How to regrade an exam that was too difficult?

There isn't enough information here to really give good advice. You suggest the exam was too difficult. It may also be that it was invalid.  It may be that some of the questions were stated in such a way as to be misleading. There are measures of the validity of such exams, by the way. They measure the validity of a question by the proportion of students who answered it incorrectly compared to how those same students did overall. Some questions are negatively correlated with overall performance.

Another issue is what your institution permits. Some have very strict rules about this. They are IMO unwarranted and counterproductive, but they may bind you.

But absent such rules, you should care more about fairness than you do about numbers. To achieve fairness you may need to drop the exam or give an alternate. You may even want to rethink your overall grading scheme.

One simple modification overall is to give course grades based on the, say, 8 best of 10 assignments/exams/whatever. Then the question of a poorly designed quiz never arises. Another way is to have quizzes every day so that no individual quiz is determinative of much of anything.

However, some of the things that you might try will leave some students unsatisfied; especially the best students who worked the hardest. You can be kind to the strugglers, but not at the expense of the superstars. The situation is worst if the system itself puts the students in competition with one another for grades. Strict curve grading is IMO immoral as it makes it into a zero sum game where I can only advance at someone else's expense. If the system doesn't permit top marks for everyone (assuming it is deserved) then it is fatally flawed.

Your purpose, I hope, is teaching, not grading. Use the exam as a teaching moment. Even have a class discussion about the questions that caused difficulty. Try to learn why people did poorly. Even permit different students to have different sorts of adjustments as needed.

I used to have fairly strict rules about such things, but the understanding was always "This is the standard and you will do no worse than X if you do Y". And I always tried to make it an advantage to learn something even if was after the deadline or the exam. Make people want to learn, not just want to maximize points.


Reviewer of PhD thesis doesn't allow me to write in the first person singular

There is an annoying truth here: What's OK in a PhD thesis and what not largely depends on the reviewers. Some people in academia have a huge inflated ego and prefer things to be done as they suggest, and the reviewer in your case is possibly among those people. You don't want to fight with them on this kind of issue.

If the reviewer has other comments that tend to create additional work without clearly improving the thesis, you may consider exchanging the reviewer.


Are there any mobile application for conference attendees?

Conference4me will do this more or less automatically. It displays the conference schedule including talk titles, authors, and abstracts, as well as maps of the venue, the list of participants, and other information. All this can be browsed offline but the app will automatically update it every several hours if it has an active internet connection. You can add sessions to your agenda and the app also makes it reasonably easy to add them to your calendar system of choice (at least it works with Google Calendar on Android).

However, the app's functionality depends on some cooperation from the conference organizers. For starters, it can only pull information from Indico, EDAS, and OpenConf, so the conference has to be organized using one of those systems, and all the relevant information has to be uploaded. Additionally, the conference organizers will have to ask the app's developers to manually set up the link between the conference website and Conference4me's data stream. It's apparently not a very involved process for the organizers, but you can't just download the app and immediately use it on any arbitrary conference with a website.


I did not earn my Master's degree. Do I mention it in my Ph.D. program and onwards and on my CV?

You don't need to emphasize or even mention such things unless asked to account for the time you spent. In general, it is a poor choice to mention things you think are failures. In any application you want to emphasize your suitability for the position and the high likelihood that you will be a success at it. Stress the positive.

But be prepared to give an honest and sensible answer if asked what you were doing for a period of time longer than a few months. It is probably fine to say that you pursued a dead end and changed course, which sounds accurate. It is also fine to say that you escaped a dysfunctional environment after being caught up in it for a while. But that isn't something for your CV or your SOP.

You will probably be asked to supply transcripts of all academic programs in some applications. You need to do that, of course. But you don't need to characterize the situation as a failure unless the institution considered it so.


How Well is a US College Degree Accepted in Québec?

A US Bachelors degree generally would be accepted, but in your case, since your degree is from a TRACS accredited college, you may have a difficult time.
For my US university (and most US universities), the policy for domestic applicants for graduate studies states:

Students must have a bachelor’s degree from a college or university
accredited by a regional accrediting association. If the degree is
from a recognized but not regionally accredited institution, the
application will be reviewed by the department and by the College of
Graduate Studies.

TRACS is NOT a regional accrediting association.  Without more details, it's not clear whether your college would qualify under the second sentence, but note that it already states further special review is necessary.
Given that your degree would not be recognized by most universities in the US (or at least not automatically), you will likely have a difficult time having your degree recognized in other countries.


I imagine that it could do wonders to your citation count

I honestly can't imagine that an unsolicited request to cite a paper actually generates enough citations to matter much.

I don't engage in this practice myself, and my response would be a cursory glance at the paper to see if it was essential (though the email should have articulated this) followed by either thanking the person for bringing it to my attention, or far more likely, simply deleting the email.


Lab computers: high end now or average system and repurchase in a couple of years?

In general, I would argue in favor of getting the best available system that fits within your budget at the time of the purchase. You might be able to save some money now by buying a less powerful system, but the danger of doing so is that you can't necessarily guarantee that in N years, when you plan to buy the replacements, that you'll have the money in the budget to do so. Long-term funding guarantees really aren't, and what is promised today might not hold up several years from now.

By getting the best available system now, you postpone the "must replace" date a while, which can give you more time to find a replacement (or the funds to replace it, as need be). Also, if your money is time-restricted in its use (you have to use it this year, for instance), there's no real incentive to skimp.


Sure. You have booked a time, make the call. If you want to be sure, ask him over the phone if it is still a good time.

Academics are busy and slow responders, so since you confirmed your emails may have been given the lowest priority.


Using a similar application essay I used before

I honestly think there is nothing wrong in applying with a similar work of yours. And I think it, well, for all the reasons you've mentioned yourself, starting with the fact that it won't be considered as plagiarism, since the primary version of it is yours as well, ending with the fact that the work is sent to the same school.
However, depending on whether you've made only minor changes to it or not, you might adjust the work a bit more, or expand it, or formulate some thoughts differently for the sake of back-up (say, if there is a chance that any of the members of the admissions know or have previously seen your primary work - then they might think that you weren't generous on the effort and,therefore, don't perceive the opportunity to be worth working more on that work or on additional ideas). After all, you're the creator, so it is still up to you to decide upon all the abovementioned things!


Where did the "Cited by" link go on Google search results?

I don't know if it can be re-enabled (seems unlikely), but a workaround could be to use the Google Scholar button* browser extension (Firefox, Chrome). You can select the title of the paper, then click the button to see its search results on Google Scholar, including a clickable "Cited by" button. Alternatively, you could directly press the button if the title is already present in your Google search terms. It is not as convenient as having the link directly in the search results, but is still easier than separately opening Google Scholar, in my opinion.
Screenshot for reference:

*No affiliation


How do I professionally communicate to a colleague that I am not interested in helping with his project anymore?

Your project is nice, but I now decided for myself that I can't invest more time in it. I'm too busy with other projects which have priority for my current research interests (so, talking to my advisor won't fix the issue).

And just repeat that same basic point when he tries to argue/discuss with you.


Having the letter of recommendation (LoR) writer send the LoR directly to the institution to which you are applying is indeed the standard procedure in the English-speaking world and increasingly beyond. In this procedure, the LoR is confidential; only the issuer and the recipient(s) should normally see it.

The process works as follows:

Online forms usually have two "sides". The first side is for you, the
applicant. You enter the name and email address of your LoR writer,
after you have obtained their approval. An email will be sent to the
LoR writer with a link to "their" side of the website, to which they
can then upload the letter and perhaps additional information.
For the offline process, you write your application, and the LoR writer sends in their LoR independently from you before the deadline.

However, in some countries (until recently e.g. in Germany and Austria) a different procedure is used, in which the LoR is handed to the applicant who then submits it together with their application (via website or offline).

I would contact the HR department at the institution where you are applying and ask for clarification, then talk to your LoR writer again. If the institution explicitly requests that you hand in the letter, you can just relay this information to your supervisor. You may also want to make your supervisor aware of different traditions of LoR writing in different countries. Alternatively, ask the HR department whether they can accept a LoR directly from your supervisor.


Do I ask the editor of the rejecting journal where to submit next?

Sometimes a referee or editor will offer an unsolicited suggestion.  When that doesn't happen, asking for suggestions would be unconventional.  As an editor, if an established professional asked me for suggestions, I'd be a little annoyed (they should be able to figure that out themselves), and I'd give a terse reply like "Sorry, I'm not sure what the best place for your paper would be."  If a beginning researcher asked me, or anyone dealing with a truly unusual situation, I would try to be more helpful.  The response you get may depend on the editor, but the worst case scenario is probably annoying the editor a little and getting no reply.  (I don't think there's any risk of dreadfully offending anyone, assuming you don't press the editor further if he/she doesn't reply or seems impatient.)  I would ask the editor only if you don't have any mentors you could ask, but in that case it could be worth a try.


(note: I have no references for the below, nor am I qualified in the topic)

First of all, the premise of your question isn't quite accurate: certainly in the UK it's very common for undergraduate degrees to have no thesis requirement. But putting that aside:

I think there are parallels with other mediaeval professions, which required proof of skill in order to become a member of a guild (the professional organisation). To be a 'master' of the guild one had to produce a 'masterpiece' (the origin of that word); this has obvious parallels with the idea of a thesis proving that an individual should be admitted to a degree (remember that historically a degree is more like a rank than an award, honour or qualification).

The MA at Oxford and Cambridge is still awarded automatically to those with a BA seven years after the start of the degree, which I believe matches the time someone in a professional guild would take to become a master.

Note also that the modern doctorate is a much more recent invention than the MA.


APA Citation of Website With No Author Mentioned

DISCLOSURE: I work for Mendeley as a software engineer. The reason I have used Mendeley is to show how it would cite this particular reference with this particular citation style using a tool familiar with academics and scholars.

Based on my findings, the citation would look like:

  Apache Struts Team. (2018). Announcements 2018. Retrieved March 28, 2019, from https://struts.apache.org/announce-2018.html

And the in-text citation would look like:

  (Apache Struts Team, 2018)

Please find below the steps I took to produce this answer:

I imported https://struts.apache.org/announce-2018.html using a Mendeley tool; I manually entered missing information in an attempt to construct a reference similar to yours:

And this how the reference looks like in Mendeley:

I can select this reference a copy/paste it using a citation style:

The formatted citation will use this citation style:

This is what you get when you paste it:

  Apache Struts Team. (2018). Announcements 2018. Retrieved March 28, 2019, from https://struts.apache.org/announce-2018.html

Then I can use another Mendeley tool to produce an "in-text" citation: (using the same citation style as in step 3)

Which gives me this in-text citation:

  (Apache Struts Team, 2018)


Can an improvement to an existing implementation be publishable?

For purposes of publishability, it doesn't really matter whether your implementation was built from scratch or from an existing codebase, or how many new lines of code it required.

What matters is whether your results contribute some new knowledge to the field....

... which we can't evaluate for you here. You need to read the literature and the previous work, and identify what you're contributing that's new. (It's not measured in lines of code.)


Tips for starting a new research direction

So the reviewers take unusually long time, don't understand parts of your work, or don't see the merit in it? As you say, it's a likely sign that the editors have a hard time finding suitable reviewers. This suggests that you should make heavier use of recommended/excluded reviewers, if the journals allow it. Pick them strategically, but also honestly, and motivate your choices. It's not necessary for all traditionalists to die if you can get more open-minded referees... On occasion, it might also be worth appealing a rejection if there are clear signs of reviewers misunderstanding the paper. Though the probability of success seems to vary a lot between fields and journals, so your mileage may vary.

It may also be the case that your papers don't have clear enough explanations of why your approach has promise or is valid. You might well explain what you're doing clearly, but fail to convince someone else that it's worth doing in the first place - especially if existing methods in the target field work fine. Typically the case for a really novel approach needs to be more convincing than that for some incremental work. Directly benchmarking it against existing methods is often useful. Try to find any patterns in reviewer responses of the "I don't see how so and so" kind and address them head on. Also try to get critical feedback from colleagues to help find any gaps in your arguments.


Is It Common For People To Write Literature Reviews On A Topic For Someone Else?

I don't know how common/typical it is, but it seems to be certainly part of a job description for a RA, especially if your implication is that you are a doctoral student.
One reason for it is just part of your training and when it comes time to do your own dissertation the practice would help.
But additionally, if the professor is exploring some new research direction it would be helpful to them to have help in assuring that they don't miss something important.
And anyone starting out in a new research area will have the same dilemma as yourself. It is hard to know where to look initially. You need to review a lot of papers and chase a lot of references. That is the nature of the task.
If it were crystal clear it probably wouldn't be necessary.
It is good that  you are humble at the start. I'd guess that the professor knows that it isn't easy and that the initial product might require refinement. Just be honest along the way about what you have "covered" and any gaps you think might still exist.


Should I email or text the professor as a apology if it seems that he is ignoring my email

I think you should apologize only if you have done something wrong. That doesn't seem too be the case here. He is likely just busy. It would be good not to flood him with things for a bit, but likely he is catching up on a backlog of work.

It is even possible that he thinks you are working fine for the moment and don't need an intervention.

Stay calm and carry on. If he is unhappy in any way you will likely hear.


"Fake" Things that are used in Experiments

At the most general term, you would call it a model. An animal model, a mannequin that models human movement/bones/flesh/weight, a drug that models the effects of XYZ in vivo. Whenever we can't use/describe nature directly, we use/describe a model.


Risks in accepting a position if candidate considers themselves unqualified and believes they will fail

The main question here is what kind of postdoc Sasha needs to appoint. Does Sasha have a specific project / task that they expect Freddie to handle? To that extend is this negotiatable?

If Sasha has a very specific task in mind that is largely un-negotiatable (e.g., because of hard commitments to a funding agency, or because there is a specific study that Sasha really wants to do), and Freddie foresees that they won't be able to actually do this, then they are only setting themselves up for failure when accepting the postdoc. The consequence will likely be a personal fallout with Sasha and a big setback to their own career. Nobody wins here, and Freddie should decline.
If Sasha is more flexible, and Freddie can do something that would be of significant value to Sasha's research programme, it is likely that things will be ok. The consequence in this case will likely be that the project gets adapted or shifted to another person, and things will work out alright. (or at least it has the same chance of working out alright than any other postdoc)

Given that Sasha knows Freddie personally, and has explicitly invited them to apply, I presume that the second case is more likely than the first - but a frank discussion between Sasha and Freddie is necessary. It is possible that Sasha is not aware that Freddie lacks these skills, or that they overestimate Freddie's ability to learn the required skills on the spot, but it is equally possible (really: more likely) that Sasha is fully aware that the project will go in a different direction with hiring Freddie, and they are ok with that.

Many academics I know (including myself) care more about the potential of a candidate to do good science in their overall field than whether they are the best fit for a specific project. In other words: I would typically rather hire a great person who is a bad fit for the specific project than a medium person who is a great fit. Ultimately, I care more about good papers being written in my team than what I care about the topic of any particular project. Freddie needs to find out if this is the case for Sasha as well.


Why do universities fund Ph.D. students in the sciences?

A good question. Why would the school make this investment (which could be closer to $100K/year)?

As pointed out, if you are TAing/grading/teaching, you are providing services that the school charges undergraduates for.
The funding of a university is not entirely like that of a business. Some of the money is a direct investment in purely academic pursuits, especially that from grants. Educating people and doing basic research is part of what that money is allocated for.
Averaged over all the graduate students, the direct value that they provide to the university in terms of research which goes on to get grants/prestige/donations/patents is substantial.
There is a non-trivial chance that you will become a wealthy donor to the school.


Are there still journals who only publish their papers in the paper form?

Yes. But they are more or less irrelevant at this point. Very, very few people will bother to read them.

One journal in my own field was strictly print until a couple of years ago. They are finally included in one database, but with a five year embargo (meaning only very old articles are available electronically). Another newer journal with a similar target audience is completely open access. Obviously, the open-access journal is getting cited more, the established paper-only one less and less.

In my opinion, the aversion to making a journal available electronically is based on old-fashioned technophobia. There is no serious rationale for it. Yes, they could get more money from actual subscriptions if libraries and/or individuals were willing to pay for them, but that's simply no longer a viable model.


I had a professor at my undergrad who would use an online service to create "mini-quizzes" throughout class; essentially, we would log into the service with our smartphones, he would place questions on his slides, and we would answer through the app/website. He could see the results live, and if enough people got something wrong he would go into more detail (this is very similar to the "iClickers" that some universities use).

I've seen some professors use Twitter as a means of enhancing the classroom - they would create a class account, and everyone would be expected to contribute by uploading photos, tweeting related news articles, and so on. I seem to recall this working best for classes in the natural sciences (biology, etc.) or fine arts (not that it couldn't be adapted for other fields, of course).

I also know of a professor at my undergrad who taught an interdisciplinary course that brought English majors, computer scientists, and a few others together to create a mobile application for a so-called "Poetry Walk" around the town. The group worked together to choose sites around town, create a piece of poetry associated with that site, and then build an app that would trigger a particular piece of poetry/spoken word based on your location.

Long story short - there's a lot of potential for mobile devices (I'm with scaaahu, if you're going to allow phones, why not allow tablets and laptops too?). It's really up to the instructor's imagination.

Based on O.R. Mapper's comment, I want to make a note that, for the foreseeable future, any activity in class that makes use of mobile devices should still not necessarily require students to have a mobile device. Simply put - this places students from less-fortunate (poorer) socioeconomic backgrounds at a major disadvantage, and it publicly reminds them of that.

The only exceptions I can think of are:

A university such as my current one  that requires all first-year students to have a laptop that meets at least certain specifications. In that case, asking students to bring their laptop is acceptable (though personally I think the requirement is a bit unfair, but that's my opinion).
A course that requires the mobile device as a central piece of the course (i.e., the mobile app development course I mentioned earlier. Though development platforms - smartphones - were still provided by the instructor in that case).

Regardless - if having a mobile device is not a requirement for enrollment, as an instructor you have a responsibility to ensure that all students have the opportunity to participate equally in the activity.


Is it weird to display ads on an academic website?

Such a website is itself an ad: for the lab, the lab's research, and for the personnel running/working at the lab.
In many ways, a lab website is like a resume. While it's not unusual for newsletters published by some local org (say, a school, church, youth group, etc) to have local ads to cover publishing costs from the neighborhood dental clinic, grocer, etc, but you wouldn't expect to find these on a resume.
Probably most people are conditioned enough to online ads that they wouldn't even notice them, but if they did it might seem a bit weird, and if they were at all intrusive it would be downright ugly looking and reflect badly on the lab. If I were working in a lab where the PI had a website with ads, I'd be embarrassed by it even though it wasn't my own responsibility. If I was visiting such a site, I might wonder if I've stumbled on some illegitimate content farm site by mistake.
I doubt a typical academic's website gets anywhere near enough traffic to make ads make much sense financially. The cost of potentially putting off a precious visitor doesn't seem worth it to me to pocket a few pennies.
If the site is hosted by the university or with any grant funds for research it is likely illegal or against some terms to make any personal profit off such a site; even if the funds are just used to pay back the site costs it's a gray area that is still probably not allowed. A university could certainly even have a policy on this even if their funds are not directly involved if anything about the website affiliates it with the university, including being an official or pseudo-official website for a lab operating out of that institution.
It's just not worth the potential conflicts from any angle I can see.


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

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

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

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

The other reason is that faculty also have research interests.

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

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

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


Is it considered plagiarism when you modify your professor's proof when solving a problem in a homework assignment?

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


Impact of parameters in experimental results of paper

Actually, I had a programming part in my masters thesis in which I wanted to show that some parameters do not have significant impact on the results. This is what I did which seems to be a combination of your methods:

I drew a plot with all the parameter remaining the same except one parameter that I want to study on. Even if the variation of the parameter does not show any significant change in the results, it does worth to show the results in a plot. It is not important that all the lines overlap. At least the reader sees that the results are the same. But, in a paragraph or at least one sentence following the graph I would talk about this. You may write that all the plots overlap, because of this and because of that; and talk about why such results happen. Also, in the caption of the plot, write something that directly says something about such insignificance.


Can I publish a paper from a work group that I happened to work on it alone?

I suggest that you be extremely careful about this. One of the most distasteful tasks of an Editor is to sort out claims of authorship in articles that have been published. You need to resolve this completely, otherwise it may be disastrous.

In resolving authorship, you must try to contact all your group mates and receive from them some acknowledgement that they wish to proceed as you suggest. If they do not agree, then I suggest that you think twice about continuing. You do not want this issue to spill over into the public arena.

You have to consider, too, the implications of your actions. What does this publication mean for the original assignment? Could the publication of this work retroactively impact on the grades of you and your colleagues? Let me be blunt -- could their grades for this assignment be reduced to zero, adversely affecting their marks, because the publication resulted in a review of your assignment? Now you could potentially be in double trouble!

Finally, say they did agree to allowing you to proceed, you might acknowledge them in your paper just the same.


Submit paper before or after going on holidays?

I would recommend submitting, because there is a great degree of uncertainty in when you will receive a response, and even with a fast response, your allowed revision time will likely be long enough to extend beyond the vacation time in any case.  If things more unexpectedly quickly, you can ask for an extension and will likely face little problem in obtaining one.

If you do this, however, you have the following responsibilities:

Make sure that you at least monitor your email when you are around, so that you can respond if necessary.
In the two-week period when you will be unable to check your email, make sure you have a vacation auto-response message set up.


How should I cite something learned second-hand (eg, from Wikipedia) when I haven't seen the primary source?

What you're referring to is an indirect source. In general, you should always work as hard as you can to find the original source. If that is not possible, all of the major style guides include a way to cite indirect sources. Note that you should not cite Wikipedia (see the "do not cite Wikipeida" note at the end of this answer). If an indirect citation is absolutely necessary, it should come from a reputable, peer-reviewed journal or other academically respected source.

According to Purdue University, the MLA rule is to name the author of the indirect source in the text and cite the work you have in-hand:

  For such indirect quotations, use "qtd. in" to indicate the source you actually consulted. For example:

    Ravitch argues that high schools are pressured to act as "social service centers, and they don't do that well" (qtd. in Weisman 259).

  Note that, in most cases, a responsible researcher will attempt to find the original source...

Williams College further clarifies that the indirect work should be included in your Works Cited list:

  ...include the indirect source in the Works Cited.

The APA rule (also from Purdue University) is to exclude the indirect source (called the "original source", below) from your reference list and only include the work you have in-hand (called the "secondary source"):

  ...name the original source in your signal phrase. List the secondary source in your reference list and include the secondary source in the parentheses.

    Johnson argued that...(as cited in Smith, 2003, p. 102).

  [...] Also, try to locate the original material and cite the original source.

The Chicago rule (once again, from Purdue) is to cite the indirect source, followed by the in-hand resource:

  ...Chicago discourages the use of [indirect sources]. In the case that an original source is utterly unavailable, however, Chicago recommends the use of "quoted in" for the note:

  Ian Hacking, The Social Construction of What? (Cambridge, MA: Harvard University Press, 1999), 103, quoted in Manuel DeLanda, A New Philosophy of Society (New York: Continuum, 2006), 2.

That said, do not cite Wikipedia in a formal document (unless, perhaps, you are actually writing about Wikipedia or collaborative editing techniques). I love Wikipedia, and I believe it is reasonably well-maintained and has a lot of good information. However, you have no way to verify if the information in an article is true -- or, if you do have a source to verify it, you would just cite that source. Aside from the tired, "Anyone can edit it!" complaint, two severe issues with Wikipedia as a citation source are:

You get whatever version of an article stands at the exact moment your web browser fetches the page. No matter how hard Wikipedia's editors work, they can't stop a bad edit from reaching your web browser if it was made seconds before you fetched the page. Wikipedia doesn't undergo any kind of pre-publication review; all review is post-publication, which means you may see totally unreviewed information. (You can mitigate this by citing a specific past revision, but it still stands that a post-publication review process means that any given revision of an article could have claims that have been reviewed by absolutely no one except the author.)
In order for a reader or reviewer to ascertain the usefulness of a source, it must have an identifiable set of authors (or, for anonymous works, at least a consistent, reasonably small set of authors). Wikipedia makes that requirement incredibly difficult to satisfy. (Again, it's possible to satisfy this requirement if you cite a specific revision of a page and find out what contributors wrote each part of a page, but it is still difficult since a potentially huge number of contributors have helped build that revision.) It's hard for a Wikipedia article to be reputable where there are no clearly identifiable authors to which a reader could attach a reputation.


Advantages/disadvantages of bundling source code from separate, related papers?

I face a similar situation. I'll tell you what I'm planning to do, although I don't claim this is the best approach. I think it's a reasonable compromise between making things easy for the reader, and making things easy for me.

First, I wrote several libraries that I keep on GitHub. One or more of these is needed to reproduce the research I'll discuss in each paper. I'll create a release for each library, with a citable DOI using Zenodo. A set of instructions is available.

Likewise, I'll have a configuration file, plus some scripts, and maybe some data, that are unique to each experiment. This is where I'll put the README file describing how to build/run everything. I'll create a GitHub repo for those as well, and create a release using Zenodo.

So each paper I write will cite all the library/other releases needed to reproduce the software.

EDIT: One advantage of this is that while the DOI will point to the exact version of everything I used for my published results, it will also be clear where people can go for the latest version of everything.


How to reference to a whole section of other paper that my paper is heavily based on

If I understand your question correctly, your problem is that you want to write a section of your thesis and indicate that the entire section paraphrases someone else's article. I would simply add a sentence near the beginning of that section that says something like "The following discussion is taken from Watson and Crick (2016)".

Generally speaking, plagiarism not an issue if you clearly cite the other person's work. Copyright is not an issue if you only use a small bit of their text and you clearly indicate that it's a direct quotation (i.e., using quotation marks or block indentation) and cite the source.

Finally, you might need to worry about whether or not you've done enough new work to merit approval of your thesis, or to merit publication. Your advisor can tell you if you've done enough new work for your thesis. The editor of the journal you want to publish in, or the organiser of the conference you want to present at, will ultimately decide if you've made a contribution worth publication in that particular venue.


Australian Research Council (ARC) grants for overseas applicants

Assuming you are willing to move to Australia, you could apply for one of the ARC fellowships.  You would need to find a host institution.  If your doctorate was awarded recently, DECRA would the best program for you.


Is mathematics becoming more applied, while engineering is becoming more math-y?

I agree with all the comments, that engineering has become more mathematical because of the rise in computers and similarly applied mathematics is growing because of its well poised position to aid in many developing engineering problems.

While I could not find any studies to back this up, I made some graphs of my own from the Web of Science.  The first two compare Applied Math
 and Pure Math.  The volatility of the Pure Math graph leads to a difficult comparison.  Similarly, I took screenshots of Engineering with Math and All Engineering. Which I believe more clearly shows a growth in engineering-math publication in the past five years or so, as compared to all engineering whose rise began earlier.

Similarly I looked into Arxiv, as it supplies a nice single source of data.  These results are for number of uploads/publications.

------------------ 2000-2004 ---- 2014-2017 ---- Growth
App. Math --------- 577 ------------- 5456 ------- 9.45
Pure Math --------- 253 ------------- 1399 ------- 5.52
Eng. Math --------- 14 --------------- 476 ----------34
All Math ---------- 14,408 --------- 102,382 ------ 7.1

While these figures are based on publications, and therefore could be caused by changes in publishing practice I think they do give decent, data-driven evidence for the claim that math is becoming more applied and engineering is becoming more mathematical.


Are scientific contributions of the article listed in the abstract?

In light of the example you linked, you should indeed state your contributions, but there is no need to state that these are your contributions. So instead of stating "The contribution in this paper is considering problem A using method B", you should use "We consider problem A using method B". Doing this would have easily saved 20 words in your example without changing any of the meaning. Even more importantly, the useless words are in the beginning, which is the only part of the abstract you can actually be sure that people will read.
The default assumption on a paper is that you are presenting something new and that new thing is why people should be reading your paper, which is why will be prominently mentioned in the abstract. So the default assumption when reading an abstract is that all results mentioned describe scientific contribution. There is thus no need to explicitly mention it.
There are of course things in the abstract that are not new contributions, but they are generally made obvious by phrasing. If your abstract starts with "We survey some recent results in ..." no one expects that the results mentioned afterwards are new. Or if you are (in)directly referencing using "The well known problem of ..." then no one will think you came up with the problem. But if a sentence starts with "We show that ...", then any reader will assume that you claim to be the first one to do so in this context.


Why are US PhDs different from European PhDs?

First, let me start off with a counter-question:

Why would you expect them to be exactly the same?

Different regions have historically different educational systems on all levels, starting from Kindergarten. Why would you expect specifically the PhD degree to have a completely uniform definition everywhere in the world? Of course there are nowadays activities to make degrees (incl. PhDs) more comparable worldwide, but these things take time. As politicians in Europe have learned as part of the so-called Bologna process, you can't just top-down decide that from now on, we are using the US system.

Of course, there are sometimes reasonable arguments for differences in system. For instance, you concluded:

  it takes longer, on average, in the US than in Europe to finish a PhD since US PhD programs require less and have more coursework compared to Eur PhD programs.

In the US, a bachelor's degree is required for starting a PhD. In Europe, almost universally, you need a master or one of the older five-year diploma studies. So we in Europe expect students to hit the ground running basically from day 1 in their PhD. On the other hand, we don't require them to do much, or any, course work because they did all of that as part of the previous studies. Of course, if you then look only at the pure time spend in what is called the PhD studies, you end up with a shorter time in Europe.

Now you can of course go deeper down the rabbit hole and ask why European universities expect PhD students to have a master's degree first. The reason for that is mostly historical - around here, we often didn't even have Bachelor's degrees until the above-mentioned Bolognia process. What happened as part of this process was that decision makers ended up deciding that pretty much the first three years of the old diploma studies became "the bachelor" while the remaining two years became "the master". Of course, this reasoning led to the public opinion of somebody with "only" a bachelor's degree as a glorified college dropout. The universities implicitly also shared this notion, as there were never substantial motions to admit bachelor degree holders to PhD programmes in most universities. Slowly, the bachelor programmes are getting more profile as something better than just the first 3/5 of an actual degree programme, and consequently their public image also improves. Universities are nowadays also taking first tender steps towards making it easier for bachelor degree holders to start a PhD - however, so far, this is mostly targeted at making it easier for international students to enroll.

Important concluding remark: I am aware that a lot of the above contained pretty sweeping generalizations, which do not hold true everywhere. Specifically, Great Britain and Ireland already historically used a different system. However, I wanted to answer with something a bit more substantial than "systems are different everywhere".


Department not allowing me to take courses from another department even though everyone else is allowed

You seem to be good at looking up university policy and rules, and reading them carefully.  So I suggest your next step would be to look up procedures for appealing academic decisions.  Also, get to know your university hierarchy.

Universities vary in how decision making is done, so it’s impossible for me to be more specific about your university.

But I will give you a trick that I’ve had good success with in a variety of educational institutions: Phone or visit the secretary of the highest-level dean you can find that sits above your department, and ask his or her advice for where in the hierarchy to bring your problem.  This secretary is often the most competent, knowledgeable person about university hierarchy in the whole institution.

And a general tip: Tell your story concisely and with a neutral tone of voice.  Begin by stating the problem.  Initially, leave out the numbered list of crazy reasons you were given (but be prepared to provide them if they ask you why the department rejected your proposal).


Journals similar to Journal of Chemical Education in style

While I am a regular reader of J. Chem. Ed., I wouldn't really say it's a good journal to read for learning the basics. It is more a journal of educators in the field of chemistry, and while I think some articles may be useful to chemistry students (including lab experiments and activities), overall its goal is to be a forum to discuss how we teach chemistry, rather than a place to learn chemistry.

For other journals about chemical education, you can find a very short list on Wikipedia. Also, as stated there, most such journals (especially for junior or high school chemical education) are localized, i.e. limited to a specific country (because of differences in curricula). Among the international ones, I would recommend Education in Chemistry, which is more readable than its sister journal Chemistry Education Research and Practice


Can an unpublished but accepted article be used for an MSc degree?

This will depend on the conference and on local copyright laws.  I can't speak to the local laws, since I don't know what local is for you.
You may be asked to sign a copyright form, and that form will have the answer for you.  For instance, it may clearly state that the paper in its exact form is not allowed to be reproduced in any way (although I strongly doubt it would, that's a weird thing for an academic paper).  My thesis was paper-based in the sense that it contained literally the papers I wrote and had accepted, in camera-ready form.  We were allowed to do this because the various publishers considered this to be appropriate use (in fact, my copyright forms all explicitly stated that inclusion in thesis documents is acceptable).
If you are not asked to sign anything about copyright, and laws in your country agree, you retain all rights and may do whatever you want.


Can a PhD student apply for another PhD program in some other university?

Yes, you can apply, just as anyone else. But yes, it is possible that people in your current program would take it as a negative. And, yes again, that the other university or program might rank you a bit lower if you already have a "suitable" position in a doctoral program. But I doubt that the last would be a large factor in most cases.

But there are a lot of reasons to switch. Some of them are very important. If you have a serious need to switch, either for personal or academic reasons, don't hesitate to explore your options and follow up on good ones. This is especially true if you don't think  you have a good path to success where you are now.

People understand that others change their minds and their directions. They understand the need to move locations and situations. They understand that some qualified students are in a bad situation.


Should I use a linear function or two linear functions to grade scores?

You should focus on getting the grading correct for students who do much better than just passing, who score within the range where you would personally draw the line between who is an expert who has completely mastered the subject and who is good but needs to study a bit more to be considered to be an expert. This line is not usually at 100% because you can make minor errors even if you are an expert, it's more typically somewhere between 80% and 100%. You then want to assign some grade, say 7 to students who are at or just above that boundary, which mans that the boundary percentage should be mapped to 6.5.

The goal of teaching is to assist students who do their best and may go on to embark on an academic career, it's not about catering to students who for whatever reasons end up not doing well. The students who are not doing well risk getting into problems; if they score sufficiently low they'll not "pass the course" but it's just a total waste of efforts to figure out how to draw the line for that.

Your attitude should be that someone who scores well below, say, 85% has de-facto failed the course, but in the gray area between, say, 60% and that 85%, they are not going to be deprived of a diploma just because they didn't do well on your exam. Whether that 60% becomes 50% or 65% should not be of any concern to you. That uncertainty should make your students who are not studying hard enough worry a bit more so that they end up studying harder.


How graduate admission committees choose between TOEFL scores?

Unless your score is significantly low in one particular section (for instance, having a 105 with 30 on all sections but a 15 on Speaking) or if the committee has a strong reason to doubt your English skills, I don't see why you should worry about resubmitting TOEFL score. You will be making far better use of your time strengthening other parts of your application (i.e., SOP, GRE, etc). Given
a sufficiently strong application, even if they doubt your ability to communicate in English, some schools will interview the applicant via Skype/phone to establish whether their English is sufficient, and not automatically discard the application.

The TOEFL score serves, in general, to establish that you have a basic ability to communicate and work in an environment where English is the main language. Meeting the usual 100+ TOEFL score for graduate applications is sufficient and higher scores are not usually heavily weighted.

To more directly answer your question about which score they will consider, that will strongly depend on the school. You can e-mail them directly to know how they will consider multiple TOEFL scores. I suspect it would be analogous to the GRE (i.e., some departments choose whichever has a higher total score, some schools pick whichever is higher by section, some schools pick the latest, some schools analyze holistically).

Note: the answer to your question may depend on your field. I am in engineering.


I’ll address you as the graduate student based on the phrasing of the question, hope I’m not being too presumptuous.
In the US, the professor can’t be your advisor if sexual or romantic relations are taking place. They can’t be on your thesis committee. They can’t be teaching a class you’re taking, can’t be supervising you as a TA, can’t be writing you a letter of recommendation, can’t be in any position of authority over you whatsoever, during the relationship and most probably at any time in the future. If none of those things are an issue and you’re a consenting adult, and barring any specific institutional policy to the contrary, you’re in the clear and are free to behave in any way that any other adult is allowed to.
Keep in mind some people in academia would still feel uncomfortable with the situation and may be critical towards you and/or the professor if they become aware of the relationship. Depending on the details, your and the professor’s professional reputation and career may be at some risk. Sex tends to make people uncomfortable, sometimes for good reasons, sometimes not.


What criteria does a research project need to match to be called open science?

To answer the first question:

I asked a similar question on twitter a while back and got a range of responses.  Those are summarized in a storify.  To paraphrase that summary ...

open access to data
open access to code
open access to publications
open source
work must be reproducible
needs to be web enabled

The last bit, and I think this is an important component, is that open science is not binary.  It occurs along a gradient.

As for you second question, I would use reproducibility as a guide.  The minimum data that needs to be accessible is that which allows for an anlalysis/project to be reproduced.  Following the gradient theme, you could open up more than this, but that it isn't necessarily required.


While the details and availability vary radically from institution to institution, some professors are given a certain budget to spend on whatever they deem appropriate (within limits).

In the United States, this is most commonly associated with more senior positions (e.g., endowed chairs). It is typically not a very large amount, but often enough to support some travel or undergraduate researchers.

In other countries, it may be structured differently.  In particular, I have heard that some universities in the Middle East have been giving extremely attractive funding packages to professors as part of their program to attract foreign talent.  My guess is that this may be the case with your professor, though it is impossible to know for certain without more information.


Is it ok to asking several profs at the same time for a letter of reference on short notice?

Because of the workload professors are under, it is not an uncommon problem. The only way to address the problem is to contact multiple professors for a recommendation; I know other people who have contact multiple professors for this purpose.

You have only asked the Professor if they would be willing to write a letter of recommendation. This means that they have not already invested any time. So, If you get multiple recommendations, you can simply email the other professor(s), "Thank you very much for agreeing. Another professor has already offered to write me a recommendation letter, so to save yourself some time you don't need to write one for me too".


PhD Dropout Applying to Unrelated Master's Program. How to explain it on SOP?

Tell the truth - whether that be it was too hard, you lost interest, you had a disagreement with the adviser, it was a financial hardship, you had personal or family issues come up, etc. etc. Whatever the reason, just tell the truth. The admissions committee have probably read enough personal statements to read between the lines. Sort of like how in a job interview if you said "I left because it wasn't a good fit", chances are you had a disagreement with your boss (or something like that).


Does dedicating to god undermine my aspiration on research in-front of review panel?

Generally, I don't think that dedications are common. In engineering, for instance, you never see a dedication except in a textbook (not common though) and PhD thesis.
Besides that, no scientific reviewer should be impacted by a dedication. There are always black sheep, who won't like it or even have a problem with it.
As reviewers or a panel are always a bit of a draw of luck, I would stay on the safe side and not put this in (any sciences/engineering).
If you are so faithful and personally committed to dedicate this work to "God" from a personal point, that's what matters. It's not necessary to state it.
But that's a decision you have to make.


How do I politely remind a professor to respond to my request for feedback

After two weeks, you're within your rights to send a very polite reminder to the professor to have a look over your stuff.

However, I wouldn't make the subject title 'kind reminder'. Be efficient and help them out, make your title 'MSc Literature Survey' or something to that effect.

As for including when you were last in contact with them in the body of the text, I would leave that out. It might just be me but it comes over as a little passive aggressive. If you're wanting someone to help you out, best not to rub them up the wrong way before they've even started.


How should one formulate a Statement of Intent for an interdisciplinary degree?

In general, the more concrete your essay is—and the more it shows that you've thought through your plans and potential options at the school to which you are applying—the more strongly it will be considered.

Moreover, if you're pursuing an unconventional path, such as applying for psychology but also going for an MFA in design, then you'll probably want to make that clear from the very outset. Otherwise you run the risk of the faculty—which normally makes admissions decisions at the graduate level—thinking you've hoodwinked them somehow. When that happens, that can make your life very uncomfortable.

So you should mention your full degree plans including, if possible, professors from both departments.

However, when it comes to writing the essay for admission, that depends a lot on the specific program you're applying to. If you are applying only for a master's program in psychology, then you should talk primarily about psychology-related topics. Your proposed work in design should amplify your psychology work, but not dominate it. On the other hand, if you're applying directly to the PhD program, and the MFA is an integral part of your plans, then you need to explain that at the outset, and should indicate what goals you'll achieve in the MFA that will help you with your PhD.


How do mathematics graduate committees view Mathematics subject GRE scores around the 60th percentile?

Does a low score in the range of 60th percentile rule one out of top 20 programs?

I am already confused by "a low score in the range of the 60th percentile." A score in the 60th percentile is, by definition, high rather than low.  A math PhD student should know that. :)

In terms of whether that score would "rule you out": again, every program and even every member of every admissions committee has to decide how to weigh the various factors.  But that is why you apply to more than one program.  I think that if your application is otherwise magnificent, you are a very likely admit at several top 20 programs.

  As an international student, I have no idea how terrible such a score is and I am considering stopping the application process to US universities since I doubt if I stand a chance.

Yes, you stand a chance, so please don't stop your application for this reason.  The smart thing to do is to divide the programs of interest to you into tiers and apply to a few schools in each tier.  For instance, my program (at UGA) is about the 50th best in the US, and for us a 60th percentile score would in all likelihood not hurt your application at all.  So it would be smart to apply to some schools in the UGA tier.  (Perhaps even UGA itself...)


Writing a commentary to a scientific journal without one's advisor

I see no reason not to send this as a single author paper.

I would, however, mention it as a courtesy to any new adviser you may acquire. If they are reasonable, they will not require being authors, but they may have input that could be useful to you, and it would certainly be useful for them to know about the paper.


What are "all the rights and privileges pertaining thereto"?

Each of my diplomas says my degree is awarded "with all of its privileges and obligations" or something close to that.  I know of neither an official codification nor a learned treatment of the privileges and obligations involved.

But, along with Thomas Aquinas, C. S. Lewis, and Mr. Spock, as opposed to David Hume and Cmdr. Data, I hold that values are logical.  So I deduce that:

The "privileges" include putting the degree on your curriculum vitae so you can get jobs requiring a degree;
The obligations include honesty about the subject matter in which you are supposed to have some expertise.


Protecting yourself when leaving PhD which involves misrepresentation of results and potentially unsafe bio-containment procedures?

I would strongly consider whistle-blowing (internal, within your organization) in this particular situation.

There are many reasons (good, bad, and hybrid) that lead people to the decision of becoming whistle-blowers: plain vanilla ethics, the desire for power & attention, willingness to protect others, legal requirements, etc. However, protecting yourself by whistle-blowing is a totally legitimate reason.

Whistle-blowing comes with some potential consequences, but here are the reasons why you might incline towards doing it:

you already made a decision to quit your program: thus, the situation influenced you (and other group members) heavily;
you already decided to switch the field of study;
this story can have direct consequences as bio-material is involved. There are very good reasons why special regulations exist for working with such materials;
the fact that the wrong-doing is happening has documental evidence: lack of the permit that is required.

If you decide to proceed, be careful in terms of the facts you present. Try to be as objective as possible without adding unnecessary emotions. Make sure that you present the facts with as little interpretation of your own as possible. Let the knife do the work facts speak for themselves.


Possibility of acceptance when the editor clearly states that another revision will likely lead to a rejection

I understood from the question that you are asking whether to do the second major revision or not since the chance of acceptance is low.

I think it's better to go through with the second major revision and see what will happen. If you think the other referee's notes (aside from the one you think is biased) are valid, and doing those revisions will enrich your paper, then do it.

Your relationship with the editor do not end with publishing this paper or refusing to publish it. You may probably deal with the editor later in your professional life, and you might submit another paper to the same journal despite how this paper will end. So you wanna maintain a relationship with the journal editor. Stopping the communication about this paper without providing a valid reason is not good idea.

Good Luck!


Is it rude to ask the status of an application?

I don't think it is inappropriate nor rude to send them an email. It's your right to be informed with your result as time is passing.


Suggestions for high school student who is visiting a professor for HS research?

As a HS student visiting a lab, a willingness to do some of the "grunt" work in exchange for a chance to do "real" research is helpful. Being able, and willing, to do literature searches on a database (e.g., pubmed), to download easy to get papers, and go to the library to get hard to find papers papers is really useful for a lab. Most researchers would happily trade their time teaching about the methods they use and love, in exchange for not having to make a run to the library. Being able to do data entry and carry out statistical tests, with guidance, in a program like SPSS, is really valuable. Being able to make charts/figures in programs like Excel, Photoshop and Illustrator is a real plus.


What can academia do with the flood of bad or subpar paper currently online?

I strongly suspect that along with the papers being poorly formatted, they also have minimal usefulness content-wise.  I think the way to solve your problem is just to use a filter of only looking at papers in peer-reviewed, properly formatted journals.  And the better ones, at that.

Yes, there is a possibility you miss something, but so what?  Euclidean perfection is not expected.  If you are doing original work, you only have limited time to spend on literature and you need to use that most efficiently.  Even if your sole task is to review the literature, you have limited time to do that.

If there is some work that was self published or poorly written but still important, than it should have been recognized (via citations) by papers in good journals.  (Then, recognizing the importance, you can spend the time to decipher the poor exposition...but again, this will be a tiny fraction.  Often zero.)

So, instead of worrying about academia (not a monolithic entity) somehow cleaning up the Augean stables for you (how would they even do that...take control of the Internet?), just change your own work habits to stay out of the muck or be very limited and targeted in your plunges into it.


Do PhD programs care about the personalities of applicants?

Yes, decisions based at least partially on personality do occur.  It's not clear to me what the legal technicalities are - for example, depending on your country there may be laws regarding things like discrimination against the mentally ill - but in practice an admissions committee can do whatever it likes, and nobody will be able to prove there was any illegal discrimination.

The way it typically works is that having a particularly pleasant or agreeable personality won't help you, but having an unpleasant personality may hurt you.  If you seem likely to be difficult to get along with, rude, disruptive, uncooperative, or otherwise problematic, then that will generally be held against you.  (This may be judged based on your personal statement, letters of recommendation, etc.)  It won't necessarily doom your chances: some committee members just won't care, and others may be willing to excuse bad behavior if you are sufficiently talented.  However, on average it will hurt your chances, sometimes substantially.


I did at least half of the work, I am not cited in the presentations

It definitely sucks when you feel like you're not getting credit for your work, and in applied math, it is certainly not standard practice to omit mention of PhD students' contributions.  In fact, I've seen many presentations where professors and industry leaders show group pictures of their entire lab, and they're proud of the team effort.

However, passive aggression is almost never effective at helping you achieve what you want.

You seem to be on better footing with your supervisor than with his colleague, so I would start there.  Once you've cooled off a bit, schedule a meeting with him and mention how you've noticed your name is absent from presentations on your work.  Be honest (and respectful) about how this hurts you, and leave room for your advisor to explain.  It could just be an honest oversight, it may be intentional-- the fact is, you don't have anything but speculation until he explains.  Mention that you've noticed the same happens with his colleague's presentations, and ask if he could talk to the guy about it.  Again, try not to assume the worst.  There isn't any real motivation for omitting someone's name when they've made serious contributions, especially in industry, where large author counts are the norm and papers don't matter nearly as much as they do in academia.


How do I create a useful learning objective?

Disclaimer: Mostly opinions.

First. I'd suggest perhaps one level down in terms of the verb choice. What the course will likely do is to introduce an array of possible mistakes in these activities so that audience can avoid committing them. So, the objectives should not be "avoiding" but rather along the line of "familiarize with", "able to list", or "be introduced to a survey of." Whether to avoid or not is really not the takeaway.

The general tip of writing objectives is to think: "If I am going to assess whether my audiences have learned my messages, what are the aspects I will be testing?" Very likely, you are not going to give them a mistake-prone situation and see if they avoid it in real life; but perhaps provide a list of scenarios and see if they can identify which one is likely going to cause a mistake, and which is a safer/more professional approach. In other words, you'll be testing their knowledge and attitude, and not their behavior after class. Yet. your current objectives are about their behaviors.

Second, perhaps add some specificity. E-mail for what? Talking to family members? Someone whose pets just died? Business? Potential dates? If someone just picked up this one page of objectives, is there enough information for the person to decide if he/she should consider your course offer?

Third, consider providing a clear set of general benefits. After learning all these objectives, what will likely happen? Will they have a better commands in communicating with people in professional setting? In other words, what are the aspirations of your course, that you won't be teaching directly, but the audience may be able to realize that if they follow your advice?

Meanwhile, beware of over-promising. Communication is at least a two-way process and even your audience did everything "right," mistake may still happen. I'd suggest perhaps more neutral wording such as "achieve high level of clarity..." so as to "minimize potential miscommunication or mistakes."


Can a company prevent a co-author of a paper from putting his name on it?

Other responses talk about the law. However, if the paper, as I assume (after all this is academia.SE), is academic, there is another set of values that rule the matter, and that is defined by the academic rules for authorial attribution of scientific contributions; unlike patent or copyright ownership, they are not waived by working for a company.

Moral rights or not - if you have significantly contributed to the paper (as evidenced by the first submission round), academically spoken, you are a co-author. Removing you is unethical and a breach of academic rules. It is academic misconduct. There is no "ghostwriting" in academia.

Laws or not: the decision to take away a doctoral title is in many countries not a legal, but an academic decision, to be decided by the academic institution that conferred it and not by court. Similar here: the judgement whether this is academic misconduct is happening on the academic, not the legal level.

Note: the fact that they demand the drafts seems to indicate that they know this and try to deprive you of the evidence that you have been co-author on a virtually identical copy; which, if in your possession, would prove that you were a co-author and should remain so for the resubmission.

This may well be a legal trick on their side to improve their position in an academic misconduct investigation. On that part of the matter, you may need the support of a lawyer if you intend to fight, because of course, the company may have the ownership of the ideas and the copyright. But not the right to remove you as co-author.


How to Correct for a Less-Than-Complete PhD career when wanting to go into academia?

That's great!  That's just how you should feel (1st 2 paragraphs, at least if you're a normal mortal).  It means (i) you're not an arrogant fill-in-your-favorite-anatomical-term-here, and (ii) you're motivated to understand things rather than just get out papers.  This is what a scholar should be.

I felt like there were too many huge gaps in my learning when I was a grad student.  I felt like that when I was a postdoc too.  I felt like that when I was a new tenure track.  I have tenure now, and I still feel that way.  I just learned a lot of basic things over the past year that I can't believe I didn't know 5 years ago.  Part of this is the impostor syndrome, but part of it is just realizing that there there is so much out there to learn.

There is so much out there, and fields are so rich after centuries/millenia of development that you can only learn bits at a time, and you need to find a balance between solving new problems/getting out papers and learning what has already been discovered.  This is true for bigshots as well as littleshots.  Ravi Vakil (an algebraic geometer at Stanford) says the following, quoted from this MSE answer:

  ...mathematics is so rich and infinite that it is impossible to learn it systematically, and if you wait to master one topic before moving on to the next, you'll never get anywhere. Instead, you'll have tendrils of knowledge extending far from your comfort zone. Then you can later backfill from these tendrils, and extend your comfort zone; this is much easier to do than learning "forwards".

I was surprised to hear one of my friends, who is a hotshot and always seemed to know everything, once tell me something like: if we weren't expected to do research, we would spend all of our time just learning the beautiful mathematics that was already discovered.

At least in math, any postdoc mentor will expect you to have gaps (otherwise you wouldn't need a postdoc), and most mentors will want to you learn a lot of new things, though it is true that some mentors focus on being productive while learning as little new as possible.  So, instead I think you should focus on finding a mentor who you think you can learn a lot from.  Here are 2 things to look for:

They work on things at least somewhat different from, or at least from a different perspective than, what you/your advisor do.  Then you will be forced to learn more new things working with them.
The professor themself seems to know a lot, so you'll learn a lot just from regular interactions with the professor and their colleagues.  This also indicates they're less likely to be of the philosophy of publishing without learning.


Are there examples of classes with students publishing their reports instead of just turning them into TA & Professor?

Disclaimer: As I've only been a graduate student at the university I'm currently attending (USA) I can only comment on my individual experience at this university in my particular field (computer science) and the classes that accompany it.

Experience: I have a publication currently accepted that is the direct result of a course I took.

Throughout my time as a graduate student I've observed several class formats as far as expected work goes, typically involving some combination of homework, exams, and projects. Those involving projects, particularly when greater emphasis is placed on the project, are those rife with opportunity for publication. An additional indication of this is if the faculty member is teaching the project-based course in his/her area of research.

If your intent is to take a class with the hope of turning your work into a publication I would recommend taking a course where the above align (project-emphasized course work being taught by a faculty member whose research area is the same as that of the topic being taught).  Additionally, I would recommend:

1) Choosing a class that aligns with your own interests and research.

2) Speak with the professor prior to the start of the class about your intention of turning the project into a publication. The professor should be able to comment on whether their project is a good opportunity for such an endeavor and perhaps be able to provide you with advice on how to be successful in completing the project and turning it into a publication.

3) In discussing with the class instructor, it would also be a good idea to discuss project expectations, particularly as they relate to (a) working with other class members and (b) the criteria that will be used to grade your work. Regarding (a), not all class members may be interested in going the extra mile to turn a project into a publication. Having this discussion with the professor up front will mitigate the chance of encountering "snags" related to this (e.g., you be given an exception to work on the project by yourself). Regarding (b), the criteria used to grade your project may be slightly different than what it takes to make a publication. Granted your intent, and what will almost certainly entail a greater amount of work, some leeway may be granted to you if tasks to create a publication and those needed to earn full marks on the project don't line up entirely. This, of course, depends on the instructor.

4) Getting [at least] some preliminary idea of the course material and ongoing research in the area of the topic of the course, prior to its start, will help. Furthermore, having some project idea (i.e., research idea) in mind, would be ideal. This can also be discussed with the professor.

I'm sure there are points and recommendation that could be made here, as well as other scenarios, which may vary by field and university, but for me, in my own unique experience, these were the highlights that led to my course-based publication. Best of luck!


How important is having research experience in the same department you are applying for?

If you want to apply to a doctoral program in statistics in the US and you have a BS in mathematics, just do it. There is no real need to take side trips into microbiology or anything else. Relatively few undergraduates in the US have any serious research experience when they apply to grad school. And in many graduate programs, serious research doesn't start immediately in any case. Some places have "warm ups" for the big event (dissertation research) but most have a lot of coursework leading up.

And of course, until you apply, you don't really know your chances.

Math is a pretty good background for statistics, of course. Much of the basis of stats is based on math. You may even have taken a probability and statistics course already.

It is odd, only because of the strange path to a goal. The winding path isn't needed here. However, microbiology might be interesting if you actually have an independent interest in it. But it isn't likely to get you much closer to acceptance in a statistics grad program.

Just. Do. It.

For the record, in Europe this might be different. But that is because both the undergrad and graduate programs are quite different than in the US.

And letters of recommendation is a separate issue, possibly serious. But it might be worth going back to your original math professors and talk to them about how they can help you. It is a hard thing to do for someone with autism, I know, but it is something you need to learn to be comfortable with to have a decent career. Hard doesn't mean impossible.


How can I secure funding for a PhD in the UK?

I was in a similar situation as you a few years ago. I have written a few answers on this SE on the topic:

General info about funding for PhDs in the UK
A bit more about the same topic
and Some information about why this is so difficult if you're not British or European

In the end, this depends on many factors, including your nationality, your field, and your institution. Funding for a PhD for a non-British and non-European person is rare, because it is the financial equivalent of 3 or so British students. You will be responsible for International Student tuition (at my old university this was about 17k£/year plus living expenses, all of which you need to have the first year prepared for in order to get your visa.

So we need more information, and your first point of enquiry should be the supervisor who wants to work with you.

To be quite honest, even with stellar grades, this would be extremely difficult unless you're very lucky. I had several PhD offers in the UK but in the end I gave up and went to Europe, and didn't look back. I would advise you consider doing a PhD in the EU - in many cases these are fully funded, with no discrimination based on nationality.

But: maybe there is something your prospective supervisor knows about. Maybe there are nationality-based scholarships. Maybe there are scholarships from your home country. The only way to know is to ask your supervisor, the International Office, and google. The remaining scholarships are very competitive (e.g. Fullbright) but worth a shot as well.


Can I get code reviewed if it might be published or referenced in a publication?

Short answer: "Do I have to mention that I had the code reviewed in the code / paper?" -> You really should, yes.  It's common practice to mention that code (or other research-related things) were discussed and reviewed with colleagues as they were developed.  A single sentence in the paper's methods section will suffice.

"Do I have to list the reviewer as a contributor to the project on the paper" -> Probably not.  The specific guidelines for what constitutes a "contributor" to a paper (usually discussed as "authorship", as in, should additional people be listed as the paper's authors) will vary from journal to journal.  Review of code or similar is generally not consider sufficient for authorship of a paper.  However, it is polite to list the names of the people who helped in the acknowledgements section, usually on the first page of the paper.

Long answer -> You really should discuss this with the professor you're working with as he/she will have a much deeper understanding of the implications, target journals, common practices, and so on.  That's your best approach.  There's no shame in having someone review your code.  It's considered a /good/ thing, so don't worry about being called out for not being good enough, etc.  Review is part of the academic process and is desirable.


I solved their problem. Should I involve them?

If you solved an open problem working independently, the polite thing to do is acknowledge the source(s) of the problem in your paper, and perhaps send a preprint to the source(s).

But, if they have not contributed towards the project, it would be inappropriate to include them as co-authors. Co-authorship is properly used to recognize joint work, not as a gift.  If you are able to write a publishable paper of your work, there is no reason etiquette would require offering them a co-authorship, based on what is written in the question here.

On the other hand, it might well be reasonable, depending on your field, to ask someone else if they would like to join with you to extend your work to something that is publishable. For example, if you cannot provide enough context or application to make a publishable paper, and they can, then you could collaborate with them.

The main drawback of the collaboration (I don't view collaboration in itself as a drawback) is that it would take time for them to work on their piece, delaying publication.

One polite alternative would be to send them your preprint and ask them whether they feel it is publishable, or whether additional material is needed. If they say that additional material is needed, that might open the door to a collaboration.

P.S. added a few days later I do agree with others here that it would be very valuable to discreetly inquire about what the others meant by "welcome to the project". The question describes them as "not colleagues" and "their only contribution has been to make me aware of the open problem I resolved"; this answer is written under the assumption that those are correct. If the others don't think they are correct, you run a significant risk of burning bridges. The advice to write a joint paper combining your work with theirs, which was also mentioned in other answers, shouldn't be dismissed too easily.


Should I submit a paper to a journal whose staff I am challenging?

First, I do not think the term "conflict of interest" applies here, so I do not expect the editors will reject you paper just because their work is somehow related with your paper. Nevertheless, it can get quite tricky to get your paper accepted by this journal and it highly depends on the editor's ability to receive criticism, but even more on the quality of your publication! So to increase your chances, you should consider the following.

Never get personal: A paper is not a place for ranting about other people. Make sure that it is very clear from the paper that it is not the people you are challenging (as expressed in your question), but only their theories. Otherwise, this will surely result in a rejection, even if your work is otherwise groundbreaking.
State the positive aspects of the editor's work, too: This highly depends on the topic. For example, if the theory still applies to some areas, state this clearly. Even if you are not sure about this aspect, you can write something like "Our analysis has given a counterexample that shows that the statement by xy et al. is not as universal as assumed, but future work is required to find the conditions under which it is valid." And even if their theory is completely bogus in you opinion, take the editors point of view, for example with statements such as "The experiments conducted by xy et al. could lead to the conclusion that ..., but future experiments presented in this paper show that the results should interpreted differently.".
Stay calm in your wording: Keep your emotions low. Do not attack or challenge their theory. Even prove the theory wrong might be too strong. See the previous paragraph for better examples which are of course highly dependent on the topic.
Do not provide attack vectors: Every weak part or minor mistake gives a good opportunity to reject your paper, before even thinking about the validity of your arguments. Too many typos -> reject, weak related work section -> reject, unreadable fonts in the figures -> reject.
Explain your arguments very good: Do not expect the editors even understand what is wrong with their theory if you explain it to them. Unfortunately, it is a human tendency is to stay at the own belief, even if the arguments are strong enough to convince a neutral person (think about all the conspiracy theories).
Expect competition: Even if the editors are very open to publish a publication that contradicts their work and your paper is generally good enough to be published, you still compete against other good papers. If the journal usually publishes x papers per year and the editors think there are x submissions that advance science more than your publication does, they will take these x submissions. Do not expect a bonus here and keep in mind that even papers that do not challenge the editors usually have a hard time of getting accepted!

All in all, it is important to submit an excellent publication!


I would focus on choosing an advisor and a project as your priorities. These will be the two most important decisions you make as a graduate student. The project you pick will be your preoccupation for the next five or so years, and your advisor will be one of the most important figures in your career. New skills and funding are secondary to these, and the issue of prestige almost shouldn't enter into your decision at all.

In particular, I would actually argue that it's not just choosing an advisor; it's choosing an advisor and a group. You will almost certainly be spending more time with your fellow group members than with your advisor. Therefore, you need to make sure that you can get along with both your advisor as well as your future colleagues. A miserable working environment is not worth the trouble, if another viable option is available.

Also, make sure that the project you want to work on interests you; it'll drive you to accomplish more, and you'll be better motivated to make it your own (which is what you need to do to succeed as a graduate student).


Do I have to disclose that I have a masters degree if I am applying to a second masters in an unrelated field

Yes, you should reveal that you already hold an MS in CS. Don't be overly concerned about the GPA, but be prepared to explain your priorities at the time that had something to do with your grades. Hiding things is generally bad practice and most such things can be checked and any time gaps will certainly be questioned.
But your overall application, including letters of reference, has to be sufficient to allow someone to predict that you will be a success.
The time gap is probably in your favor here as people understand that others can change. Make sure that your statement of purpose is forward looking and points to success and clear goals.


Are Honoris Causa degree worth as much as PhD?

I think your question indicates a fundamental misunderstanding of what a honorary degree is, and who gets one. Fundamentally, an honorary degree cannot be compared to a regular PhD. All the rules for getting a PhD fly out the window, as do all the perceived benefits for doing a PhD. If you get an honorary PhD, nobody will suddenly assume that you possess the subject knowledge of the holder of a regular PhD.

Similarly, you seem to assume that an honorary degree is somehow an easy way towards a PhD. This is not the case. By and large, by the time you get an honorary degree, you either already have enough degrees or you will never need one again in your life.

  Can that person be called a doctor at all?

Yes, as long as you don't pretend to have a "regular" PhD.

  can an Honoris causa graduate give lectures at a university?

Sure. Everybody can give a lecture given that he gets invited or appointed to do so. In the usual case, somebody important enough to receive an honorary doctorate is also somebody that an university would love to get for a lecture.

  Is it possible for one to get an honorary degree in science, or engineering

Sure.

  How much demonstrated work would it take to get one?

Usually none.


No one can answer this question but you.

Having said that, some points to ponder:

There exist funded research based masters programs. Depending on the field and geography they will vary substantially in quality, but conceivably you could delay answering that question by going somewhere for a Masters and seeing how well that goes.
Grades are going to have an effect on you getting in. In terms of success, what really matters is grit. Smarts get you somewhere, but you need to learn to tolerate challenge and failure to succeed in research.
If you have nothing else on your plate, in terms of family or ambitions, then now is the time to experiment with possible paths. So long as you don't define your self-worth based on success in a PhD, the worst that could happen is you decide research isn't for you.
Is it research you want to do, or is research just the only entrance into a field you can see. Sometimes people think they want to do research, but it's because that is the only job they know in that field. Maybe spend some time thinking about alternative entrances into the field you're interested in!


How to deal with an author who worked on an analysis that never made it into the paper?

I had a situation like this come up once, where one person did an extensive analysis that turned out not to be particularly useful, so there was no point in including any details of it in the paper.  However, we did feel that having the analysis done did lead (indirectly) to a better understanding of what we were studying.  Moreover, we also felt that the person who did the analysis deserved some measure of credit in the final paper.  So we put a very short mention (one to three sentences) in the manuscript, just stating that we had done the analysis, but that it had not led to any useful conclusions, for such-and-such reasons.  Since the paper included this, it was unquestionably appropriate to include the person who had done the bulk of that analysis as an author.

I would suggest that you could do something similar, so your colleague could unambiguously be considered an author.


My Phd advisor does not appreciate anything I do, and provides no help

I feel you follow the wrong advisor. It seems normal for some people who are in academic. It is pretty unpleasant.


Also, the first piece is actually of limited technical use but introduces the concepts, notations, and methods required for the further pieces.

The main question is whether this work is of independent interest or use to anybody but you.  All research is incomplete in some sense, and that doesn't bother people (everyone likes opportunities for further work).  So the issue is whether your paper is incomplete in the sense of not accomplishing anything interesting yet, or incomplete in the sense that there is still much more to do.

If there are people who want to read it now, on its own, then that's an argument for publishing it now.  If it has little value except as preparation for the next paper, and that paper is already written, then it might be OK, but getting it accepted on its own may be tough.  If it has little value except as preparation for a future paper that does not yet exist and might not pan out, then it will be really difficult to publish it.


Is it always necessary to mathematically define an existing algorithm (which can easily be researched elsewhere) in a paper?

In my experience, most of the times, when someone tries to "clearly describe in English" what an algorithm does avoiding mathematical notation, the result is not as clear as intended. Ask yourself if that is the case also for your description.
Math exists precisely because it makes it clear and unambiguous to speak about combinatorial concepts.


FERPA: Can I anonymously quote a student?

Can you: YES

Should you: NO

Imagine if the quote/anecdote got back to your student. While no one else would know who said it, the student who said it would know. Even if it never makes it back to that student, other students will know you are making fun of students. That is not good for your reputation or for student learning.


My supervisor does not want to publish my research

If you are the sole author of a work then you can publish it. However, if your supervisor needs to be listed as a co-author for contributing content, not just custom or courtesy, then he can block it as any co-author can.

On the other hand, even if he must be co-author on a joint work, you can probably write an independent paper and publish it without any "permission." This would only be false if you have signed some agreement with the professor or the university to yield rights to them. That would be unusual for dissertations, but you would be aware of it if it bound you, I think.

Note that the ideas that you develop in your studies are free to be used. It sounds like your supervisor is trying to "own" ideas. Other than patent, that isn't allowed in the laws of most places. You might also seek guidance from the research office of your university. They will know whether you are bound or not, though they may lean in the direction of the university.

If you try to publish and he then interferes it will be the time to escalate the issue.

But if your work depends on the work of others you have to consider their rights as well. Normally properly citing that work is enough. Contracts can be limiting of course.


Right way of requesting research project from a professor as a non-affiliate

It is acceptable, but not the best strategy. Getting the attention of a top professor is like fishing a very picky fish: you need a good bait. In my experience, it is easier to approach them by offering something rather than by asking for something. Also, the approach should be genuine. This is, you approach them because you want to work on something that might fit his/her research interests not just because you want to see his/her name tied to yours in a paper.
IDEAS: Professors salivate when they see an interesting idea.
Just follow all the etiquette rules. Be polite and respectful as you would be with any other person. Also, try to be precise, they are busy people.

More importantly: Publications are not strictly necessary to be admitted to a decent PhD.

If you have some project in mind, write it and send it to the Professor in question. Tell him/her that you are interested in working on such project and that given his/her research interests, you think that the project would be greatly benefited with his/her ideas and that you would appreciate collaborating with him/her on it.