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I have egregiously sloppy (possibly falsified) data that I need to correct. How should I go about this?
Several years ago, I did a summer project as an undergrad with a PI not at my undergrad institution (I'm in grad school now). Now, the project is finished and he wants to publish it with data that I've gathered.
The problem is, after checking my data, that the spreadsheets that I used to calculate the data are very inaccurate, to say the least. I can't remember exactly what I did, but there do seem to be some egregious inaccuracies (as in, values from the wrong dataset) in my spreadsheet compared to the raw data from the instrument either that I was colossally bad at copying data over correctly (all of the data in my spreadsheet do appear in the raw data someplace, but not necessarily in the right location, the right dataset, etc.), or worse, I'm terrified that I may have done it deliberately at the time. (How would someone be able to tell?) I did analysis with the faulty data back then and produced graphs.
Obviously, I will have to supply the correct data analysis before it gets published. But is it ok to explain it as "I majorly screwed up the analysis and made a lot of data entry errors, here's the corrected version"? I'm hoping that my PI will just use my corrected data and analysis and just focus on that instead trying to pore over my wrong spreadsheets to individually compare all the changes, many of which are embarrassing at best and look suspicious at worst. I am not under any suspicion of wrongdoing thus far.
I redid my data analysis with correct data entry and the results look messier on most of the things I messed up, though they do not affect the underlying trends. Not sure what this means - how likely is it for honest error to have the effect of making data look cleaner than it actually is? Also, my god, I was awful - mishmashing data from one trial with another, copying data from the wrong wavelengths and/or from the wrong trial, wrong normalization numbers, etc. etc. etc.
If you were a professor and you were approached by a student who says that made egregious errors on past data analysis and the corrected data looks not nearly as good, what would you think? Would you think they were honestly trying to fix a mistake, or trying to save face and cover for past misconduct?

How is it that your own data dwell in some Schrödinger-esque contraption in which they are either falsified or merely erroneous? Do you mean to say you've actually falsified these data but are trying to be coy and test whether it can go unnoticed as you correct them? Or looking for a reason to keep it in the altered form?

A bit of a tangential point, but this is also why you should not be doing data work in spreadsheets.  Data work should be done through code, without altering the originals, so that it can be reproduced and audited.

@Jeff This. Data should be always available in the original raw form as it was created by the measurement device or at the time of the experiment. That version of data goes into Fort Knox and is never ever modified.

I never modified the original raw data. I did egregiously miscopy that raw data into spreadsheets where I do my calculations.

I find it hard to believe your implication that you do not know whether you deliberately mishandled the data in the past. Do you have any reason for not knowing for sure?

@user21820 I did this research more than half a decade ago. I had to email my former PI just to have the data since I no longer had it. When I saw it, I couldn't believe the inaccuracies in my spreadsheets - while I did not alter any of the original raw data, I often miscopied the data into the spreadsheets to such an extent that I found it difficult to believe that it was ordinary carelessness. The graphs also seemed a bit nicer with the inaccurate data entry/analysis.

@8263xiao: Hmm. I don't have a problem remembering whether I was deliberately dishonest or not, even a decade ago. From your last comment, it sounds like you do not have a habit of being dishonest, and you do not remember intentionally being dishonest. If that is so, take it at face value, because carelessness can cause a huge amount of errors. In particular, a mouse-slip might cause an entire chunk of text to be dragged from one point to another, and if middle-click does a paste operation then an accidental middle-click can overwrite data with data from somewhere else without you knowing.

People who has perfect memory cannot get this. I totally can. Many times in my life including when I was young, I had situations where I could not remember some pieces of information, other people would deem "impossible to forget". One of the situation was very similar, I was accused of a misconduct, and I could not remember the exact chain of events, that would clear my name, I could not confidently say I did not do it. I suffered the punishment, and then a witness that was unwilling to come forward during the process, approached me and informed me that I in fact did not do it. It does happen

@AndrewSavinykh I agree completely. I am capable of forgetting not only what day and month it is, but what I did that morning. This is not an unbelievable story.

Using or not using Excel vs retaining the original raw data have nothing to do with each other.  It has to do with using proper methodology, not what tool you are using.  And also, Excel formulas are code (and I say that as a professional programmer).

Anything like "I majorly screwed up the analysis and made a lot of data-entry errors…" will stand only to your shame.
"That version was corrupted. Here's the corrected version…" should work.
None of that changes the fact that your exposition might look detailed but in fact, it's merely wordy…

@AndrewSavinykh: Did you ever have any situations where you didn't remember if you intended to engage in misconduct? It's one thing to not know whether you are doing it (even in the present you might not know whether something constitutes misconduct...), it's another thing to not know whether you intended to engage in misconduct.

@user541686: As Andrew writes, it may be difficult for people with good memories to “get” how this kind of bad memory can work. In my adult professional life I’ve never committed such misconduct; but in high school, I did (if I remember right) fabricate data on a couple of science projects/assignments, and in undergrad, I remember at least being tempted to do it again on one project. I don’t think I did in the end, but I don’t remember for sure.  It’s hard to distinguish in memory between the feeling of serious temptation/considering it, and actually doing it.

@BryanKrause  one way I could see it happening would be to intermingle test data with real data.  If the OP was using modified copies of the real data to test various cases within their analysis path and was sloppy about keeping track of which files were which when copying data around.  Similar to  Andrew Savinykh; after 6 years I could see myself wondering if maybe I wasn't just way sloppier than I thought possible but in a moment of stupidity/insanity did something worse and then dumped all recollection down a self sealing memory hole.

While the only consequences to me were just a trip to the ER and a permanent scar, I managed to bury the fact that a childhood accident whose circumstances made no sense was that rather than pushing back on bad how to instructions (to swing a hammer with my right hand despite being left handed) I did something that I thought would just result in an "OWWW!" after which my point for "that's the wrong way to do it" would have been made for about 25 years.

I infer from the question that you still have the raw data. In that case, I think you need to re-do all the steps in which errors could be introduced (such as data entry, spread-sheet calculations, analysis of trends). Then see what effect the corrections have on the conclusions of your paper, and rewrite as necessary. I realize that this sounds like a lot of work, essentially repeating most of what you had done earlier, but since you apparently did it wrong the first time, you now need to do it right.
Meanwhile, you should tell the PI about the problem and your plans for correcting it. If I correctly understand the situation, the raw data are the only reliable information currently available. You should make sure he knows that, so that he (and others working with him) won't build further research on a foundation of wrong results.

I do still have the raw data, and I did redo the analyses prior to asking my question. Most of the errors were in the data entry - copy/pasting numbers from the wrong places, and there was quite a lot of that such that it's almost inexplicable. The effect was that the trends stayed the same but the error got bigger. There were other things I had to do with the spreadsheets, such as re-organizing and making a new graph, so I just sent him the spreadsheets/graphs I corrected. Hopefully he takes it well and doesn't react with anger or suspicion of previous wrongdoing.

And, most importantly, stop doing science with spreadsheets

Everyone will have their own reaction, of course, but the more important thing is that you point out the errors and the need to correct them. Going forward with bad data is the worst outcome.
Work up the best data you can and tell the prof that the older data was seriously flawed.
I think most people will accept your honesty, even if it means some delay. And most will forgive at least some of it due to your lack of experience at the time.
Hopefully the original data is still available making corrections possible.
But, you also need to be honest with yourself about how this all happened. I can think of a few very bad scenarios that I hope weren't contributing factors. There are actual medical conditions that might have such an effect. You don't want a recurrence.

I did. Hopefully that will satisfy him. My previous work was admittedly atrocious (I was definitely a very sloppy undergrad), and my fear of suspicion is because the corrected data looks messier and has much larger error bars.

@Buffy If the internship was relevant to a grade or a reference, the discovery of fabrication of data may unravel the conditions for OP being in grad school. It is very much to be hoped that the data were just misgenerated in a fit of sleep deprivation rather than in an act of intentional fabrication. I know that I would wash my hands off a student that I suspect of previously fabricating data. This is the one capital scientific misconduct that a reputation can not recover from, in my opinion.

How would such an act of fabrication be proven vs. genuine error? Also, I already sent him the corrected data analysis - how would a PI react to their former student saying they made a lot of mistakes in data analysis and provided corrections? The raw data is unaltered and available.

"And most will forgive at least some of it due to your lack of experience at the time." I think so, too, but publishing data generated by an undergraduate student without double checking is also a mistake, maybe also caused by lack of experience. Both student and advisor will have learned something from this. (Not saying anything about the intentional vs. accidental discussion which can only be decided by looking at the actual data.)

A mistake is unfortunate, fabrication is evil. Intentions matter. If it was a mistake, it's still not nice (it is a nuisance to have sloppy collaborators, but if they learn to become more careful, one may accept that they improved). Bad intentions will however leave an ever-lingering suspiciion.

@CaptainEmacs, I took "falsification" as hyperbole based on fear rather than fact. But, yes, intentional falsification is of a different order than sloppiness.

@Buffy It's the OP's own words. I must confess I find it hard to put myself in the shoes of someone who does not even remember how their data came about. I remember the circumstances about the development of practically every paper I did as a first/main author. That's why I suspected that the situation might be the result of lack of sleep (or otherwise under extreme time pressure).

I'll take your questions one at a time.

I'm terrified that I may have done it deliberately at the time. (How would someone be able to tell?)

I'm not sure if by "someone" you mean you, or the person you send this to.  I can definitely imagine looking back at my own work from undergrad and doubting the integrity of it if it looked fishy.  If I were trying to figure out whether I had done it intentionally, I would look for patterns in the errors (e.g. maybe treatment group is only ever misrecorded for data points that pattern against the tested hypothesis), and see if they jog your memory.  I suppose that's probably what I'd do if I were trying to figure out whether someone else had done something intentional, but I seriously doubt most people would bother.

But is it ok to explain it as "I majorly fucked up the analysis and made a lot of data entry errors, here's the corrected version"?

Absolutely.  You were an undergrad and it's the prof's responsibility to check your work and to ensure you know what you're doing.  Also, the unfortunate reality is that lots of profs intentionally teach students in their labs to mishandle data to "improve" results, so that's a potential explanation here too.  Because of that, I'd be more likely to say something like "Looking back at the data now, I'm finding a lot of errors, so many that I don't think correcting them is feasible, so unfortunately I believe that this data would have to be reanalysed from scratch to proceed with the project." That is, tread lightly if you can't recall the origin of the discrepancies, but make your own position clear.
Also, it is absolutely not your responsibility to provide corrected data if you don't want to continue with the project.  I assume as an undergrad you were either paid or volunteering in exchange for the training/experience, and I assume neither of those is true of your relationship with this PI/lab now.  I recommend asking yourself whether you honestly want to continue with this project before putting any more work into this.

I redid my data analysis with correct data entry and the results look messier on most of the things I messed up, though they do not affect the underlying trends. Not sure what this means - how likely is it for honest error to have the effect of making data look cleaner than it actually is?

More likely than not.  Unfortunately, we're a lot more likely to double-check steps in our work if we don't like the look of the data, no matter how thorough/neutral we might intend to be.

If you were a professor and you were approached by a student who says that made egregious errors on past data analysis and the corrected data looks not nearly as good, what would you think? Would you think they were honestly trying to fix a mistake, or trying to save face and cover for past misconduct?

Depends on the student and the professor. Personally I trust the students that I work with or I wouldn't be working with them, so I would believe them.  And I promise you, every researcher has encountered egregious errors in their past work at one point or another, often at this very stage of preparing/doublechecking for publication.

Now looking back again, the most suspicious thing I saw in the data was that I had copied only some of the results of different trial into a spreadsheet for a particular trial. While certainly that is possible with error (I may have had both trials' raw data open at the time and thus it was possible to mix up), there were more data points in the trial I erroneously copied from, which resulted in the original trial having more points than it actually did, matching the other trial. 1/

It's possible that when I was analyzing the data I misremembered the setups for each trial and thought they were both the same, and I may have set up my spreadsheet that way and the mixups gave me the wrong impression that I had the additional points for both. But that does look suspicious. For my corrected version, I just reported fewer data points, consistent with what I saw in the correct raw data. It didn't really change the overall results but did make them a bit more noisy. 2/

My former PI never delved into the spreadsheets or compared them to raw data; I only showed him graphs. I don't think he ever pressured me to "improve" results per se, though as an undergrad I was definitely very insecure, eager to please, but not particularly professional/competent. I do want to get this published, but certainly not with bad data. I do have the original raw data that I now analyzed correctly, and I told him I found a number of errors in my past analysis. Hopefully he believes me and looks mainly at the updated/new analysis without delving into the past too much. /3

I think my PI trusts me, perhaps undeservedly so back then as an undergrad. It is absolutely my responsibility to correct the data because it will be reflected in the scientific record and not doing so would tarnish us both. I just hope that he trusts that I'm now on top of things and that he's not painstakingly combing through what I already told him is invalid analysis, for both our sakes. /fin

If you can't remember what happened, I'd give yourself the benefit of the doubt and assume it was an honest mistake unless and until you discover evidence to the contrary. Basically treat your work as you would someone else's. It's really no different at this point, since you can't remember what you did. Your work is as much a black box to you as someone else's would be.

@bob What would be evidence to the contrary?

I'm not sure honestly. Notes in the Excel workbook that indicate dishonest intent ("round down to minimize appearance of errors")? Maybe someone else could comment here? But basically if it doesn't scream "this looks like academic dishonesty", I'd take a deep breathe and relax. It probably wasn't. This of course is taking at face value an inability to remember what happened.

@8263xiao: Since your bad data never got published, any mistakes (intentional or otherwise) are at least semi-private, and in your past.  Clearly you know better now, and can just start fresh from the raw data (which you know hasn't been intentionally tampered with), with better analysis tools and methodology that you've learned since then.

@PeterCordes I think the issue is, now looking back at it again, that the data inaccuracies are very suspicious and could be consistent with misconduct; if someone meticulously combs through my old spreadsheets, that is a conclusion they could easily draw as the inaccuracies made the graphs look better. It is true that the scientific record will not be tainted by this, and I was not stupid/malicious enough to tamper with raw data. 1/

@PeterCordes So I did start fresh from the raw data and redid everything. I had changes I wanted to make to the analysis anyways because I learned a lot in the years after that project. It's just that the possibility that based on my past inaccuracies someone could reasonably conclude that I was acting dishonorably, even if I am not doing so now, even if I already informed my PI my past spreadsheets were flawed and their contents should not be the basis of the paper, that worries me. /fin


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how can i publish paper in open access journal?
I found a hybrid journal that accepts an open access option. When I submitted my paper, there was no choice to choose open access and it is submitted now, how can I tell the journal that I need to publish with open access, or will the choice of open access be at then end of the reviewing process?

thanks for replying , so it will be at the end of the reviewing process , but excuse me i found that some papers were reviewed and published with in  two months with open access and the other without this option took a long time for reviewing , is there any relation or just luck ?

There is not enough information to tell. That could easily be a function of luck, how fast the reviewers are, suitability of the original manuscript, time authors take for revisions etc.

Open access is usually (but not always) offered after the peer review process is complete - i.e. after your paper is accepted.
For now there's nothing to do except wait.

And be prepared to be shocked (shocked, I say) when they tell you the cost of open access.

@Buffy Shouldn't be too shocking at that point; don't most journals make the fees clear at the time of submission?

@BryanKrause, some users here have been shocked (shocked, I say), so maybe not all.

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What should I do when the review process takes longer than expected?
First case: my paper got minor revisions and is "under review" since 27/10. Is it normal to take all this time for minor revisions? Can I ask the editor to remind the reviewers or can I ask for their deadline?
Second Case: other paper sent to an issue with these details:

Final manuscript due: 14 November, 2022
Tentative publication date: 14 February, 2023

but it is under review since 23/9. I sent a message to the editor of the issue with no response, so I sent another one to the editor of the journal and received this reply:

The journal aims to complete the peer-review process in the shortest time possible without sacrificing quality and integrity. However, a number of factors influence the actual time it takes to complete the process, most notably the availability and responsiveness of qualified and able reviewer.

What should I do with this paper? Can I ask the editor of the journal to contact the editor of the issue to inquire about the problem or if the dates of their issue changed?

(1) Please ask a question in your title and (2) please don't use code formatting for things that aren't code.

I tried to edit the post and hope can get a response

There is nothing to do, actually. Writing again will have little effect other than to increase the workload of the editor, reviewers (perhaps), and staff. The response you got says it clearly. The system doesn't work on strict deadlines, and can't since humans are involved.
You won't change any decisions or affect any deadlines or scheduling by writing. It is just noise that might require someone to compose a reply like the one you've already gotten. Patience is warranted.
If you require information for some other purpose, you can ask for that, saying why, but if it is just worry and/or curiosity, then I recommend that you let it go.

Thanks a lot for the answer . excuse me , what if the status change to under review again with different date ? does that mean the other reviewer didn't review it and the editor assign new reviewers ? and if so , will the duration for the reviewing process be another months :-( or just will review the comments

It can mean a lot of things, including disagreements among reviewers, non responsive reviewers, etc. The time can't really be well estimated. They strive for efficiency but it is an elusive target. Too many moving parts, not well connected.

@user1 you seem to be checking the status a lot. That is not healthy. You have submitted your papers, so you have done all you could. Now it is out of your hands. There is no action you can take that will influence what happens. Any micro-second you spend on these papers is wasted time. So don't check on it. Forget these papers existed. Instead spent that time on things you can change: your next paper, doing nice things for your neighbors, co-workers, who-ever, or just relax. All of that is more productive than looking at the status, which is random noise most of the time anyhow.

Thanks a lot for the advice but those paper for my phd-defense that has a deadline so i'm feeling confused and stress . i hope i can get an accept nearly

FWIW, accepted (in press) papers are almost as good as published ones; PhD students starting too late with their publications is a very common thing.

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Fellow lab researcher adds me as (fake) author because his funds come from my fellowship
I received a 3 year fellowship for a 3-year PhD in computer science at a well known lab in my topic. I am in my last year and things haven't gone well. I don't have any impressive research results, feel unmotivated and only have a single publication when my peers have 3-5. Of course I am to blame for that.
Recently, my supervisor added me as an author in a publication I contributed nothing to. I told him that this is unethical and asked him to remove my name. He then told me that it is not that big of a deal and that the rest of the paper was funded partly by my fellowship. Some months passed and again without being asked, I was added as a (fake) author in another publication.
What should I do? I believe that the other authors think getting my name on publications is something I need because, as I said, my publication history is very weak, but I would rather fail in getting the PhD than having it based on fake authorships. Also I believe that they are short on funding and need to put my name on their publications to use part of my funding.

Your fellowship provided money besides your salary?

Yes it provided money for my supervision and for "research needs" eg software,hardware etc.

Were you involved in purchasing/selecting that soft/hardware?

You are right that you should not be an author on a paper in which
you did not contribute as an author.

It is important for anyone writing a paper to include all authors
that should be authors, and not to name anyone as an author who does
not agree to be an author; at your request, you should not be
included as an author if you don't want to be.

However...

It is very unlikely that any harm will come to you for being listed on a paper as an author as a junior researcher, much more likely you will benefit. The exception would be if there is something else ethically or scientifically wrong with the work that does not allow you to stand by it (an extreme example would be fabricated results). I believe your colleague/supervisors actions here are intended to be in your interests, even if they are not in the ethics of the field.

The systemic problems with gift authorship are mostly about senior researchers bullying their way onto papers where they do not belong, gaining benefit for no academic contribution besides perhaps funding. There is not nearly as much concern about junior researchers being over-credited; if anything, the opposite seems to come up more often.

Consider that your colleagues may find your input and work in the lab valuable to them, and that while you feel your contributions do not amount to anything towards their papers, even insightful side discussions can be critical to the development of a paper. Consider also that they may consider parts of your group work as a collaborative effort whereas you are focused on your individual role: if your group approaches a problem with three possible solutions, and each of three people take on one of those solutions, the total work could be considered a joint effort regardless of which effort is successful first, and the unsuccessful paths may be considered not merely as failures but as constructive efforts towards narrowing the remaining possibilities.

You should not agree to authorship merely as a way of letting them capture your funding, but I would think deeply about whether any of your contributions in the lab could be thought of as part of authorship of these works, and if so, ask that you can be more closely involved in the drafting of those papers (even if it's just re-checking analyses that were done, or contributing references and background to the introduction or discussion) so you can feel more comfortable being included as an author.

Let me add a secondary note to the answer of Bryan Krause.
While you are correct that this very probably crosses proper ethical boundaries it is generally a mistake to get into a fight with your supervisor as they have too much control over your advancement.
You could complain to the journal, of course, but the backlash would come to you and also reflect badly on the other students. Just as a matter of personal survival, I suggest letting it go.
You registered your objections, which was correct and bit bold, if risky.

Sit for a talk about your research and priorities with your advisor.
Be explicit about the "I would rather fail in getting the PhD" part, but also be careful with wording about fake authorships while doing so. Implications of unethical behavior are unlikely to be met well, and while you might choose to burn all the bridges, it is not necessarily what you desire, at the end of the day. Instead, a milder wording like "I really want my degree to be based on my own accomplishments and would rather not get it otherwise" might go better.
Consider their stake at the arrangement - they likely feel the need to successfully graduate you, and there is some external pressure. Possibly, to them "the student did not do much but I have pulled some strings here and there and they got to graduation nonetheless" is something to be almost proud of.
I do not agree with Bryan's implications of "gift authorship this way is not doing systemic harm so it is okay to accept it" - this is your own ethical stance, it might make your life "harder" but it is a very valid decision to follow that route nonetheless. The advice to view your contributions to the lab in a different light and not just focus on the funding is excellent, though.
So, talk to your advisor. Make decisions. Avoid drifting to the deadline passively observing it approaching. Figure out what is important to you and pursue it.


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Frequently checking NSF website for new grant?
Shall one frequently check the NSF website for newly released grant opportunities?
How often does NSF release a new grant in fields like Machine Learning or Deep Learning? Per Month? Per half a year?

You can get on NSF's mailing list for new grant solicitations...

The best way to stay up to date with NSF grants opportunities or any grant opportunities is to sign up for email alerts or for the funder's RSS feed. Both of these options are available for the NSF. See: https://beta.nsf.gov/funding/opportunities to the right above the search bar. Additionally there are for-pay grant/funding alert systems that your university may subscribe to. Do get in touch with your funding support office for more information about using those.

Thanks! That helps!


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If previously submitted and marked paper is plagiarised by others, is it collusion?
Assuming a student wrote a paper on their own and submitted it to turnitin.  AFTER they graduated, if their paper is accessed (with consent) by an undergraduate student who is studying a same course and the paper is plagiarised by that student (without consent), is it collusion?

It could be collusion or not, but it can certainly be charged as such. Collusion requires knowledge and consent. But the source of the paper certainly enabled the plagiarism even if unintentionally.
But giving the paper to the other student is improper in any case since it interferes with the learning of that student, unless the professor was also informed. It attempts to short-circuit learning by making it "seem" like the student has some knowledge that they don't possess.
Some things that seem like "help" are actually hinderances. Students need to learn through their own efforts if they are to later successfully use their knowledge.

Thanks for your answer.  Can I further ask that is collusion applies to graduates?  Becuase in the case I mentioned, the one who leaked the paper is a graduate rather than current student.  Moreover, I am a little confuse about the fine line: for example, if a graduate post his own attempt on past year exam question on internet, and students plagiarise it, does it count collusion?  Thank you.

The timing is immaterial. While posting exam material in a public place is inadvisable, there is no collusion. Professors shouldn't really reuse such things, but the reality is that they do. Fraternities in the US (did, do) kept extensive files of exam materials for use by future members (files as in file drawers). That was a form of collusion because of its intent. If professors know this and don't reuse old exams then it is benign and can be a source of study material. However, reading solutions is not the same as producing solutions, so it also can sabotage learning.

sorry just one more question: so if what is leaked is just past exam paper attempt or study notes but not a paper, there is no collusion?

I disagree - collusion would be the original author actively assisting someone copying their material. Just letting somebody else read a paper of yours is not collusion.

@JonCuster, I think you mis-read what I wrote. As I said, intent matters. But there are other "bad" things than collusion. It "could be" collusion but there is not sufficient information here.

At various universities, at least some student papers are explicitly made public. This includes PhD theses, but includes many other things as well. No one would accuse the author of collusion should somebody else plagiarize from them. Why would a privately shared paper necessarily be treated differently? There are many good reasons to do so, including providing a review of background literature, sharing references, and providing a solid foundation so the other student can extend the work.

Again, you are misreading. I don't claim it is necessarily collusion. And you are clearly comparing apples to oranges here. It could be "charged" as collusion by an external reviewer not knowing all the facts such as intent, etc.


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Where are historical research papers stored?
I have been reading some historical papers in the field of computer science, economics and game theory. I have noticed that some of the really old ones such as Equilibrium points in n-person games by John Nash (1949) accessed from PNAS has minor inconsistencies and flecks in the ink, indicating it could have been typeset with a commercial cold typesetting machine¹ that is appropriate for the era.
I spoke to a friend about this and they mentioned accessing some of Turing's original papers. They claim that the scan of the paper appears more modern and contains less of these historical artifacts within the typography. This leads me to another assumption: some historical papers were not preserved and we are forced to refer to the oldest known reprints.
Logically, this begs the final question: who handles storage and archival of original scientific papers and how do they do it? The following sub-questions also arise:

is this process standardised in any way;
if so, is the degree of standardisation dependent on university, country or is it international?
Is there any way to verify originality of documents?
If there are multiple entities performing the archival duty, where does one look for them?

¹ My assumption could be wrong here as I am not an expert on the history of scientific writing and its typography. Please be sceptical about this.

Many (most?) still-exisiting journals have been digitized in the last 30 years. How much effort went into cleaning the scanned versions up varies widely. Many have been OCR'd as well, but not all. Pre-Internet, back issues were bound in thick books and stored down on Level 4 in the library basement where, if you weren't careful, you could be eaten by a grue.

1949 is not really old. People still often read papers from the 19th century and earlier.

Where are historical research papers stored? Yes, libraries, but there are other archives, including the archives in long-standing large organisations, private archives and libraries, and museums. For example, the Association for Computing Machinery has opened up its first 50 years of publications in celebration of its 75th anniversary.
Who handles storage and archival of original scientific papers and how do they do it? Many large organisations employ specialist archivists or librarians to look after items. They are trained to degree level and beyond and use methods developed over the 100s and 1000s of years libraries and museums have been in existence.
Is this process standardised in any way? There are best practices, well-tried methods, and standards used.
If so, is the degree of standardisation dependent on university, country or is it international? Librarians are very professional with many national and international organisations and publications. Preservation of human knowledge has always been taken extremely seriously. Plenty of examples in (recent) history of madmen trying to destroy knowledge for their benefit.
Is there any way to verify the originality of documents? Go back to the original source. Alternatively, an original copy in an independent library/archive. In the UK there is Legal Deposit. Everything published must be submitted to the British Library.
If there are multiple entities performing the archival duty, where does one look for them? Ask a librarian! Most libraries operate in cooperation with national libraries. Libraries can, and often will, borrow from other libraries. In the UK there are six libraries of legal deposit (The British Library, National Library of Scotland; National Library of Wales; Bodleian Libraries, University of Oxford; Cambridge University Library; Library of Trinity College Dublin). Their contents are available to other libraries and visitors.

This is a good answer, but I think it could be improved by pointing out that the answers to the main original questions are extremely obvious

There are 6 libraries of deposit in the UK - you have omitted the British Library

Thanks, corrected the list of legal deposit libraries.

The answer is libraries and librarians

I love this answer because it points out that there are people whose job it is to preserve knowledge :-)

It is amazing that people seem to have forgotten about the existence of libraries and librarians

Because they no longer set foot in libraries. I haven't been to my university's library to look at books or articles in years (probably ten or more years).

Worth noting libraries have separate functionalities of providing everyday use books in circulation for the public and also preserving archives of old texts. You aren't going to be walking in and checking out an original 1000 year old manuscript. There also exist private and public archives that focus on that archival aspect over the everyday use. So this answer could be fleshed out more or turned into a separate answer.

@WolfgangBangerth well, yes. But there's a bit of a cycle there. It's become more and more common for university libraries to archive away older journal editions so you can't go and look even if you want to. Found this particularly irritating when dealing with poor digital copies and being then unable to get to the physical copy the library did have!

When I was a student, there were materials from the 16th century in the library, perhaps earlier.

You want things that you don’t have. I’ve lived in Asia for a few decades, where there are no good libraries of materials written in English. I’m ecstatic when I get to visit Oxford or Cambridge, and can spend a day in their wonderful old libraries.

I notice that many old library books are for sale on the internet. I like the fact that I can buy them, but it disturbs me that libraries are getting rid of books. Do they typically scan them before ditching them?

A lot of old journals are bound to volumes in the basement of the library. Suprisingly I once retrieved an original paper from 1932 (written in German) at a Singapore varsities scientific library (I expected them to have to order it, but they had it in the basement).
Some libraries switch to microfiche when they need to clear up some storage. Generally there should be one (or two) original copies at the national library in the country where the journal was published. (not every country has a national library though).
For the Nash one, probably any tier 1 university will have an original.

+1  U.S. Universities (that were in existence then) will likely have PNAS all the way back to Volume 1 from 1919.


text:
General tips for starting a master's thesis
In September I'll be starting my second year in my master's in which I'm writing my master's thesis. I have everything set up and I am starting to go through some of the literature during the summer.
As this is my first 'larger' project I am involved with, I wanted to ask for some tips on how to handle and structure a thesis, or larger research projects in general. I want to implement some good practices when starting my thesis and try to avoid common mistakes made by grad students.
I'm open for any kind of answers, from personal anecdotes and 'lessons learned' to e.g. software for organizing ideas like Obsidian.

Document everything! OK, this might depend a bit on what kind of work you are doing, but for me as a lab rat that is one of the most important things. Once you sit down to write your thesis it makes such a difference if you have good structured notes to go back and remind yourself of exactly what experiment you did and when/how, what observations you made, what conclusions you drew, etc. This is important even for experiments that didn't work.
Also in a really big project it is really easy to get lost and feel like you don't really know what goal it is you are actually working to. It will take some time for you to wrap your head around everything, so try to break it up into smaller problems. This is also where your supervisor's guidance can be really important. I have sometimes made the mistake of not asking my supervisor for help when I've been stuck and they could have given me a push in the right direction. Better to ask one too many times than one too few :)

Thanks for your answer! I'm keeping some kind of log already of what I'm doing, and I'm trying to create a general structure in my note-taking.  I'll keep in mind what you mentioned about breaking everything up into smaller problems. That'll help with the digestion of large amounts of material.

The best time to start organising ideas and taking note is from the first year. The second best time is now. So, you're still good to go.
In your writing up, have/develop a story line. Your literature, methodology, findings/results and discussion all end up fitting into your narrative (story line); not just discussion.
For your literature, annotation and referencing, you can't go wrong with Zotero. I actually moved away from Mendeley to Zotero due to Mendeley encrypting their SQLite db.
If your institution offers Endnote, feel free to use as alternative to Zotero.
I'm aware you mentioned master's thesis. Tips for PhD writing will equally be important.
Andy Stapleton provide guidance for writing thesis and good ol' tools/tips.
Just to mention that most universities have good resources for writing up. Check with your university's writing center and postgraduate center/school.

Martin Adams has a comprehensive tour of Obsidian for PHD Students

Maybe I wasn't too clear, but the thesis in my case only starts in the second year. So in that sense I am a bit early by starting in the summer. I'm generally also interested in stuff like keeping a log, that aren't necessarily fully connected to the writing of the thesis itself. In any case, thanks for your answer!

You're on track and being proactive enough. The actual writing up will be iterative. Starting now on thoughts, approach, tools including structured log taking and literature mgt would go a long way.

When the writing gets full gear, your structured logs and literature will be invaluable ... "I'm generally also interested in stuff like keeping a log, that aren't necessarily fully connected to the writing of the thesis itself"

Do you have any concrete tips on how/what to log? For now I'm just keeping track of what I read with some comments on the content.


text:
Asking my PhD mentor to be my referee for PhD position
I'm a Master student in Belgium, 2nd year, doing my Master thesis. I have a supervisor/promoter (university professor) and a PhD student as a daily mentor, we work together and get along great.
I started looking up PhD positions in and out of the country, and most positions ask for 3 referees informations. I'm an international student in Belgium, so I only knew my professors since last year, and I don't know how to ask them, I asked my current thesis supervisor and he accepted, but the other professors I was never close to them, so would it be ok to ask the daily mentor to be a referee instead? She's a PhD student in her 4th year with more than enough experience in the field.
If not, how do I even open the topic with the other professors? I don't know if they remember me. I was never an outstanding student, but I got by just fine.

You can also ask some of your former teachers, especially those with whom you had a good connection. Also ask your thesis supervisor for some suggestions.

Yes, you can ask her for a letter, though one from a professor would be much (much) better. The tradeoff is that while she knows you well and can speak to your skills, she has not yet proven herself in academia, so some (not all) will discount such  letter.
But, I suggest that you ask her for advice about who would be a good letter writer. You and she might together approach one of the professors who knows you a bit better than others.
And, some places put much more emphasis on such letters than others. They are quite important in the US, but less so in some other countries. Other parts of your record may be more important.

I see, I will ask her then, thank you!

You should also ask the prof who agreed to write a LOR for you. Probably profs have had experience with similar situations.

Got it, thank you!


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Potential PhD Advisor wants to know my decision to accept or not before the 04/15 deadline
I received an offer from a top US engineering Ph.D. Program. Let's say this is Program A. I also have another offer program B. Currently, I am waiting on program C's decisions. The potential advisor from C is very positive he will have full funding + offer for me soon. All A, B, and C are my TOP choices and TOP engineering Ph.D. programs in the U.S.
My preference is as follows with a 'confidence value of my preference' estimated in brackets.
A_offered (0.90) > C_waiting (0.87) > B_offered (0.83)
My dilemma is that the advisor from A emailed me that they want to know my decision a couple of weeks before the 04/15 deadline. An official offer letter was attached to that email.
Though I am leaning toward program A, I am still looking into program B and waiting on program C's offer.
Would it be okay to respectfully ask the advisor from A that I will need more time to make my decision?
And, if I do ask him for more time, is there a possibility that he will rescind my official offer?

This is not the same question, but the info is relevant: https://academia.stackexchange.com/questions/143505/how-bad-is-it-to-accept-a-competitive-fellowship-then-reject-it-before-april-15?rq=1

Do they say why they would like an early response? Could 3/15 just be a typo of 4/15?

@Dawn I don't believe so. The earlier date is stipulated as the same on both the mail and the offer letter.

Yes, you can absolutely say you need more time. The April 15 deadline is the only real deadline here. It may be that it would be convenient for the faculty member to have you decide earlier, but they should not be pressuring you strongly for an earlier decision. It is okay for them to ask, but not to push.
You can say something like - you are waiting to hear the details of one more likely offer and would like to weigh it fully. You can also offer to let the faculty member know as soon as possible (can keep this vague) after you receive the details of the final outstanding offer.

thank you for your honest answer. I am just worried A) if I ask for an extension that they might rescind my official offer. Even if they do say "Please note that acceptance of this offer is non-binding until 04/15" and B) If I do ask for an extension, should I mention I do have other offers/waiting on them? Or Should I just be vague and just say "I would appreciate some more time." Thus, its the brutally honest vs. a-bit honest deliemna.

I don't see anything wrong with saying you are waiting on another offer that you would like to consider fully. Rescinding the offer would be totally illogical. It is possible that it happens, but not the sort of thing that a reputable program would do -- it would be very strong signal that you were dealing with an unethical advisor. For more information about non-binding acceptances, see the link I posted above as a comment.

My read of the situation is that if you are going to definitely reject them, they want to know as soon as possible. It seems like soft encouragement for an early reply, not a demand.

Deadlines are deadlines, sometimes they can be bent, but I would not expect a significant extension. After all, the advisor from A needs to submit their decision as well, starting your work together by missing deadlines is surely not the most professional thing ever.
The ball is in your court: you have all the information from that advisor and it is clear you may wait until the start of April to make that decision. They have nothing to gain from the extension: either you apply to A anyway (why would you need an extension then?) or you decide to go with C (why spend time and resources and go out of your way for them to specifically bail on you?). It just makes no sense!
From your description, the advisor has handled the communication so far very professionally. You should live up to that standard, too. There are times when you have to make decision based on incomplete information and cannot guarantee that the course of action is the best possible one.
What you could do is to inform the advisor at C that you have a hard offer which imposes a certain deadline on you. Do not mention where you got this offer from nor the deadline itself: instead, state a deadline of your own (say, March, 25th). This passes the ball on and if the advisor at C drops it, well, not much you could do. If they really want you in their lab, they should make a counter-offer with some way to guarantee you it would work out. "We will have funding sometime soon, promise" is not the way to do any business together, much less long-term commitments. Maybe "I have talked to all the people responsible for the funding and they have promised me it will be allocated" is enough, but "I am sure I will manage to get it" is not.

Disagree. This is a misread of the situation as 4/15 is the real deadline. Any other date is a personal preference by A.

@Lodinn Thank you for your answer. I agree he has been professional in his offer and communication with me. I have no dissatisfaction with that. But they do mention that my official offer "Please note that acceptance of this offer is non-binding until 04/15" but at the same time asking for my reply by 03/15. I do believe that I am in my rights to respectfully ask for more time... but what if they rescind. And, plus I don't want to start off the wrong page with my potential advisor.

Note here that the 4/15 deadline/policy is specific to the US. People who are at non-US universities don't have the same set of policies to deal with and individual advisors have more power to make deadlines.

Yes, maybe I should have highlighted that all three are US Ph.D. programs.

@KTJ The reply by 03/15 is a bit unreasonable demand, IMHO - I've interpreted "a couple of weeks before the 04/15 deadline" more literally. That is, you are technically free to wait until 4/15, but it is better if you could notify them a bit in advance (say, before 4/8) so to accommodate them as well. To that end, a single extra week probably won't change as much, which is what I meant by "not a significant extension". A month, however, is quite significant, and I would push back on that.

Considering that (in the U.S.) quite a few "second round offers" go out just on April 15, due to "first round offers" being declined at the last minute, etc., the questioner here may not have definitive info about other possible offers until essentially April 15. So, to "compromise" at deciding a week earlier, etc., would (possibly) be a bad compromise, given the mechanics. Grad admissions people/advisors/etc obviously would prefer to have their own strategizing about this simplified, but the stakes are much higher for students, and my opinion is that we should "just deal with" complications.

@paulgarrett hey thanks for your response. Could you elaborate on your last statement, "my opinion is that we should "just deal with" complications"?

The "we" is faculty and admissions committees and university administrations dealing with grad students. These decisions are a very big thing for grad students, and they shouldn't be bullied or "guilted" into making decisions before the standard date in the U.S., just for the minor convenience of faculty and admissions committees.


text:
Dealing with an exploitative co-author
I have, unfortunately, ended up working with a truly awful co-author on three separate projects. The problem with this co-author is easy to summarise: he contributes almost nothing to the projects, and yet he wants to make all the decisions. As you can probably guess, he is fairly senior (and substantially more senior than me).
To give an example, let me tell you about the second project we worked on. The co-author played no role in coming up with the idea of the paper. He played no role in designing the experiment on which the paper is based. He did none of the data analysis, and also didn’t write the paper up. In fact, he only saw the paper well after it had been circulated for comments! His only ‘contribution’ has been to take the completed paper, and then make some (terrible) edits to the finished version, thereby making it slightly worse.
Given his lack of contribution, you might think that he would feel lucky to be listed as a co-author at all. Unfortunately (for me), he doesn’t exactly feel this way. Instead, he thinks that he gets to make all the important decisions, including the decision of where and when to publish the paper. Moreover, he decided that we need to run some extra experiments before he will ‘sign off’ the paper for submission. That was over a year ago — and we still haven’t submitted the paper.
I could you about the other projects, but the story is the same. He contributes nothing to the paper until it is finished, at which point he makes some terrible edits. He then thinks that he gets to decide on everything — including whether his terrible edits can be altered and (more importantly) when and where we submit the paper.
You might ask why I ever agreed to work with him. The answer is that my friend (who contributes a lot to the projects) persuaded me to — and this coauthor is my friend’s employer. This makes it very difficult to resolve the situation.
I should perhaps add that this co-author co-owns the data on which the experiments are based. I think this probably makes it impossible to remove him as a co-author on the papers. In fairness, one could also view this as his contribution to the projects (he co-owns the company that has been running the experiments).
I really need some advice about what to do. On the one hand, I want to tell him how I feel about what he has put me through over the last two years. I have also considered contacting my university (and his university) to escalate my complaints. On the other hand, I feel pretty powerless here. What he has done is not exactly plagiarism, and he does co-owns the data which we use in the papers. In addition, he is fairly well known and could retaliate by trying to sabotage my career.
I should also explain the very specific conflict we have currently. We have recently finished our third (and final) project together. He has done his usual thing of making some terrible edits, right at the end and once the paper is completed. I now want to submit. However, he wants to delay submission (he won’t give a timeline), mainly so he has more time to make edits. Hence the conflict.

Just on the 'terrible edits' -- are they reasonable?  If not, refer him/her to the rule book.  Otherwise, I would just let it go.   A senior person should in theory knows what is acceptable and the path(s) that lead to the most publishing success in a given area.  In my area (engineering), I've seen poorly written but technically very sound papers.   However, you may not feel happy to have authored such poorly presented papers.  End of the day, people are interested in ideas -- you don't get cited for having written a nice  looking paper.

Can you clarify the question? Are you looking for advice on ending your relationship with this guy? On publishing the existing work? On something else?

My question is mainly about how to go about publishing the existing work. He wants an unspecified amount of time to make further edits, perhaps so he can feel that he has contributed something (albeit at the final stage).

I suggest that you do what is necessary to get to the end of this project, even if it is somewhat unsatisfactory and just move on. If they have made some "decisions" on the structure of the project/paper then they probably can claim authorship and can probably just demand it in any case.
I assume that you also have valid authorship and can't be removed. You could, yourself, refuse to permit the work to be published, but I don't recommend that (actually recommend against it).
You can't prevent what this person will do to your friend no matter your course of action.
But move toward the exits and salvage what you can from this burning edifice. Don't bother to complain to him. It won't help anything. If he tries to remove you and publish without your authorship you can then complain to the publisher.
Sadly, this isn't a unique situation.

Thank you for your comments -- I appreciate the advice.

"Sadly, this isn't a unique situation." True. Academia is full of people with big egos who are used to make decisions and defend them against other people with equally bis egos. Therefore, OP could practice here how to communicate with such people (I am trying trying to find the positive aspect here).

@apostdoc38933: I agree with this answer. Even researchers who are very friendly and nice people outside of academia tend to, when they have seniority, freely use arguments from authority (e.g. "you should do what I say because I have got many papers published and you have not!") to get their way. It is worse in your case (i.e. unfriendly and awful), so just get it done by whatever means and then leave the toxic relationship as fast as you can.

@user21820 To me, the original post sounded more along the lines of "I give you the money, manpower and equipment to run the experiments so I get to sign off on your projects". Chest thumping about papers published for this kind of PIs/contributors is important on an earlier stage, when they get to the power to make those decisions in the first place. And some are good administrators, but bad scientists. Not all of them are able to completely give up on their desire to be at least a little hands-on with research even when they can't do it competently any more.

@Lodinn: Definitely not. The asker wrote: "He did none of the data analysis, and also didn’t write the paper up. In fact, he only saw the paper well after it had been circulated for comments! [...] He has done his usual thing of making some terrible edits, right at the end and once the paper is completed.". Both of these indicate that the person is not at all attempting to still do some research, but rather being an obnoxious boss.

@user21820 You missed the point - or, at least, read "hands-on" as something much "closer to the ground" than I implied. The reality for quite a few senior researchers I've met seems to be thus: they have built a successful career out of managing research and saw their ideas flourish, and are far more into the management work than "actual research". They have no possible hope to be intimately acquainted with the modern toolkit and often, no time to design nor run the experiment. And yet, that research is what drives them. They try to stay in touch the way they still can... And it is obnoxious.

@Lodinn: Lol so you agree with my conclusion despite the differing interpretation. I can't be sure my interpretation (that it is a toxic relationship) is more likely, though I have literally seen this kind of really intrusive editing being done by superiors (and there is still a difference between toxic and non-toxic relationship, with very clear differences in behaviour). Anyway, never mind! =)

@user21820 There are two separate issues. Yes, I wanted to show the other side of the coin (at least the way I perceive it; being able to sympathize with it at least). But the reason I replied initially is that the "argument from authority" in this interaction is not "I know this field better", but rather "I pay you to do research the way I want it, when you procure the money you set the terms". Different interpretation, but no real leverage in the latter case. Scientific merit and relevance of earlier works can be debated, but they don't really matter here. A bit different power dynamic.

@Lodinn: I got that, but I don't see much difference either, because the type of intrusive editing based on argument from authority that I have seen is really not based on skills or knowledge. Let me give you an example: The superior does not understand much of the paper but makes twenty different edits at one go, causing many statements to become false, and causing distinct variables to become the same. The point is that publishing more simply implies nothing about the value of their edits, but this kind of people often edit just for the sake of sticking fingers in.

This sounds very familiar. I once worked for a PI who behaved in a very similar way, down to the total lack of participation, the terrible edits, the arrogance, and the insistence on being in charge. In one case, the edits consisted of some wording rewrites and adding his name in various places in the author contributions where it didn't belong. He then finished off by sending us (his co-authors) a lecture on grammar by email.
The project I was working on (two of them) were both sort of derived from his "intellectual property". And I think one of the projects used data he provided.
I don't think I have much advice to offer except to say that it sounds like there is little if anything you can do about this. Your problem person realises, I'm sure, that he has leverage, and that there is little you can do. Also, based on my experience of academia, complaining will almost certainly be useless, and possibly worse than useless, if your co-author learns of it. Sorry.
I also imagine this sort of thing is not uncommon, at least with PIs dealing with his/her own students/postdocs. It might even be common. For obvious reasons, data about such things is hard to get. My experience on working in collaborative projects is that "senior" people are extremely disinclined to do any actual work on the project, though they are more than happy to have their name on it. My impression is that this is how (some) people get ahead in academia, by taking credit for other people's work. The capitalist analog is obvious.
Your case is different, in that you are dealing with a colleague's employer. The good news is that because this is the case, you can get away from it relatively easily.
I suggest finishing the project with him, if you can, and I also recommend that you avoid, if possible, starting new projects involving this person in the future. Because the stress is probably not worth it. You say you've worked on three different projects with this person. That seems like a lot, and I would avoid a fourth unless there is some truly compelling reason for it. Also, I would not stress about the unfinished project. It sounds like there is little you can do to speed it up without creating more friction, and it's probably not worth it. But don't withdraw from the project either. It sounds like it will probably move forward and get published eventually.

"The capitalist analog is obvious" - yes, but in capitalism, they are not taking credit for others' work. Instead, they claim that greasing the cogs of the machine may be adding more value than being another cog. To me, being the Big Boss is a ton of responsibilities taking you away from what you actually love doing so that it would get done better in general. Hardly an enviable position. For all we know, this stereotypical "lazy boss" from OP's description might be working their ass off trying to get funding and approval for the project and the rest is them coping.

@Lodinn No, but they are profiting from others work. Hence the analogy. "Credit" has no  meaning in capitalism.

I have, unfortunately, ended up working with a truly awful co-author on three separate projects.

Well, that's the problem right there isn't it; that number is two too many.

This doesn't seem to give any useful advice on dealing with the author's current situation. It does seem to say, "don't get into those situations," but doesn't provide any advice on how to do that, either.

+1...the question is "what should I do" and the answer is "stop collaborating with this guy." An ideal answer might explain how to wind down the collaboration and publish the existing work, but that's tricky because the optimal course of action will depend on the personalities involved (and perhaps the technical details too).

It might be three projects which were started concurrently, for all we know. The question does say this ordeal has lasted for two years, but that doesn't necessarily mean that any additional commitments were made after it became clear that this person wasn't a good collaborator.

@kaya3 That'd be still an overcommitment then.


text:
Resources for searching research internships
I'm a master's student in computer science and ML, currently on the lookout for research positions within my field. I'm aware that finding such opportunities can be quite challenging, given the decentralized nature of job postings for research/scientific roles. Unlike the more centralized platforms for industry positions, such as LinkedIn, it seems there's no equivalent "go-to" place for research jobs.
My goal is to find a platform where I can filter opportunities based on criteria such as location, specialization, and perhaps the type of research.
Could anyone share their experiences or recommend websites where I could start my search?
edit: both  academic and industry are applicable

Are you looking for academic or industry-based internships?

You can start your search at ScholarshipDB.net. On this page, you can find multiple research positions, internships, postdocs, etc. They are not directly published in ScholarshipDB.net, they are retrieved I assume automatically but the corresponding origin of the opportunity is provided.
You can also try AcademicPositions.
If you are interested in Germany try Research in Germany or MyScience; for Switzerland try Academics; for Austria try AIT.
I hope any of them helps you.


text:
MS/PhD Pass Qualifying Exam and Finding an Advisor
There are three outcomes in my department's qualifying exam: PhD pass, Master's pass, and fail. I am fairly certain that I will not PhD pass and will only Master's pass. I still have a chance to retake the exam next summer, but I was wondering how I should proceed from here.
In our department, PhD advisors are only assigned after a PhD pass.  However, if one fails completely, there is a thesis option to finish the MS. I think I did well enough to MS pass, as the threshold for that is quite low according to some of my professors. I don't see why I wouldn't be able to take the MS thesis option even if I MS pass -- our department is small and I don't think the professors are overloaded with supervising students.
I still want to complete my PhD in this department long term, but I am worried that an extra year without an advisor would leave me behind. Would it be acceptable to ask a professor (who very clearly states on his website that he will not advise a PhD student until they PhD pass) to advise me for an MS thesis, and then hopefully if I pass next year use that MS thesis work as part of my PhD dissertation/thesis work?
I do not care that much and understand if this professor supervises me less because he is my MS advisor vs. PhD advisor, but is this a silly idea? Would it be received in a negative light, like something analogous to "grade-grubbing" or trying to play the rules?
Thanks!
Background: I was admitted as a PhD student out of undergrad and will be starting my second year in a mathematical field in the US.

Is the MS Thesis option in your department an option that is frequently used, or only an option that theoretically exists on paper?  Does this professor actually supervise any MS theses?  I'm a mathematics professor who would usually be reluctant to supervise MS theses because I usually don't have any suitable projects.

I'm not sure if I would go so far as to say it is frequently (> 25% of MS students) used, but I know some MS students who did not sit in for the test this year because they discussed with the grad. director to do the thesis option. As for the professor, he specifically mentions that he is open to master's students (also undergrads) to do research so I feel like he has some projects.

To be honest, you should wait until you get your results. Don't speculate, as it makes things worse. Go out for a hike, take some time off, disconnect from the computer. But, you should definitely have a plan A, B, C, etc...

Yes, an MS thesis can be continued into a PhD dissertation, I've seen it happen, but it is rare. That is certainly one option, but there is no shame in waiting another year to take qualifiers again. I did something similar too, as I failed my first qualifying attempt. It crushed my soul, and I was about to drop out.

But, I doubled down on studying, focusing in the areas I was weak at. I retook it and passed! I just recently graduated with my PhD, so looking back at it, I am glad I gave myself that second chance.

Kind of like that time when Kakarot almost killed me on that pathetic rock called 'earth'. Haha, weakling! (lol, sorry I just can't resist the humor)

@VegetathePrinceofSaiyans, you probably have a proper answer here.

Have you taken the exam and are waiting for results, or is the exam in your future?

As Buffy points out, I may be able to flesh out an answer here. Like I say in the comments, you should really wait until you get your results. Speculating and ruminating are pretty bad for your mental health. It creates unnecessary stress, and of course, you want to minimize your stress because you will get plenty of other things to worry about later. Don't sweat the small stuff.
Now, regardless of your results, you should have already a plan A, plan B, plan C, etc... Like they say, "don't put all of your eggs in one basket". I had a similar experience, where I needed multiple options after taking (and failing) my first attempt at a qualifying exam. I too was worried after taking it, but making a list of options helped me to cope with these feelings of anxiety. For example, it may look like this:

Plan A: Pass qualifying exam and ask Dr. X to mentor me. It was the best case scenario.
Plan B: Fail the exam, but I am given a second attempt (hopefully). Study and take it again. Also, have a contingency plan, which can look like getting a MS (possibly with a thesis) on the side, in case I fail that second attempt.
Plan C: If no second attempt allowed, still finish the MS. But also cultivate other options, such as applying to another program. I was considering mechanical engineering as another option. Maybe also get a certificate in a hot technical area so I can go and find a job after my MS.

And so on... As you know in math, the optimal path from point A to B is a straight line. But, things very rarely go as planned without hiccups. It is actually advised to have secondary plans, as it is better to be proactive rather than reactive. Also, yes, in my university, it wasn't a guarantee that you'd always get a second chance after failing a qualifying exam. I was beyond grateful that I was allowed to continue and take it again.
Now, in case you want to go with the MS with thesis option, yes I have had one friend who transferred his credits from a MS to a PhD (in the same school), so he continued his research with that same advisor. It can happen, just not the most common option. But I would bet that you'd still need to retake the qualifier if you are given an MS pass and you want to continue into a PhD dissertation. In my institution, there was no MS pass officially, just pass or fail.
Another thing is how to deal with rejection. It happens everywhere, and you failing a qualifying exam is by no means a reflection of you as a person. I personally failed that first time because I had a panic attack and was under new anxiety meds too. Out of 4 subjects, I passed 3 initially. So I just had to retake the portion that I failed. I buckled down and studied smarter, took care of myself (went to gym, therapy), and surrounded myself with good friends, not toxic ones. Things went much better second time around and I passed! I went on to get my PhD, with prestigious internships and 3 publications (1 which was a first-author publication). Not bad at all!
I highly encourage you to give yourself the benefit of the doubt. If you got accepted to a PhD program, you already are better than what you give yourself credit for. Keep going, as perseverance is a highly desired trait in any trade.


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My Master’s advisor is slowly killing me
I am Master’s student and finished 1.5 years. After first year, you are supposed to start your experiments but most people start even earlier. My advisor or PI or professor ,whatever you want to call, wrote a project for 7 months at the end of my first year and it was rejected. She is editing it and is gonna send it again but it will take at least 2-3 months. I don’t have that much time. I am already sure that I will have to lengthen it at least one semester. But I want to learn nice methods and write a nice thesis. But I didn’t even entered the lab. I didn’t do any experiments. When I ask her, she gets mad and tells me to be patient and that we don’t have money yet. I am doing a internship in another lab in a different country.
I did experiments on her field but my data is kind of shit. I was hoping that my data would be okay and I could write grant application on my own and could do experiments more with this method but my data is shit and needs a lot of troubleshooting. My advisor does nor have knowledge on this. I want to go to another lab who is established, have already an ongoing project.

What's your actual question?

Should I change my advisor with one who has ongoing project (she is in a different uni so I will need consent from my own advisor) or stick with her, write grant application and take risk?

Every university has a set of rules about the way projects should be conducted and the milestones. They also have internal and external oversight mechanisms that should oversee the work of supervisors and the progress of students. Failure of a student is bad for a university's reputation.
You must have a second supervisor who is not part of the same department.  You must also have had a project plan outlined at the start of your Masters Degree.  Use these information and levers to force your supervisor to move forward.
I also wonder if you have given the correct and full information here. In your message you say:
"My advisor or PI or professor ,whatever you want to call, wrote a project for 7 months at the end of my first year and it was rejected. She is editing it and is gonna send it again but it will take at least 2-3 months."
I do not understand how your supervisor wrote a project? what does that even mean?
if you mean the supervisor wrote the project definition and plan and took 7 months, then I would say you should have taken that work upon yourself or at least helped her. It would have been your opportunity to define a project in the way you want it and include the type of work you like to do.
Finally, I advise you to do the following (without fail). Have meetings with your supervisor at pre-arranged time slots and not on her way to and from a Lab or office. After each meeting write an email with three or four lines giving the summary of what was discussed and the listing what was agreed that you will do and what was agreed that she will do.  Then send her that email as a meeting note.
At following meetings go through the list of actions for you and list of actions for the supervisor. If any of the actions have been completed write down the outcome and if not write down the level of progress and reason for delay. Add any new actions that may be necessary. Write up the new meeting notes and send it to her.
As a student you should know the value of documentation and keeping trace of agreed and approved actions. You will see that in due course your project will move forward faster than before because you need to take control of it.

Wrote a project as in for grant application. We have to get a grant from government or else we don’t have money for experiments. I can’t really change the project and she and other two professors wanted to write it in certain way. She assigned me parts to write and I wrote them but they needed to edit a lot together and also write methods. When this started, I didn’t know how to write experiment plans out of nowhere, i was just fresh out of bachelors, I did not know any of those methods.
And no, i don’t have any other advisor, just her and no one oversees her.

but you say two other professors were also involved in writing it.

Yes, but they are not my advisors, they are assistant professors in the same department. Mine is head of the department. Other two don’t really care if I graduate with strong thesis or not. The thesis plan we wrote to send the institute is nearly as simple as my bachelor thesis. I couldn’t say no or add more experiments cause she repeatedly said we will be lucky if we do things we wrote. She said I could even graduate with the data I got from internship? Is this a normal way of thinking?

"Every university has a set of rules about the way projects should be conducted"... "You must have a second supervisor who is not part of the same department" - we don't know where the OP is located, so we can't say this for sure. +1 for your paragraph starting "Finally", though whether this works depends heavily on whether the supervisor agrees to this approach.

Thank you. I think everyone assumes I am from Europe or US but I am not and department is imcompetent. I am not the only one who is having problems, other 4 master students also are having problems but unfortunately, I am the only one without a set project going on for me. All of them started and they came after me.


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Is it correct that staying in postdoc position for more than 3 years is a negative thing?
I am working as a postdoc at a reputable university. The salary and funds are quite good, no less than an assistant professor at our university. However, some of my friends are saying that staying in a postdoc position for more than 3 years is a negative thing. Especially since I currently have an offer for a non tenure track assistant professor position from an average-rank university.
Is it correct that staying in a postdoc position for more than 3 years is a negative thing?

It might be dependent on the specific system. As well on the post doc age, and his/her feeling concerning an advancement at the current institution, as well as a multitude of factors linked to private life.

It depends on the person evalutaing. Some will see this as negative, most will probably look at your scientific achievements and ability to aquire funding during this time.

This will also depend on the field. For example, Biomed researchers seem to stay as post-docs longer than, say, engineering researchers.

What's your career goal?

This is a question which depends highly on specific circumstances, and thus cannot be answered universally in a reliable way.
Some important parameters:

country (East Europe? Russia? USA? UK? China? India? Iraq?)
field of study: norms in your field of study? How competitive is your area? (Is it history or machine learning?)
More specific parameters: do you have better alternatives?
Etc.

That said, it is generally (read: on average, considered across all possible parameters distributed with uniform probability) correct, in my opinion, that staying too long as a postdoc is negatively correlated with getting a permanent academic position. This is because empirically "aged" academics are perceived negatively sometimes by recruitment committees.


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Postdoc with only 5 publications 3 years after graduation
I am a polymer chemist doing a postdoc. I would like to pursue my career as a researcher. However, I have only 5 publications (all first author) 3.5 years after my PhD graduation. 2 more should be submitted within 6 months.
Will it be possible to continue my career as a research scientist?

depends very much on how many others in your situation do have…

If the publications are published on generally acknowledged top-level journals in your area, then your productivity looks good to me.

This is very field dependent. But do you mean in academia or in industry?

Any. I would prefer accademia as I have mostly been in accademia. But no need to have the grade of professor or lecturer. If I can be a scientist staff for a while, I  haopy.

I suggest using the experimental method to answer your question.

I know nothing about your field, nor the general expectations there, but you've clearly been active. "Only 5" may be an overly pessimistic view.
The way to know whether you are employable either in academia or industry is to apply to a few places. Don't wait until your postdoc ends, though. And gather colleagues willing to support any applications.
If your field requires extensive lab equipment in order to do research, then you might be limited in the places that you can work, unless you have a way to fund that equipment through grants and such. So, you might also think about how you should go about that. Bringing a grant with you to a new job is definitely a plus in the hiring process for most purposes.

A couple of peer reviewed articles per year sounds a respectable record. Why doubt yourself? Equally, why assume anyone can predict your future on so little information? What interests you? What path do you wish to pursue? What makes your work important? Are you a good person to have in a team? Do you need support from others or do you give support to others? Does academic prestige matter more to you than money? All these questions, and more, need answering before anyone can see or assess you properly.


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Possible options for an unhappy graduate student
I am a first year PhD student in Mathematics at a US university but I cannot adopt myself to the environment of my current program. I feel this program is not right for me. Unfortunately, I have to stay in this university for at least one more year because the deadlines of application for most of the universities I want to apply to are already over.
Is it possible to quit the program after one year if I have good standing and possibly ask for a recommendation from the professor whom I have classes with?

https://academia.stackexchange.com/questions/82681/phd-candidate-to-resign-and-reapply-asking-recommendation-from-thesis-advisor

You want to be discussing this with your faculty advisor. Assuming you have one and have a good relationship with them.  You may get some useful advice. Maybe your current situation is not hopeless.  Or maybe you do need to make large changes. But your prof will have knowledge that you don't. Especially on how not to burn bridges behind you.

You are not required to stay at your university until you get a position in another PhD program.  You can get a job instead.  At the moment, they are plentiful.
Yes, you can ask for recommendations.


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Second PhD or MSc if one requires more research experience in a field
I have a PhD in agronomy. I now want to get more hands-on experience in  plant breeding. Most post doctoral positions I see require applicants to  have graduated no more than 2 years before applying.
I don't fit into this category as I have graduated long after the past 2 years. Do I apply for another PhD or a masters instead, to enable me to enhance my research skills in this area?

I wonder what other paths you might have to a full career. Both of those seem sub-optimal.

Preferable would be a postdoc in a close to relevant area that overlaps with your new and old interests, more so with the former.
While earning a second PhD or MSc can have benefits, they will usually not outweigh that of a PostDoc. It is not uncommon to change your field slightly when doing a postdoc.
Perhaps a research job in a company in the industry can give you the experience you seek? I would suggest getting in touch with a career counsellor to discover your other options as well.

Somewhat typically for this SE, the answer is "Just do it". Don't know how approach your advisor? Just do it. Don't know how to write a proposal? Just do it. Don't know how to do more research in X? Just do it. Formalities are important to observe for a career, but they are still secondary to the substance of your work.
You have a certain skillset, and a desire to do things outside of it, as is common in academia. Landing a job is a mutual thing: there is something of value to the employer (your skills), and something of value to you (getting paid and learning). Your background seems to overlap sufficiently with the desired target, so there seems no reason to get more formal education full-time. Find a group that does what you want and at least a bit of what you can do (or feasibly has a need in that) and apply there. Education-wise... one might end up getting certifications along their career path, but getting stuck in school perpetually is just no good.


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How do I know the impact factor of a certain journal is true?
I am new in publishing, I have never published a paper, and nowaday there are too many online journals. That made me suspicious about their reputation, and it is not easy for me as a beginner in publishing to decide whether they are faithful about their impact factor or not.
Let me be precise, I wonder if anybody know about this journal? it says it has impact factor 2.31, can anyone please confirm that?
If you believe this is not a correct place to ask this question can you please tell me where should I ask?

Recent Science (the published of said journal) is on Beall's list: http://scholarlyoa.com/publishers/ and could be considered predatory. Avoid. I also did not find the journal on Thomson Reuters master list (which is the "official" impact factor as I understand it). See also http://en.wikipedia.org/wiki/Journal_Citation_Reports

See http://academia.stackexchange.com/questions/101/how-do-you-judge-the-quality-of-a-journal

I double checked. The journal "International Journal Of Mathematical Sciences" doesn't exist on JCR, hence has no impact factor assigned. There are 4 journals with "mathematical science" in the title, and the highest has impact factor of 1.52 (COMMUN MATH SCI). Avoid!

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Time to decision/uncommunicative Journal
My co-authors and I submitted a paper to the Journal of Ichthyology and Herpetology at the end of February. We have not heard anything from them about the stage of our submission in the review process, despite an email to the editor at the beginning of April. We have only gotten a response from one associate editor after a mass email to them in an attempt to find out if it had been assigned to someone. At this point, we are over the average time to decision that the journal themselves highlights (http://www.ichthyologyandherpetology.org/blog).
Does anyone have experience with the recent publication process of Ichthyology and Herpetology/Copeia, or attempts to communicate with them? The most experienced PI on our team is growing increasingly restless with them. My worry is that even if we tell them we are retracting the article, they won't acknowledge it.

This seems like a question so specialized that the likelihood that anyone here actually knows is approximately zero.

Also related: Do I need to wait for a journal to "consent" to paper withdrawal before submitting elsewhere?


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How do I systematically identify and select literature?
I want to do a content analysis on particular content published in current textbooks in my discipline specific to my country. For example, Canadian political science textbooks.
I’m not sure how to systematically identify and select the textbooks.
One article with a similar approach used best-selling textbooks in their country within a given time period, then analyzed particular content published in the textbooks for their analysis.
Is this a good approach? Or are there better metrics to determine leading textbooks specific to a discipline and country?