rightly?) feel that you have too much prior work to make up.


Is it acceptable to ask my professor for help for another class during her office hours? I am in two classes (1 and 2), and my 1 professor never answers emails or holds office hours now that we're online. There is also no TA. Oh well, there's nothing I can do except include this information in my review at the end of the class.

I happen to know that my 2 professor has taught 1 sections in the recent past, and she attends her office hours without fail. If I give precedence to any student hoping to learn 2 during my professor's office hours, then is it acceptable to attend with the intention of getting help for my 1 class?

This might depend on local custom, but I don't think there is any reason that you shouldn't ask for help. You may be sent to the other professor or just told that the one you ask hasn't the time for you. But asking is fine.

Of course it is also appropriate to say why you ask the one and not the other. But having a relationship with a professor makes it easier to discuss things with than with someone more distant.

The professor will set boundaries if necessary. You don't need to be overly concerned with whether you are interfering with other students.


What counts as self-plagiarism? I'm an undergraduate and would like to write about certain topics and post the documents online, available to everyone to read and probably indexed by search engines very soon.

However, I think that if I do this, I'm very likely to have written about the topics of my bachelor or master thesis/theses before I write it/them. What I post online is planned to be high-quality but of course not scientifically published.

If I copy parts of these works without stating I wrote and made them publicly available earlier, does it qualify as self-plagiarism? If so, does it still count if I create the documents now, copy parts of them into my thesis, but only upload them after I (hopefully) got my degree?

Are the rules the same around the world or does it depend on things like the country, the academic discipline, the university, the kind of degree or other scientific work, or other things? If it does, please tell me what's relevant in the comments so I can add that information. However, since adding the probably most relevant details isn't hard: I'm a German computer science student studying in Germany.

If I post the documents pseudonymously, do I have to prove they are written by me or does the examination office have to attempt to prove they aren't written by me? Does it make a difference whether I use a pseudonym which is clearly not a person's name? If I do, how would I quote myself if I have to?

This question is about a similar topic but I don't think mine is a duplicate of it because the linked question is about publishing in a journal, not about writing one's bachelor or master thesis.

Cite your online reference, just as you would cite some other online reference.  In neither case is it plagiarism, because you're citing it.  And in the case of your own online work, you can take credit for it as if it were not cited, as long as this work does not appear previously to when you published online.


In text listing style - how to use? Any downsides? I'm currently considering to use a in line (in text) listing style, such as:

'Some things are quite good. (i) Thing A can do this and that, which is awesome because of this and that. (ii) Thing B can do, ... . (iv) Some people also say that this and that, therefore thing Z is great.'

I've got more important points already highlighted through bullets, therefore I don't want to use bullets again for this minor information, plus I want to logically link the single points through sentences, but still provide an easy way to pick out the key words quickly.

First question: I've seen this style in quite a few papers. Is it considered to be a "good" style, or are there any downsides to this approach? Should I not use this style? Does the reader get confused by this?

Second question: Shall the brackets and latin number be bold, only the number, or nothing?

Third question: Should I place the enumeration element right infront of the keyword, or at the beginning of the sentence containing the keyword?

Yes it is a good/acceptable style. At least in the fields where I have looked the format is standard. in fact bullets or numbered lists should be used more sparingly and I think the following is a good guideline: use bullets/itemization when there is a lot of text going into each. 'Lot' in this case is a complete sentence or more. Use the format you mention when you need a word or partial sentence for each item.
there are several ways to do this you can use 'i)' or '(i)' or (1)' or '(a)' etc. The choice may differ depending on what else you have in your paper. If you have figures that contains several panes, for example, a, b, c, d, you may decide to use Roman or regular numerals for your lists. if you have several lists you should avoid repeating the same item descriptor and, for example, use Roman numerals for one and Arabic for another.
This depends on the context. you should place them where it is appropriate to read them. this means before each part of the construction. In your example you have divided everything into separate sentences but I think you should make a construct with semicolons instead: "There are three things of importance: (1) thing A; (2) thing B; and (3) Thing C."


I lost my students' quizzes due to a theft, what should I do? I am a teacher assistant for a big course and I am expected to conduct weekly quizzes. Last week, my bag containing a week's worth of quizzes got stolen. My question is what should I tell my students and is there a fair way to make it up to them?

Report it to the police. Report it to the department.

You don't have anything that requires making up to the students. Of course you should be fair to them and not let this hurt them (e.g., no grade for this quiz, but allow students to take an optional alternative assignment to take its place).


Ethics of scraping "public" data sources to obtain email addresses I am wondering whether the following research practice is ethical.

A software engineering researcher downloads source code repositories from Github, a large source of publicly available open source code.  The researcher searches the git commit logs to find email addresses of software developers who have committed to a project, and uses these email addresses to send them an email asking them to participate in a survey.  If the recipient clicks on the link to the survey, the survey contains an appropriate briefing and obtains informed consent.  The researcher follows all institutional and legal requirements related to human subjects research.  The researcher limits the number of emails sent to only the number of participants they think they will need to test their hypotheses.  However, at least one recipient of this email is annoyed that the researcher obtained their email address in this fashion and sent them unsolicited email.

Is this an ethical research practice?  In particular, what would be the relevant ethical principles or ethical framework for analyzing this question?  I've read a bunch of papers and backgrounders on ethics in human subject research and in engineering research, but they seem focused on other issues.  Are there accepted norms or guidelines relating to this sort of situation?  Has it been considered in other fields, such as the social sciences?

A possible argument that the practice is ethical: The data source is publicly available, and the email addresses were collected from this publicly available data.  Developers chose to make their software repository publicly available, and they should assume that any information contained in it are public.  Developers who don't want to be contacted could have configured their git client specially to use a different email address.  The research will benefit our understanding of the science of software development.  Subjects have an opportunity to decide whether or not to participate in the survey.  Participant confidentiality will be protected, and all responses will be treated anonymously.  The research complies with all legal and compliance requirements.  From a legal perspective, the emails are not "spam", since the unsolicited email was not sent for a commercial purpose.

A possible argument that the practice is unethical: Software developers probably would not expect someone to scrape email addresses from the git commit logs.  Their email address might be contained in a publicly available data set, but some developers might expect/consider the information private, or at least not public and free for unrestricted use.  Some developers might object that it is one thing to use email addresses that are publicly listed on their Github profile page, but it is another thing to extract private email addresses that are provided as part of their git configuration, and that their understanding of social norms is that the email addresses automatically inserted into the commit logs by their git client were not intended for this purpose.  Some software developers might object to having an unwanted email message in their inbox or find the practices "creepy".

Please note: I am not asking about IRBs, legal requirements, or compliance.  I am super-familiar with those considerations.  Assume that the researcher has complied faithfully with all of those requirements that are applicable in their country.  I'm not asking about that aspect.  In my view, researchers have an independent obligation to conduct research in an ethical manner, and to exercise their own judgement in avoiding unethical behavior, even if is legally permitted or approved by an IRB.

A relevant guideline from the Council of American Survey Research Organizations' Code of Standards and Ethics for Survey Research:

  Research Organizations are required to verify that individuals contacted for research by email have
  a reasonable expectation that they will receive email contact for research. Such agreement can be
  assumed when ALL of the following conditions exist:

  A substantive pre-existing relationship exists between the individuals contacted and the
  Research Organization, the Client supplying email addresses, or the Internet Sample Providers
  supplying the email addresses (the latter being so identified in the email invitation);
  Survey email invitees have a reasonable expectation, based on the pre-existing relationship
  where survey email invitees have specifically opted in for Internet research with the research
  company or Sample Provider, or in the case of Client-supplied lists that they may be contacted
  for research and invitees have not opted out of email communications;
  Survey email invitations clearly communicate the name of the sample provider, the relationship
  of the individual to that provider, and clearly offer the choice to be removed from future email
  contact.
  The email sample list excludes all individuals who have previously requested removal from
  future email contact in an appropriate and timely manner.
  Participants in the email sample were not recruited via unsolicited email invitations.

It would seem here that GitHub users do not have a reasonable expectation that they will be contacted for research.


Is there a preferable time of year when one should apply for a PhD in the UK? [Edited] I am very shortly going to be sending off my PhD application. I cannot apply quite yet because I am waiting on my bachelor's documentation which was withheld (library fines which are now cleared) but now it is in processing, and I do have my transcript. I have my master's documentation. The BA uni say they don't know when the cert will be ready, it could be a week or two, or longer presumably. The deadlines for PhD applications are set as the summer, but I know that many faculties like to have the applications in sooner because they want to decide on their student quantities. Is there some kind of unspoken deadline that I should shoot for in general [e.g. late Feb, Apr etc] or does it vary by institution? Does one lessen one's chances of acceptance if applying nearer to the official early summer deadlines?

I should mention that a staff member in my choice of PhD uni has already approved my proposal and agreed to be my supervisor. Should I apply anyway without the BA cert and just say it is in processing [without going into reasons why]? I am not applying for funding.

Question:
Is there a preferable time of year when one should apply for a PhD in the UK?

Answer:
This very much depends on the university, programme, funding, etc. So it's hard to generalise a single "preferable time".
But, that being said, many STEM programmes (which are not on a rolling admission) and funding opportunities tend to have application deadlines between around mid-September and around mid-February.

Question:
Does one lessen one's chances of acceptance if applying nearer to the official early summer deadlines?

Answer:
Not unless it says somewhere that places may be filled before the application deadline.

Question:
Should you apply without the BA cert and just say it is in processing (without going into reasons why)?

Answer:
Typically, applicants are not required to submit proof of any qualifications in the early stages of the application process. They are required, however, to submit an official academic transcript.
It is only in the later stages of the application process, e.g. after receiving a conditional offer, that applicants have to provide supporting documentation as evidence for meeting each condition of the offer.

My advice is that you get in touch with the admissions office of the place you are applying to, and ask them directly about the details of the application process and your BA cert.


How do you hide your past online identity when you enter Academia? I worked before as a freelancer writer where I would review some tech products (phones, websites, online services... etc) and post them on YouTube (channels which I do not control), and both my voice and picture were appearing in these videos.
Now that I graduated from my Masters program, I want to pursue my PhD and teach in the university. I would like to start publishing some papers as well in my field.
However, my past online identity is haunting me; Anyone can search my name and instead of finding my Google Scholar page as the first result, they would see me talking about the features of iPhone 7 in a YouTube video, and it is embarrassing for me. Some political articles that I published online are also embarrassing for me as I enter the academic world.
Do most people in academia suffer from the same thing? How can one get rid of this past online identity before entering the professional academic life? And how can I be sure no one uses parts of this old identity against me in the future?

Firstly look into the possibility of changing your YouTube name. If this is not possible, see if you can create a new YT account and move the videos into this.
Whatever about YouTube, your academic name is better being different to your commonly used name: we are all entitled to a life away from our work and from any "reputation" that follows from this. How best to select your academic name depends on:

The country you are in

The commonness of your first name, middle name(s) and surname

Naming conventions in your country

So, for example, if your YouTube name is Pablo Garcia, your middle name is Enrique and your mother's name is Sota you might publish under the name P.E. Garcia Sota. Likewise if you live in Netherlands and your YouTube name is Johan Van Dijk, you might, if your middle name is Willem, publish under J.W.V. Dyck as the latter form is often used in English publications. English native-speakers might use a number of first name initials and maybe omit the usual one if it is unusual enough to be searchable. Irish people have the legal option of using the Gaelic version of their name. Doubtless there are other possibilities in other countries, there may even be regional naming conventions in parts of France and Germany.
Look into the options in your own country and then do some trial searches on the main engines. Be careful to avoid a name that already has an existing big persona attached to it, especially in academia, as Google searches will associate you with them. Use Google Scholar to help with this.
Discuss your final selections with those close to you.


Should I mention my co-authors while tweeting about our publications? Assume we have a paper published in a conference or journal. Should I mention my co-authors while posting some content of the paper (or just paper's link) on Twitter or Facebook?

Let's assume I am aware of their Twitter or Facebook accounts.

It would be a polite thing to do to at least link the co-authors, for example, something along the lines of:

  Paper title, paper link, #co-author

It also depends on the amount of space available in your tweet - their names will be written on the paper itself in any case. At the very least, let them know that you are tweeting/posting the link/paper, which would give them an opportunity to retweet/share it.


Is it plagiarism if I copy somebody else's answer I already solved but misplaced? For an assignment, I was supposed to do some tedious calculations and essentially compute a certain number of things and then just list them as answers, one after another, without the calculations. There were about 15 of these things that I had to list.

I did this, and then misplaced the paper on which I had written them. I was sitting in class getting ready to hand in my paper when I realized this. It was the last paper in the stack and I guess it just got lost somewhere.

So what I did was that I found the solution online, and then just listed those things down again and turned it in. The problem is made worse by the fact that I listed the 15 things down in the same order as the solution found online. There wasn't a "natural" order to the things, apart from maybe the first and last thing, and therefore, there were 13! = 6227020800 different ways of listing them, and so of course it will look very suspicious if somebody noticed that I just happened to have the same order as this other solution.

Is this plagiarism? What should I do if this is caught? I am considering writing a mail to my instructor right now, but I could also leave it be and hope it is not caught.

EDIT:

One of the answers below raised another question. What if my original solution was wrong? In this case, I definitely cheated by copying from the correct solution, but, since I did not know whether my original solution was wrong, I did not cheat intentionally, so .... ?

Is it plagiarism if I copy somebody else's answer...

Yes. Without even reading anything else you wrote. This is exactly what the word "plagiarism" means.


symbol list and nomenclature I received this comment from a reviewer in journal of "Optimal Control Application and Methods": "The notations need to be added in the revision to add the readability, because many symbols appeared are not very familiar with the readers. For instance, what is the meaning of <…> in (2) and (3)?"

Is it necessary add a nomenclature with a list of used symbols of variables, operators and abbreviations?
Is there any specific position for this section ?

Is it necessary add a nomenclature with a list of used symbols of
  variables, operators and abbreviations?

You should treat this comment like any other comment from a reviewer: It tells you that one potential reader of your paper (and, if the editor did a good job, a qualified one) had a hard time understanding your paper. Hence, you should improve the presentation of your paper in this respect, so you should make the effort and help potential readers. (There may be the chance that this particular journel even requests a nomenclature, but I did not check this…)

  Is there any specific position for this section ?

For this, there are two good answers here.


How to get authoritative bibliographic information about journals When I collect bibliographic material, I seem to get grossly inconsistent information.
Papers from the same journal are often linked to different publishers, the same journal or publisher is often stylized differently (e.g. Wiley, Wiley-Liss, Wiley & Sons), location information about the same publisher is different (see What address to put in bibliography for Springer (and others)?).

Maybe I'm a bit obsessive, but I would like to be consistent when citing papers from the same journal/publisher, especially in my thesis.

Is there any source for authoritative information about journals and publishers?
Also: Is there a good guide for the semantics of the different fields in a bib entry?  If I knew, for example, that what goes into the publisher field should be the registered trademark or the trade name, I could work out some of these on my own.

(BTW: I'm using Citeulike's mechanism for getting bibliographic info for most of the papers I cite.)

I always like to go back to first principles when considering questions like this.  The purpose of a citation is to allow another researcher to find the reference in question.

The conventions for citation were developed many decades ago, when documents were always looked up in print, having information like the publisher was critical. These days, we live in an era of search enginers and highly international publishers.  That means that:

Often there is no such thing as a definitive publisher name or address, because it depends on what perspective you take.
There is no unified database for anything, anywhere.  If it is valuable, there are many versions of it, and they will contain conflicting information.
Authors and title are typically all that's actually needed to uniquely identify a document.

What's typically really important to get right is: author, title, and publication venue (journal, conference, [chapter in] book).  Many citation formats won't even show the publisher or address.  Likewise, online-only publications like the PLoS journals don't even have a meaningful address or page numbers.  For the rest of the fields: don't give incorrect information, but any of the reasonable variants of correct information is fine.


How can I publish an academic paper independent of work while working at a company? I have been working on some independent research for a few years now, and I'm finally at the point where I'm seriously considering publishing a Computer Science/Mathematical Algorithm in an Academic Journal.

I presently work as a Software Development Engineer at a major tech firm. I have never published a paper before, though I do have my Masters and have gone through the process of writing a research paper before.

My specific questions are:

If my research paper is completely unrelated and independent of anything I do at work (nor am I even in a research type position), what - if any - obligations do I have to my work place? Do I need to seek their approval before publishing a research paper?
If so, do I need to supply them with my research paper - or merely
provide an abstract/description of the research to them?
Will an Academic Journal require me to submit evidence that there is no
workplace-conflict as an Independent Researcher?

Thanks :)

If my research paper is completely unrelated and independent of anything I do at work (nor am I even in a research type position), what - if any - obligations do I have to my work place? Do I need to seek their approval before publishing a research paper?

You would have to read whatever NDA you signed, as this is specific to your situation. IANAL, but I think the most likely answer is there is no problem with this. You aren't allowed to divulge company secrets, but this is something you worked on independently (somewhat of a hobby).

  Will an Academic Journal require me to submit evidence that there is no workplace-conflict as an Independent Researcher?

The short answer is no. The long answer is that many journals would require you to disclose if you have any conflicts of interest that would affect the validity of your results. For example, if your paper is about the effectiveness of a particular algorithm used at Uber for matching riders to drivers, and you work at Uber, you would need to disclose that as a conflict of interest. However, as you have already said that your research topic is unrelated to your work at your job, it probably would not constitute a possible conflict of interest.

Submitting evidence would be even less likely, I wouldn't worry about that unless asked.

However, note that you will have to choose an affiliation when you submit, which means you probably will want to think about how you want your name to be listed. This is just for informational purposes. Perhaps you can be listed as affiliated with your company, or maybe you can arrange to have no affiliation.


Common scenario and situation leading to similar questionnaire -- Is it plagiarism? I recently had to make a questionnaire for my research. For this questionnaire, I tried taking some ideas from other examples for the questions. Another student was working on the same topic and did her questionnaire before mine, but didn't publish any results yet. After comparing my questionnaire with hers, it was clear that some questions are a remarkably similar, due to covering the same topic, same country, same society and same climate. The other student made a complaint that I have copied some of the questions from her questionnaire.

Could anyone please help me know whether did I commit plagiarism? How should I deal with the present situation?

tried to obtain some ideas from other examples for the questions

That has the hallmark signs of plagiarism, although without seeing the original sources and your questionnaire it is hard to give a definitive answer. It is okay to look at other sources for ideas. Paraphrasing is okay also. Copying, or even changing a few words, is not okay without proper attribution. In general it is okay, and often desirable, to reuse an existing questionnaire, or parts of an existing questionnaire, in a new study, but you need to provide attribution to the original questionnaire.

As to the similarity between you and the other student, this depends on if you used her questionnaire for ideas. If you never saw her questionnaire, then you clearly did not plagiarize from her. It is possible that both of you got ideas from the same source, in which case you both plagiarized someone else.

You need to determine if you plagiarized and if you did plagiarize, who you plagiarized from. If you plagiarized from the student, you need to tell her and your supervisor. If you plagiarized from a third party, you need to tell your supervisor. You should also inform the student that your questionnaire contains plagiarism, but that you did not plagiarize her. You should also tell her that you are telling your supervisor.


Do you have to have PhD or employed in academia to publish a textbook? I am interested in publishing a statistics textbook (e.g. through Duxbery, Springer, etc.). I do not have PhD in Statistics, nor am I employed in university or college as an instructor/professor (but I have BS and MS in Statistics).

Do I have to have PhD and/or have career in academia to publish statistics textbook with those publishers?

Thank you,

No, there are never any degree requirements in academic publications.

I am in the field of mathematics, and I have some colleagues who published academic books while in graduate school and even, in a few cases, as undergraduates.  There are also academic textbooks published by people who have no degrees whatsoever in that field.

It is possible that the editors and reviewers will look into your credentials and may apply a bit more scrutiny to someone without a terminal degree...but more scrutiny when it comes to textbook publishing is not necessarily a bad thing.  In any case, if the book really is good they'll be happy to publish it no matter who you are.


How long the curse of bad education remains in academic career? It is understandable if considering the educational record (where s/he has studied and how is his/her transcript) of an applicant applied for junior academic positions such as postdoctoral fellow or assistant professor. BUT, for senior academics, the factors for judging a potential full professor is his/her research, teaching, publications, and other academic achievements.

I read in a few job ads for full professors in Europe (mainly Scandinavia), one of the application materials is unofficial transcripts. It seems that the initial review is substantially based on the applicant education achievements two decades ago.

I wonder how much the education of an applicant affects his/her chance to be appointed as a full professor? Does a bad education (having low GPA at PhD level) always affects someone's academic career, even at highest levels?

From a European perspective: the only time I was ever asked for transcripts was for PhD admission. After that, nobody every asked me for transcripts.

Administrative people asked me for a proof of my degree (a copy of the degree itself, without grades, is what I gave). They only wanted to check I was eligible for the position's formal requirements (having a PhD to become post-doc or assistant professor).
Scientists asked me for my publications, my thesis, the list of topics I had taught, etc. They did not care the least about my grades in undergrad or graduate education.

So, I think the ads you saw asking for transcripts, especially for senior positions, are by far a minority. Once you have a PhD, most people won't care about your earlier educational record, since it is not a good predictor of how awesome you will be as a researcher.


Applying for job while 3/4 done with MS program I am currently a MS student finishing my last (2nd) year. I have just applied to a top company of my field in my city (perhaps the nation as well). I did a video, phone, and on-site interview. They understand that I have just 1 class left next semester, but also need to finish my thesis (which is maybe 25% done?). I have informed them that I can work a full 40hrs a week (I am actually currently working about 35 hrs on top of 2 classes, TAing, thesis work). I have received an offer to start in January that is generally quite high for a new MS grad in my field. To be honest, I am much more interested in the work I would be doing at this company.

Should I take the offer and start working while taking the class/work on thesis? Or don't take it ?

Usually a masters thesis is a full time job, especially closer to the end of the thesis. Honestly, I would not recommend working 40h/week on top of working on a masters thesis, as long as the fields are not closely related. But of course this depends on individual factors which we can not appraise without knowing you and your thesis / course work.

Some questions which might help:

How much of your thesis can be finished before January?
Will it be possible to reduce the working hours to complete your studies if necessary (without being paid during that time)?
How well can you handle stress?
Would it be possible to start with 20-30h/week whilst you have to study?

In the long run, it is not a good idea to screw your thesis for a job. It is the most important grade! When people apply for a position at my lab, I am mainly looking at their thesis topic and grade - the rest is less important.

Maybe you can twist it another way: At our university it is common that students are doing their thesis in cooperation with a company - maybe you could switch your thesis topic and combine job and thesis.


Citing two authors with the same surname – is it worth noting that they are distinct people? In the paper I am currently writing I cite works by Bill Smith and Fred Smith.

I refer to them both several times, as several of Bill Smith’s papers provide the basis for some of the techniques I am using, and Fred Smith’s work provides origin for the dataset I am using.
This dataset is commonly called The Smith Corpus.

Currently my paper has a paragraph (boldface mine):

  We use the Smith Corpus (Smith 2010), as prepared by Johnson et al (2015).
  This corpus is partitioned into test, development and  training subsets, and has minor clean-up from the original data collected by Smith (2010).
  It is also used by Smith et al (2016) and Otter et al (2016).

Where the all uses of Smith, except the last refer to Fred Smith.
Only Smith et al (2016) refers to Bill Smith.

Anyone who checks the references section will realize that these are different people.
But the citation style I am using, is a surname–year style.
So on a casual reading, one might expect the dataset in question to have been introduced in one of Bill Smith’s papers. However, this is incorrect: It is first used in this area by a third author, John Johnson (whom I also cite), then later by Bill Smith, and Sam Otter.

Bill Smith he refers to the corpus as the Smith Corpus in his paper – without qualification in any way.

Is there anything I should be doing about this possible confusion?
Or can I trust the reader to check the reference list if they want the details on who actually did what?

The ~5 page style guide for this conference says

  Citations: Citations within the text appear in
  parentheses as (Gusfield, 1997) or, if the author’s
  name appears in the text itself, as Gus-
  field (1997). Using the provided LATEX style, the
  former is accomplished using \cite and the latter
  with \shortcite or \newcite. Collapse multiple
  citations as in (Gusfield, 1997; Aho and Ullman,
  1972); this is accomplished with the provided
  style using commas within the \cite command,
  e.g., \cite{Gusfield:97,Aho:72}. Append
  lowercase letters to the year in cases of ambiguities.
  Treat double authors as in (Aho and Ullman,
  1972), but write as in (Chandra et al., 1981)
  when more than two authors are involved.
  ...
  We will reject without review any papers that do
  not follow the official style guidelines, anonymity
  conditions and page limits.

This level of guidance is typical for CS conferences in my field.

While I can of-course decide to make up my own rules for what to do in this case that is not covered clearly by their style guide -- and they probably won't desk-reject for it -- what additional rules should I use (if any)?

Check your style guide. Many surname-year styles, such as APA, have provisions for exactly this problem.

  But do you know how to proceed when a reference list includes publications by two or more different primary authors with the same surname? When this occurs, include the lead author’s initials in all text citations, even if the year of publication differs (see the sixth edition of the Publication Manual, p. 176). Including the initials helps the reader avoid confusion within the text and locate the entry in the reference list.

http://blog.apastyle.org/apastyle/2014/01/when-to-use-author-initials-for-text-citations.html

In your case, this would lead to:

  We use the Smith corpus (F. Smith 2010), as prepared by Johnson et al. (2015).
  This corpus is partitioned into test, development and training subsets, and has minor clean-up from the original data collected by F. Smith (2010).

  It is also uses by B. Smith et al (2016), and Otter et al (2016).

Note that since "Smith corpus" is a name of a corpus, rather than a citation, it can remain without the initial.

Also note that in APA style, all citations to any Smith papers have to have the initial. So even if this is the only time you mention B. Smith et al 2016, all of your references to F. Smith 2010 have to have the initial. This is a little annoying but nicely unambiguous.


Preprint on CV - should I include journal I submitted to? I'm in a discipline where it is common to make preprints publicly available on arXiv as soon as they're ready to be submitted to a journal, so naturally I list them on my CV. Before the review comes in I would just list the paper as "Preprint" and after it's been officially accepted I would list it as "To appear in XYZ". I wonder what is the best course of action between those two states, that is, after the paper has received positive reviews but there are still corrections to be applied and it has not been officially accepted (but I'm willing to bet that it will be). Is it reasonable mention that the paper is "Submitted to XYZ" in such a case? That has the benefit of providing more complete information, and is definitely a statement that I can justify if pressed. Or is it always preferable to stick with "Preprint" until officially accepted?

No, do not list the journal you submitted it to.  Frankly, it means nothing: anyone can submit anything to any journal.

Of course, you want to your CV to accurately reflect how much work you've been doing lately, but there's always a chance that the paper gets rejected in the in-between phase.  A good enough compromise is to just post the arXiv info, when it was revised (this reflects that it's been recently reviewed), and perhaps "Accepted."  Once you get the proofs, you can change to "To appear in [Journal]."


Is it rude to visit a professors office during the summer if they have not responded to my email? I understand that a somewhat similar question has been asked before, but my parameters here are slightly different. Essentially, I have been emailing a professor since early April about joining their lab. They have responded and inquired what sort of projects I would be interested in. They also remarked that they would be interested in meeting after the semester is over. Well, after final grades were input I sent an email and... no dice after two-ish weeks. This is no surprise, given that I know a student who got a response from them months after sending an email. The thing is, I am trying to join their project over the summer and well, precious summer days are about to start passing pretty fast.
In summary, I am moving close to campus next week, and I am wondering if it would be rude or brutish to go to their office location physically to follow up. Is this a bad idea? The difference between this situation and the last person who asked is that this is during summer and COVID times. I also just finished my freshman year if that matters.
EDIT: as a corollary, I could also try calling the office. Though that almost seems more incessant than showing up in my opinion. Thoughts?

It's not rude.  It quite probably is futile.

Many faculty are not in their offices very often normally.
Many faculty are in their offices less in the summer - in particular, they are unlikely to have scheduled office hours.
During a pandemic, you might not be able to go into the building anyway.

If the professor does not feel safe meeting in person during a pandemic, they'll just tell you to contact them some other way when you show up.
Do not go to a professor's office if you are sick.  Also, do not go anywhere, except for medical care.


How damaging is it to have been a co-author of a retracted paper? Many years ago, when I was very new to the world of scientific paper publishing, I was a co-author to a paper that was subsequently retracted after an investigation of the findings. This was before I did my PhD (was a Master's student in a different field that I am currently in).

To explain, my role in the data collection and analysis was quite specific, and in the investigation it was deemed that my part of the work was verifiable and sound. In hindsight, I have long realised that I should have taken on a more active role in proof-reading the article as a whole, cross checking the findings and being more active in the article writing process. For that, I have always taken responsibility - so, even though I do not have anything to do with the lead author anymore - I am not blaming anyone.

Since then, I have been co-author and first author of over a dozen more papers - many are published without difficulty (we check, cross-check and check everything again nowadays).

But, the question remains, in terms of applying for postdocs, funding, grants and the like - how damaging is it to have been a co-author of a retracted paper?

The effect of retractions on scientific careers has been studied, and the conclusion is essentially that retractions don't hurt scientists who are behaving carefully and ethically.

For your case, it sounds like you were clearly exonerated, and that your only fault was being a junior researcher who wasn't proactive about ensuring honesty on the part of your collaborators.  Since you've since gone on to be more fully educated as a researcher and to establish a good publication record, I would not expect that this past retraction is likely to have any significant effect on your current prospects.


Paper keywords: singular or plural? When listing keywords for a paper written in English, is it better to write keywords in singular or plural form?

I am interested in both keywords stored in meta-data:

and keywords listed at the beginning of the paper:

It doesn't really matter. Adopt the style that the journal or conference you are submitting to seems to prefer if there are no instructions given by the venue.


Can a person become a professor in English without having a Bachelor degree in English? Some universities allow students to get enrolled in English studies without having a Bachelor degree in English.

If someone completes an MA and PhD without a Bachelor, can that person become a professor in English?

Of course you can.  Yes, once you complete a Ph.D. in English, you will not need a bachelor's degree and you will not need a master's degree when you search for a job.

Entry into a Ph.D. program in English may be done by those with bachelor's degrees in other, related fields.  Or by those with appropriate experience outside academia.

And let's face it:  Once you are awarded the Nobel Prize in Literature, practically any English department will hire you as a professor, even if you have no degrees at all.


Sending a copyright transfer The following sentences is in the Submission Guidelines of a journal:

  Once a paper has been accepted for publication, the authors are assumed to have the copyright transferred to World Scientific Publishing Company.

I have an accepted paper in this journal, but I have not been requested to submit  the copyright to the publisher yet. Must I send a copyright to the publisher?

The key word in that statement is assumed. That means that they believe that your submission and their acceptance of your manuscript implies that you have agreed to transfer the copyright to them. They are basically saying "you don't need to send a form transferring copyright, because you did so by allowing them to publish.

If there is a reason this is not the case—for instance, all the authors are US government employees, so that the work is in the public domain—then the publisher should be alerted for guidance.


Help - drowning in non-thesis related work from supervisors during PhD I’m not quite sure how to handle this situation and hoping you may be able to help!

I am over a year into my PhD and have supervisors who, although we don’t have a bad relationship from their point of view (they would likely say it is good), in my opinion I have a very formal, structured and slightly cold relationship (comparing to previous managers in other jobs).

At the beginning of my PhD they were keen to get me involved in projects they have going on in their department that would help them analyse data and produce papers, I was told this was my way of saying thank you to the team (I assumed saying thank you for supervising me) and this would not gain me a name on their paper. Admit-ably at the start I was very keen to impress them and additionally thought getting stuck into some work for them could also help me get in the flow of what I might do for my own thesis. Over a year later and these projects continue and are only getting bigger each meeting we have. The tasks (and timeframe expected) mean I would need to spend on average 10-15 hours a week on these projects to get them anywhere near completion. I have noted to them in my last meeting this is a lot of work and I think I am unable to meet their desired deadline but this is not really taken on board. As our relationship is extremely formal I feel like I can’t really explain how overwhelmed I feel or how unfair I feel like this is. Its never been an option as to whether I want to or can take these projects on, they are expected to be done ASAP and I feel like I am being treated how you may a member of staff whose sole role it is to complete this additional work.

Having talked to friends and other PhD students they would call this unfair, toxic and flat out refuse to do it. However I am really mindful I want to keep in good faith with my supervisors, they are experts in the field I want to work in and there is no option of another supervisor to switch to without completely hindering my thesis and remainder of my PhD. I’d be better off quitting.

My idea would be to give it my best shot with finishing the majority of the project (even if it will be tough to do) , ensuring I am keeping minutes from our meetings which highlight that this is their project. Hoping that in future, if I've done a good chunk for them, they will let me away with not finishing acknowledging I have bigger priorities (my thesis). If this doesn’t work I would consider getting my university involved however I’d really rather not resort to this.

I know I’m being a wuss with this approach but I want to be diplomatic.
Any advice? Do you think it is normal for (some, I am aware not all) supervisors to do this?

p.s I don't care too much about not being mentioned in authorship for their papers, I'd much rather get on with my own project and have my thesis run smoothly. I just want to try and finish and be unscathed!

This is an unpleasent, but not uncommon situation. You say you "feel like I am being treated how you may a member of staff", and in fact many supervisors, particularly in the bio-medical world do treat their students exactly this way. For many students are the only mechanism to get any hands to do research. It is a bad thing, but it is common.

Firstly, no one should ever ask you to do work that won't get you an authorship, unless its group maintenance sort of work (organising the seminar rota, or making sure there is always milk in the fridge etc, monitoring everyones disk space usage). I know you say you don't care about this, but you should. Authorship is the currency of academia. It is how we are paid for our work.

Secondly SOME amount of off-topic work helping others is part of the payment you make to them for training you. When the time comes, you might need help from someone else to achieve something your project requires, but you are not capable of. However, you need to be careful of this becoming too much. In the run of things, your 10-15 hours a week is probably on the edge of what might be considered too much. If you are work 50 hours a week, then thats 20%-30% of your time. Not nothing, but not leaving no time for your own work, probably just starting to interfere.

Finally, expecting someone to do something immediately, when they are doing it as a favour is plain bad manners.

You have two approaches. First, if your supervisors are being cold and formal, then be formal back: arrange a set of expectations that both sides are expected to uphold. This doesn't have to be confrontational, it can be approached from a neutral stand point.

You time scales make it sound like you are in the UK. In which case, you should have an adviser - an academic in the department that is not scientifically related to your project. They are there for exactly this reason. The way this usually works here is that we have meetings with our advisees and if they report this sort of worry we go to their supervisor and say "I ask student X about their day-to-day and the answer made us worry that they are spending insufficient time on their primary project" - makes it sound like the advisor worked it out rather than you complained.


Is there any website for announcements of journal's special issues? I was wondering if there is a site or something where I can find announcements for all (most of) the special issues of journals (upcoming and past) . For example of Springer, IEEE, Elsevier, ...

If I search for this now, I find scattered call for papers. Also, I can't seem to find this on wikicfp.

No, there is not.

Speaking as somebody who has dealt with a number of special issues on both sides of the editorial table, there is simply too little coherence in how different journals advertise their special issues.  Sometimes it's hard even to find a coherent explanation of how a journal is approaching special issues even on its own website.

Maybe somebody like Google could address this, but it would be a hard problem requiring either serious investment in human curation or serious natural language processing mojo.


Should I prefer a grad-school recommendation from a PhD holder who doesn't know me well, or an MS holder who does? I work at a start-up as a research intern, and I'm looking to get a recommendation letter from somebody within the company for my graduate application. I'm primarily looking at one of two people:

Person A: He has a PhD from a top-5 university, well recognized in the industry space he's in, and is also the CTO at the company I work at. I do know him semi-well and thinks I'm talented, but I've talked to him very rarely as he wasn't my manager.

Person B: He has an M.S. from a top-20 university, pretty recent graduate, and is a researcher at this company. I know him pretty well, as he's my manager and we have very frequent meetings; he would be able to discuss my research potential in heavy detail.

I'm at a loss as to who I should ask for this letter. I'm really, really leaning towards Person A since he's an alumni of the university I have as my top choice, but Person B would know me much better.

Person A. Person B, as a recent graduate, is not really in a position to assess your caliber as a researcher -- he is still settling into his own career. He cannot compare you to dozens of others he has known at this stage of your career. Further, he is hardly in a position to judge your suitability for a PhD program, not having one himself. There is a fairly firm unwritten rule that grad school LoRs have to come from faculty, not grad students or post-docs -- I imagine person B is the industry equivalent of a post-doc.

You may want to ask Person A if they would appreciate notes or a draft letter from Person B. This is one way to get more specifics into your letter. Another way is to write your own notes and provide them, just to "remind him" about the things you've been involved in. Alternatively, if your school accepts extra letters, you can ask both.


Non-EU PhD title in Germany I am a German PhD student in South America and am worried about whether my PhD title will be accepted in Germany (as Dr.) and internationally in general.

If you successfully complete a PhD in the EU, you are allowed to carry the title "Dr.", as any PhD in Germany does.

I am working in a faculty with a professor with international experience, who, for research reasons, left a reasonably strong department in Europe for the position in South America, which is incidentally one of the strongest two departments in South America.

I am attending international conferences every now and then, have two papers published in international journals (one jointly, one alone) and two more papers in preparation.

For all I know, I can reasonably expect that my research performance (and eventually, my PhD thesis) is not below the European standard.

The default format for PhDs from a non-EU country is something like "Hans Wurst (Doutorado, Universidade de Ipanema)", which looks like I should just use my self-confidence instead and not mention that I did a PhD unless someone asks.

I don't know if it's off-topic, because this might just be "too localized", but of course I am wondering if it is possible to have my PhD accredited to use my PhD title in Germany like any "normal" PhD.

I'm also wondering, whether the international community is as strict as German law, or whether I should just call myself "Hans Wurst, PhD" on job applications, my professional webpage, etc. (where the place will be listed somewhere), and hope nobody tells me it should be "Hans Wurst (Doutorado, Universidade de Ipanema)" instead.

Did I make a mistake in my career planning in that the only title that is worth carrying (until full tenure, I guess) I can't carry without a large number of not-so-fancy accessories?

How your PhD is counted depends a lot on from which country you obtained it. Currently, degrees from Australia, Canada, Japan, Israel, and most doctoral-granting American universities are recognized as fully equivalent to "Dr." Beyond that, however, the PhD is listed as a PhD, so long as it's been granted by an institution accredited to give out doctoral degrees. (It has to be legitimately "earned.") You just would not technically be allowed to call yourself "Herr Dr. Hans Wurst"; you'd be "Herr Hans Wurst, Ph.D." (or whatever the formal name of your degree is).

Unfortunately, the classification of the degree does matter in Germany. Someone who holds a Dr. rer. nat. (sciences), for instance, will have a harder time getting a position in an engineering faculty than someone who holds a Dr.-Ing. (engineering). PhD's may or may not count as being equivalent to either degree, unless the specific regulations of the universities allow for this. (This can make a difference in setting up thesis committees, depending upon the regulations of the faculty in question. Yes, it's really annoying, but that's the way the system is set up.)

Fortunately, as Nate says in his answer, the rest of the world is nowhere near as strict as German law (even the modified version now in effect).

Also, you can apply to the Zentralstelle für ausländisches Bildungswesen (Central Authority for Foreign Education) for recognition of a foreign-obtained degree as equivalent to the corresponding German degree.


Are there any for-profit schools that have achieved a good reputation in academia? Is the for-profit model feasible to higher education institutions? In other words,  are there any for-profit schools that have achieved a good reputation in academia (teaching and/or research)?

This answer is about the US.

  Are there any for-profit schools that have achieved a good reputation in academia?

As far as I can tell, the answer is (1) we don't know, but (2) probably not.

The reason it's difficult to know the answer to this question is that although there is a variety of mechanisms for judging the quality of education at non-profit schools, such mechanisms either don't exist or aren't working well in the for-profit sector. US News and World Report doesn't rank for-profit schools. There are accrediting bodies, but the ones that handle accreditation for for-profit schools seem to be lap dogs of the industry.

Because of the lack of data, people in the federal government who have been trying to crack down on fraud have been forced to use various proxies as measures of educational quality. For example, they look at the percentage of graduates who default on the government-sponsored loans that they used to go to for-profit colleges. People have also tried to figure out what percentage of students at these schools actually end up employed in their field of study. All of these statistics are at best indirect measures of quality, for-profit colleges tend to come out very low on these measures, and the colleges tend to give out fraudulent numbers to try to make themselves look good by these measures.

You can try to try to pick out a specific college, or a certain program at a certain college, as a success story. I didn't have much luck at that when I googled. One article mentioned Microsoft certifications as an example of something reasonable that you could pay a for-profit college to help you prepare for. But when I started looking up information on Microsoft certifications, it basically sounded like a scam in which the instructors are really not vetted at all, and the purpose of the program is to achieve sales and vendor lock-in.

Another example I've heard about is that often community colleges don't have enough capacity to handle the demand for certain programs like nursing. In theory, it would seem to make sense for the private sector to take up the slack. As private, non-union businesses, they are more agile. But the reality seems to be that these programs are of extremely low quality. For example, stories abound of students taking a semester-long nursing course in which five or six different instructors come and go before the course is over.


Is ever answering "No Basis for Judgement" on a reference request a red-flag I am filling out a reference form for a student I supervised on a medium sized project who is applying for graduate studies.
The student is great, of all that I have supervised in this way they are significantly the best on a number of metrics.
They are also the only student who has ever applied for graduate studies.
It has a bunch of questions where i am ask to rate them on there e.g. analytical ability.
One of the questions on the form is:
"Rank relative to others you have recommended for PhD studies"
with options like To 1%, top 10% etc.
The last option is "No Basis for Judgement".
Since they are the only person I have recommended for a PhD program, that seems like the correct answer.
Since I don't have anyone else to compare them to who I have recommended.
But I am wondering if I am I am interpretting it too literally.
and I should actually be answering this question with my total assessment of them (though there is another field for that); or with comparison to people who could have but didn't ask me for a reference; or to the set of people i expect would exist.
Especially I worry that saying "No Basis For Judgement" might be taken as a red-flag by the program administrator.

Usually you can supply context either as comments on the form or as a separate letter.  This is where you can explain you “no basis for judgement”.  It is not uncommon (although maybe so for this specific question): you may simply not have the historical pool of students to make an informed comparison.
You can use comments or a letter to simply restate what you just included in your post, and this should be enough to justify an honest opinion AND provide useful additional information for a committee.


Can I publish a paper in mathematics education on a computer program? I am a PhD student in mathematics education. As a part of my thesis, in the last year I designed a learning environment for tablets, similar to a computer game. The program is designed for children ages 6-10.

Up until now, I have not tested the program with any children, only some preliminary tests with fellow students.

Is it possible to publish this?

The program is quite complex and I fear that a single article detailing the program structure and the mathematics it can transport as well as the findings in the working sessions and interviews with the children may turn out to be too long.

I agree with user2768's comment that it will be most convincing if you can publish a user study and/or test of the program's impact. However, if your program is designed around some part of learning theory that is important but hard to implement, or focuses on a neglected area of mathematics, the program itself may generate interest. You allude to interviews with children when designing the program--so if you can illuminate what the misconceptions are that kids have (or other needs you found) and how the program is designed to address those, that might be compelling.

You may want to take a look at the Bootstrap project, which started as a teacher's classroom tool to teach algebra and became a dissertation topic and then an educational tool.  http://www.bootstrapworld.org/community/

It's also not fully clear to me how far along in your thesis you are. You'd benefit from reading about Design-Based Research (see, e.g., the 2004 special issue of the Journal of Learning Sciences, starting with this article by Barab & Squire: https://www.tandfonline.com/doi/abs/10.1207/s15327809jls1301_1?journalCode=hlns20), and possibly also this conference paper on how to build that into a dissertation: http://ro.ecu.edu.au/ecuworks/1612/ This method may offer you a framework to help you publish design work-in-progress, as well as knowledge you gain as you test and develop it.

Also, you may want to ask your advisor about good outlets to publish this, and whether getting a paper out at this point is a top goal. Since most education conferences are non-archival (double-check whether the individual conference publishes archival proceedings), this may also be a good thing to submit to a conference.


What are some bad effects of bullets in presentations? I get confused with some comments of JeffE on this question. Those are:

  ...avoid bullets entirely.

  Powerpoint doesn't kill people. Bullets kill people.

The comments got a lot of upvotes, so there are many people agree with them. And I don't understand why.

I use block and itemize extensively, and I think they provide a clear structure to my presentation. The bullets are the key points that I want to present on that slide.

So why people think they are so bad?

I have to emphasize that the question above asked about teaching, while I only give presentations. Are there any differences?

UPDATE

Thank you for the excellent answers (I still want to hear from JeffE). I can kind of understand that using only bullets is not enough, but avoiding them entirely is a personal opinion, not a general rule.

By the way, the best presentation I've seen so far is the last lecture of Randy Pausch, in which he used a fair amount of bullets.

TL;DR: A bulleted list onlys show one kind of relationship (either sequence or membership in a set). If you want to show another kind of relationship, it's better to use something else. If you want to show sequence/membership AND something else, you can either use a different visual tool (not a list) or a list + additional dimensions.

Bullets are useful to help speakers remember what they wanted to talk about, but they're not a powerful way to visually convey ideas and relationships between ideas.

To quote Edward Tufte in The Cognitive Style of Powerpoint:

  By leaving out the narrative between the points, the bullet outline
  ignores and conceals the causal assumptions and analytic structure of the
  reasoning.

He in turn quotes the Harvard Business Review:

  Bullets leave critical relationships unspecified. Lists can communicate
  only three logical relationships: sequence (first to last in time); priority (least to most important or vice versa); or simple membership in a set (these items relate to one another in some way, but the nature of that  relationship remains unstated). And a list can show only one of those relationships at a time.

Bullets may be OK when you want to convey sequence or membership in a set. But even then, lists often have more than one dimension, in which case there are almost certainly better ways to present this than just as a plain text list with bullets. For example, take this slide showing an outline of a talk by Tom Rondeau:

and compare it to the classic way to show an outline with a list:

The point of this example is to show that the "plain" list, which is a fairly standard way to show an outline, conveys one dimension. The list version conveys sequence, which bullets can do fairly well (the parenthesis attempt to add another dimension, but it's subtle). The graphical version shows the sequence of the talk and also adds a color dimension to show the content of each section and its classification.

You could of course add extra dimensions to the list, too. This image was contributed by Eddie:

But if you are just listing points and not trying to show order, priority, or membership, all the more reason to stay away from lists.

Also see Bullets versus sentences in posters (I hate bullets in posters).


Is it necessary for a journal submission to include the names of the authors' departments? I would like to know if it is an unwritten rule to include the names of the departments of the authors' of a journal submission?

Strictly speaking, it is usually a written rule, as journals have written rules governing what they expect from submitting authors, and this usually includes information about their affiliation. It is an unwritten rule in the sense that tere is no rule that all journals should follow the same format, but it is very common to include the authors' affiliation.

Sometimes this information is helpful as different departments belong to different "schools". So knowing the department alone can sometimes help you "place" the article in wider debates. Sometimes, it helps disentangle people with the same last name and the same initials. Regardless, this information only helps when you are an insider to the (sub-(sub-(sub-)))discipline discussed in the journal. However, those insiders are a legitimate audience for a journal, so I don't see a problem here.


Publishing company's reps refusing to send desk copies to my home. Any way around this? A certain popular publishing company won't send a textbook to my home, for a course I'm teaching this Fall; It's a new edition for this year. I understand they have policies, but I was expecting some kind of favor during the COVID business. It isn't easy to get the textbook if it's shipped to the campus right now, because the college is completely locked down. Has anyone found ways to convince publishers to send them out to home addresses?

Just say “thanks for your help, and mention an equivalent from a different publisher”... also drop in how many copies you would need :)... they need sales and work hard to get them.
Also consider contacting their boss by email, saying you wanted to consider their book but you crossed them off as you can’t inspect the book.


Does poor grammar on a shared message board for school annoy teachers? From the experience of a student, these are the types of people I notice on class messaging boards:
Person 1. Writes almost six-seven paragraphs for a single question that could be asked in two sentences. All sentences are grammatically correct and punctuated. Always includes greeting and salutation.
Person 2. Writes about three paragraphs. Most sentences have proper grammar. Either salutation or greeting.
Person 3. Writes one or two sentences. Most I's are not capitalized and poor grammar.
Person 4. Random letters mixed in, most sentences are gibberish.
Does this annoy teachers? Especially from junior high through high school where this is common.
Most teachers reply even to the most nonsensical messages, which is nice of them, but it is annoying to me (as a student) when someone doesn't take the time and effort to add a period at the end of their sentence.
So, from the perspective of a teacher or professor, are People 3 and 4's (as shown above) behavior on a shared message board obnoxious?

Teachers could very well be annoyed by 3 and 4, but would probably answer nonetheless.  They might also reach out to the poor writers and offer tips.  Posting writing rules for the messaging board in advance might help also.


Asking a complete stranger for a subreview for a conference? This question is about Computer Science firstly, I don't know if it applies to other domains

I am a PC member of some international conference in my field. I got a large number of papers to review, so I need to find subreviewers for many of them. Most of the time I would give the paper to a colleague that I know would be interested in reading it ... but I know only so many people interested in so many different topics, and there remains some papers for which I have no idea of whom could review it.

So I'm doing the following: search the web for any researcher in this domain who is active, has publications matching the keywords of the paper, does not seem to have any conflict of interest with the authors, and, preferably, published to this conference before.... and ask this person to act as subreviewer.

Is this common practice? I have received conference papers from complete strangers before, but this was only rare occasions (say a few percent), but I feel I'm doing this for almost 1/4th of my assigned papers. Is there any way to address this person, other than the standard EasyChair message?

I am a CS guy and can answer this question.

Yes of course. That is what conference chairs do perhaps. As you told the person has already published in past conferences like this. If some researcher is active in the field of his/her research arena and agreeing to review the manuscript. This is what is called peer-review. My recommendation would be to contact the researchers through academic e-mail ids of theirs to make it more transparent.


Should I oppose reviewers whose results I show to be wrong? I am submitting a mathematics paper to a journal. This paper contains a section where I claim that some results made by some authors in different published articles are false. I give a counterexample to support my claim and also show where their proofs are flawed.

Should I oppose these authors as reviewers when I submit the manuscript? In this case what should I write in the “reason” section?

If possible, it is good form to contact these people a few days before you submit so they can "check" your counterexample.  Phrase your counterexample in a constructive manner v.g. avoid saying it is false but rather suggest their proof is incomplete.

If these people are reasonable, they will double check, confirm that the counterexample is valid, thank you for it, and maybe cite your own work.  If they are not reasonable you have still been gracious.

People don't like to be criticized in public - nobody likes it.  Avoid "springing a trap" that will get these people in a bad mood if they learn of your counterexample in a journal or as referee of the paper.