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Class Appears to Lack Support - Does the issue lie with me?
A quick qualification: I usually associate failures in a class with it being my fault, like a lack of studying and such.
Background: I am on the last few courses of my degree. I work full time and have a job that requires me to think a fair amount, so these days I usually limit my class load to 1-2 courses a semester. It can be difficult to have the brain power to study after a long day of work, but I try to shift things around at work to have easier tasks on days leading up to an exam...etc.
Issue: This semester I am taking a course on DSP (Digital Signal Processing). I have had this professor before, and while he was a little disorganized previously I was able to get a good understanding of the previous courses material and get a B in the course. I feel the previous course was more technical and difficult mathematics wise, but I am struggling this semester. I feel like I understand the lectures, which if I had to estimate I'd say I'm 90% confident in. However, when it comes to the actual use of the material, I'm more like 20% confident. The source of issues this semester are:

No syllabus. I'm used to a syllabus at least containing tentative scheduling, this semester the "syllabus" is just a copy and paste of the ABET requirements.
Professor doesn't appear to have any known plans for how many exams we'll have, when we will have them, or how exactly the material will be split up among the exams.
We have projects. Initially the projects were supposed to be due at the end of the semester. He then randomly changed his mind and made a project due with only a few days noticed. The projects can be completed in a day or two, but that is assuming I can immediately respond to a change in schedule.
Similar issue with the exams, he'll randomly tell us we will have an exam a week before.
There was initially some review homework problem assignments for background material, but since then there have been no homeworks.
We have lecture notes we can view, but they're a bit disorganized. Even worse, I didn't take many notes in class because he said they were available online. Some were, but he waited until after the first exam to release some of the notes, some of which were required for the first exam.
He has no grader this semester, so what is graded has no feedback. I did poorly on my first exam, partly because I didn't know exactly what I needed to study, but all of the "feedback" I got was my grade. We submitted the exam online, so I don't get any feedback for what I missed. For me it's quite helpful to know at least where I went wrong, was my error a small error that cascaded out? Things like that help me learn and improve. The feedback I received for my last project was "50/100 output incorrect"... which of course I knew by the fact that the output didn't work, so it didn't assist me in knowing how it was incorrect or where I went wrong.
He has provided his past exams, but no solutions to the exams. Since I have no feedback from anything else, such solutions can assist in me attempting the problems, knowing where I have an issue, and looking at the solutions to understand what and where so that I can resolve my misunderstandings. He previously stated that he held back solutions as he felt it would hurt those studying (how I am not sure), but stated he would upload them since I asked... he has yet to upload them and I have an exam tomorrow.
The provided past exams only vaguely match the given exams. No direction is given as to what will be on the exams, like what class of problems...etc. Last he said in class is, "It's difficult to give information on what to study for the exam since it's cumulative." Which I understand, but a class of potential problems to study would be quite helpful. If I practice those but lack the needed cumulative knowledge, I can proceed to brush up on that knowledge before I continue. For the first exams I was relegated to printing out the past exams and marking problems that sounded familiar or something I should know, so that I could study those.
He mentions that the past exams won't match our new exams anyways since he is trying to incorporate more Matlab. Which is fine, but I feel he doesn't cover Matlab enough to give us an exam on it. We've only covered Matlab material in two lectures, and the feedback from the projects is too lacking to be of use as a study aid.

In summary, I feel like there is a lack of organization leading to me feeling lost on what to study, how to study, how to improve on things I missed, and in general feel more lost than if I were doing an MIT OCW class and teaching myself.
It has been suggested to me to complain or report the professor, since I paid for this course and feel like I am not getting much, if any, support. However, I am not a person that likes to do this, and on top of that, normally I prefer to blame myself for my lacking achievements rather than the professor. I see a lot of people blame professors for their own failings, and I try to avoid doing the same. Though, his last emails wording suggests that he is getting frustrated with the class as well and annoyed that "very few" (out of an 8 person class) failed to get the project working.
Some extenuating circumstances, maybe. He mentioned that he had to cancel class one day due to an unexpected medical appointment, for a place that is a few hours away. Normally you don't do this unless you're visiting a specialists in my opinion. Recently he canceled two other classes, and assigned another project and said we'll have another exam ("take home", which I'll simply do at work during what would be normal class hours). Though he didn't provide a reason for this absence, I'd guess perhaps the same reason.
Bottom line, do my grievances seem legitimate, or are some of my expectations out of line?

This sounds like the professor has issues going on in his personal life, which happens to all of us from time to time. If possible, you might go to office hours or talk to him after class. Don't address his problems, but instead tell him you are struggling with the presentation and ask for his suggestions on how to do better. Ultimately, that's the goal, whether the root problem lies with you or with him.

I can certainly appreciate the issues. Unfortunately,I may have waited too long to bring up the issues to him. I originally was hoping it would get more organized as we continued, so I didn't say anything (thinking maybe personal issues created a small bump in the road). But I am now a few days before the last day to drop and I am not confident I can recover in time. Perhaps I'll keep this in mind for future reference, early communication before it becomes too late.

@JarrodChristman The decision on whether to drop may be a good hook for a discussion with the professor. Explain your need to know about deadlines in advance so that you can plan your entire workload including your job.

There are some things that the professor should improve and there are other things that you should improve. I think it is a shared responsibility in this situation.
There might be some reasons, medical and other, for a certain lack of organization, but it certainly doesn't seem ideal. Even if he is trying to mutate the course into something more modern (matlab) it would account for some disorganization.
But the biggest problem that is the responsibility of the prof, is the lack of assignments and feedback. Students need reinforcement of the ideas in a course (assignments) and they need feedback on their attempts.
But much of the rest of it is up to you. He seems to be doing some things well, in my opinion, making lectures available online, for example. Even having new exams quite different from old ones is a good thing. The old exams can give you practice even if they are unrelated to what will be asked now. But you need some feedback on your attempts. But note that having an answer key to the old exams is not really appropriate feedback. Working toward a known answer is not the same as working out an answer unaided. He is even warning you that the new exams will be different.
He should, however, find a way to get you feedback. If there are issues that prevent him from doing it himself, he should be at least trying to work out some way for that feedback to come from somewhere. If you are at a large place, then a TA could be employed. If at a smallish place, then a senior student might also be given a grading task.
But, as for your own responsibility, you need to practice more, even if there is no way to really get feedback. If you have a book, or could acquire one, that has exercises, you can do them even when not assigned. I once learned a lot in a certain course by creating my own examples and problems and exploring solutions.  I was able, however, to verify my solutions even without feedback. The practice alone did me good and I got a deep understanding of a small part of the course and insight that served me well overall.
Don't depend on remembering or learning from lectures. You say you don't take notes. That is a serious issue. Taking notes (by hand - on paper) is a reinforcement mechanism that will serve you well. It will also help you see what isn't there and what you need to explore in questions or in outside reading. Take a lot of notes. Spend some time summarizing them.
Seeing isn't learning. Only work that reinforces it will lead to learning. You need to do that, of course, even when the prof is extremely organized and provides the feedback. But, he should be providing that, of course.

Thank you for taking a balanced approach. I can see your point with note taking. I used to take notes but found I never referenced them, however, maybe I would still benefit from the reinforcement side effects of note taking.
For studying on my own, I think the issue is that I usually use assigned homeworks (whether graded or not) as a jumping off point, so I know what "class" of problems to search for on my own. It may be that I'm a bit lost since I have no assignments, and he doesn't follow the book exactly. But, I can see where that is something I should improve upon skill wise.


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What are the chances of being rejected in situation when applying for post. doc. without PhD supervisor's reference with valid reason?
I have a horrible experience with my PhD advisor. He is the worst person to have as a PhD advisor. I should have judged him before but after 4th year of my program, I got what kind of a person he is.
Despite all these, I continued for my degree and will finish it in a year. I have almost decided if I apply for post-doc position, I'll not include his recommendation letter.
One big reason for this is the a "very serious academic misconduct" He did with me. I have documentation with proofs.
I will be very grateful for your suggestions/experience regarding my situation.

Welcome to Academia.SE. What is exactly your question?

What was the "very serious academic misconduct", plagiarism?

is swapping advisors completely out of the question at this point? Assuming that this is as terrible as you claim, someone on the university would probably facilitate that..

Are you afraid he will write bad stuff on you? That would just look bad on him, and if you actually have proof of his misconduct, you could retaliate. He's not going to risk that unless he's mad. Or are you just sulking, thinking you can raze him by not asking for a recommendation? In that case, think again.

@peterh yes plagiarism (published)

@Fabio Dias : it is already too late for me and I'll graduate in next year. If this happened to me during my first couple of years, I'll definitely swap the advisor.

@nero_bin I saw people changing advisors on the day of depositing the thesis, 60 days before the defence... Please do check with the chair/dean/etc of your department. Or embrace the advisor and get a good LoR. Advisors help a lot, not only for posdocs...

One of the largest fears of the people judging your applications is that they will be falsely accused for some "serious misconduct". And now you want to apply to them, accusing your ex-prof with a "serious misconduct" in your application.
You are harming yourself and not him.
If you decided to not start anything against him, you abstained your right to intervene. Accusing a prof with some serious is a really hard thing, best if you are far, far away from anything even similar to that.
If you didn't do anything at the time he committed the misconduct, and if you "defame" him later, retroactively, it looks very bad for you.
Even if you have documents and proof. The first question what would you hear: "And why didn't you do anything at the time?"
Despite that you had the obvious reason to not do anything at the time.
Furthermore, the people judging your applications probably won't know what he did. The strength of your application should be the possible strongest in their eyes, and not in yours. Missing his recommendation letter may be understable - for you -, but it will look very differently for them.
They will simply think that you don't have a recommendation letter because you are bad. And anything what you say about the case, will most likely further decrease your estimated value in their eyes.
Logic would dictate, the best would be in your case if you could somehow utilize the power of your proofs to let him to help you on your academic career. However, any possibility I can think for that, would be far more risky for you, as for him.
I am sorry to say, but I suggest to play this: "everything were happy, look what a wonderful LoR I've got". This maximizes your chances in the future.

Thanks for your answer @peterh. Your answers makes a lot of sense. Since I'm international student, I felt this is irony why your future career depends mostly on your PhD advisor and not on your own ability.  I almost felt like even if  you are hardcore science students, you need to play politics based on your situation.

@nero_bin It depends much more on your actual product as in the job market. Being an international student is non-issue. How important thing was what he plagiarized? If it was the discovery of your life, then it is a different case.

There is a point of being international student. I found that if I'am from well known countries, he will know that I know the rules better and will not do dare to do that stuff. Another point is in my home case, it does not matter who you worked with  for your degree - it doesn't have that great importance as in here in us.

@nero_bin Direct discrimination would be far more risky for the committers as for the targets. Indirect, hidden discrimination often happens, but this whole thing looks unrealistic to me. Can you convert the thing into a nice motive for the Prof, to give you the possible best LoR? Saying, that you could even help him in his projects?

@perteh I got from everybody and you as well that If I want to continue to work in academics then I've to play politics. If I want to find job outside, then all of these does not matter. But I learnt a very good lesson and this lesson is going to protect me in future.

@nero_bin Thank you very much! I think it is not very deep politics. The case is extreme (plagiarism by a prof, it is nearly unimaginable), but the related politics is not very deep. It is only about to tune your face where you want to get in. The profit-oriented job market is far worse in this sense.

@nero_bin Btw, I think this site can help you a lot in "political" matters. For example, if you had asked this question at the moment that the prof committed that, you could have got likely much sympatetical answer(s). If you have a problem, time is crucial, ask it on the spot!

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Can a thesis not answer the research question and still be good?
I have written a thesis about applying some AI techniques to a simulation that my professor introduced. To make this happen, I had to implement a very large amount of software, because the simulation works in another language, follows different principles etc.
After 6 months of hard work, I did not reach my goal. I was not able to actually implement the AI technique I wished to apply to the problem. I created a lot of reusable components that future developers (and in fact other students as I was told) will want to use. But the actual question and also the title of the thesis (which both had to be fixed ahead of time and cannot be changed once it has been started) don't match the main body of my work.
Can a thesis still be considered good even if the question was not answered because it was not "reached"? If not, why? If yes, why? I can imagine this going either way but I'd like to hear opinions and experiences.
Basically I would require another 1-2 months and maybe someone to work on the problem as a team to get new ideas. I believe I still worked in a scientific manor (I prioritized reusability and usefullness over just reaching the question but without it being easily reusable) and no one ever said science is only good if it never misses a deadline. But I can also imagine an argument that simply states an unanswered research question is a bad work.
My original intention was to apply this AI technique to the common example research problems (like Atari games or locomotion) but my professor insisted I apply it to his field of work (energy market simulation). I had to agree if I wanted him to take my thesis and I didn't know how complex the mapping of his problem to the commonly used tools would be. The argument "a good researcher is also capable of creating a reasonable problem scope" therefore is a little unfair as he sort of forced me to extend it.
Alternative B I write a preface / authors comment at the beginning, stating that the title/research question won't be matched but due to university regulations may not be changed retrospectively.
Alternative C: A fellow researcher recommended me to just change the question and content but ignore the title. I hand in my thesis under the forced title but publish it under a more suitable title. That seems a little "fake" as I don't want to lie about my original goal and me missing the final goal.

Edit: Most suggestions go along the lines of "depends on your professor or institution". While I fear this is probably the only right answer that helps me personally, it doesn't seem right that it depends on the professors attitude or personal opinion. From an abstract perspective, is it OK to rate a scientific work as a bad work if it fails to reach a previously defined target when new information came to light along the way? Probably not. But is it common practice to change the research question at the end to better match / suit the line of argumentation? It seems to me the question should reflect what the researcher asked him/herself when he/she started the inquiry. If the results are not what was expected, that doesn't mean it's bad results.

Seem to have read this question the other day - and answered it....

Your school forces you to write about exactly the question that was given out when you first started?!? Idiocracy knows no limits.

@Karl I may be able to change the question (I am still waiting for an answer of my professor but it has been waiting 2 weeks now despite several emails) but the title is fixed and with 3 weeks left, it's tough to restructure the whole line of arguments now anyways.

Have you asked your professor what you should do? The answer to this question is: expectations vary.

@Dawn he doesn't respond to my inquiries anymore. I could contact my other contact person but she usually just refers to him as the authority that must make the decision.

Sounds like you need to set up a meeting or attend his office hours.

Related to your edit: I think it depends on what you mean by research question. It could mean hypothesis (in my field, we would not usually change that) or contribution (that will change). It also depends on what you mean by the "beginning" of a research project. There is a lot of work in my field that happens before you establish the testable hypothesis and the experiment/analysis. During this process, you have already begun research, but you have not begun the research that will go in the paper.

A research question in my case was really a question. "can deep RL based agents learn from other agents in the PowerTAC setting?" It's no hypothesis nor a contribution. Well a hypothesis in a way that it "may be, let's find out".

No one cares about the title of a master thesis.
Go with C, then you describe what you did and you can safely say that the time-constraints did not allow you to fully investigate all the topics.

The short answer to your question is yes, you can have a good result even if you don't (completely) answer the original question. However, the advice you really need is from your professor. Don't express negative feelings about how he "forced" you or anything like that. Ask him for his analysis of your work and how to best position it.
Many research questions take a long time to resolve. Don't be discouraged by that.
But the work isn't a failure, and you, especially, shouldn't think of it that way. You want to ask yourself, however, "What, exactly, did I demonstrate in this work". Your wording of the rest should revolve around answering that question and showing how you did a good job of it.
You can have a final section that discusses how this work is part of a larger work and briefly describe the problem you started out to solve.
However, some of your statements confuse me. You seem to be saying that at some earlier point you gave a title to the university that makes a claim of success to the earlier question, and that that can't be revised. Such a policy would surprise me and I would make doubly certain that you are correct. But advice from your professor would also be valuable here.
When it comes time to publish your work, there is no rule anywhere that I know of that restricts you in the title of the paper(s) that get produced. So even if you are sort of "stuck" with an inappropriate title, you can just treat it long term as an anomaly. You then have a little joke you can share with future students if you stay in academia.

Yes, it can. Research is too flexible to be sure about a year in advance. Perhaps you found out that the question is the wrong one to ask, or perhaps someone proved that a different method is superior - it'd be foolish to persist on the same path then.
In any case, talk to your professor, who will know what your institution's policies are.

while my professor didn't answer, his assistant who is supposed to be my contact person did. She told me to just stick with my current trajectory and discuss the shortcomings in the conclusion and explain what stopped my from completing the question. I guess the short answer would be "time" and the long answer will be some pretext why I couldn't develop software faster in the 6 months to get to the goal in time.

Is thesis complete or good enough depends mostly upon observations from your committee and department. Can it be published in peer reviewed journal is a different question. I would say “a well defended thesis is good thesis”. Thesis is never done unless you and your committee declare it’s done and so does it’s quality. Get it done, move on, and if you want to publish, polish it. If not, chapter closed. Start a new chapter.

No one cares about the title of a master thesis, apart from generally understanding what will be its topic/semantic area.
Go with C. Then, when you present your thesis:

Experts in the field can and will recognize that the title was overambitious, then when you describe what you did you can safely say that the time-constraints did not allow you to fully investigate all the topics.
Other people will not realize the mismatch unless you explicitly point at it. But they can still understand the breadth of what you actually did. You can therefore present what you did, and its implications towards reaching the goals that you "missed".

I found the answer I gave to the other question :
You can have a valid result showing that the "XXX method" is not the best in YYY situation - that is, or can be, useful work for someone who does not waste their time on that possibility.
They can then focus on a different direction - which you can also do ie checking out if the Tabu search works for ZZ or AA for example..

The issue is not that I wanted to try to apply XXX on YYY but it didn't work. I wanted to apply XXX to YYY but the professor insisted it would be ZZZ for which it turned out I had to implement A, B, C, and D. I implemented A - D but then time was gone and I was not able to apply XXX to ZZZ anymore.

Then that was your problem - you should not apply XXX "ON" YYY but you shoud apply XXX "TO" YYY....

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What would my Higher National Diploma be considered in the United States?
I am currently studying my BTEC HND(Higher National Diploma) from a United Kingdom approved centre and i was planning to apply to the United States after complete this diploma. However i have no information of what to expect out of the United States. What will my diploma be considered in the country and will it be easy to apply to universities regarding my discipline. I've added a link below explaining and introducing HND for those who are not fimilar with the program.
Thank You in Advance
Infromation about HND From Pearson Education

From the website:

BTEC Higher Nationals are internationally-recognised Higher Education qualifications at level 4 and 5 that are equivalent to the first and second years of a university degree, providing progression to both university and employment.

This means it will probably be considered as something like an associates degree. Some 4-year US universities might give you credit towards undergraduate classes. I doubt any well-respected university would give you credits towards a graduate degree. It is probably insufficient to get admitted directly to a graduate program.

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Potential supervisor replied but did not explicitly say if he is ready to supervise
I sent an email to a potential supervisor for PhD in Computer Science with a concise introduction, research I am exploring and a brief about how one of his publication is relevant to my research. Put in some good question around it as well. Then I asked if he is willing to take PhD candidates in his lab.
I received a response within half an hour of sending the mail. Though the content is a bit ambiguous. It says, "Thanks. There is just one position available in a particular stream. So please go ahead and apply."
How do I interpret it? Does this mean he is ready to supervise? He didn't put in any response to my question though. How do I reply to him further as I'll have to mention in the application if the supervisor is ready to take me in.

"Dear Professor Blank: Thanks very much for your response. The application asks if you are ready to take me in.  How should I answer this?"

@NateEldredge That is very helpful, thanks. Should I also reiterate my questions about his publication and if he is willing to discuss my potential research before the application?

I'm confused. Are you an undergrad trying to line up an advisor (presumably to talk about in your SoP, or to list on the application)? Or in the university already trying to find an advisor? What is the "application" for?

@cag51 I am CS post graduate and having an industry experience of 6 years. Looking for PhD in CS. I am looking to line up an advisor to mention on the application

Here is how I would interpret it:
The professor has no knowledge of the details of the application process. He may also have little power to directly influence whether he has a student or not, because there is little funding available and it is shared between several topics/groups/subjects/faculties. He would probably take you on if you make it through the various barriers (how happy he would be about it is unclear; some academics have more control than others over whether they take students), but he's not going to invest much time in you before then.

Precisely, this is what happened later when I dropped another message as per Nate's advice along with a query if he would like to discuss my research idea in detail. He said he doesn't have time right now and mentioned that I should go ahead with answering a Yes for the question in the application asking whether the professor has already corresponded with me.

I think the suggestion in the comments is reasonable, but for the sake of providing an answer in the answer section, I will present an alternative.
Yes, list him on the application. What's the worst that can happen?

If he will supervise you, then there is no issue.
If he does not want to supervise you, he cannot raise a stink without looking like an idiot, since he wrote "please go ahead and apply."

I think the most pertinent take-away from his message is that there is only one opening in the stream. My guess is that he is planning to supervise whoever gets that spot (it sounds like that spot will be pretty competitive, so whoever gets it is likely to be pretty good).

The question asks how do I get back to the professor with the questions mentioned and not how to bypass him! This is not about what worse could happen, this is about how to ensure things get done in a phased and proper manner to increase my chances. I have been rejected ones before, so I need to ensure the 'worse' doesn't happen again.

Based on your follow-up to the accepted answer, I would argue that I was exactly correct -- he didn't appreciate the follow-up, but was fine with you listing him on the application. :-)

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How to speak fluent English being a mathematics teacher?
I am an assistant professor of mathematics (and pursuing in service Ph.D in mathematics ) a non native English speaker. I was not bad at English during my school days. Gradually, my effeciancy in speaking English seems to have gone down badly through years of pursuing mathematics (a dry subject without language). How do i improve myself now with minimum time and effort?

First step: stop pursuing math without language. Math uses the same English that everything else does.

The premise that math is a dry subject without language is very inaccurate, and is a symptom...

If it is for classes, concentrate on explaining the concepts clearly and use good examples and practice problems - the students can survive a few grammar errors when they see you put the effort in...

This question would be a good fit for http://languagelearning.stackexchange.com/ . I would recommend leaving the part about mathematics being "dry subject without language" out, or being more precise about it, and being more precise about your goals than "improve myself".

I think minimum time and effort as a goal will defeat you. They are also somewhat inconsistent. To reduce the time (a bit) take a course in speaking that forces you to actually do it. But that takes effort. To reduce effort, just practice as you go along, increasing time.
But the way to learn to do pretty much anything is to practice it and get feedback. In the case of teaching, if you are doing so in small classes, you can just inform students that you aren't a native speaker and are open to being corrected. But that takes a bit of courage and isn't without risk.
If you are in a situation in which you can speak your native language, then try to resist doing so as much as is possible (and polite). Force yourself to speak English in all possible situations.
You can ask colleagues to correct you if you trust them, of course. Again, it takes some courage and patience both from you and them.
If you asked how can I become an Olympic Swimmer with minimal time and effort, the answer would be "You can't". It is similar here.

@holla - perhaps an overloaded term...minimal could mean "very little" or "the minimum possible." Learning to speak a new language with very little effort is likely impossible as Buffy says; learning to speak it with "the minimum possible" effort is a reasonable question, but arguably in the wrong forum (since being a mathematician has very little impact on the language learning process).

There is an organization called Toastmasters, which aims to help people improve their public speaking through practice. It's organized in local clubs, which have membership fees (they're usually not very costly). You could consider finding a local Toastmasters club and joining it (note that different clubs may have membership restrictions). The activities usually center around people delivering short speeches and responding to impromptu questions. Toastmasters appears to be international.


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(Canada) How likely/unlikely is it to get accepted to a direct entry PhD program?
I am now torn apart between leaving Canada to do a masters program in a foreign country, which will put a huge financial burden on me, I don't even know if I can afford it, and I would also become isolated from my family and would likely have to break up with my GF.
I also could spend the next year doing research with a professor at a local university while also working, but I am sick of working, all I want is to do research, all I want is to learn math.
If I can get accepted into a direct entry PhD program, delaying entrance is worth it, because I can start the program a year earlier. But if it's very unlikely, then I would have ruined my chance to get back on track into the only thing that really matters to me for trying to optimize for some less important (but still valuable) variables.
So in short, is it likely to get accepted into a direct entry PhD? I understand each institution, program and professor is different, and that it depends on the candidate, I just want a general idea.
Edit:
I am considering it, but if I am going to do a masters anyway, from a purely academic perspective, there would be no reason to delay my studies and simply go to the foreign university. It would be much easier to justify and additional "GAP year" as a way to invest my time into improving my profile to be accepted into a PhD program directly and skip the masters alltogether, mostly because I know for a fact I want a PhD, I know for a fact I want to do research.
Direct entry simply means bachelors to PhD, i.e skipping the masters, currently the plan is next September (2020 not 2019).
I had a 3.67 GPA, however if we take away 4 japanese courses (that I tok out of interest) it's 3.72, 3.8 in CS courses, 3.98 in math courses (I have a pure math minor).
I did honours but did not publish the research (some non negligible additional work was needed to get it published and I graduated right then, then moved to a different city).
I am in a rush to start because that's all I wanted to do for the longest time, I let my family convince me to work for a while to see what the "real world is like", and after working and doing undergrad research, I understand with full clarity that I'd rather do research for 20k a year than work for 100k a year. I want to learn more math.

Ask the person you would like to supervise your PhD.

They said "there's no guarantee that you will get the position even if you do a good job, maybe I won't have the funding".
Which is fair, but there's other universities and supervisors I could also apply to and see what happens.

That's a better answer than you can get from Stack Exchange.

@Makogan Given your edits, I think you are worrying too much about a "gap year." Skipping your Masters might just mean you spend that much longer getting started in your PhD. The Masters is a good time to take advanced classes, learn to read papers, etc. Also, if you are starting with a CS background, I definitely would recommend a Masters if you're switching to Math. A Canadian Masters will help, not hinder, your research career.

I am not trying to switch into math, rather the kind of work I have been doing since my undergrad, is mathematical in nature (I have to work with parametric surfaces, calculuse, differential equations, statistics...) quite a bit. But my focus is still CS, i.e I want to do a CS PhD that involves a lot of math (still within the field I have been working so far which is computer graphics)
And it wouldn;t be a gap year, it would be two of them.

@Makogan if you're interested in Graphics, look at the UBC PhD Track Master's program. It's a master's program where you have the option to transfer to PhD after a year. UBC also has an excellent program for graphics. https://www.cs.ubc.ca/students/grad/prospective-grads/grad-programs/phd-track-msc-program

@jmite Thank you so much for this tip, this is awesome!

@Makogan if you're a Canadian citizen or PR then you should also definitely applying to the NSERC CGS-M scholarship.

@jmite Can I apply if I have a pending application for PR? (i.e I applied but have received no reply yet)

@makogan no clue. Google is your friend

Is there any reason you're not considering a Canadian Master's program? They're usually funded, and doing a Master's is pretty standard before doing a PhD in Canada.
What do you mean by "direct entry"? If you mean starting this September, then your odds are quite low. If you mean "straight from Bachelor's to PhD" then that's a different story.
What are your grades like? Do you have any undergraduate research experience? Skipping the Master's is generally reserved for "exceptional students" in Canada, so your odds depend on how your Bachelor's went.

I know some schools have a "PhD Track Master's" where you start in a Master's and transfer to PhD after a year. Maybe that's for you?
Graduate studies is a long haul. Don't be in a rush to start it if it doesn't work for your life.

Good answer taking into account the Canadian system

To answer the titular question: yes, direct entry from a BSc to a PhD definitely is possible. This may be anecdotal evidence, but I know several who pulled it off. In practice though, MASc to PhD is much more common. To go straight from a BSc to a PhD, the bar in terms of grades, previous research experience, publications etc is higher. From my anecdotal evidence, you will probably need an 'A' grade overall and previous publications.
In the end though, it is down to each individual department and more importantly each individual professor. If you can convince a professor to take you on and he has funding, he can vouch for you on the departmental level to help you secure the department-level scholarships needed provided you clear the minimum grade requirements (which are higher for BSc -> PhD than BSc -> MASc). Your best bet would be to ask about direct entry on a case by case basis by contacting professors you are interested in working with. I have found that professors are usually much more eager to take on PhD students rather than MASc students if they can help it. I speculate this is probably due to the fact that they will be able to get more work done tying a potential student down for 4 years than for two.
Joining at the masters level then subsequently switching to a PhD after a term or two is also possible and common from what I have heard as the previous poster pointed out.


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When to apply for master scholarships?
So I am a bit confused as to how the standard scholarship application works (North America, mainly Canada). When applying to a masters program, most schools ask me if I have applied to any scholarships and to list them. However, when looking to apply to any scholarships, one of the prerequisites for most is to have already been accepted to an academic program.
This is confusing to me, should I apply to scholarships before applying to my masters, should I apply after receiving a positive reply from at least one institution?
I understand that specific scholarships will have their own details, but this is a general question. How do I approach not starving if I get accepted to a masters?

schools ask me if I have applied to any scholarships and to list them. However, [...] one of the prerequisites for most [scholarships] is to have already been accepted --- There might be a reasonable explanation for this, but I have to admit I found this funny (in a sad way). It reminds me of the "catch 22" situation with many entry level jobs, something that used to be a problem for me 30-40 years ago, although now I mainly have the opposite problem.

I'm guessing that the intent of this is to determine if you are in the somewhat rare case of not needing funding. If you can say that you will be funded from other sources (scholarships from another country, for example) then funding is one factor the committee need not consider. But if you need funding, then they also need to find ways to provide it if you are accepted. Or at least think about that, since if you are accepted without any funding, then there is a higher chance that you won't actually come.
So, follow the rules of any scholarship application, of course, and answer this question honestly. Apply when you meet the criteria.
I doubt that they expect you to have funding already arranged. But they would consider it a plus if you do.

Depending on your program, most if not all recommend applying for external scholarships prior to acceptance into the program (as if you are already going to attend). For the big government scholarships, the application date for study beginning next Fall has already past, but provincial awards (such as OGS in Ontario) are open until early December. Internal awards are decided during the application process usually. It doesn't look great if you apply to a program without attempting to get any external funding, but it's not absolutely necessary.


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Is it better to list a non academic reference that knows me really well, or an academic reference that is less familiar with my work?
During university I had 3 professors I did close work with and that were really familiar with my work. Unfortunately one of them retired and as such is no longer willing to give me a reference letter.
I have been working in my field at a startup, and the CTO of the startup knows my work really well and is willing to write a recommendation letter for me.
Is it better to contact professors that remember who I am but with whom I only took a couple of courses and as such may not be totally familiar with my work ethic/skills, or is it better to list my CTO who doesn't have a PhD.
Edit: Field of study is Computer Science

How about listing both references?

@ToothpickAnemone I only have 3 slots, I can;t list 4 people

General Answer
This will in part depend on what type of graduate program you are looking at.
If this is for professional school (business, law, medicine, etc.), I would think that a letter of recommendation from non-faculty would be relatively common. Such a letter (such as in the case of an MBA program) could actually be favored over a letter from a pure academic.
Conversely, let's even suppose you are trying to get into a master's program in a purely academic discipline. (For sake of argument, let's say pure maths). You need to have some letters that can speak to your academics and scholastic abilities directly.
However....
If you already have two solid letters from professors who can speak to your academic qualities, a letter from someone in "industry" who can speak to the more non-academic aspects of your profile might add a positive depth to your application that would not be achieved by having three academic references.
Speaking for myself personally, if I was to receive an application from a student who had two academic references and one reference from a CTO, I would likely be more inclined to look at the application with deeper consideration. The non-academic reference could provide a dimension of insight into the applicant that would not be accomplished with three academic references.
Long story short, I would much prefer to have a non-academic letter of recommendation that gives a fuller and more complete picture of an applicant than a letter of recommendation from a professor than does not know a student well.

Situation Specific
Based on some inferred information from your profile, it seems that you are likely trying to get into a program in the computer science fields. If you have a quality letter of recommendation from a well credentialed CTO (i.e. not someone who runs a company worth US$200 from their mother's basement), I would by all means include it in your application. Many programs want students who have connections to industry. It helps them make inroads with their alumni network into new employers and new fields of collaboration.

The startup currently has 30+ employees and has deals with companies in every continent except antartica, would that be credentialed enough? (Legit question)

@Makogan That sounds significant enough for me.


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Self-censorship to prevent grievance being filed by classmate
I am currently an undergraduate student in my last year at a Canadian university. Today, I gave a presentation about anti-censorship technology being developed at my institution. We were required to ask questions to the audience at the end of the presentation and one of mine was a multiple choice question that asked where the technology would not work, with answers that included "The People's Republic of China" and "Republic of China" among others.
One of the students in the class who grew up in China asked a leading question about why I had two options, to which I responded: "there are two countries that call themselves China". He became extremely aggressive at that point and stated that I shouldn't be pushing my political beliefs on the class (the class was about technology and business), and yelled a standard Chinese political line about a united China in the middle of class. In the moment, I quickly just apologized that he was offended by it and somehow got the presentation back on track.
I spoke with the professor later in the day and he said the student came to him with a list of demands, which included, among other things, a public apology in class, alteration of my slide deck before posting it to the discussion board, and a meeting between him, the professor, and I.
I believe I am in the right when it comes to this topic and during my discussion with my professor, he agreed that students have a right to freedom of speech. He left it to me to decide what actions on the demands list, if any, I would be willing to do.
I feel some remorse, as I didn't think that the question would be taken so violently by a member of the audience, but the level of intensity in my classmate is extreme. He stared at me consistently for the rest of class and, to be honest, made me somewhat uncomfortable.
I agreed to the meeting to start, but what else should I do? Disciplinary actions, like legal trials, tend to not always work out for the person who is in the right - there are many innocent people in jail. I want to stand up for freedom of speech, but don't want to be crucified under a formal review because one of the reviewers may have also been indoctrinated by growing up in China and share the same views. I'm sure just like anything, if you dig hard enough, you can find something to get me on if the administration wanted to.
The irony that I see in this whole presentation is that it was about anti-censorship, and my classmate wants me to censor myself and only accept his version of truth - which is actually a lie.

I don't know how these processes tend to go, but since you seem to be surprised by this student's reaction, I think the first thing you should do is read more about the issue. Knowing just how massive a hot button it is will help you a) figure out where the student is coming from, and b) decide how important fighting about it is to you.

I sincerely doubt a Canadian university is going to do anything to you at all. I wouldn't do any of his "demands." You don't answer to him. I also would not involve myself in an argument over Taiwanese sovereignty during finals. Just ignore him.

This isn't really an answer to your current problem, but in the future it might be easiest to put something like "Taiwan/Republic of China." This allows you to acknowledge that Taiwan does indeed call itself the Republic of China while also pointing out what it is to those who don't know that Taiwan calls itself that (many Americans don't, at least). It also gives you a bit of plausible deniability if Mainland Chinese students complain, because you're just listing the two names a particular region is most well-known by rather than committing solely to the one that the PRC doesn't like.

I was aware of the debate going on over sovereignty, but did not expect a country all the way around the world to have students that would violently react to an opposite viewpoint. I referred to every contentious country by its full name, I called North Korea "The Democratic People's Republic of Korea" as well, but left undisputed countries like Russia as just "Russia". I think calling a people/nation by their preferred name is the most respectful thing to do. I don't call people Steve who tell me their name is Dave.

@Anyon and b) decide how important fighting about it is to you. It sounds to me like OP is already quite well-informed about free speech and its importance to him.

I am a Chinese citizen, and I HATE this kind of people who force their opinion on others (and not like your opinion is unethical or anything). After all, this isn't China where you can have the government censor anything you don't like! Personally, I do support a united China, but I won't force everyone to believe the same. Not to mention that what you did is perfectly reasonable (the Republic of China exists, whether they like it or not). Please, by all means ignore him. If he is disrupting class, make him "shut up". I apologize on behalf of him!

I appreicated everyone who contributed so I figured I would share the outcome.
The meeting ended up fizzling out to nothing. He started it with spending 10 minutes trying to convince the professor and I that the PRC owned the ROC using various corporate websites and online sources. He also tried to make a comparison to Quebec, but I didn't really get the point of that. Ultimately, he asked if I believed that the two Chinas were distinct countries and I told him that I really don't care to shut him up - he seemed satisfied at that and nothing else came of it in that class.

You are, it appears, being bullied. You will encounter people with strong, even irrational feelings irrelevant to you and your work with some regularity over your career. Engaging is seldom useful. You are not responsible for his demands, and this issue is not one in which it appears you want to involve yourself. In your coming meeting, engage as little as possible with his narrative. Bring all topics back to how you are being made uncomfortable, and how you wish to be left alone.  You are correct in your statement, but don't seek to assert that. Just let this angry individual exit your life without engaging with his angry demands. If he escalates, your department will certainly help you; use that.

@mike, Let us know how it all turns out.

Canada is a country where people generally hold free speech in very high regard. Even in the extremely unlikely event that the student will be successful in his efforts to get you disciplined by your university, I find it impossible to imagine that you could not with very little effort (say, a couple of Facebook posts complaining about your mistreatment) turn this into a huge scandal that would get the decision overturned due to overwhelming public pressure. I agree with others’ assessment that you have done nothing wrong and are being bullied into expressing speech you do not agree with and suppressing your own fully legitimate speech and thoughts.
With that said, in my opinion none of us has the moral right to tell you what to do, since you alone will have to bear the consequences of your decision. At the very least, the thought of having someone who disapproves of you so intensely would make anyone uncomfortable, and could be a strong motivating factor in the direction of deciding to try to make amends and cave into their demands, unreasonable though they may be. No one wants to have enemies. So you’ll just have to decide on your own how far you’re willing to go with this.
Finally, I must say I am disappointed with your professor. It would be more appropriate for him to tell the other student very firmly and clearly that he has no business pursuing any action against you, and refuse to discuss the matter further or even communicate to you any of the student’s “demands”. This is not exemplary behavior for an educator.
To be clear, my answer is based on general principles of free speech and has nothing to do with any particular opinions I may or may not hold regarding China and/or Taiwan.

@Roland I’m not faulting the professor for not intervening in the moment. But I am definitely faulting the professor for “He left it to me to decide what actions on the demands list, if any, I would be willing to do.” The professor should stand up for his students’ right to express their (legitimate, non-hateful) speech in his class. By even agreeing to communicate the list of demands to OP and have a discussion about them, he is lending those demands a perceived legitimacy they don’t have, and to some extent enabling the other student’s bullying.

The irony that I see in this whole presentation is that it was about anti-censorship, and my classmate wants me to censor myself and only accept his version of truth - which is actually a lie.

That's one, but there's also a lot of irony in

He ... stated that I shouldn't be pushing my political beliefs on the class

Since you've agreed to the meeting, you should think through what you aim to get out of it. Specifically: what points do you want to make? What concessions do you want the other party to make, and what concessions are you willing to make? How important to you is reconciliation with the other party?
If you rank reconciliation highly, then unless there are technical reasons why the answer to the question differs for the PRC and the RoC it seems that you might be able to concede the slide modification. You might even choose to concede the apology, conditional on the other party also making a public apology.
If you're willing to burn bridges, you could choose to go on the offensive and insist on an apology (in the meeting, not necessarily in public) before you're willing to discuss anything else, with a fallback plan of filing a grievance yourself if you don't receive it. Or you could lay a trap by clarifying that the other party thinks that pushing political beliefs in the lecture theatre requires a public apology, and then when he confirms this asking when he intends to make it - although be warned that your professor might not be amused.
Either way, if you think that a grievance in either direction is likely, it would be worth your while to find what relevant written policies you can, read them carefully, and take a copy to the meeting.


text:
Will the transferred manuscript at the new journal (B) be sent back to the same reviewers at the transferring journal (A)?
I submitted a manuscript to Journal A. After review, 2 reviewers were positively endorsed for publication. However, 1 reviewer and editor suggests publishing it in another journal (B) in the same system. So We agreed, revised, and transferred to Journal B. So my question is:
Will the transferred manuscript at the new journal (B) be sent back to the same reviewers at the transferring journal (A)? or they will invite a fresh new set of reviewers?
Thanks
Note: Journal A is higher than B in ranking, same system.

Could anyone with editorial experience/handling this kind of transfer manuscript answer this question? Thanks

I don't think there is any useful general answer.  I think it would be quite normal to consider inviting the same reviewers (unless the journal has a policy against it). However, there are many reasons an editor might decide not to do so. In particular, if the target readership of the new journal is different from the first, there may be an argument for getting reviewers from this community. Also, if the original reviews were positive the editor may feel that further reviews from those people would not provide additional useful information. Everything depends on the circumstances.

It is what it is. You will get a decision eventually. How they reach it is up to them.

It's even imaginable that the editor for B will accept the paper without further review. There were two positive reviews for A, and a third review that apparently found the paper suitable for B.  Maybe the two positive reviewers found the paper good for A  but specifically not for B, but if that's not the case, the B editor could conclude that there's already enough positive information to accept the paper.

It could also happen that the referees of A serve for B as well. In that case, depending also on the contact among editors as well your accompanying letter (if any), the whole procedure at B can be shortened and have a positive outcome.

I would expect that where the editor suggests "transferring" to a specific journal, it is because there is some arrangement that this can be done while keeping the same reviewers (assuming that they are happy for this to happen, but I don't see why they would object). Unless the new version of the paper has significant differences, the next review should be relatively quick. This has happened to me.
It is of course not uncommon for reviewers, if they don't think the paper is strong enough for the current journal, to suggest a specific other journal which would be suitable, and you shouldn't read anything into that (other than "if I were reviewing for journal B, I would recommend acceptance). But if the editor endorses that suggestion, and particularly if they use the word "transfer" rather than "resubmit", it suggests they think they can expedite the process for journal B.

Probably not - because the new journal B does not know which reviewers were invited by A. This information, as well as the reviews received by journal A, is not usually shared between journals.
The manuscript could still be sent to the same reviewers, but that would mean the editors of A and B independently agreed that [reviewer] is an expert on the topic who can review the paper.


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Should I resubmit?
I received the following rejection letter from the journal editor. It does not look like “rejection and resubmission” to me. Should I revise and resubmit? Is there any chance of acceptance?

... I very much regret to inform you that your manuscript has been rejected. Below are the comments and recommendations for this manuscript.
If you wish, please consider the suggestions made by the reviewers and/or Editor's Office and, possibly, consider submitting a new version to the journal.  If it meets the journal requirements, we will then send it out for independent peer review.  It has been our experience that those who follow the reviewers' comments and re-submit their paper generally are successful in publishing in ABC.  However, the decision to rewrite the paper rests with you...

The wording is clumsy and unusual but essentially this is an invitation to revise and resubmit with responses to reviewer comments as per the normal peer review process, isn't it?

What do the reviews actually say?

Your options are to take the reviewers advice and then resubmit, submit elsewhere, or just forget about submission. Of the three, the first seems, to me at least, to be the best option.
The last option seems clearly undesirable, but even the second may well leave you in exactly the same situation with a few months gone by.
But, the paper is yours and you can choose. Nor does it "belong" to the reviewers and you can choose to ignore some of their advice in a rewrite, though you should have reasons for that if you do. It is generally wise to "consider" every comment made by reviewers and at least rewrite "in the spirit" of the comments if they are reasonable.
It may be, of course, that the reviewers didn't understand what you were trying to say. But that is generally an indication that you haven't expressed yourself well enough that experienced people can follow your arguments and evidence. And that is also reason to rewrite.
I assume you are asking because you are at the beginning of your career and don't have a lot of experience with this. Just the practice of rewriting is probably worth it to improve your exposition style and to shore up any holes in your arguments. It is a learning process if nothing else.
And note that their instructions seem to be quite positive about the outcome of a rewrite. I'd recommend you do it. But the paper is yours.

That looks like a standard Reject and Resubmit to me. Therefore, provided you take into account reviewers' and editors' suggestions/comments and answer on their questions (if any), it is worth considering a resubmission to this journal.
There might be additional connotations to be read from the particular comments given by reviewers which would require a dramatic change in the methodology, results' collection OR some fundamental issues with the paper. It is quite likely that the resubmission is reviewed by the same set of reviewers which has its pros and cons.
Overall, given solely the information in the question, I would seriously consider resubmission upon careful examination of the review.


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Teaching at university (pathway 3 and teaching-oriented positions)
In England, in principle, there are three pathways to professorship, or in general to teaching permanent positions at universities. The third one is for academic staff whose responsibilities are primarily to cover essential teaching, educational needs and, for more senior grades, pedagogic research.
But, in practice, scientific faculties do not allow almost anyone to get a professorship that way. In Bristol, in particular, I only know of people in the Graduate School of Education having become professors through pathway 3.
Is there in Europe a real possibility, in disciplines like physics, mathematics, engineering, to work in academia as a university lecturer primarily?
One way of rephrasing this would be:
Are there in any European countries any teaching-oriented positions in scientific disciplines at universities?

Many places in Europe try to follow US examples, and that involves promoting research first, as a way of educating the faculty itself. Of course a acclaimed handbook author like Tom Cormen would almost always get the job anyway.
It is noted that there is many more postdoc positions than professorial positions worldwide.
Even if there are professors that focus mostly on teaching, they would not be advertised by universities trying to attract research funding.

Even Tom Cormen got his faculty position on the strength of his research, not on the fame of the textbook he wrote (with two and later three other coauthors whose names appear later in the alphabet).

I'd note that the US has a wide spectrum of types of colleges & universities: those that stop at PhD, MS, BS and associates degrees. To a first-order approximation, only the doctoral-granting schools are historically "research first" with low teaching loads, the rest being mainly teaching-oriented. All types can have tenured faculty. Basically if you want to teach doctoral students, you will need to get the funding for them too.


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Bibliometrics analyses with Pubmed metadata
I just started to have interest into bibliometric analyses, and so far I am struggling to understand the tons of copyright policies. However, these are (from my opinion) quite vague and with too much grey areas.
Let’s say that I constrain my analyses on the metadata from Pubmed (not PMC) considering basic classes in it (i.e., title, publication year, citation number, MeSH terms, author names…);
but I never touch or analyze the abstracts (text mining or anything alike whatsoever on abstracts).

Do you think that such analyses would pass without copyright infringements?

I'd definitely suggest to contact PubMed and ask this question directly.

Publication metadata does not have license restrictions. I work for the European partner of Pubmed - Europe PMC, and you can get metadata for every article available in Pubmed via the open API (https://europepmc.org/RestfulWebService).
In some countries publication abstract may be under copyright. For UK and USA it is possible to reproduce abstracts if your use of this data falls under "fair dealing claim" (see https://www.copyrightservice.co.uk/ukcs/docs/edupack.pdf).


text:
Is a software developer entitled to participate to paper?
I'm an external consultant who has been brought to develop a software suite to collect, analyze and reduce data for a project (with oral assurance that I would participate to any paper to come from this project).
Since then, the IT engineer assigned to the project has filed a complaint arguing that hiring me was a waste of lab resources (even if the suite was provided on time with no overcost) which resulted being in not being hired for the follow-up to this project.
Drama aside, I know that a publication resulting from the data processed through the suite I developed is underway. I tried to voice my right to examine, but was denied, again on the IT engineer's (who is participating to the paper) good word: he argues that I have no right to participate as developing software is neither original nor a research task.
From my point of view, this is simply not true: The software I've developed was tailor-made for this project and incorporate elements based on the state of the art in both data collection and analysis.
I know that what qualifies someone to be included in the authors of a paper varies widely among fields of work (my previous experience is a Ph.D. in solid-state physics, I'm talking about medical research here). Am I justified in wanting to be included in the paper?
I can see several reasons why it's important to me:

I want to validate the interpretation done.
Getting a paper for this project was for me a mean to prove my proficiency to further clients in this field of study.
Pride, also ? :)

One of the further questions is: had money change hands? Typically, if something is bought off you as a sub-contractor, you waive some rights. This should not be the sole factor, however. Did you try politely asking?

Based on what you say, I believe ethically you would be listed as an author on the grounds that data analysis in an integral part of research. At least, this is what I would do. I would do this trying to keep things professional even if personally I came to dislike the software developer.
However, in practice, it may depend on the contract you signed. If there was nothing in the contract, things get trickier as the situations seems already deteriorated. Is there anyone in the research group, apart from the IT engineer, that can vouch for your work and argue for your inclusion?
If you did not sign off the copyright to the software, you may have legal grounds for not having the research group use it (again, depends on the contract), although this would be harsh. An alternative would be to publish your own paper on the software, just as a data analysis tool if it is general purpose enough to be of use to others. That would give you even larger credit. Note however that most likely the software would need to be available free of charge to other researchers.
(As a minor point, I do not understand your first bullet point. If you are not on the paper, why is it important to you that the others interpret the results correctly?)

Assuming, of course, that all the details are as you report, then yes, you have a valid claim to be included, though it may be difficult or impossible to realize. You are being abused. If you contribute materially to the paper then you should be included or, at a minimum, recognized in the paper. It may well be that there would be no paper without your contribution.
Remedies may be difficult to obtain, however. Was the assurance purely oral, or is there some record of it - email, for example? Can you get support from the person who gave you the assurance?
While you may not be successful here, you should, in future, make sure that you have a complete understanding, in writing, of how your work will be recognized or if you are just a hired-gun to do contract work. Live and learn, perhaps, but guard yourself as best you can against unforeseen circumstances and bad actors.


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Tenure Track application: Time for committee to respond after interviewing references
I have a case where I applied for a tenure-track position in a R1 research institution. A month after the application, all my references were contacted and were asked for a telephone interview, which I got to know from all my references. This was a good sign and I expected the committee to contact me soon (in about a month after the interviews). Now it's been two and a half months since they interviewed my references but no contact yet. I am not sure what is going on and how should I deal with this. Should I email them asking about the status of the application?
Update
It's more than 8 months after my first application for this position. Significant changes happened to my CV to bolster my application. I had no hopes, but I dropped an email saying that this is my updated CV, please update in your records in case they are still reviewing.
The programme manager updated my CV in the application replied that the review is still undergoing and they have yet to finalize applicants.
Any idea what might be going on?

This might be nothing more than end of year business, and people going off, making it hard to get a committee together. It could also be that the committee is deadlocked. I doubt that it would harm you to ask, but it might be better if your advisor did so.

It could also be that you're out of the running and that other candidates are being considered or that funding for the position has been canceled and the position won't be filled.  However, it can't ask to send a polite email to the search committee chair asking about the status of the search.

@Buffy: I don't think it is appropriate to get the advisor involved here.  The candidate should communicate with the search committee directly.  It would probably be against the rules for the committee to share anything about someone's candidacy with anybody but the candidate themselves.

@NateEldredge, no argument. I was thinking that they might be able to say something about the state of the search, not the candidate. But your answer is likely the correct one.

Any idea what might be going on? — I'm going to go out on a limb and guess that their review is still ongoing and they have yet to finalize applicants, just like the program manager said.  The good news is that they haven't decided not to interview you.

Yes, it's certainly fine to email them and ask.
However, I'm afraid you probably won't get good news.  A common workflow for tenure-track searches is that after one round of review, they only contact the candidates who were selected to move on to the next round.  It's likely that this has happened by now, so if you haven't heard from them, it probably means you're not one of the candidates they're actively considering.
You technically haven't been rejected yet, because in principle, if the selected candidates don't work out, they could go back and reconsider the rest.  Indeed, official rejection letters often are not sent until after the search is complete and someone has been hired (or they've given up).  But this isn't a good sign.

Thanks for all your comments. I think my dilemma lies in the fact that the committee has taken efforts to contact all my references and do an interview with them meaning probably I made the first round. So, I am still not sure if its just delayed slow process or I am out of running. If I am not out of running, I would not want to look desperate by asking the status, but if I am out of running then its better to know right away.

@PranavPandit: My personal guess is that you're out of the running, but there's no way to know for sure except by asking.  I wouldn't worry about "looking desperate"; that's unlikely to have any effect on your chances.  If anything it may be helpful to let them know you are still on the market.

Unfortunately, after 8 months with no interview or any further news, I would assume your application has been unsuccessful.
Hiring practices differ between fields and countries, so you should ask someone (e.g., your advisor) who is familiar with these practices to confirm what is the usual time.
Unfortunately, it is not unusual to simply never hear back from a job application. I applied for tenure-track jobs in the US about a year ago. Some universities got back to me and arranged interviews (within 3 months of applying) and offered me a job (within 5 months of applying). Some sent me rejections (as late as 8 months after applying). But most simply never responded. Alas that's the way it is.
Did the position description you applied to specify a start date? If that start date has passed, I think it's safe to say the search is over.


text:
All Reviewers Assigned : Nature Communications revised manuscript: What does it means?
I have a revised manuscript which I submitted to Nature Communications. The status of the manuscript says 'Reviewers Assigned' for about 24 days. What does it mean? Is it under review by the reviewers? Or reviewers are not responding to the editor after the request to review the revised manuscript by the editor? Just want to clarify, that this question is specific to the editorial process of 'Nature Communications' which is not usual and not related to generalized peer review process. I think I am asking this question especially because Nature Journals have their own editorial workflow which is not as same a typical workflow of many journals.

Update on the question. After being under the status 'All reviewers assigned', the manuscript status changed back to 'Manuscript Under consideration'.
This is more confusing as generally, 'Manuscript Under consideration' means that the editor is considering the manuscript for peer review. Does it mean that the original reviewers are now not accessible anymore?

Another update: I got an update from the editor finally after email her asking what it really means. The manuscript was under review when it was showing 'all reviewers assigned' and when the status changed to 'under consideration' it means that reviews are back with her and she is discussing it with her collegues.

It means reviewers have been invited, but you can't read anything more than that. Whether or not reviewers have accepted the invitation is usually confidential information available only to journal staff. Depending on the range of statuses the journal uses, this status might even mean that some reviews have been received.
In any case, there's nothing to do except wait and see.

It can mean many things, if the status has been same since you resubmitted your manuscript then editor might still be waiting for all the reviewers to send the editors their review reports, in some cases when one reviewer is too much busy and needs more time to finalize his review report, editors waits for him to send his comments then they contact the author and make a decision on the basis of these reports and send you acceptance, rejection or revision based on their reports.
Also if one reviewers has recommended for rejection and one or two reviewers has endorsed the publication then editor weighs the comments of all the reviewers and then make the final decision.


text:
I published an article developing and applying a method that I thought new. Someone had developed it before, outside of my applied field
I am writing my PhD thesis now. It comprises, in particular, one published article in a Q1 journal. This is a compilation thesis, and thus articles are pasted directly. For context, we apply machine learning techniques to biology, and publish in biology journals.
Here is the issue: When trying to solve a problem, I upgraded a machine learning method with a modification. Since, at the time, I was not good at all at reviewing literature, I thought that no one had had this idea before, and I called the method X. Now, while writing the thesis document and properly reviewing literature, I just discovered that this methodology already exists in the machine learning field, and it is called Y (which, by the way, is a better name). In addition, several more advanced adaptations also exist.
What is the best way to proceed here? The thesis has an introduction, and I am thinking maybe citing the article describing Y and saying we do the same thing and call it differently, I think it is the best course of action. I am deeply worried that I did not really contribute with anything new and concerned that someone may think that this is plagiarism.
Of course, none of the co-authors (it is just three of us), nor the reviewers, noticed this.

Yes, this is a PhD thesis. Corrected, thanks.

This sort of thing can happen to anyone, I suppose.

The, to me, most striking example of not-actual-novelty is the Fast Fourier Transform, which is commonly attributed to Cooley and Tukey (1965) but was in fact already used all the way back in 1805 by Gauss!

@leftaroundabout ... and finally named after J Fourier :)

I would acknowledge that you've since found that someone else did something similar/the same thing. You can still describe how you originally came to your findings and the checks/tests you performed independently.
Independent discovery is not plagiarism when you don't know about the previous finding. Hiding that someone else already found something you thought was original is quite suspicious though. Now that you know, act as though you know.
It's common that things are discovered more than once. Communication barriers used to play a big role, through language, physical distance, and distance in time (things get forgotten or their applications are not evident immediately). Today, many of these barriers are reduced, but instead there is simply so much information out there that it's easy for things to be lost in the background, especially when terminology differs.

describe how you originally came to your findings and the checks/tests you performed independently. ... #rediscovery. #reproducibility

+1 for that last paragraph. One famous example from communications: BCH codes were named after the inventors Raj Chandra Bose, D.K. Ray-Chaudhuri and Alexis Hocquenghem, however, the latter (Hocquenghem) discovered them indepedently of the other two.

+1 for "especially when terminology differs" - more than once, I have come across papers that described, on an abstract level, the same thing I was about to write, but that used a totally different vocabulary than the literature I was basing my work on.

is another important point to mention that it may be up to their PhD committee to say if the work still qualifies towards the degree ?

+1, especially for noting that the communication issues have shifted from "too many barriers" to "too much information". Today all this information to parse can build-up a lot of "background noise" for sure.

@MikeM It really should, but certainly not all PhD committees/graduate programs are reasonable, I've seen some really unreasonable policies mentioned on this site.

Change your claim.  Instead of 'This thesis proposes a novel method X for ...' to 'This thesis presents the first study that shows how method Y can be applied to field Z'.
The strategy is to present a new angle (or research question) or details.  Usually, this is 'easy' (though requires a bit of thought) because you and the author of method Y took a different path/direction or research aim.

+1 ... shows how method Y can be applied to field Z

Since method X was already published, I think it is fair to state in the introduction of the thesis that this was an independent development. Of course one should state in the discussion that it is essentially method Y, but also that this connection was only realized later.

Honesty is always a win. While this means to "downgrade" one's claim from "we developed the novel method X" to "we apply method Y to field Z"; one can, especially in a thesis which is not page/word limited, discuss the whole process: we developed method X and later realized that X is essentially equivalent to the method Y; and here's why this is the case, and here's why X/Y is better than Y/X, etc. etc. No matter whether your method X is novel or not; you developed it, tell the world about it.

This type of thing is not as unusual as you might think; rediscoveries are common and sometimes they slip into the literature because the relevant parties are not aware of the previous work.  Just be clear and honest in your dissertation about what happened, and note it where relevant when citing this work in future.
Going forward, you should refer to the relevant method as Method Y (since it was first and you say that this is the better name) and cite both papers, but perhaps add a footnote noting that your own paper was an independent rediscovery of the method and noting why you've chosen to go with the previous method name.  This is not plagiarism, but you are correct that this circumstance reduces the novelty of your own work.  Your paper might still have value in presenting the same method in a different way and that would still be a novel contribution in a different sense.  In any case, keep pushing forward with your research and pivot to new forms of novel contribution in your field.

If nothing else, it provides value from confirming the results of the other work -- something entirely too rare in science.

@Mark  one of the most serious problems in science today.

This happens all the time (in my field, econometrics, mainly applied). I'll review papers for meta-analysis and two completely different authors will have done very very very very similar work, almost down to the specifications, and yet they came to these decisions independently. So I would cite the other authors, highlight your differences, and talk about how your method might be useful for your applications.