text:
Scanned detailed comments for a paper review
Sometimes I find my self reviewing papers with authors who are not very capable English writers. I am a non-native speaker myself, and I know how difficult it can be to proof-read a paper in English, in particular if you don't have access to any native English speaker. If the scientific content of the paper is otherwise good, I therefore try to do what I can to correct grammar, poorly constructed sentences, spelling mistakes etc.
It often results in very long referee reports, which take ages for me to type. I was wondering if it would be proper form to simply scan a version annotated by hand, and attach it to the referee report? If you received such a thing, would you be grateful for the time spent, or would you consider it lazy that I did not type in all the suggestions in a proper report?

Correcting spelling and grammar is not a reviewer's responsibility.

I know. But if the content is good, then it is a shame if an otherwise sensible paper is illegible because of poor grammar and spelling.

Journals have, or should have, copyeditors who do that.

I agree that they should (otherwise - what are they paid for?), but unless you publish in a high profile journal, it is my experience that they don't.

If you receive the paper as a pdf, then it is possible to annotate the pdf directly so there is no confusion about what and where the corrections should be.

@SolarMike: annotating the PDF will usually tag your notes with your name or at least your initials, defeating anonymity.

@StephanKolassa It depends on software you are using and how it is configured.

A scanned referee report is fine, so long as it is legible.  This requires good handwriting, patience, and a good scanner.

Completely agreed with this answer, except re “a good scanner”: these days, there are plenty of scanner apps available that produce good-quality “scans” from a phone camera.  In iOS, for instance, you can use the default Notes app — start a note, click the “insert image” button, and it offers a scan as one of the options.   (In my online teaching last semester, I encouraged students to submit handwritten homeworks scanned with apps, and the results were good enough quality that there was no extra friction during grading.)

Please don't feel obligated to proofread manuscripts as a part of review process. This is not a reviewer's responsibility. Journals are supposed to have proofreading services and/or to encourage authors to send their manuscripts for proofreading / editing. It is sufficient to comment on whether or not language check is required for the manuscript to be accepted.
Proofreading takes a lot of your time, which you are not compensated for. Unless you are  also a professional proofreader, you can inadvertently introduce some occasional mistakes on top of correcting others. Moreover, if reviewers keep doing a proofreader's job, it will create an unjustified expectation on both journal's and author's side that proofreading is a reviewer's job. As a reviewer, I am frustrated with authors sending their manuscripts in a very poor state (not even spellchecked using a computer), which slows down the review process. It is important to remember that journals and authors benefit from publication directly, while reviewers do their service on a  voluntary basis and for the good of the whole community.

Journal paid proofreaders, aren't, I think, domain experts. Some of their advice changes the meaning in unfortunate ways.

@Buffy Ultimately, it's down to each journal whom they hire. If paid proofreaders introduce a small number of errors, they can be corrected by authors. If they introduce a lot of errors, authors will complain and journals will be forced to hire better ones. Reviewers should not involve themselves in this process.

I disagree that discouraging the OP is a good thing. They are a volunteer, they can go beyond the minimum if they like. I applaud it, actually. If you don't like the state of a manuscript sent to you for review, you are also free to reject it.

@Buffy It depends. In academia, we often fail to impostor syndrome and spend enormous amount of personal time and effort doing things "beyond minimum". This is easily exploited by for-profit publishers and/or Universities, capitalising on unpaid academic overtime or voluntary review process. It is important to alert early career colleagues that some areas of work are actually someone else's responsibility (and they are paid to do it).

Just as @Buffy, I'm skeptical of the "doing too much will create an unjustified expectation" line of argument wherever it is being made. It leads to janteloven, which is hardly what we need more of in science. And you can prevent the expectations from rising by openly declaring that what you are doing is unusual and you're doing it because the paper is really worth it or because the author is new or something like this. (It also gives you a new reason to decline referee requests if you don't think the paper is worth it.)

My impression is that professional proofreading services are always a double-edged sword in science, if not a sword with the blade pointing the wrong way. The proofreaders rarely know the science well, let alone the specific subject of the papers. Last time a paper of mine went through professional proofreading, "we coordinatize the space" became "we coordinate the space". I found it because I looked over the (handwritten and scanned, in 2019!) page proofs, but I doubt many authors actually do so (it takes time, and is ultimately pointless if you think of arXiv as the point of truth).

I'd like to add a concern: Adding scanned documents or annotated PDFs might unwillingly disclose your identity. It is good practice to keep reviewer anonymous for authors. If you are recognized by your handwriting, by PDF metadata, or just the practice of adding scans (which might be unique in your narrow sub-field), that would be a bad side effect.

The remark about PDF metadata applies to all referee reports submitted as PDF (e.g., most reports in my subject), not just scanned ones. Actually, scanned PDFs are less likely to contain identifying metadata. Good editors will probably scrub metadata from PDFs automatically via script (e.g., "qpdf --empty --pages [original PDF file] 1-z -- [output PDF file]"). As a referee you are not responsible for doing your darndest to get rid of metadata at all cost.

You can do this as long as you get your meaning across. I can't speak for other editors, but I'm happy to receive any reviewer report at all (since I'm after all taking up your time), and won't begrudge you for not typing it out.
However, I'm skeptical it is the most efficient way. Today's copyeditors have a lot of shorthand symbols (example) that often makes writing more efficient than typing (this depends on the copyeditor; I know some who prefer to type anyway). Still, even if you are familiar with copyeditor symbols, there's no guarantee the authors are.
If you can't use the symbols, then the advantage of writing is you can clearly mark where the changes are and don't have to write "on page 3 second paragraph, change X to Y". But you can do that electronically too, e.g. here's how to do it in Adobe Acrobat. At that point the only advantage of writing is if you're dealing with heavy mathematical symbols that aren't easily written electronically. If you are making lots of these corrections and typing is inconvenient, then sure, although I suspect if these are necessary then the manuscript has more flaws than a proofreader can solve.
Bottom line: if it really is the best way for you, feel free to write & scan; however, there's a good chance there exist tools that make doing it electronically more efficient, to save nothing of the paper/trees saved.


text:
How to communicate with the co-authors regarding the work (paper)
I am working on a project, where I am the author of the idea. Also, I found the data (open-source) that can work well with the idea of the paper.
I invited one of my colleagues to work with me on this project. We have agreed that I will be the first author.
As this is the first time for me to work on a paper, I really do not understand the role of communication with the co-author. So, can I share with the co-author the analysis of the data (before writing the paper? In other words, can I show the co-author my works and software codes? or I must write the paper (my role) and then they can look at it. I ask this question for two reasons:

To understand my roles and duties.
To avoid bothering my colleague with my work.

Can someone help me with this point, please?

This is a very strange question definitely telling that the concept of writing a paper, and generally doing research, has different meaning in different fields. I wonder how/why your question even has emerged.

Can you help me understand "Mathematical Science"? (from your profile) Is it Applied Mathematics or something else. To my mind mathematics and science are quite different disciplines. Help?

@Buffy Hi. Thanks for your comment. it is a statistical modelling.

Co-authors should be involved in every step of the scientific progress. Some might be more involved in some steps than others, due to differences in expertise or involvement, but generally:

you should meet and discuss ideas and plans
you should meet and discuss results/interpretations
you should both contribute to writing

"meet and discuss" can be via email or in person, or a combination of both. These can be scheduled meetings or meetings at the coffee machine. Discussions can be more or less deep, depending on your needs and expertise (e.g. whether you need to share code or not is a specific question for your case, hard to answer in general - however, do ask for their input in case you want to). Writing usually loads heavily on one person (probably you), with the other(s) giving comments and feedback at major milestones.
You should definitely share and discuss progress before writing the paper, and before having written the paper. If you collaborator (as it seems) is not your supervisor, it is probably going to be your role to keep the project running. At the same time, if this person is not your supervisor, or you are already a bit more senior, you might not want to share every minor step of your work. Even if you can work quite independently, it could be good to give a status report every few weeks to keep them informed of the progress, and keep them on board. And, most importantly, to give them an opportunity to contribute.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

sort: votes


text:
Replying potential PhD supervisor with documents
I applied for PhD at a University and receive a mail from the supervisor, he asked me to mail my cv and transcript. I am thinking to reply like this:

Dear Professor XXX,
Thank you for your reply.
I have attached my grade sheet and resume, with references, to this email.
Thanks for your consideration.
YYY

Is it sufficient and decent?

I am not a native English speaker and haven't mailed many  profs so

Yes, this is sufficient and decent.
Only point I'd note is that if your transcript is not in English, be sure to include a translation. You might also need an explanation of what the grades actually mean (e.g. is your grade measured on a 4.0 scale, or on a 100-point scale?).

Glad my edit was ok then...

Thank @SolarMike and Allure

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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How much is an average time of waiting to receive a reply from Professional co-author?
I have sent my manuscript to a professor of math about one month ago. This manuscript was written according to his encouragement for a joint research work. He told me that send him what I have done from my side, and then he will add additional materials from his own side. I want to send a tracking email about the status of that. Should I do that or I must wait for his reply?

Do you really mean "tracking email"? Like these?: https://academia.stackexchange.com/questions/82869/is-it-rude-to-use-tracking-softwares-for-the-emails-that-you-send-to-potential-a Never, ever use these.

If by tracking email you mean an email sends you a notification when the recipient opens it, then it's probably a bad idea.

Can you elaborate on the history?  When did he tell you that, when was your last communication about it, how much does the joint work date back?

The academic clock can run slow. Be aware.

In the non-Covid times, some researchers would take summers off, say June to August.  In that case, you could not expect a reply until he returns to civilization in September.

@GEdgar True, but I have yet to find someone that goes into hibernation for three months like a bear and does not even answer e-mails.

"I want to send an email email asking him for an update about the
status of that. Should I do that or I must wait for his reply?"

Absolutely. Why? Because it has been 1 month and you have not received any communication from him yet. Usually after waiting a full 7 days, it is not inappropriate to send a follow-up email.

"How much is an average time of waiting to recieve a reply from
Professional co-author?"

It varies. Some people reply the same day, some the same hour, but it's also not uncommon for people to take a month or two to reply.
Usually it is not inappropriate to ask for an update 7 days after the first email. Another one after another 7 days can also often be considered okay. It's when you send more than 2 follow-up emails, or when you do not wait ~7 days between them, that it might start to be seen as "nagging", but even then that's not always the case. Please send him a follow-up email and ask us what to do if you still have problems after that. My guess is that he'll reply (since he asked you for the manuscript).

It should read "the vast majority take a month or three"

When communication becomes difficult, when human sensitivity comes into play, don't write mail after mail: call your collaborator by phone. Maybe on phone you can get them to make a credible promise; maybe they will make you understand how overburdened they are right now; maybe they will enjoy a little chat with you; hopefully, your relation with them will grow through direct conversation.

Calling collaborators on the phone without any prior arrangement or emergency seems horribly intrusive to me.


text:
How should I thank mentors that I connect with via the Internet?
I am an incoming undergraduate student, and I have reached out to people who are currently pursuing/once pursued the field that I'm interested in (it's physics if it matters), via the Internet. Most of them are willing to help me and have given me a lot of good advice. Thus, I really want to thank them for doing that while potentially improving their impressions of me. However, since I have never met most of them in person (even if we did, most of our communications still happen online), I have a hard time thinking of a way to express my gratitude. Here are some details of my situation:

I know very little about them as a person (their hobbies, preferences etc.). The conversations we had focused almost exclusively on their chosen fields - most of the time, they answer my questions and provide guidance.
People who have helped me are in various stages in their study/career right now. Specifically, undergraduate, Master's, PhD and postdoc. Thus, I think that they may prefer different types of gifts.
I've heard of people writing thank you letters to their mentors. However, I feel that doesn't apply to my situation since my relationship with my mentors doesn't have an explicit end. For example, the length of our relationship isn't defined by the length of a course or a program. Thus, I feel that writing them a letter that talks about our past interactions would be perceived as a signal that I no longer want to continue our relationships.
I tried to treat those who invited me to talk in person with drinks or meals (if they let me). I would like to hear your thoughts on whether or not it is a good way to express gratitude as food doesn't last very long. Should I keep doing that or even go out of my way to invite them when I travel to places where they live?
Alternatively, I am thinking of mailing them tangible gifts. But again, I am unsure about what to purchase yet.

A simple email is really all you need. Thank them for their help and update them on your recent progress, say by mentioning that you have been accepted to ...
Don't bother with gifts as they will embarrass many people and might be considered improper. The one exception I can think of is the situation in which you are from a different country or culture. Then a token tourist level souvenir from your country might be fine. Something like this if you are from Sweden (not the world's biggest, though). I find it harder to come up with anything appropriate if you are from the same culture/country, though. The gift should have personal value, rather than tangible value.
Later, when you finish a doctorate, say, and get a great job, you might think of something more elaborate.
But for people you have met and who have helped you, say a teacher, it is a good thing to go back after several years and thank them personally for their mentorship. Just a meeting in a hallway with the statement of thanks for their help and guidance is a deeply satisfying thing to do and to receive.


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Being incorrectly assigned as a thesis reviewer?
I am 3rd year PhD student now. Today I was approached by a master student from my lab asking me to be his external reviewer. There are several things that bother me in that situation:

To my great surprise, education department did not object when he filled my name into 'external reviewer' field in his form about a month ago. My personal suggestion is that they did not check that I'm from the same lab.
I was acknowledged of that situation just now, not when he filled the form.
His defense is within a week, so I'm not sure if he will be able to defend without external review.
I actually helped him with advises being unaware of my role as external reviewer.

Q1: Would it be considered as an academical dishonesty if I write my review for his work as external reviewer?
Q2: How should I approach that ugly situation?
P.S.
I am not inclined at all to ruin his last two years of study, but even if I make a review of his work, it will definitely not be good.
Edit:
The formulation of who can be an external reviewer from education department is extremely vague:

The External Reviewer can be appointed from among Faculty or Researchers of /university name/ outside of the Students’ Educational Program.
  The Reviewers can also be expert representatives of other higher education organizations or employees of other organizations from the professional sphere corresponding to the topic of the Thesis.

So he asked you just now if you want to be the reviewer? Did you say yes? Also, do you now the precise rules in your uni what a reviewer has to do and who is allowed to be a reviewer?

Did the student have a primary supervisor? How many reviewers does a master's thesis usually get? Does the student have the required number and you are extra or are you the obligatory "external"? You were not asked whether you are happy to supervise? Is that required in your department? Did you inform the exams office that you gave advice to the student and that you are in the same lab and asked whether, under these circumstances, you are allowed to mark the work as external? BTW, do you know the work of the student so well that you know you will mark him down? If yes, how?

The description of who can be an external reviewer is extremely vague, as far as I know it: The External Reviewer can be appointed from among Faculty or Researchers of /name/ outside of the Students’ Educational Program. The Reviewers can also be expert representatives of other higher education organizations or employees of other organizations from the professional sphere corresponding to the topic of the Thesis.

It was a bit unclear whether you are, indeed, in the same lab. Clarify?

@CaptainEmacs, I just do not know all the requirements he have for a review, I got my masters from another uni. There are no formal requirements for masters supervision, but I was kindly asked to do that by my supervisor.

Speak of all this to your PhD advisor

So your supervisor said you should be the reviewer or what?

Ask your supervisor and mention the issues that you see and whether you count as external. Proceed from there. If your supervisor is a marker, do not mention your concerns concerning the mark, though, or you taint the decision-finding process.

I voted to close as "unclear". You haven't said anything about your advisor's position in this. It was improper, IMO, if you weren't consulted before your name was added, but it is possible that your advisor sees it as an opportunity for you. It is also unclear if filling in your name was just providing a "suggestion" for a reviewer, rather than a "selection". Lots of possible nuance here.

"if I make a review of his work, it will definitely not be good." But please stay objective. Your own work will be reviewed at your PhD defense.... A harsh review could backfire on you....

You have a conflict of interest which is NOT your fault: declare it officially
You have been nominated for a duty in respect of which there is a conflict of interest of which the persons responsible for ratifying your nomination for said duty may be unaware. Given that you did not consent to the nomination, this is not your fault, but you have an ethical obligation to declare the conflict of interest officially and in writing. Once the conflict of interest has been declared and recorded officially, responsibility for adjudicating the appropriateness of your nomination rests with the persons responsible for ratifying your nomination.
Whether the conflict of interest is acceptable depends on local regulations and custom, but what you describe strikes me as problematic enough to disqualify you from being an external reviewer. But, based on how you describe things, the situation is not your fault. The professional response is to raise the issues with the person responsible for organising the review/examination/defence. I will address your four numbered points individually.

Re §1: being "from the same lab" strikes me as failing to meet the criterion of being "outside of the Students’ Educational Program" (but maybe the institution has a different interpretation? To be honest, I find their definition already very lax, since I would consider "external" to mean "not working at the same institution").
Re §2: in many places, the custom is for the external examiner/reviewer to be approached prior to being nominated, but this is not universal; at the same time, unless there is something in your contract about taking-up examining duties of this sort whenever requested, you should feel free to refuse.
Re §3: the short notice is not your problem, so you should feel free to refuse on that basis alone.
Re §4: this is the most serious issue, but it is not your fault, so you should be completely open about it.

Your questions
Q1: I would consider it dishonest if a reviewer/examiner failed to declare a conflict of interest, which is to what the problems you describe amount.
Q2: Contact the relevant office/convenor/official, and disclose the conflict of interest in writing. Explain that you did not agree to be nominated for the role of external assessor duty. Then:
option A (ask either to be excused or for confirmation to proceed)
Ask the office/convenor/official either

to excuse you from the assessment duty (this is the professional course of action if a conflict of interest is deemed unacceptable) or
confirm in writing that you can undertake the assessment duty despite your conflict of interest (if this happens, keep the relevant letter/message, and bring it to the defence -- that way, if you are challenged about acting as external assessor, you can show the letter/message and thus not be blamed for the situation).

option B (say you are excusing yourself on the grounds of conflict of interest)
If you feel strongly that the conflict of interest is unacceptable, you can, alternatively, simply notify the office/convenor/official that you refuse to act as external reviewer due to the conflict of interest. It is perfectly reasonable and professional to say this, unless you have misunderstood the nature of the role.
option C (say you cannot do it in the timeframe)
If you feel the institution does not take conflicts of interest seriously, you may wish to refuse due to the short notice of the examining engagement.
Finally
Do not keep quiet about the conflict of interest out of some desire to protect the Master's student. He/she may have acted inappropriately by nominating you; if so. it would be far better for him/her if this mistake is rectified before the defence, not after.
If you keep quiet and somebody else discovers this conflict of interest, it could have serious ramifications for the Master's student and you may be regarded as having behaved unprofessionally or even unethically. If, on the other hand, you declare the conflict of interest officially, then any blowback would be to the person/official who permitted you to serve as external assessor despite being told about the conflict of interest (because, when questioned about it, you would say, "yes, of course I was aware of the conflict of interest, and declared it accordingly to the dean and the rest of the panel; as you can see from this message dated ___, the dean confirmed that I can still act as external assessor; I was a bit uneasy about it, but I was not about to argue with the dean").

Sorry, I don't understand how it is, in any way, a conflict of interest. Are you suggesting that if one person goes up, the other must go down? Please clarify.

I see two conflicts of interest: first, being in the same lab; secondly, as the OP says, "I actually helped him with advises [sic]". Both of these would, in my eyes, disqualify the OP from being an external assessor. Maybe the OP's institution has a different concept. The relevant authorities should be aware of the first conflict (same lab), but it is very possible that they are unaware of the second (OP assisted the candidate). Therefore, it is imperative that the OP declare it, otherwise he/she may be accused of collaborating with the candidate to rig the examination.


text:
Is it ethical to present the performance of an implementation that uses undisclosed optimizations?
Our research group sometimes does the following:

There is some problem P, and we are writing a paper about a novel technique T.
In one of the sections of the paper, we try to empirically show that T is a great technique.
To do this, we create an implementation I of technique T, and also look at other existing software products/artifacts J, K, L which also solve problem P (but not using technique T).
Generally, our implementation I is better than J, K, L, and this serves as good empirical evidence for the hypothesis that T is a great technique

However, our implementation I usually uses several other optimizations T1, T2, T3 and
the paper does not discuss these optimizations. Now, I believe that we would not have beat implementations J, K, L if we only used T without T1, T2, T3. I also believe that just adding the optimizations T1, T2, T3 to any of J, K, L would still be not as good as I (which uses T + T1, T2, T3).
I think these are (one or more of) the possible rationalizations of doing this:

Technique T1, T2, T3 are minor optimizations. (This is subjective, but I generally disagree that they are minor. My opinion is that our PI is a gifted programmer and consistently underestimates how difficult it is to implement something.)
Talking about technique T1, T2, T3 is "bloat" for the paper, and takes away attention from T, which is the main idea. If we do this, this might distract the reviewers, and there is a possibility that they wouldn't agree with the hypothesis that T is a great technique.
Sometimes the software artifacts J, K, L are very well-known and well-engineered tools. If this is the case, one may say that our results are good evidence for the hypothesis T is a great technique anyway, since the implementation I is an underdog in terms of man-hours spent in producing it.
If they are not minor, it may be worthwhile keeping T1, T2, T3 for a different paper, or an extended version of the paper, or a "tool" paper.

But more importantly, this feels unethical to me because:

We are misrepresenting the impact of technique T, which is what the paper is about.
It reduces the "utility" of our paper. If someone needs to solve P, and discovers our paper, they will be in for some unpleasant surprises if they try to implement technique T.
It also doesn't help that we rarely publish our source code

Is it ethical to present the performance of an implementation that uses more optimizations than we discuss?

I urge you to think carefully about whether you really need symbolic names (T1, J, etc.) for anything here. I think they obfuscate your point.

You're comparing your technique T plus optimizations T1,T2,T3 with software products/artifacts J,K,L. I would understand "software product" to mean not just a technique but a technique plus optimizations. I.e., "products" would include optimizations. If that understanding is correct, then your comparisons might be fair. Nevertheless, I agree with Buffy that you should say something about this in the paper, explaining the situation as well as you can (presumably without access to the optimizations of J, K, L, as these are probably proprietary).

"If we do this, this might distract the reviewers, and there is a possibility that they wouldn't agree with the hypothesis that T is a great technique." And possibly they might be right with this concern. That's what ablation studies are for.

The problem is that I cannot trust your results at all.
You claim that you have improvements due to T. But since you added optimisations T1, T2 and T3, there is no way to verify that any improvements are indeed caused by T. Neither for me nor for you. You should only publish this if you can also provide either the unoptimised version, and the unoptimised version with T, so we can check the improvement from unoptimised to (unoptimised with T), or your current version with T removed, so we can compare (optimised without T) to (optimised with T).
Of course you could just create a paper that demonstrates T + T1 + T2 + T3 being an improvement to having neither of them.

If the other optimizations are responsible for the result and they aren't disclosed, then, yes, it is unethical. If, in fact, your results show that that T alone isn't better than the other alternatives and you misrepresent that it is better, you are being unethical.
You need full disclosure here and you should probably view it as an opportunity. Academic publishing should be about reality, not marketing some technique.
I would think that a paper that demonstrated the combination of things, and not just "T" alone was superior would be a better paper then one that misrepresents the value of T.
As it is, you seem to be wanting to publish a "hoped for" result, not the actual result. Yes, ethical problem.

In general, claiming that X is evidence of Y while not disclosing Z, a fact that makes it clear that X is not quite as strong evidence for Y as you are claiming, is dishonest and unethical.
Your situation clearly falls within this set of behaviors. So yes, it is unethical.
Thinking about the bigger picture here, what seems to me to be the larger problem is that your group is publishing code-based papers without disclosing the code. If you were required to release the code, the sort of gamesmanship you are talking about would be much more difficult to engage in, because the “hidden” optimizations would be easy for others to detect.
Conversely, in an environment where authors are not required to release their code but can still claim breakthroughs evidenced by their private code, it is almost certain that various forms of cheating and gamesmanship would take place; the temptation would be too great, and making performance claims that are unverifiable by anyone who doesn’t have access to your code is just too easy for it not to become commonplace.
So, while your group’s behavior is indeed unethical, I’d say the larger culprit here is the bad publication culture of your field, in which papers can easily get away with making unethical and dishonest claims.

"I have a truly marvelous algorithm to solve the halting problem which this margin is too narrow to contain."

I hope you can see that your back-to-back statements are contradictory:

Now, I believe that we would not have beat implementations J, K, L if we only used T without T1, T2, T3. I also believe that just adding the optimizations T1, T2, T3 to any of J, K, L would still be not as good as I (which uses T + T1, T2, T3).

They correspond respectively to T < J and T + T* > J + T* -- that is, the unoptimized new method loses to the unoptimized packages and the optimised new method would still beat the hypothetically optimised packages.
I suppose that could theoretically be true since computational gains aren't always additive. But it's not obvious how that could be true, and I don't think you are sure whether it is true or not, and if you are not sure about the subject of your expertise then doesn't that make it fertile grounds for research? Shouldn't your group also investigate whether T* are truly optimisations and publish that they are or aren't?
So, ethical concerns aside (and they are real!) your group is simply leaving easy papers unwritten if you keep not documenting all the improvements you're making. If your group is really a paper-focused group, why not write those papers?

How improvements are not additive, an example: A Fourier transform can be evaluated in O(n^2) steps using a very simple algorithm, or in O(n n * log n) steps using a Fast Fourier Transformation (FFT). If the original algorithm did Fourer transforms unnecessarily, and the improvement removes them, and the calculation was very slow, then you get a massive improvement. If instead you switch to FFT as an optimisation, that also gives a massive improvement, but then avoiding Fourier transforms willl have much less benefits.


text:
How to defend plagiarism in my bachelor's thesis
I study at a university in Europe and recently received an e-mail from the exam commission regarding the submission of my bachelor thesis. I am under suspicion for plagiarism and to be honest I don't know what to do, as the consequences are severe and I had no intention of committing plagarism.
To give you some background information: I intend to start the Master Accountancy after summer and  all I need to do now is pass my thesis. My supervisor got sick a couple of weeks before the deadline and therefore our final meeting was postponed until only a week before the deadline. In this meeting she told me that my thesis was too complex and it would be difficult to efficiently use SPSS. She adviced to change a lot of stuff and I eventually had to rewrite big parts of my thesis. Due to the limited time until the deadline I had left, I used an old student's thesis for inspiration (as we partially had the same research question and often made the same references). I had no intention of copying or being inspired this much by this thesis. As I said, my own research questions reflected his a lot and I read the thesis many times through. Naturally then, it took up a large portion of my working memory during these days and I appearantly was disproportionally influenced to the point my thesis started to reflect the paper too much.
I now need to send an e-mail back to the exam commission with an explanation with what happened. What scares me the most is that should the exam commission decide that I plagiarized my thesis, I am not allowed to resit the thesis for one whole semester (6 months) after the students who failed the resit re-do their theses. This would mean that I would be restricted for the thesis for  1.5 years. This would be such a shame, as I finished everything else, and already was planning to start my Master in a couple of months. All of this is really starting to affect me mentally.
Does anyone have any idea what is best to do next? Please keep in mind that I am under ''suspicion of fraud'' for now. I am not sure what to respond to the exam committe and how to convince them otherwise. It was never my intention to do this, but it was done unintentiolly in the rush of the nearing deadline and having to re-write a big part of the thesis in a short time span (due to my supervisor not being available for feedback, due to illnes). I now see that my thesis indeed reflects the paper disproportionally. I am out of ideas on what to do. I ideally want to convince the exam commission that it truly was not my intention, so that I don't have to wait 1.5 years to start my master's. I would be glad if I can convince them to reduce the punishment.

Did you cite the other thesis in yours?

No I did not, I used it more as a ''lay-out'' than as an information source. However, our topics were very similar and apparantly this influenced my own writing to the extent that it started to reflect the other thesis too much. Any tips on what to tell the exam commission are more than welcome!

Eh, forgive me but I'm feeling pretty skeptical of your story. "Layout" sounds to me more like "ah, this thesis is organized with an introduction chapter, then three chapters discussing different experiments, then a summary chapter that suggests future avenues for study". That's useful info you might get from another person's thesis that no one would expect you to cite. It sounds instead like you took much more content. Even if you didn't copy whole sentences, if it's similar enough to raise suspicion, you almost certainly took enough to cite it...

I don't really feel comfortable giving an answer for "how can I best avoid the consequences of academic misconduct". I think the other answers cover it as well as they can. Consider that not everyone put in your situation would commit misconduct, and consider that it seems your primary concern is that you've been caught.

Please come back with an update as soon as you have the final decision!

Tell the truth. It depends on how much you copied and how whether what you wrote here will count as an excuse or not. There is nothing else you can do.

You are right, I plan to tell the truth. However, I am still scared to say the wrong thing, as the result would be to waste 1.5 of my study life. My response to the exam commission is of great importance, and I still deciding how I should formulate this best.

Don't overthink it. They know you are nervous,and they won't hold that against you. Be prepared like Mark told you, but otherwise the situation is the way the situation is and you cannot change it.

Hard to say without knowing your thesis, the other thesis, and how you referred to this earlier thesis. But - working on a similar topic and therefore having a similar story and references isn't plagiarism, even though some automatic systems might set off a warning.
My suggestion, assuming that you didn't plagiarize and referred to other people's work accordingly, would be to (a) explain that you understand their concerns given the closeness of topics/questions, and (b) offer your availability to meet and cooperate in figuring out whether or not you crossed a border or not.
Before the meeting, if you get one, make sure to work through both your thesis and the earlier thesis and identify sections that could be seen as plagiarized, but also make sure you know where your work is different and unique. Be critical of your own work, but at the same time defend it (if you think that it is defensible) using scientific arguments, not emotional ones.

Thank you for your response! I plan to be honest to the commission. However I did not cite the other thesis at all. It was never my intention to use it as a source of information, but rather as a ''lay-out'', as we had similar topics. Apparently it unconsciously affected my writing too much. As I am writing this right now, I see that even though this is the truth, it is not believable for the commission. Any tips are welcome!

@Michael You seem to be missing the point, which is that plagiarism does not require some evil, secret, premeditated intention to be plagiarism. The main issue is not that what you're saying is "not believable". I believe it, but it still sounds to me like what you did may very well be plagiarism. The main issue is rather that if you "read the thesis many times through" and it massively influenced the way you wrote your own thesis, then you should have acknowledged the intellectual debt you owe to this thesis by citing it. It's as simple as that.

In general, we are not judged by our intentions, but by our actions.
What you are describing sounds an awful lot like plagiarism (though as others point out, this is hard to tell without actually seeing the two works).
You may not have intended it; you may not have realized you were acting in an unprofessional manner; you may have come with the best intentions. Ultimately, you took someone else's work and heavily relied on it (not sure whether your definition of "inspiration" means that you copied their words, or just their content) and it's also unclear whether you acknowledged the other thesis by citing it.
The best thing you can do right now is to be honest, explain what happened and hope that the disciplinary committee appreciates your honesty enough to let you graduate in time.
I personally am a lot more lenient with students who show genuine remorse and understanding of where they were wrong, rather than wasting my time with disciplinary proceedings. Perhaps your institution works in a similar manner, and you will be allowed to write your thesis again with no significant delays. In that case - make sure you do things right! Ask for deadline extensions rather than freak out and do something you'll regret.

Thank you for response! Should I not have to wait 1.5 years and get an opportunity, I will not take any risks. Unfortunately, I am still not sure what to put in the e-mail I will send back.
I copied nothing literally, but having looked at both thesis today, I have to admit my thesis does reflect the other quite a lot. However, we do have similar topics, and therefore it would only be normal that we refer to the same research and theories in our thesis. But again,  I do understand why the supervisor would suspect plagiarism.

Devil's advocate here.
First: tell the truth.
Based on what I read in your question, I assume you copied large part of the previous thesis, so either you are a poor poker player, or you are very clumsy and instead of defending yourself you are putting even more suspicion on your acts. You have nothing to loose by saying the truth, but by saying something that is percevied false, you have a lot to loose: please remember it is not a trial, but it is a commitee "judging" you. In fact, they must come to a decision based on what you wrote and how you will behave in front of them. I see two possible outcome:

you will be judged as a student under a lot of pressure that may have copied,

or

you will be judged as a liar and a plagiarist that tries to cover up the fact of copying from a previous thesis.

Second: 1.5 years is NOTHING
In that span of time you can learn a foreign language (spanish?german?Python?sql?) sufficently to be professionaly proficient in that language. So in 1.5 years you will have a lot of open doors, and even more after your master.
Yes, you may need to work at McDonald for 1.5 years to sustain yourself. That is not absolutely wrong, you will start to get a couple of things about how big companies address account problem, and how the divide between affordable (and healthy food and working poor salaries is getting larger and larger.
Good luck, please remember that rules are often in place to protect someone from him/her/themselves ...


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I was caught cheating in my exam, how should I deal with it?
Since High School, I have cheated a lot in exams. But in college it became a habit and I developed successful ways of doing it, without getting caught throughout first and second year. But I eventually got caught, and I feel horrible about it, it was the most humiliating thing ever, but I guess karma comes to us all.
A lot of the other students know that I've cheated a lot throughout the course and lost respect for me, so they'll be happy now. This time, I cheated in the same way that has worked a lot for me in the past. I recorded full essays on my phone, put it in my pocket with earphones hidden up my jumper and sleeves, and I rested my head on my hand with the earbud in my ear, listening to the recorded material. I knew early on that this invigilator was more wary of my body language than any others have been before, she was a lot younger than any others and probably more alert about technology. I became a bit unsettled, and she noticed that as well. When the first essay finished, I put my arm down and she immediately came over to me and investigated me. My major mistake this time was that, instead of putting my phone in my pocket and covering the wire with my jumper, I had it between my legs with the wire sticking down the middle of my trousers. She saw the wire, bent down and pointed at it asking 'what's this?' then rolled up my sleeve and found the ear socket inside. I was busted, so I gave her my phone and earphones, then she took my paper of me and gave me a new one to restart. It wasn't subtle, the whole class knew about it and I saw a lot of them turning around to look at me. She then phoned her invigilator boss and told her about it to make sure she handled it correctly, and she said clearly 'I just caught a student cheating' in front of everyone. I just sat there for the rest of the time, not knowing anything because I didn't study for it, and wrote a letter to the marker about it. At the end, everyone left the room staring at me while she took a photo of the evidence.
I burst into tears when I was left with the invigilator on my own, and she told me to speak to my tutor. He told me that I'd fail the module, and I emailed the programme leader about it, who said he would wait for the invigilator's report. I think I'm going to have to go through a disciplinary hearing, but I have to protect myself. I can't admit that I've cheated in just about every exam in the three years I've been there, I'll have to say that this was a one off thing because of personal problems and lack of preparation.
But it's not a good feeling having a conscience guilty of such dishonesty, and more lies to tell. I can't get expelled from the course, because I want to get my degree, but I'll deal with failing the module and having a disciplinary record.
Am I just an evil person by nature? I know I don't deserve to be on the course having not been caught so many times, yet I'm doing everything I can to stay. A lot of people say honesty is the best policy, but I don't believe that is true within the business of living and getting success.
Also, how will a disciplinary record affect my future? Will employers/other education institutions know of it after I leave?

It seems to me like you only feel bad about the consequences of getting caught, not at all about the cheating you've done. Given your admitted history of cheating and complete lack of remorse, you certainly deserve to be expelled. Keep in mind that it's your dishonesty that has led you to this position, do you really want to double down on that?

I'm mildly shocked by the fact that your moral system has failed to develop beyond the stage of "doing whatever I can to get ahead as long as I'm not caught". You need to re-examine your fundamental assumptions of life.

Also, how will a disciplinary record affect my future? Will employers/other education institutions know of it after I leave?
I think the piece you're missing here -- and this is life advice, not college advice -- is that your future employer will find out very quickly simply because you don't know a lot. If you cheated on all of your exams instead of studying, you likely did not learn very much. You may have been able to hide this from your college so far because they only check on you during exams. But you won't be able to hide this from your employer because they will need to see results from your work, on a more or less permanent basis. If you did not learn anything in college, this will become apparent very quickly in work life.
In the long term, you have two options: (i) take a job that does not require a lot of skills, likely does not pay very much, and may not be very fulfilling, or (ii) study and acquire skills that qualify you for a better job. That choice is for you to make.

I think the problem is that I've been studying a course that isn't where my heart I truly set. If I enjoyed what I was learning, and was interested by it, I wouldn't resort to cheat. That's why I'm leaving this year and focusing on what I really enjoy. And for these exams, everyone forgets everything after about a month (as a class we discussed it) so it won't really affect our future. They're just short-term memory analysis by seeing how much information we can cram into our heads within a few weeks, after we've done the other projects and essay coursework

Even in the most desirable job, there will be times when it becomes a grind. If you don't learn to work honestly at something when it isn't fun you are unlikely to succeed at anything.

@Jamie: You're rationalizing bad behavior. But that's not a strategy to be successful.

"If you cheated on all of your exams instead of studying, you likely did not learn very much." If exam questions can be answered by just listening to an audio stream, one may question the real-world value of the exam.

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Formatting of grants
I am lucky (or potentially unlucky) enough that a grant applications that I am working on does not have any formatting specifications and instead just has a limit of 5000 words. There are some suggested sections, that will be be variable in terms of length (some will have 200 words and others over 1000), and it is likely that everyone will need to add additional sections. I am used to grant applications using poorly created MS Word forms with predefined sections that allow no formatting and are a single column with narrow margins/long line widths and single spacing.
I am looking for a style guide (or recommendations) about how to format the grant and the pros/cons of different formatting styles. I am both interested in the physical layout on the page, use of figures and tables, as well as advice on sectioning and the order of sections. I use LaTeX if that matters, but am happy for MS word advice also.
For example, do I go single column or double column and wide or narrow margins? The suggested sections do not include an obvious place for aim. Is it worth starting with an an overview that defines the problem and the outlines the proposed research or is 5000 words short enough that you do not need it?

I envy you the fact that it is only a word count that counts. I am in a system where everything has to fit a certain number of pages with 12pt Times-Roman and 2.5 cm margins.
With the word limit as your main limitation you have the possibility to illustrate your application more freely. If suitable, I strongly suggest you try to come up with conceptual graphics to strengthen the text and make difficult concepts  easier to grasp. This can be a huge advantage. Since your are not limited to pages you can afford complex and larger illustrations than otherwise possible.
As for typesetting, you use LaTeX (as do I) which produces excellent text. Trust the LaTeX settings for text width, line-spacing etc. to get a readable text. Too long or too short lines makes the text difficult to read. See the geometry package for details if you are not already using it. EDIT: I do not think two-column format is good for proposals. It is a way to put as much text into a small area and also involves using smalller type sizes, typically around 9 in order to get enough characters into a line to make it readable. Since the number of pages is not a limit, I would aim for something which is as easily read as possible, typically 11-12 pt single columns. the margin widths can be determined so as to get reasonable line lengths. I do not think wide or narrow margins make a difference but wider margins make the page more attractive than narrow (basically a typographical design issue).
EDIT: With one-column format you can add figures at full width and with the no-page-limit do not have to worry about the size of the graphics (in the sense of having to make it as small as possible so to not use up space. I think a straight-forward simple formatting is best. There is no need to be overly creative. What conveys the message without resistance is the best.
One of the more useful concepts in grant writing I have come across is given in the book Writing Successful Science Proposals by Andrew J. Friedland and Carol L. Folt which outlines a two-paragraph summary, akin to an abstract whith which you introduce your proposal. The point of this is to quickly and concisely convey the key points of the proposal to the reader. This involves starting from the big picture metion key gaps in knowledge, how to tackle them (methods), preliminary results (if existent) and expected results. I obviously cannot copy the book content here but the point is to make the reader of the proposal completely clear over what to expect in the proposal and so all details given is just putting substance to the known structure. I believe this is what you aim for in what you call an overview section.
EDIT: After having started your text with a brief introduction, you simply follow up by the usual type of structure:

background (to focus on the gap of knowledge to be targeted)
objectives
project outline
time table (milestones; can be a gantt plot)
if applicable: research group/resources
references
For references I would go for footnote type references since the harvard-style citations uses up many characters. It is also possible to abbreviate the reference list by omitting the paper title, similar to what is done in Nature and Science.

By submitting a grant proposal you're asking the funding agency to give you some resources (funding) to investigate some problem.  Very early in the proposal you should make the case, clearly and succinctly, why you --- and not someone else --- should be given those resources:

The problem:

what is the issue you propose to investigate?
why is it worth investigating?

The current state of knowledge:

what are the shortcomings or gaps in the current state of the art?
why are those gaps or shortcomings important and worth addressing?

The proposed research:

how do you propose to approach these gaps or shortcomings?
what specific research questions will you address in the course of your investigations?
what will be the impact if your investigation is successful?

Likelihood of success:

what makes you qualified to do this research?
what preliminary evidence do you have that suggests that your proposed approach is likely to succeed?

I would suggest addressing these points in an "Executive Summary" or "Background" section, of at most one or 1 1/2 pages, at the very beginning of the proposal.  This will give the reviewer a high-level view of what you're planning to do and help set the context for the more detailed discussion in the rest of the proposal.

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How can physicists help in theoretical biology, besides math and fresh perspectives?
By googling this keyword: "theoretical biology" and physics, I get many interesting pages, such as:

Physics meets biology: Bridging the culture gap
Biology is more theoretical than physics
Why physicists like models, and why biologists should
Biology is the new physics (note that this article's title is somewhat misleading in my opinion)

All pages I found mostly (or only, if I remember correctly) focus on the advantages of the physicists are their math background and being a neophyte so sometimes able to bring fresh perspectives to a problem. But that means a mathematician is also adequate to this.
My undergraduate dissertation is about biophysics, so I actually know that there are things that a physicist can help in biology. But mostly I see them in molecular biology. What else can physicists actually help with given their background?

I don't think this is on topic for this SE; the question concerns the subject matter of persons within academia, not academia itself. Your question is not as technical, but it is analogous to asking something like, 'how can the path integral be used in stochastic calculus?' to give an example in the case of physics and finance.

it's not really that analogous. If I were you, I would ask that question in Mathematics.SE or Physics.SE or Economy.SE. At first I have doubted like you, but after seeing the [tag:changing-fields] tag, I think this question is on topic.

This question appears to be off-topic because it is about the content of research, rather than its process (per the help centre).

@Davidmh do you think that this question will suit in the meta or in Biology.SE?

FWIW this would not be on topic on [physics.SE].

@DavidZ so how about meta and Biology.SE?

Definitely not on a meta site either, since it's not a question about a Stack Exchange site. I couldn't say about [biology.SE], though; I don't know their scope.

@DavidZ: What should I do to improve this question?

@Ooker I don't know. The reason this question is off topic here and on Physics is not that it's bad. So I don't think anyone is saying it needs to be improved at all. It's simply outside the scope of the sites.

@Ooker I think this would be a very good question for a discussion forum, or even a workshop on Theoretical Biology. I think it is very difficult to give a single handed answer. If you find a suitable place, please link it and ping me.

@Davidmh Will this question satisfy you? What physics knowledge can be applied to biology in organisms and ecosystems?

One important contribution of physics to many areas is that physics is the origin of much of our understanding of complex systems phenomena, including emergence, chaotic systems, network effects, and phase transitions. Many areas of biology are still trapped in a hyper-reductionist framework (e.g., is FOXP2 the gene for speech) rather than realizing that such questions are poorly framed. Many biologists are embracing systems thinking, but the tools of physics are still not very widely dispersed overall, and collaboration that brings together such expertise with biological expertise (non-biologists are often frightfully naive about many realities of biology) can be of great value.
There are many other possibilities too, but this is a very important category that I think may be a good start...


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Is it acceptable for an undergraduate researcher to ask to work on a project that will yield publishable results?
I am currently a summer student working on a project suggested by my supervisor. While the project will not directly result in any publication, it will open up avenues for further research for the group. I have completed the main objective for the project ahead of schedule.
When I originally started working with my supervisor, I expressed that two of my goals for the summer were to (1) contribute to the group in a meaningful way and (2) the possibility of publication. I feel that (1) will be satisfied by my current work, but (2) will not. I have one more month left on my research term.
I originally agreed to my supervisor's project suggestion on faith; I didn't understand the scope or scale of the other possibilities and I trusted that it would satisfy both of our goals.
Would it be too forward of me to ask to contribute to something that will result in publication (considering that I am an undergraduate and given that there is only one month left)? I would like to work on a publishable result, but I also don't want to mooch off of the hard work of my group members.

I don't know if a month is enough time to really make publishable contributions to something you're brand new to, but it's definitely worth mentioning again that you had hoped to start building your publication record and to ask if there is anything you could do. Perhaps there is something publishable in the work you've already done? Worst thing you can do is not ask.

Is it acceptable for an undergraduate researcher to ask to work on a project that will yield publishable results?

Yes, of course! There is nothing wrong with expressing your goals for the research project to your supervisor, and I think any reasonable research supervisor would appreciate that sort of honesty from their mentees.

When I originally started working with my supervisor, I expressed that two of my goals for the summer were to (1) contribute to the group in a meaningful way and (2) the possibility of publication.

Sounds like a reasonable list of goals to me. But, for your 2nd goal, the possibility of a publication coming out of your work is only that: a "possibility." As you may be relatively new to research, it is probably a good idea for you to keep in mind that not all research projects result in publishable results (as this question highlights).

Would it be too forward of me to ask to contribute to something that will result in publication (considering that I am an undergraduate and given that there is only one month left)?

This is where it gets a bit trickier. You only have one month left on the project, and it may be difficult for your supervisor to find something meaningful, and publishable, to work on in that relatively short amount of time.
On top of that, there may be other factors working "against" you. For example, suppose that there is a gap your group is looking to fill, but you do not have the background necessary to make a meaningful contribution. What are they to do in this case? Drop everything they are doing to get you up to speed? I think you can see that this may be an unreasonable request.
For all I know, you are an extremely bright student who is more than capable of making a breakthrough on a tight deadline. But, if there are gaps in your knowledge, and it would take someone a nontrivial amount of effort to get you up to speed, then that could be problematic. There are other researchers in the group, and depending on the group dynamics, it may be difficult (or easy) for them to make accommodations for you on such short notice.
In the end, I think you should definitely have a chat with your supervisor, give them the lowdown on what you'd like to accomplish in your last month. Then, listen.

Nothing wrong with asking. If your data is OK, it is conceivable that the data could be included in a published work. Gaining authorship on this paper is another story that I wouldn't count on given you are only around for another month.


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What advice would you give to an undergraduate research assistant?
I'm an undergraduate research assistant on an experimental physics project. I'm becoming aware that the skill set I learned from my classroom learning doesn't necessarily transfer over to the research world. My question is: how can I develop this new research skill set and become the best research assistant possible?
What are traits of exceptional researchers? What skills should I focus on developing early? What are common mistakes in mindset, time management, project choice, etc. that should be avoided?
What advice would you give to yourself at the start of your research career?
Please let me know if there is any literature out there on this topic.

See this question (possible duplicate?).

Work hard.  Be persistent.

By the way, there are many books with titles like Letters/Advice to a Young Mathematician/Scientist you may be interested in.


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How to overcome a reverential fear when meeting the topmost minds in your field?
Once upon a time on one fortuitous conference, I stumbled upon one of the most outstanding and revered academician in my field. I had a nice question nicely formulated in my head, but when I finally met this towering intellectual figure I was struck with nigh-religious trepidation and lost my marbles for a brief moment. So my question is: When meeting the Einsteins/mega-stars of your subject how do you secure your composure?

Why would you fear them in the first place? They're just people.

@potato Well, yes and no. As an undergrad, I've sometimes met with professors who act like the students should bow down at their feet just to get time to talk to them. Ironically, these tend not to be people at the top of their fields (or even departments). But as you go through such a system, PIs seem less and less like... people.

@Potato I've waited for one prof for nearly an hour before for a pre-set appointment. Got no apologies at the end, and was told that they had another meeting to go to so could I wait a little longer. I did not, and never went back. But I certainly don't view some faculty as "just people" that I can talk to normally.

@vidory They may not be your close friends, but they are your colleagues. "Reverential fear" seems unreasonable.

Focus on having an authentic, human interaction.  I see this as similar I don't care how many people give their congratulations -- if one more person comes up and says how much they enjoyed it, it feels good.  Especially if the congratulator says something about his favorite part or aspect.  - - -  You can start with a specific thank-you and go from there.  (I wouldn't necessarily start the conversation with a question.)


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What will my academic path look like after testing out of high school math classes?
I am currently a 15-year-old in the 9th grade, and I am studying to test out all of my high school math classes, which is something I didn't realize I could do in the 8th grade and would have if I had. I contacted faculty, and if all goes well, I'll test out of Geometry, Algebra II, Precalculus, and AP Calculus BC. I also hope that once at college, I can test out of Linear Algebra.
I have also been studying Japanese for a few years, and know the meaning of all the required Jōyō Kanji, although I lack vocabulary otherwise. Because of this background, I plan to Major in Pure Mathematics, and Minor in Japanese Studies.
If I end up taking classes at Delta, (a nearby community college) I would not be able to take Topology, Complex Analysis, Real Analysis, or Abstract Algebra. Instead, I would take Multivariable Calculus, Linear Algebra (if I fail to test out of it), and an ODE course, as Delta only has a Transfer Math program, and no Japanese language program.
I've been told that my high school will also pay for my college classes while enrolled in high school, although the only people they have ever done this for went to Delta during high school, and they were seniors in the 12th grade.
That being said, I have a few general questions about college that that fall under the umbrella of the title.

Would it make sense to apply for colleges as anything other than a Senior, or dual enroll in non-community colleges?
What will writing a thesis be like for someone with no Math paper writing experience?
I have below-average grades in everything but Math, how much will this affect me?
As a high school freshman, I've yet to take the SAT, how much will this affect me?
For the math people reading this, how do you recommend studying math on my own?
My mother doesn't want me to test out of my math classes, because "they teach me hard work,"
and because she wants me to raise my other grades first before doing something "fun". How do I deal with that?

Watch out for your overall GPA. Dual enrollment programs often have a minimum GPA requirement--because the thought is that if you're not successful in all your classes, adding a college-level course is a burden. FYI, this stackexchange is for graduate students, lecturers, professors, not for undergraduate or high school students. Your question is likely to be closed shortly. You may want to take the [tour]. For Japanese, try Duolingo or look into doing an intensive summer program.

This question is manifestly not about "undergrad" math (whatever that means, and many meanings are, in my opinion, foolish)... since it is exactly about a young person who is not waiting passively to learn/do mathematics. I myself had a vaguely similar arc, and have some hopefully-useful comments which I will write out tomorrow. I do seriously hope that people will not belittle/downvote/whatever this question... The extreme disconnect of timing about math versus other subjects, and parents' expectations, etc., is a genuine issue for some kids. More later.

If you can get a passing grade on the AP Calculus BC class while you are in 9th grade, you would probably be successful in an early college.  I recommend http://simons-rock.edu.  If you have reasonable writing ability, you would be likely to get a full scholarship.  Community colleges are not designed for students who are ~5 years ahead of average.

My mother doesn't want me to test out of my math classes, because "they teach me hard work," Testing out of math classes and taking more advanced math classes would be harder, not easier.  Study for and get a good score on the AP tests.  While standardized tests are bad, they do at least demonstrate that you can work hard.

Whatever you do, please keep in mind that there are many other things one needs in order to become a healthy and happy person besides studying and career. Please don't forget to constantly improve your social skills (however good they may be now) and develop new hobbies, be interested in the world.

Be careful not to confuse being good at tests with actually understanding the topic. Either is possible without the other, but while being good at tests is the important thing until maybe late undergrad, it is an entirely useless skill afterwards. As knowledge in mathematics is quite cumulative, lack of understanding can result in you being far behind quite suddenly. You seem to have already diagnosed that problem in your Japanese, so be on the lookout for the same in maths. In short, don't be the maths equivalent of the guy who knows all kanji, but isn't able to form any coherent sentence.

I highly recommend the Art of Problem Solving. https://artofproblemsolving.com/

@AnonymousPhysicist Not even; I wouldn't say I worked particularly hard on my AP tests and passed them all.


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Citing a general fact but applying it to a specific point I'm making in a sentence
Here are two sentences from a paper I'm writing:

In addition to being context specific, competencies try to describe what a person needs to succeed in a context at a useful level of abstraction. This point is perhaps best illustrated by contrasting competencies to its more concrete evolutionary predecessor job analysis (Scott & Reynolds, 2010).

The first sentence is something a point that I, the author, am making.
The more general fact that 'job analysis is an evolutionary predecessor to competencies' is from Scott and Reynolds (2010).
It's a bit ambiguous: you could read the sentence as it is Scott and Reynolds (2010) who are saying that the "point could be well illustrated by contrasting" which is imprecise.
To remove ambiguity, I could write something like:

Job analysis is the evolutionary predecessor to competencies (Scott & Reynolds, 2010). The former is more concrete and the latter more abstract. Comparing the two is useful to illustrate what competencies are.

But it really breaks up the flow of the paragraph, creating a more awkward reading experience for the reader.
Is having the sort of ambiguity of the first example, for the sake of flow and narrative, bad or wrong citation practice?
Edit: So my question here is about clarity and explicitness of citations. How clear should a text be as to what is attributed to whom? When does it get too sloppy or unclear who said what?

I do not think this site is about writing a paper, not in the sense supposed by this question.

@Alchimista my question is about citation conventions, tried to clarify with an edit

What Scott & Reynolds did? They introduced/developed something called "competencies" (it is even not clear competencies is a model/system/etc)? If so you can put a comma after it, and then say "competencies, the latter approach discussed in Ref. #. But this is nothing about conventions.

I can only say I find the second version much clearer and better to read.


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Appeal on overpunishment for exceeding word count was denied – how to proceed?
I made an academic appeal over the marking of an essay, which was 13 words over the word limit.  The mark on the word-count section was unexpected, but was not consistent with the formal university word-limit marking rubric. (I cannot change the essay anymore.) Unexpectedly, my appeal was denied.
How should I further advance the appeal?
Here is what I considered so far:

Rely on independent student advocate, found by internal university contact. The issue with this is that I don’t know whether they play their role effectively. My first appeal was already denied. And before marking academic appeal, I did request for independent student advocate to be involved and witness debate of academic appeals process.
Approach an ombudsman and independent student advocate to invite them observe the entire process of complaints to the university registrar (invitation goes before arrival of formal approach, so there are witnesses to breakdowns in procedures)? This seems workable solution, and is an option I believe I can trust.
Consult the family lawyer to engage in challenges and observe the review process to make sure no more maladministration.
Perhaps a combination of 2 and 3? This may be too aggressive, but seems to have a higher chance of success than 2 or 3.

Is my thinking sound? Is there a better way I haven’t thought of?
Details on word count inconsistency are as follows......
a/ There are 5 gradated sections for word count limits.  There is no hard public published specification on when you transition from one gradated section to another.  There is no published specification that suggests that if 5 (or 10 or 15)% over word limit then you lose marks.  The marking rubric is vague and does not specify what percentage over word limits, transition you from one gradated marking section to the next one down.
It is at the marker's discretion
b/ My essay had a word limit of 2500 words.  My submitted essay had a word count of 2513 words, or 13 words (0.5 %) over the word limit. From my understanding based on experience from submitting previous essays within this department and university system, it should have gotten in the top section (because it was within the previous experience of applied margin of errors before mark degradation), or one down from the top gradated section.  The mark I got for the word count section was the 2nd section from the bottom.
c/ I did email the instructor (before essay deadline) for guidance on when word count limits transition from one formal marking section to another, eg 5% or 10% etc.  The instructor never replied to this query.
d/ the word limits was only for the main body of the essay only -where the substantive argument is.  Word count does not include title, references, bibliography, footnotes.
e/ the essay word count was not changed after first formal deadline.  It was the same word count at the time of submission of first formal deadline, as it was at the time of academic appeals denial.
Would you like any other details?

My instructor viewed a draft 400 words over the word limit on the wednesday before the essay deadline - I was able to reduce this to 13 words(over the word limit)by the time of essay deadline submission.  I cannot further reduce essay length word count after essay deadline submission......its a different set of circumstances to change the "assignment" outside the rules of the game.  For our university, to be able to change the "assignment" after the first formal assignment deadline, you need to apply for "special consideration" - I didn't qualify for this at the time

My instructor got the roughly 400 words (over word limit) draft essay by email on the wednesday (3 days before deadline)..... so there is a record of that. Neither the instructor nor I, have anything but respectful relations with each other

Question reopened and comments purged (since all should be addressed; if not, repost). @Anti-Tao: Please check whether everything is correct. Also, can you please [edit] your question to specify how bad your grade was (in comparison to what you consider the fair grading) and what impact this has on your studies? This may allow us to give better answers.

What's the word limit order of magnitude? Are abstract and title, as well as footnotes included in the word limit? You need to find inconsistency or inaccuracy in description to battle this, or unreasonable difficulties in computing the word count in your document (which may be the case if any of the above was difficult to estimate) or I see little recourse for you if the word limit was known beforehand. Even if myself I would consider a hard word limit ridiculous, it was part of the task.

The question is still missing details on what the penalty given was and what the official guidelines stated. The fact that the essay was originally much longer and was later cut down after turning it in (as was mentioned by OP in a comment) also seems potentially relevant, depending on what the official guidelines state.

Proceeding with a lawyer seems to be the best option because you are in a dispute with the rules. Arguing within the university system won't work well because the rules are going to be upheld. The core of the argument is essentially that sticking rigorously to the rules is unreasonable, and that has to be argued outside of the university system where the university will be forced to defend the reasons for having the rules and enforcing these rules so strictly. They then cannot engage in a circular argument involving those same rules.

With the added details, it certainly seems harsh to move that far for such a small amount in excess (though how you could ever expect to be placed in the top one is beyond me). The details about changing word count is still missing (the comment was deleted along with the rest, so I can't see it, but I recall you mentioned originally submitting something 400 words too long).

@TobiasKildetoft: I undeleted those comments. If you can, please edit whatever part you consider relevant into the question.

@Wrzlprmft Actually, on re-reading them I see that I misremembered them. Having sent a too long draft ahead of time is probably not relevant anyway).

It is hard to be sympathetic, actually. You seem to have made a lot of assumptions. You seem to be overly judgmental of the actions of others and not accepting your own errors. It is easy enough, today, to check your word count. It only takes a few moments and minimal effort. You are suggesting bringing in lawyers for what is, in essence, a request for special treatment. My advice is to swallow this and do better in future.

What was the actual penalty? "Second section of the bottom" doesn't tell us how severe the actual penalty was.

@JeffE vague application of marking rubric - all students get is a total overall mark (based up on a vague formula combining all sections of the grading rubric), not individual marks per section - at least in this assignment

Let me try again: How much higher would your grade have been without the penalty for going over the word limit?  10 points out of 100?  Two letter grades?  If you can't give a precise answer, then why are you complaining about this specific penalty?

There are other issues with the marking of the paper, based on the marker's comments in the paper - hard to convey here,  without actually seeing the comments in context of the relevant sections of the paper.  I am attempting to use the clear word count issue to initiate at least a partial remarking, but hopefully a full remarking.  There have been observations by other individuals, which "I" took to indicate the paper was grossly under-marked (for whatever reason) - not an accusation against the instructors. I need clarification of those comments and marks, due my great efforts in writing

@JeffE - also a principle at stake here for me. I am sick of just accepting poor treatment, when there are proper ways of doing things.  As for marks, it is unclear how much more a partial remarking on word count would add - due to vagueness of marking rubric.  Or how much more a full remarking by a independent impartial competent marker would add, due to vaguness of comments and marking rubric.  I am rather at the end of my tether, and feel like I need to make a stand. There is a strong emotional element in response to being constantly pushed, and I am taking this opportunity to push back.

Also, finally, I see an opportunity to push back, that I have confidence in that I have good chances of success in.  I haven't had this assessment of chances of winning before.

Your post sets out details of the substantive matters in your case, but it does not give any information on the adjudication rules and the avenues for appeal in the rules.  You have already appealed to the university, and this failed.  You refer to this as your "first appeal", but you have not made clear whether there are any other steps of appeal allowed in the process.  If there is another step of appeal allowed in the rules then you may avail yourself of this; if not, then that is the end of the (internal) adjudication process.  Thus, the first thing you need to do, if you are interested in pursuing this, is to read the university process for appeals of marks, and see if you have exhausted the internal appeal process.
If you decide to contact a student advocate, ombudsman, or lawyer, their first step will be to find out what has happened so far, and whether you have any additional right of appeal within the university rules.  A paid lawyer will happily attend meetings, hearings, etc., with you, but that will be very expensive.  For a student advocate or ombudsman, they will make their own decisions on what, if any, actions they wish to take to mediate the matter, and they would be unlikely to agree to attend the entire process.  The substantive complaint you have sounds weak to me, and presumes various things that are not requirements by the university.  Moreover, if the appeal process is already exhausted then you unlikely even to get to an assessment on the merits (since that has presumably already been done).  If there is no further right of appeal, the most likely outcome is that the university will write to you (or your lawyer, ombudsman, etc.) stating that the appeal process has already occurred and is now concluded.

Accept it and move on.  Consider:

You had a clear rule for the word count
You violated that rule
You appealed and were denied

And that's it.  Engaging in other extreme forms of behavior, such as trying to involve a lawyer (!), will surely sour the attitude of everyone involved toward you.
To address one point specifically, when you didn't hear back from the professor about word count rules, you should probably have defaulted to following the rules to the letter.  I personally try to always respond to the emails I get, but I admit I vastly deprioritize emails that are asking me things with clear answers already available - such as a word count limit.

Your best course of action is going to be to accept things and move on.
Unless the marks you've lost on this essay make the difference between getting your degree or not, the damage to your reputation incurred by any of your options will significantly outweigh the gains.


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Can I accept an offer from a MS program, but continue applying to other schools?
I have accepted an offer to a MS program, but after further consideration, have decided I am unhappy with the program and the location of the school. Would there be consequences if I applied to more programs? Would I be burning bridges? If it makes any difference, I am unfunded and would enter as a coursework student. I would like to switch to the research-track after a semester, but I am not currently taking up a spot in a PI's group.

Most likely, every reasonable prof will understand your situation (as you are unhappy and unfounded). Whatever the unreasonable might say, better not listen to them.

Actually, to behave in a completely ethical manner, if you don't intent to honor your acceptance, then you should withdraw. But that is based on the basic idea that failure to do so could deny an opportunity to someone else. And, in light of the other things you say, I'll have to guess that the probability of that in this case is small.
In some programs, it would be very important that you withdraw. For example if you have been accepted into a program with limited slots that are difficult to fill and that require expensive resources - medical programs, say. But that isn't the case here.
In fact, the program that accepted you has probably accepted a few more people than they need to (course based masters) expecting that a few won't show up. It is fairly typical and is normally a good thing for them to do.
I think that in the narrow case that you describe you can probably go on for a while leaving it as it is. Any transgression would be small. But you should inform them when you know that you won't honor the offer.
I think the only consequences would be to your conscience.


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Is there a copyright in researchgate
If I upload my research to researchgate, will this guarantee me copyright? Because I sent my research there and I added it to the site with ease and no one has reviewed it before sending it.

What do you mean by "guarantee me copyright"?

https://explore.researchgate.net/display/support/Copyright

@GoodDeeds I mean, will no one steal my research?

Related: https://academia.stackexchange.com/q/17145/68109

Are you talking about making otherwise unpublished results available on ReasearchGate?

Note that copyright law varies around the world, so your own country's law will apply. In the US and some other places, your copyright rights begin when you make something eligible public in pretty much any way, including Researchgate or your own website. Other places require a specific registration process, though that may be disappearing.
Note, however, that Researchgate is also used for copyright infringement when people who don't hold rights to papers upload them anyway. But you can certainly put your own work there.

The concept of "owning" and "stealing" of research is a bit subtle. No one could claim priority, once you publish in any form, unless they already have a valid claim themselves. But you can't "own" ideas.

Because I sent my research there and I added it to the site with ease and no one has reviewed it before sending it

This is because Researchgate is NOT a peer-reviewed journal, NOT a book publisher and so on. It is a social network for scientists so that you'd have relevant research in your morning feed instead of funny cat pictures. It is quite brilliant as a concept, but absolutely NOT a substitute for proper publishing. In some fields, uploading preprints there instead of arXiv may be a common practice.
There also seem to be two important misconceptions, but Buffy and Wetenschaap have already addressed them - copyright is NOT the same as the proper attribution of ideas: you may be giving the publisher exclusive rights to distribute your work in some cases, and uploading it elsewhere might be a breach of contract. With all that said, indeed, there's never a guarantee someone else won't "steal"/misattribute your work ignoring every possible concern about the intellectual property.


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How to remember what one studies, when there are a lot of things to remember
I'm currently pursuing my bachelor's in Mechanical engineering and I am facing this issue since a long time. I study a subject completely and then forget it overtime as I continue to study new subjects. I thought repetition could probably serve me well. But if I start revisiting a subject all over again, it takes a lot of time, and then I'm in the dilemma of choosing to revise a previously done subject or study a new subject.
How can I overcome forgetting without wasting much of my time?

First, and most important, there is more to learning than "remembering". Your goal in learning something like engineering (or math or science or ...) is competence in the field. That is, applying what you learn. If you can do that, then remembering specific facts (if that is what you mean) is less important and they are likely to rise to the top when doing applications.
Another major goal of an education is to gain insight into the workings of the field. How do the ideas fit together to form a unified whole. That can be just as difficult to achieve as competence, though they are related. And again, the facts will be implied by the insights, making them easier to recall, but also easier to look up in reference material as needed.
But, learning requires two things (as I've written here pretty often): reinforcement and feedback. Reinforcement comes through practice and it changes the brain. Feedback is to assure that you don't reinforce things that are incorrect. Most coursework is designed to provide these two aspects along with the presentation of material in a coherent way. For the "change the brain" idea see The Art of Changing the Brain by James E Zull.
But there is a way to enhance learning and enable retention that go hand in hand. Here is a description of something called the Hipster PDA, which is nothing more than a deck of index cards. The value in learning is that the creation of the cards and the revision of notes is in reinforcement. If you write things out by hand you get strong reinforcement.
But the added value for retention is that you can carry around with you at all times a few of the cards (10 - 20, say) and review them when you have a few moments; waiting in Starbucks, perhaps. If you write important ideas on the fronts of the cards, leaving the backs blank, you have a way to make notes when you think of things or see some relationships to other ideas. If you use different colored cards you can keep different  kinds of ideas easily classified.
And, you don't waste any time at all. We all wind up waiting impatiently for things. Even carrying a notebook at all times is a big help. Bound notebooks (Moleskine) are very good for this. Date every page. Leave room for updates.

Tips for Remembering What You've Learned

It's scientifically established that students will learn better when they like the subject of the class.

It's also known that students learn better when they like their teacher.

Given these facts, even if right now you do not think you like the class or the instructor, try to like them anyhow.
It's a similar concept to getting more nutrition from a food you enjoyed.  You will retain more when you actually like, value, and appreciate the subject matter.
Aside from doing your best to enjoy/think positively about the subject, it also helps to apply what you've learned in some way.  Think about how what you are learning affects your life or that of others, or how it can be applied to solving problems, etc.
The Best Tip
But the very best tip of all (I saved the best for last) is this:
Teach it!
That's right--when you have begun to grasp the subject matter, find someone to whom you may explain it.  When your mind is applied to the task of explaining what you have just learned, it is forced to organize your thoughts, which may still be somewhat sketchy, and to make sense of them.  One cannot teach what one does not understand.  Furthermore, the very fact of teaching it gives opportunity to repeat the knowledge and make a practical application of it to someone else.

Yes, the standard joke is that math grad students finally really learn calculus after being a teaching assistant for it 5 years in a row, and then teaching it another 5 or 10. And teaching first and second-year grad courses several times is what finally cemented my knowledge of that stuff. :)


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I got rejected for my PhD application to a German university, but the university informed me of another PhD hiring. Is it a positive sign?
Last year, I applied for a research assistant position at a German university in the STEM field aimed at a PhD degree. I prepared all the documents required, including recommendation letters from professors in my current school. I also got an e-mail from the university confirming my application.
However, I was not informed about the status of my application for a long time (about two months), even close to the desired starting day for the PhD I had not heard back from them. I also checked my spam folder every day. So I sent an e-mail to the university to ask what was going on. They said that my application was rejected but it seems that somehow the result was not communicated, and they don't know why. I didn't understand the situation, but I could do nothing but accept the given result.
Soon after, I got an e-mail from the university informing me that they will open another hiring process soon. It says that they decided to hire a more convincing applicant at the time, but they hope that I consider applying once again. I never got this kind of e-mail before, so I'm now a bit confused.
Is it normal for German universities to announce new hiring to all previous applicants, or is this only for me? I might be overthinking too much, but I'm guessing they are just being nice. (Maybe as I was not informed of my previous application because of their mistake.) My supervisor said that it might be a positive sign, so he encouraged me to apply again. But I'm suspicious whether the university really wants me to re-apply. I was not even invited to the interview, and all I got was a short rejection mail. I won't apply again if the same result is repeated, as I don't want to waste my time. What should I do? Should I seriously consider applying again?

Who sent the email? And is there any reason why you might only be invited to apply for formal reasons (e.g. you are part of an underrepresented group)?

@user151413 The email was sent by a secretary at the department, and there is no formal reason why I should be invited. I think I'm not the only one, but I have never received this kind of mail before so I'm wondering.

The key thing to know about the German system is that a lot of the decision making power lies with the individual professors. As such, what is normal can differ even within the same department, depending on who is hiring. In any case, since you have your documents ready, i would argue that simply reapplying takes less time than writing an SE-question and waiting for answers. In particular when there is a good chance that you simply never got an interview because they misplaced your application before sending the invites for those.

I would take it as a positive sign.
Note that in Germany, PhD/postdoc hirings usually work via professors, not via the department or university. This means that it is quite likely that whoever makes the decision in the hiring wanted you to apply again.
In case they wouldn't want to hire you, there doesn't seem to be any incentive to encourage you to apply, as it would only create extra work for them.
I wouldn't take the fact they didn't invite you last time as a negative sign: It could simply be that the last time, they had someone they definitely wanted to have (be it because of the specialization of the person, or it was someone the professor knew very well, or who had a very specific and strong letter, ... ), but for some reason, the hiring didn't ultimately work out. If that was the case, it was in fact kind that they did not formally invite several people to give talks: This would have just created unnecessary work for everyone.
So if I were you, and I were still interested in the position, I would definitely apply.

If you want another chance at the position, you should apply again. Nobody here can guarantee anything about how the process will turn out. Possibly they are 'just being nice', but usually, universities don't want to spend more time to 'just be nice'.
The fact that you hadn't heard anything for a long time with your first application can mean anything. Probably it means what they told you. Universities have no reason to be dishonest in this process. There is a good chance that you will be rejected in the second application as well, since it is possible that they sent the invitation to apply to the second position to everybody that applied the first time. You can always apply and see what happens.