text:
Can I apply to other postdocs after accepting an unofficial postdoc offer?
I am a PhD student in Applied mathematics. I submitted my PhD thesis (not yet defended) and am applying for postdocs. Until now I have gotten two unofficial postdoc offers: the PIs unofficially informed me about the offers mentioning the salary and duration. I accepted one offer by emailing the PI. However, I have not signed any contract yet. Till I get an official letter can I also apply to other places?
Any help/suggestions will be useful. Thanks in advance.

Do you want to keep applying because you would prefer another position, or because you are worried that the first offer is not official and might not happen? In other words, if you get another position which one would you take? In my experience the informal answer for a postdoc contract can be trusted, it's just that it can take time for the institution to issue the formal contract.

@erwan: thanks. It is the second one: it is not official. I want to go to that position which I accepted by email.

Till I get any official letter can I apply to other places also ?

Depending on the laws in your country, it is likely that you are allowed to do so without breaking any law. However you should be very careful about damaging your reputation in case you end up committing to several positions.
In my experience, in academia an unofficial commitment can be trusted and official paperwork can take some time to be issued. This depends on many things obviously, in particular how much you trust the PI who offers the job.
Since you mention that your main concern is about having a backup plan, I would recommend inquiring with the future PI (or the administration of the future institution) about their administrative procedure. Why not also mention to the PI that you are considering other offers? This could motivate them to speed up the process. And in case you feel that they are stalling, then you have a good reason to look elsewhere.

@NajibIdrissi fair enough, I updated my answer accordingly.

In my experience, in academia an unofficial commitment can be trusted — In my experience (in the US), the intention behind a verbal offer can almost always be trusted, but sometimes things go wrong. Which is why my experienced colleagues phrase their verbal offers very carefully, and why I advise my studetns not to “accept” anything less than a formal written offer.

@Erwan: In order to join the accepted postdoc phd thesis needs to be defended. In our country thesis is sent to two reviewers (one in country and another outside). Till now one review report has come, another is pending. All these procedure can take some time. In that time I want to apply for other places also.

@RIchardWilliams: actually it's fairly common to start a postdoc position even before defending the PhD, provided the defense is planned soon; this depends on the rules and usages in the institution and on the agreement of the PI, of course. Usually administrative constraints are not the main issue, what matters more is to make sure that the time frame is right: can you be available when the contract is expected to start? This can sometimes be negotiated, you can ask the PI.

Until you have accepted a signed offer in writing, you don't have a job and should continue to search for one.
If you've verbally accepted a verbal offer, you are free to continue to be cautious and continue to search, but you might want to prioritize accepting the eventual written offer that matches that verbal offer.
Of course they might send you a written offer that differs significantly from that verbal offer, in which case, feel free to decline it.

How important is your personal honor to you? How important is your academic reputation? I strongly recommend that you consider your acceptance as final, even though not yet legally enforceable, unless you come to an agreement with the PI in question that you want to withdraw "firm" acceptance until such time as the arrangement can be made official.
The proper (ethical) course of action is to communicate with the PI. You don't want to get a reputation that your word can't be trusted. Nor that you are willing to leave others "in the lurch" while seeking personal advancement. The negative consequences can all be on you and your academic reputation.
Of course, the PI can than withdraw the offer altogether if you don't come to agreement, so state your case carefully. But there is nothing unethical about changing your mind and communicating that to the PI. You just need to try to work out a suitable accommodation that is acceptable to both.
However, if you consider yourself bound, the only downside of looking elsewhere is that you may be wasting resources of the places you apply to. It may provide backup to you, but it would also be good to be honest with those new institutions that you are in the final stages of an acceptance. But then, if you get a new offer, you are in a deeper bind, unless the earlier offer wasn't as serious as it seems.
When you get such an offer it is even better to be clear in your intentions. If you are a bit tentative and feel at risk, you can say that the offer seems acceptable, but that it needs to be official before you can really accept it. In such a case you are clearly free to continue your search and even accept another offer. But even if you say that you would accept it if offered formally, you have given your word and shouldn't go back on it. But in this latter case you need assurance that it will be offered formally.
Consider for a moment the opposite situation in which they offer you a position verbally, which you accept, but then they continue their search without notifying you that it isn't really an offer. Suppose they then hire someone else instead.

No idea why this was downvoted. Sometimes it makes me sad how much push-back there is on academia.se to basic ethics. We see it also in answers regarding why cheating is bad.


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How commonly do researchers spend a long time (>10) years on soft money?
In Academia, a soft money research position is one where uncertain money comes from an external source.  The employee or xyr supervisor/boss might need to secure funding every couple of years or so, in order for the position to continue.  The way out would be tenure or a government job.
An obvious soft money position is the post-doctoral fellowship, but many post-docs might not find a faculty position directly.  For example, if the University of California at Los Angeles (UCLA) advertises a soft money assistant researcher position, they have a defined path of promotion steps.  UCLA defines four steps of assistant researcher (2 years max), three steps of associate researcher (2 years max), and nine steps of researcher (3 years max until step IV, possibly indefinite from step V).   If coming in at step I of assistant researcher, it might, theoretically, take 4*2+3*2+4*3=26 years of positions in steps of 2 years (first 14 years) and 3 years (last 12 years), until one might be appointed indefinately, if I'm reading things correctly.  Needless to say, not ideal from an employee's point of view.
Although time-limited positions and soft money might not mean exactly the same thing, I suppose they often go hand in hand.  That raises the question: how common is it for researchers to spend a long time, say more than 10 years, in soft money positions?  It's one thing to "drop out" of Academia when finishing a PhD at 28 years, it's another thing to move from postdoc to assistant researcher to associate researcher, only to finally discover, at age 45, that you're not good enough for tenure, and lack the necessary skills and experience for a teaching position.  Oops.
In Science, Technology and Engineering (STEM) fields in the USA and Canada, how common is it for researchers to spend more than 10 years in time-limited soft-money research positions?

My bad. Deleted the comment.

The way out would be tenure or a government job.

There seems to be a misconception here, namely that tenure is necessarily a way out from soft-money positions.  Instead, it's possible to get a tenured soft-money position.  This means the university provides no salary or other funding (which are supposed to come from grants), but they can't decide to eliminate your affiliation with the university.  This is obviously not as secure as being paid by the university, but it still means something.  Controversial research can't be held against you, and the department can no longer decide you don't meet their standards.  (The latter is actually a genuine risk.  Sometimes someone is allowed to hang around in a soft-money position for many years despite not being respected by some of the department, because nobody cares enough to try to get rid of them.  Then one year a new chair comes in and decides to clean up the department by imposing higher standards.)
Most soft-money positions do not lead to any sort of tenure, and it's rare to have an "up or out" scenario in which someone must achieve tenure or leave.  In particular, the scenario described in the question, in which someone pursues a soft-money position for twenty years and is then denied tenure and forced to leave, is not standard or common.
In particular, I don't think the UCLA positions the question links to are "time-limited" in any harmful way.  My reading is that once you reach Researcher V or above, you can sit at that rank indefinitely.  The time limits on lower levels ensure that junior researchers will get periodic raises and titles the reflect their increased experience.  There is no tenure in this career track at UCLA; there is periodic review, but I'd guess that it's not particularly severe (intended to make sure people remain productive, not to weed out otherwise promising researchers).  It's certainly not a career track with anything like the security or stability of a tenured position, but aside from that it looks pretty reasonable.

In Science, Technology and Engineering (STEM) fields in the USA and Canada, how common is it for researchers to spend more than 10 years in time-limited soft-money research positions?

It varies enormously between fields and departments.  In medicine, soft-money positions are pretty common and they can be prestigious and relatively secure.  In mathematics, very few people support themselves entirely from grants.  In computer science, it's in between.
As a rule of thumb, in the U.S. long-term soft-money positions are not a route towards a tenured hard-money position.  It can happen, but this is not the typical or expected outcome.  Instead, they are a parallel career track.  One way to gauge how common this track is at institutions you care about is to look at departmental directories and count titles like "researcher", "research associate", "research scientist", etc.

That's an interesting answer. I should also add that we academics tend to get a bit obsessed with formal tenure. Having a job that is basically secure but you get reviewed every other year before your contract is renewed isn't bad at all in terms of job security when you compare it to most jobs in industry.

A good example of a soft-money with tenure is Woods Hole Oceanographic Institute (WHOI).  Their faculty must both build a tenure case and raise money to self-support and support their engineers and technicians.  WHOI is an example of an institution that uses pooled-risk and bridge funding to make things less precarious for their soft-money PIs.

@xLeitix Is it?  Would it, for example, be possible to get a mortgage, if you cannot show an indefinite employment contract?  (I know that in Germany, for example, it isn't)

@gerrit I don't know the german rules specifically, but I know plenty of people that bought a flat / house while on temporary contracts (in Austria, Switzerland, Netherlands, and Scandinavia). I don't think that none of them needed a mortgage.

@gerrit xLeitix's comment has a double negative so I think he means that they did need mortgages.

In the US, you can get a mortgage by showing an income stream that will meet the mortgage requirements. With a big enough down payment, you can even get a mortgage while on unemployment. Most US jobs have no contract and can be lost at will, so the banks don't tend to care about the length of your future contract (which would be 0 for most people). I was asked for proof of current employment, a copy of my pay stub and a list of all jobs for the last two years. But, the US home loan market is (was) quite a bit easier than the German market.

In the U.S., at least, long-term careers on various forms of "soft money" are a lot more common than it looks from inside the "core" academia of graduate school and tenure-track faculty positions.  In reality, the research ecosystem is very complex, with all sorts of niches that aren't necessarily apparent from the outside.  My own experience as a grad student was that I didn't even know any of these options existed until a colleague reached out and invited me into the non-traditional side of academia.
I know of many people who have had long and fulfilling careers, all the way to retirement (if they ever really retire), entirely on soft money.  Some of them have been with a single university or company for that entire time.  More often, they shift around from position to position over time, between university, government, small company, large company, consultancy, foundation, non-profit, standards organization, etc., in patterns dictated by the evolution of those organizations and how the research opportunities are shifting.  Unlike with postdocs, this often doesn't require moving, particularly near a high-tech hub: Boston and the Bay Area are obvious examples, but many large cities have research sectors that interact with the local universities in all sorts of non-obvious ways.
The distinction between "soft" and "hard" money is not always as obvious as it appears, either.  For example, there are organizations that pool soft-money risk, or have core positions that are effectively hard because they are pooled between many external grants.  Even university professors can often have the option to "soften" their positions by buying out of teaching responsibilities.
From my experience, it seems that there are three main classes of soft-money researcher, showing up in all of these environments:

Primary investigators: just like normal faculty PIs, but with a higher cost and no teaching commitments.  A PI who can establish a strong research direction and funding stream can hold a position nearly as secure as tenured faculty.
High-skill implementer: these are people who don't necessarily lead their own projects, but who work full-time for PIs in executing projects.  Engineers, analysts, programmers, lab technicians, etc.  Really good implementers are always in high demand for research, and can have a long and productive research career when teamed with the right sort of PIs.
Exploited labor: these are either implementers who haven't developed/proved their skill, people trying to become PIs who haven't made it yet, or researchers who are stuck in an exploitative environment.  This is the type of soft money that seems to be most common in certain parts of traditional academia and can be "eternal postdoc limbo" (or its fake-hard-money cousin: "adjunct faculty limbo").  Unfortunately, it can often be hard for a researcher to tell if they're in this category and whether it's a passing stage or a trap they need to break out of.

Life in these worlds can be very different than in the teaching-centric parts of academia, but an awful lot of interesting things happen in them, and it offers much more variety in career options for a graduating Ph.D. with an inclination to research than I think most people know about.

In central europe, things look much the same as jakebeal explains in his strong answer. In reality, I think only a small minority of academics actually follow the theoretical trajectory of "PhD student - [short time as postdoc] - junior prof - tenured prof" around here. A simple reason for this is that the notion of tenured-track "junior professors" (whatever this position is formally called differs from country to country) is in fact a new-ish invention around here, and actual positions of this type are still very, very rare. My alma mater with more than 100 CS profs. had less than 5 calls for single tenure-track CS positions lifetime.
The career trajectory of an academic in central europe is generally much less standardized. The first step is always doing a PhD, but what comes in the next 10 to 15 years is different from candidate to candidate. Common career stations seem to include: (1) traditional postdoc positions, (2) working as a senior postdoc / soft-money PI (3) spending a few years in related industry, (4) founding your own startup (and, often, running it into the ground :) ), (5) working as a research scientist in a government or industry lab, or (6) going abroad (to the US or asia) for any of the options 1-5.
Some will then, after spending 10+ years in a combination  of the options above, directly re-enter the regular university system as a tenured (full) professor. The majority, of course, will at some point before that drop out of academia entirely (e.g, their startup succeeds, they find work in industry more fulfilling and better paid, or they simply decide that their research isn't good enough to have a real shot at professorship).

From the sample of my colleagues (in Germany, math), I have no people following (3) and  (4) but a substantial number of people following (7) tenure-tack or non-tenure-track junior prof.

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How can academia defend itself against journal website hijackings?
This is fresh off the press:*

How to hijack a journal. J. Bohannon. Science 350 no. 6263, p. 903. 20 November 2015.

I just saw it and I find it intensely worrying. In short, it appears that scam attacks on legitimate journals are now going beyond fake websites of the form 'sciencernag.com', to actually taking control of the internet domain name of journals.
The symptoms of such an attack might look something like this: you want to submit a publication to this hot new open access Journal of Scientific Results your collaborator just told you about. You look for the journal name on Google and you click on the top result. It looks essentially fine: correct website feel, new papers on the front page, etc. Out of curiosity, you might wander over to Thomson Reuters to see what they say about JSR, and maybe even notice that the website listed is the one you just went to. So you go over and you submit your paper, and when they ask you for article processing charges you might go ahead and pay them.
However, the journal website is in fact in control of a group of scammers, through a combination of means apparently to do mostly with the jittery ways in which the administration of web domains takes place. (The true JSR might be at a new website, trying to draw traffic there but powerless to stop the new owners of the domain.)
This sort of attack seems pretty much impossible to avoid as a reader or author caught unawares. (This is unlike, say, falling in the hands of a predatory journal, where much can be done by consulting Jeffrey Beall's list of potential predatory journals and publishers.) Bohannon's piece suggests that to verify the authenticity of a journal website against such an attack, a cautious visitor might try the following.

Dadkhah suggested two ways to spot a hijacking. First, check the domain registration data online by performing a WHOIS query. (It's not an acronym, but rather a computer protocol to look up “who is” behind a particular domain.) If the registration date is recent but the journal has been around for years, that's the first clue. Also suspicious is if the domain's country of registration is different from the journal's publisher, or if the publisher's name and contact information are kept anonymous by private domain registrars.

This seems incredibly onerous to me. It might be justified if one is about to fork over manuscripts or money to a smaller journal, but it's definitely much more sleuthing than I'd find reasonable for just casual browsing. However, it's not clear to me that there are any surefire alternatives to this (and even then, WHOIS queries can only run up suspicions, but they might miss e.g. what happened to Acta Physico-Chimica Sinica). Bohannon has provided a list of hijacked journal websites as supplemental data to the piece, but this is not necessarily complete and it would need someone curating it with a dedication to match Beall's to keep it updated.
I'm asking this mostly to raise awareness, but I do have a genuine question. Are there methods and institutions within academia that could be used to prevent or hinder these sorts of attacks? This sort of thing is probably not new in business, where it is very often sink or swim for companies (so there is more awareness that you need to protect your brand against things like this) but there is also more scope for companies to reinvent themselves (whereas it is very hard for an academic journal to change its name or website and expect their entire community to be aware of the change, unless it makes a big splash like the recent shift in Lingua did).
So academia has its own particular weaknesses to this sort of thing, but we also have a bigger set of structures and institutions that can work to prevent things like attacks on reputation from working. (In fact, it is the fact that one of these mechanisms - the Thomson Reuters listings - has failed that makes this such a serious thing, even if the actual scope is probably still relatively small.) What broader tools could we as a community implement to try and hinder this sort of stuff, and how would those mechanisms look?
* So hot off the press, in fact, that it was published in the future as of this posting.

It seems to me that this is a problem for any business/institution/organization with a website - if so, I'd wager the same techniques they use (good organization security, preventative measures, etc.) apply.

Those are techniques for individual businesses, though. On a broader scale, the business community simply lets careless organizations die. Taking that viewpoint means that even a small, new, creative journal gets judged by academia not by its academic proposals but by how well it navigates the thornier sides of the internet, with no backup from the community. I'm not sure I'd like that sort of world.

Have you seen the Target/Home Depot/OPM breach? It's a problem that affects organizations of all sizes - from your mom-and-pop DIY-website to major corporate entities to governments.  I don't much like it either, but it's a heckuva lot harder to secure something than it is to break it - ask any 3-year-old who breaks a toy and then wants to put it back together :) I agree though - it's a scary world.

I might add - if your question is "how can the broader academic community protect the integrity of specific journals", that may be slightly more feasible/pointed.  But protecting all journals, new and old, big and small? It's going to be thorny at best.  Grouping them together under a larger org like the IEEE or ACM helps, but it's not a panacea.

I did indeed see them, but these are attacks of a different kind - not usually an actual electronic hack, but mostly a social engineering scam much more akin to the ones that get you to hand over money and papers to a phantom conference that never happens. These are targeted against academics and they work (or they work particularly well) because of the peculiarities of the field. And similarly to predatory publishers, where we can and need to create mechanisms to limit the damage, I feel that we also need to limit the ways in which how we run business helps these groups.

I'm voting to close this question as off-topic because this is a boat-programming question about domain-name security and phishing.

There is nothing special about a publisher's domain being hijacked compared to, say, any other online retailer. Indeed, it's probably far less lucrative to do, because only a very small proportion of visitors to the site are there to spend money, as opposed to reading articles (which is unlikely to work on a scam site, thus exposing it rapidly). I don't see that there's anything unique to academia about this, so it may be off-topic.

I disagree with this closure for the reasons I've already stated, but I guess burying our heads in the sand and ignoring the problem is also a workable solution.

What broader tools could we as a community implement to try and hinder this sort of stuff, and how would those mechanisms look?

In the long term, if we reduced and eventually eliminated our dependence on commercial publishers, and worked towards a future where all scientific research was free to everyone everywhere, then we would eliminate any possible financial incentive for scammers to hijack the process.

I'm not sure I agree. The incentive is there as long as any money changes hands (including advertising and APCs), and it doesn't go away even if the articles are free to read or even to reuse. I was looking for slightly more realistic, mid-term solutions, though.

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Do Nature journals wrongly claim copyright in their published pdfs?
I just noticed this and I'm slightly confused by a small detail.
The Nature Publishing Group states in its Publishing Licences page that the copyright on articles remains with the author:

NPG does not require authors of original (primary) research papers to assign copyright of their published contributions. Authors grant NPG an exclusive licence to publish, in return for which they can reuse their papers in their future printed work without first requiring permission from the publisher of the journal.

Moreover, this is supported by the Licence to Publish agreement, which explicitly states that

[...] the Authors grant to NPG [...], subject to clause 2 below, the
  exclusive licence (a) to publish, reproduce, distribute, display and store the Contribution in all forms [...].

and

Ownership of copyright remains with the Authors, and provided that, when reproducing the Contribution or extracts from it, the Authors acknowledge first and reference publication in the Journal, the Authors retain the following nonexclusive rights: [...].

However, the published articles have a clear Macmillan copyright marker. Taking this paper as an example:

Is NPG wrongly asserting copyright to the entire article? It is my understanding that they could still be claiming copyright over the copy-editing and formatting, but since they have explicitly opted for a licence to publish instead of a copyright transfer, it seems to me that they should be crediting the authors with the copyright, e.g. along the lines of

© 2015 Qian Wang, Edward T. F. Rogers, Behrad Gholipour, Chih-Ming Wang, Guanghui Yuan, Jinghua Teng and Nikolay I. Zheludev. All rights reserved.

for the above-quoted example, with whatever legalese they felt necessary to indicate that they own the exclusive publishing licence.
Is there some interesting detail about copyrights that I'm missing here? Or is this simply a fudge?

I understand that this is not a big question and that it is on the edges of this site's purview, but I still think it is interesting. If the community decides that this is too much on the legal-question-answerable-only-by-a-lawyer, would migration to Law Stack Exchange be appropriate?

I read that as only asserting copyright over the other content on the page (the site header and footer, links to other articles, etc).  For the paper itself there is a "rights and permissions" button that seems to explain the copyright status of the paper more clearly.

Hmmm, you mean "Copyright © 2015, Rights Managed by Nature Publishing Group" here? That is pretty ambiguous, I would say. The copyright mark on the website footer could be interpreted either way (compare with the much more detailed markings on the SE network), but the example I give is from the pdf, which does seem to assert copyright over the entire work.

@NateEldredge I reckon they're claiming copyright over the whole page.  Not the article as such but the presentation of it.  Consider that many publishers won't allow you to self-archive the post-print without paying for full open access.

I think this is a question where all we can say we are not lawyers, and few of us has detailed knowledge of (international) copyright law that one seriously can argue. If you have a practical problem eg uploading the paper to an archive or reproducing others figures, the most fruitful would be first asking the publisher about the specific issue and what they mean by these copyrights.

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What solutions exist to store data in text files and future-proof against tampering?
A recent question in Information and Security Stack Exchange,

How to know whether a textfile has been edited or tampered with

raises a very good point: if one wants to archive experimental data in an open, text-based format, in the long term, it is desirable to have tools to prevent the tampering of the files, or at least detect the tampering if and when it happens.
The answers at infosec are good, but they feel somewhat abstract and hard to implement for a busy PI whose hands are already full trying to run a research lab. It may be, on the other hand, that solutions already exist that fulfil at least some of the requirements, or that they will appear not too long in the future; it's certainly reasonable to suspect that some form of tamper-resistant data or lab-book signature scheme is already in use at least in commercial research organizations.
This question is relatively hard to pose correctly, as there is an inherent vagueness in the requirements, and it is probably better to keep it general. The main problem is, given a set of text-based data files, how to signatures, or similar devices, that can be used in the future to provide guarantees that the data has not been tampered with. Are there any specific solutions that will do this in an accessible way?

Do you want to track changes (see: version control) OR do you want to ensure that a file is unaltered (e.g. due to malicious users, connection failures; see: md5 checksum)?

Also, if you haven't taken it into consideration for the storage, you'll want to look at ways to avoid/detect/correct for data rot.

I don't have anything particular in mind - I mostly think it's an appropriate time to have a parallel thread here to the InfoSec one, focused more on usable solutions than abstract signature schemes. I think both tamper-detection and change tracking solutions would be interesting in this context.

@E.P. What is your question here that is about academia?  This seems to me to still belong on infosec.

@jakebeal I suspect there is or will develop a market of tools geared directly at academics; in any case, as I said, academics tend to need plug-and-play solutions rather than abstract schemes that one could potentially implement oneself. In any case cf. this or this questions.

I'm voting to close this question as off-topic because it is a question about information security, no part of which is specific to academia.

@PiotrMigdal, MD5 has been broken. Not enough to be able to doctor text files, but anyway. Use something else. You'd need a digital signature, like PGP or GPG offer.

Wow, you guys really are harsh.

In addition to good recommendations on the InfoSec SE site, some of which are not that difficult to implement (for example, digital signing), I would suggest another rather straightforward solution (unless your data is extremely large or extremely sensitive): simply use one of Git repositories, such as GitHub or GitLab, or research data repositories, such as Zenodo or figshare.
Git and Git-based services now support large files, plus you will have an added benefit of versioning for data files that you can match with your research workflows to enable reproducibility.
Check my related answer on some arguments for potential preference for Zenodo vs. figshare.

A private Github repository (they are in general very inexpensive) is my method of choice. They 1. Can be funded by your department with most likely no objections to the cost, 2. Allow for versioning of files with timestamps and version comparisons, 3. Offer collaboration features for your colleagues and have access controls if need be, 4. Are hosted so you don't have to worry about backing up data, 5. Are private to only the collaborators and can be made public if you feel like it. However, Github and similar services are don't work well with non-text data (no file diffs can be done).

@ChrisCirefice: Private repositories is what I implied in my answer (and, BTW, research data repository services offer them as well). As for diffs for non-text (binary) data files via Git services, your statement is not exactly true: 1) you can use Git attributes (see "Diffing Binary Files" on this page); 2) for image files, there are various approaches, such as GitHub's built-in one or this one.

The OP explicitly asks about text files, so Github should be good. Plus: I wouldn't trust any file format other than TXT and CSV to be legible in the long run. File formats change. Worst of all are proprietary file formats where you may not even have the necessary license in five years. Bottom line: store everything possible as TXT or CSV.

Unfortunately, using GitHub isn't really a long-lasting solution. It only lasts as long as Github's servers do, and depending on the success of a corporation isn't exactly future-proof.

@RogerFan: Your point is valid (in the context of long-term preservation). However, there are, at least, three approaches that alleviate the problem: 1) instead of hosted cloud versions, use of on-premise versions, i.e. GitHub Enterprise or GitLab EE; 2) deploying archiving solutions to several solid cloud infrastructures, i.e. Amazon Web Services, Microsoft Azure and Google Compute Engine, and keep data in sync (chances of all three companies disappear are pretty slim); 3) use Zenodo, which is built around CERN infrastructure and backed by EU, which guarantees the long-term data preservation.

A common tools for checking data integrity is to use MD5 checksum. If you have unix-based system, you can do it form command line:
$ md5 some_file.csv

or (md5sum, depending on your system).
It gives some hexadecimal number (like dc50353b4a1e5d99cb49b65e33b18916) which will (almost certainly) change with any changes to the file.

The only problem with this is that you need to maintain a reliable  and trustworthy way of disseminating the correct hash to end users. In this short term this is pretty easy, but if you want to archive data for potentially years or decades it can be difficult.

@RogerFan Short term: just put md5 on your website. Long term: same, but in archive in which you are storing your data (and which archive is good is another question).

@PiotrMigdal: Storing md5 hashes where you store data files is akin storing keys in the open in the vicinity of locks they protect. Bad people can simply tamper data files and then regenerate corresponding hashes and replace the original ones with them, all in the same archive. Unless you track filesystem changes, you will have no idea that the data files have been tampered.

@AleksandrBlekh No, it is not the best analogy. Unlike keys, you want to have as much people having a copy of it (which, in short, is the only way to ensure it is uncorrupt). And if you put your md5 hash in article (publication) content, or some text, it is much more likely to be cross-archived that a (potentially big) file. What is ironic, git does not protect against malicious use (one force-push and you are done).

@PiotrMigdal: I agree - it is not the best analogy. However, I was just trying to make a point, which, by the way, assumed a centralized archival solution (perhaps, I misunderstood you, as I thought that was your assumption). Anyway, it seems to me that the solution you're talking about is distributed and, thus, IMHO might be implemented, using blockchain technology. As for potential malicious use of git via force-push, I don't understand how it could be malicious, if all repository operations are logged.

something... something... BLOCKCHAIN?


text:
Does Hill University (USA) have legitimate accreditation?
I need to know if Hill University is accredited. Especially in the field of MBA degrees.

Why do you say "Hill University (USA)"? I don't see anything on their site that suggests any particular connection to the United States.

It's a diploma mill. Don't waste your time or your money.

The Hill University's, website dead as of Sept 2015*, accreditation page did not make it clear which of their degrees were accredited, instead the two accrediting bodies (IOEAB and OKOLA) are listed at this random website as "fake degree accreditation agencies". They are also the accrediting agencies used by Speedy Degrees which would suggest to me that accreditation by those bodies is more or less meaningless.
Further, the web domain is .com and not .edu which is highly atypical for US universities. The requirements for .edu domain require a US location and "proper" accreditation. While not using a .edu domain could be related to the online nature of the university, it is also a warning sign that the accreditation might be questionable.
* Recent reports by NYTimes and UIUC list this university as a fake.

Their webpages also use stock images, another strong indicator of an unaccredited degree mill.  Google Search-by-Image is one of the easier ways to detect imposter institutions.

In fact, the entire text of that page is clearly plagiarized from http://www.edinburgheducation.net/accreditation.html ... which may itself be an imposter.

It might be the other way round, since the EE webpage mentikns Hill as if they did a faulty search-and-replace http://www.edinburgheducation.net/about.html

Note: .edu now requires "proper" accreditation, but people who had .edu domains before the early 2000s were grandfathered in; .edu doesn't necessarily guarantee proper accreditation.

For what it's worth, it is possible for an online-only university which has a recognized US accreditation to get a .edu domain.  Example.  So the fact that Hill University doesn't have one is more likely related to lack of accreditation than its business model.

A list of accrediting organizations for US universities is available from Wikipedia. Note that in general individual degree programs are not accredited; only the universities as a whole are.

@FerasAlSoufi I suggest doing your own web searches on both the individual behind the first web site you list, and the organizations behind the other three, before deciding.

Please modify the answer to account for what Nate has said.


text:
Lack of undergraduate research experience and impact on PhD applications
I am currently a second year (final semester) undergraduate enrolled in Nagoya University's G30 program. After I graduate, I intend pursue a PhD in the chemical sciences, and I am looking to apply to universities in the United States and the UK. So far, I have been doing well academically--I'm at the top of my class and have cumulative GPA of 4.08/4.3.
Unfortunately, till date I haven't been able to secure any research experience whatsoever in my university, and not for lack of trying. I have approached research groups in my departments whose work I found interesting, but have been turned down by all of them. The rules prevent them from taking on undergraduates students who are not in their 4th year, and they have stuck by them adamantly.
I do get to work on a research project in my fourth year as part of my graduation requirement, however, I do find it disheartening that I can't start early.
Regardless, I am still approaching people, looking for a break and also looking into other avenues outside of university.
However, what if nothing works out--would one year of research experience be sufficient? Personally, I don't think it is enough to prepare me well for graduate school. Moreover, I am concerned about how an admissions committee will view this lack of of research experience?
Additionally, in the UK, most universities that I am interested in encourage applicants to get in touch with faculty/potential advisors before the make a formal application. By my estimate, I ought to be doing this sometime during my third (early 6th semester) year, and thus would have had probably little to no experience conducting research in a laboratory. How can I overcome this potential handicap, and get them to take me seriously?

Keep going at it!
If local colleagues only take students from 4th year onwards, there must be good reasons - like fairness, openness, transparency, risk assessment... Look forward to your 4th year and beyond :)
Also, how typical is your 'lack of experience'? If all students of your 'class' share this, you will not stand out negatively, and PhD recruiters will expect you by default to have limited experience. Then of course if you manage to acquire relevant experience, that will make you stand out from the crowd.
Your question 'what if not...?' seems to go far beyond your original point and your main ambition.
Take it as a game and keep the flame alive. Keep looking for opportunities, and you are bound to find one that will fit your circumstances.
Another way to go at it could be to approach higher education institutions where you would be interested in applying, and ask them what their expectations are in terms of lab work experience.
This way you will have a clear vision of the standard you have to meet to have a good chance of being offered a place, and potentially a scholarship.
You will not have to second-guess what they want any more, and you can focus on achieving what they look for, and more.


text:
My mum was recently diagnosed with cancer. Should I tell my supervisor?
Yesterday, my mum was recently diagnosed with cancer. However, we have yet to know what stage is her cancer and whether the cancer can still be removed from her body or it has metastasized to other parts of organs. This is a major health concern and it will of course affect my health and mental being for the next several years.
I am a PhD student and I thankfully successfully submitted my thesis a few months ago. So far, I have yet to receive the news regarding my viva. Given the history of my university and accounts from other students' experiences, my department is very tardy in processing viva examinations. It can take up to six months for students to finally undergo the viva and then a few months for correction afterwards. Now I have to worry and be stressful for two things: my mum's health condition and my viva.
I want to e-mail my supervisor about the possibility of speeding up my viva process. I have been well prepared for my viva for a month. I have re-read my thesis multiple times and re-read the journals that I cited. I really hope that my department can speed up my viva so I can move on with my life (getting a good job, taking care of my mum, etc.). Delaying my viva will certainly damage my well-being. However, I don't know whether emailing my supervisor will undermine my professionalism (the art of separating personal and work).
I am in my 20s with no experience of experiencing sudden loss of my loved ones and this news will definitely affect me in the immediate future. And I don't write this post to look for sympathy or anything. This news will certainly make me appreciate life and moments that we have now.
Should I e-mail my supervisor to state my current condition and hopefully she could do something regarding my PhD limbo?
EDIT: I do have a very good relationship with my supervisor. However, I don't want to come across as someone who tries to milk this tragedy for my own gain. Therefore, I am juggling the decision whether it will be fine or not to tell my supervisor and at the same time to request viva speed up.

By 'right', do you mean 'by law' or 'by social norms'?

If you don't tell, good chances your advisor will notice that something is going on. Personally, I would like to know, not only because it will have impact on the production, but because I care about my students. I would do everything on my power to help. I don't believe I'm rare in this aspect :)

The question in the title (does supervisor have a "right" to know) is not really the same as the question in the body (would telling my supervisor be helpful).

@ff524 I submitted a revised title.

I had a lot of terrible things happen last month, like my Grandmother dying after being diagnosed with stage 4 cancer, my coworker committing suicide, and my cat dying. I told my Principle Investigator that I've had a lot of crazy stuff going on, and she was so kind and compassionate.

If you are ib  good relation your supervisor will (try) to help. Why not to tell him her that you right want to speed up the process? This is not to ask for marks. It is a complete different story. It can be the case of foreigner with any type of urge and limbo situation (as what country next ? To give an idea. To which school shall I put my son for the next year. ...and so on). All the best.

Many countries have rules in place that allow employees to take paid or unpaid leave to care for an ill relative. No shame or unprofessionalism should result from making a request to accommodate a need to deal with a loved one's illness.
If you have a good relationship with your advisor, then your advisor should understand.
(That said, the advisor may or may not have much control over the viva, depending on who is responsible for scheduling and organizing it, and who else must attend. But you won't lose anything by asking.)

Regardless of whether there's a legal requirement to grant leave, I'm confident that leave will be granted if requested.

What happened/might happen should not affect you severely for several years. If it does affect your mental well-being for more than a few months, to a degree where you are not able to work most of the time, you can and should get professional help, which might even be provided at your university.
Usually, there will be times where you feel fine, and times where you might want to stay in bed all day - therefore it would generally be good that your supervisor knows what is going on.
If it is possible to speed up your process of defending your PhD will depend on local regulations. In your case, it might be best to talk with your supervisor (not just email him/her) to inform him/her about your and your mom's situation, and to see together if there are ways that your supervisor can support you (e.g. by speeding up the final steps required for your PhD). That is, if you have a relatively good relationship with your supervisor.

good, answer, what if students are at the beginning of Ph.D., first year. what would you suggest them then?

@SSimon The same, why should it differ? It might be even less of a problem, because it could be possible to work less for a while, or work from home (depending on the research), to spend more time with one's relatives.

Really? WOW unexpected, since usually there is contract in olace

@SSimon How could a contract change anything?

Personally, I would tell them - just so they know.
They could ask you what you would like to do : earlier date or later date and then see what is possible.
They won't tell anyone else so it won't go public so that is not a worry.
However, Best wishes to you and Mum.

Do not hide behind your problems
If your mum's health directly affects your ability to work and your supervisor notices or will soon notice, explain yourself. Do not make up any excuses, because there is nothing to be sorry for. Just...
State the facts
Tell them what happened and that it is currently influencing you as you are understandably worried. Do not, again, use this to "hide behind", just state it as a fact and mention that you are trying to do your best.
Take the help you are offered
At that point, as you stated you have a good relationship with your supervisor, they might already offer you help or tips. They are a human being, they have been going through one or the other hard situation in their life as well. They are your supervisor, they have an interest in you succeeding.
Ask for help
Some people might be hesitant to offer help. Maybe they just don't know what you need, maybe they do not want to feel that they do not believe in your ability to handle your own problems. Maybe they are just overwhelmed with their own life. If you need specific help from a specific person, feel free to ask. Asking does not hurt. Don't request things (yet), but ask tentatively. Ask for what you can do first, before asking for what they can do for you. Ask "Is there anything I can do to speed up my viva, so I can focus on being there for my mum?"
Request what you are entitled to
If things get worse, you might be entitled to time off to care for a sick relative, for example. Not everybody around you will know that or think of it, so request these benefits when you need them instead of waiting until you are offered them.
But most importantly:
Stay calm
Maybe a long, hard journey is ahead of you. Maybe things turn out better than expected. For now, do not create worst-case scenarios until your mum has a full diagnosis. Also, do not paint worst-case scenarios for others. This might be influencing for years, or it might be a bad scare, but could be over in much less time. (I have seen both happen amongst family friends and acquaintances. Interestingly, the people who were scared most after the initial diagnosis fought the cancer fast and completely in less than 18 months. Some are calmly living with it for years now. I am not trying to play down your worries, but keep an open mind for the good scenarios. That will enable you to be much stronger for yourself and your mum.)

Stay calm.
Your mother has been diagnosed with cancer and that is terrible news. But, I truly encourage you to remain optimistic.
Remain optimistic.
Cancer treatments have advanced significantly and the outlook upon diagnoisis is generally good. (You haven't provided details on the specific type of cancer, so I won't speculate further.)
(In)Action.
At this stage, I personally don't recommend taking any action with regards to academia. Look after yourself; wait for a full diagnosis. Try walking, exercise, or even working, anything that helps you get through the wait.
Viva. You've submitted your thesis. Congratulations! The hard work is already done. The viva process varies country-to-country, so it is difficult to provide specific details. But, the time-frame probably cannot be shortened by much, because time is required to evaluate your thesis (which is probably a long document). Your supervisor might be able to help speed-up the process, but the evaluation procedure is probably conducted externally, so it is unclear what speed-up can be achieved.
Once you and your mum have received her full diagnosis, you'll be able to think more clearly about the future. Perhaps ask another question then. For the moment, stay calm, remain optimistic, and look after yourself.

(Possibly) Going beyond the scope of the question, one can ask: When should I tell my supervisor about a personal issue? I personally recommend telling a supervisor when that issue has the potential to negatively impact your work over a prolonged period.


text:
Do any scientific publishers have a stated commitment to authors regarding copyright infringement?
Within the debate of whether science should move to an Open Access / CC-license scheme, or remain with a more traditional scheme where the authors transfer copyright to the publisher, one argument that gets made relatively often is that the latter provides a better defence against copyright breaches. I would like to know how much this argument actually works in favour of the author.
One good example of this argument is made in the position paper Publishers seek copyright transfers (or transfers or licenses of exclusive rights) to ensure proper administration & enforcement of author rights, by the STM Association, which states among other points that

In general, publishers in the field of science, technology and medicine (STM) prefer assignments over licences, mainly because:

authors are rarely in a position to defend themselves against infringers, plagiarists, pirates and free-riders, partly due to financial considerations; [...]

Thus, an assignment enables the publisher: [...]

to react more rapidly to copyright infringements, unauthorised derivatives and plagiarism;

This position is endorsed, for example, by the IOP, in their Introduction to Copyright leaflet.
However, this argument only works in as much as the interests of the publisher and the author are aligned, which is not necessarily the case.

For one, it may be in the publisher's interest to stop copyright violations agreed to, or initiated, by the author, as in the Elsevier takedown notices to academia.edu last december. (Note, though, that I am not claiming these are wrong or that it is right for authors to violate agreements they have signed.)

On the other hand, if a copyright violation occurs and the author objects to it, it may or may not be a good business case for the publisher to take legal action against it, and the sort of outcomes that will be acceptable to the publisher may not be in line with what the author needs.

Dealing with bad-faith copyright violations is definitely a problem and Open Access is not ideally equipped to deal with them. (That is: if someone brazenly republishes in violation of a CC license (i.e. lack of attribution, unendorsed+unlabelled modifications, commercial use of a CC-BY-NC article, or such), how can the author sue?) However, it's not clear to me that the alternative does work in the interest of the author.
So, my question is: do any scientific publishers have stated policies about their actions in the case of copyright violations, or stated commitments to authors regarding this? It would seem a fair counterpart of the publishing contract, where the author hands over the rights of the text in return for a commitment to disseminate and defend it, but this is not usually how the scientific publishing business works in my experience.
Failing that, I would be interested in evidence, either public, statistical or anecdotal, about publishers' behaviour in such cases, though I know these are not easy to come by.

This is not really germane to your question, but in the case you mention in your third-to-last paragraph, it seemed that the issue was actually that the republication did not violate the CC license (but maybe the author wasn't aware that was the case, and if she had thought more carefully, would rather have published under a license that did not allow such republication).

@Nate I know that case is complicated, but the licence violations I do think may have happened are improper attribution (i.e. lack of citation and licencing status in a publicly-available TOC) and unendorsed modifications. In any case, and regardless of whether they happened in that case, the question stands: if such licence violations do happen, what recourse do authors have to defend their IP and moral rights? And, conversely, (my question here,) does switching to traditional publishing offer a guarantee against that?

@E.P. but that case is not complicated--it is simply a case of authors not understanding the terms of the license.  It is explicitly stated in plain language--not complex legalese--that commercial derivatives can be made.  And this is to the advantage of the author because it means that if you're making, say, a reasonably priced textbook you can put it in there without chasing down the author for permission (it was already granted in CC-BY), thus the author gets more exposure.  If it bothers the author that it also licenses it for an unreasonably priced text, CC-BY is not for them, period.

@msouth I'm taking the reference out because it just clouds this issue. I agree that the authors' reaction was overblown and they should have read and understood the license in the first place. Have you actually looked at the book, though? There is no attribution of the journals where most (all?) of the contained articles appeared. There are also editorial changes w.r.t. the author-sanctioned versions, as I understand it, which are not clearly labeled as such.

I cannot properly answer your question, but: I don't really see a difference between normal copyright and CC regarding bad-faith copyright infringement and plagiarism. CC-license do comply to copyright laws, they just let you decide which rights you want to share with users. The point thus is: is the author backed by an institution (like the publisher or the university?) That can happen or not, and does not depend on the license of the article itself.

Moreover, in the specific case of self-archiving you often have a timestamp of the moment of upload, and that is useful for fighting copyright infringement.

@Aubrey the situation for CC papers is complicated but it is not the question I'm asking here. Timestamps are great if you go to court but doing so is expensive and time-consuming. Publishers claim that their institutional clout can make that easier; the question is whether it does in practice and how formally  committed they are to that defense.

Nicely formulated and interesting question (+1). While I don't have any direct experience to back up my point of view, I very much doubt that publishers have time, resources and, most importantly, intent to react on and comprehensively analyze every potential copyright violation globally across all their corresponding outlets. While @CapeCode's answer is nice (+1), I'm pretty sure that it is more of an exclusion from the typical behavior of publishers. (to be continued)

(cont'd) Stated simply, using the OP's own words, publishers and authors IMHO do not have their interests aligned due to their practically monopolistic influence on authors through establishing their dependence via branding, rankings and other questionable mechanisms. Just my two cents.

Since you also ask for anecdotal evidence, I have a first hand experience with a commercial publisher (Wolters Kluwer) that reacted quickly and professionally to my message reporting prohibited commercial use of my work. This particular journal gives free access to articles after a one year embargo.
An internet magazine based in India copied verbatim large parts of the introduction and abstract of one of my papers with some words in between to try to make it look like an original journalistic report. The 'article' was available for a fee.
Since I formally transferred my rights to the publisher in the author agreement, I really only reported the issue out of interest for the outcome. They took contact with the 'company' that subsequently retracted the content from their website.
I suspect established publishers like Wolters Kluwer have significantly more legal firepower than a one-person operation run from an internet cafe in Hyderabad.

Out of curiosity, how well was your original paper referenced in this 'report'?

@E.P. there was no mention of my paper in the freely-available 'preview' in which I found the lifted paragraphs. I obviously did not purchase the full article (I doubt that there was even one).


text:
What are good practices for sharing protocols online
We're beginning a fairly large effort to share the vast number of protocols accumulated in our lab and pushing them all to the cloud. Naturally, you don't want the knowledge of older graduate students lost when they graduate.
We have had experience with putting all of this information into OpenWetWare but there is a small but non-trivial learning curve with the wiki-format. Another possibility would be to create living documents with google docs and organize the links in a wiki format. Finally, there is always the dropbox method of having a bunch of files in folders. I was curious about good methods to create a repository of protocols.

By protocol, do you mean a lab methodology, or the object you study (as in network protocol)?

Lab method/technique.

Do you wanna make such protocols kind of "living documents", so as to enable peers to improve them along the time?!

Thanks to Stack Exchange, I've recently started to become familiar with Markdown and in particular its variants, including MultiMarkdown and Pandoc. These might be the ideal alternative, as they're very easy to master—after all, it's what powers sites like this one!—and yet powerful enough that it can handle most of your needs.
Individual users can write their protocols in a simple, easy-to-read text format, and then output that to HTML, PDF, Word files, or whatever. Then all you need is a master page to catalog everything, and a web site manager who's skilled enough with a command prompt to handle the conversions using one of those tools. The format's flexible enough to handle hyperlinks as well as graphics with a minimum of fuss.
The other advantage of having a text-based system is that it makes version control very easy as well.


text:
Good practices with lab wikis?
OpenWetWare and Google Sites have been effective strategies in curating lab knowledge. I was curious about what are effective ways to create an effective wiki. Factors include:

Ease of use and low learning curve
Speed of sharing and diversity of shared files
Privacy and protection from sabotage
Organizational flow
Legally sharing papers/manuscripts

to protect from sabatoge, make sure that a login is required.

In addition to @David's suggestion, also only accept connection from on campus IPs (you can usually VPN if you are at home). But for security issues such as this, best thing to do is to consult your local IT department to tailor something to your needs.

In one of the labs (about a dozen people) I work with, we use a MediaWiki install given to use by the university that requires log-in to view everything but the front page or to edit. Although the learning curve is not steep (most people already know how to use Wikipedia) it has been hard to convince the undergraduate lab members to use the wiki. It mostly serves as a place for:

short project summaries (since the lab has many different projects)
notes/minutes from lab meetings, a place to store slides and presentations, and
link repository (for instance I maintain a big collection of links to relevant StackExchange questions).

With a former supervisor, we used to have a private MediaWiki install that was used by a our small group (3 or 4 people). Since we worked on theory/math it contained:

short tutorials on how to do automated calculations as experiments for testing potential theorems (before trying to prove them), and
collection of special cases that we had calculated by hand.

It was relatively well maintained by the prof, and a pretty good guide for understanding some of the work behind his earlier papers.
I also keep a personal private TiddlyWiki, there I keep:

notes from papers I've read (although I am slowly moving this over to Mendeley)
collections of relevant links from the internet
a more structured index of the folders and files on my harddrive (through local links) that is easier to navigate and search than my file system directly.
partial documentation of code and notes on partial results of simulations
administrative stuff like members of mailing lists, and groups I organize.

For me, the most useful was the private Wiki, the second most useful was the small group wiki because of the good maintenance by my prof, and least useful is the large lab wiki.

A wiki is a platform, which you can use in whatever way you see fit. Personally, I've used them academically for the following purposes:
Lab notebook
I was running cognitive psychology experiments on subjects. I would make a top-level page that contained links to a separate page for all of my research projects. On each research project page, I had links to separate pages for each of the following:

Study protocols (behavioral testing, brain scanning, data cleaning, data analysis) - separate pages for each
Change log to the paradigm itself
Troubleshooting notes... as I encountered problems, write them down here
Subjects (one page per subject

Each subject page contained notes on each session, results, general info ("subject performed poorly today, possibly due to stress from midterms"), as well as the results of their data analysis.
Publication repository
This wiki was basically a place for me to store papers. Many wikis allow embedding of pdfs, and I would store pages as follows. The top-level page segmented topics. Each topic page contained links to pages about individual papers, as well as links to ongoing summaries of my reading. This was where I would write down my thoughts and conclusions after reading papers, and made it easier for me to combine my thoughts on multiple papers... after reading a new article, I would review what I had written there and try to somehow incorporate the new article in my ideas (if relevant, more often than not it wasn't).

These are just two ideas, and they were just used by me, not my whole lab. I'm sure you can think of more (managing lab meetings, managing collaborations, managing lab-wide protocols, etc).


text:
What can be done to possibly avoid corrupt practices in the blind peer review process?
During my short career as a researcher I observed a few seemingly unethical behaviors by Editors and Associate Editors:

being asked to include a particular new author in order to be accepted
being asked to cite articles with no apparent link with my article
being told by the conference TCP (one of the top conference) to reject all the articles I review
In one unique case, I reviewed an article and recommended strong rejection, it was subsequently accepted without revision. Reviewing the authors profile and handling editor, I found one of the author is an Associate Editor for another journal. It appears that both help each to publish articles in their journals.

All the above experiences were observed in well-reputed journals and conferences. Given all this, how what can I do to "clean this mess" in academic the journal/conference review process?

How do you deduce that I want opinion or discussion? I want to hear the answers from other members.
By the way instead of closing you can make edits in my question.

@Monika agreed! in addition of over controlling students. I know few professors from developed countries who offer money from project funds to students from country like india, pakistan, bangladesh etc. to include their name in article. Paying 200-300USD from project and get thousand of dollars incentives is a good business.

To prevent this question from being closed as "being a rant," you might want to edit the title of the post to something like "What can be done to possibly avoid corrupt practices in the blind peer review process?"

@St.Inkbug it is specific question and if you scroll down I have answered and asked community to provide their opinion. I can see the opposition is coming from the editorial board members. I am also AE of few journals now. If you we don't stand and clean up this mess, then this whole system will lose its credibility. Its not atypical you can see other community members do agree and experienced similar corruption.

@Monika this nexus is strong :)
This question is voted to be close soon.

OP has absolute right to share his/her story, and I hope they do it. However, SE is not a blog for sharing stories. This is a Q&A forum, and this story is not a good Q so far.

@Monika if you agree with this question, then please vote for reopen.

No-one said OP's story is not important. It is very important. But OP does not have a clear, answerable question here, so it does not fit SE format. If OP can turn their story into a question, it will be welcome here. But I am not OP and I can't ask question based on their experience.

I don't see why this question can't be answered without invoking opinion. "How to fight back and clean this mess from academic journals/conferences?" - "it can't be done" is such an answer. Open to changing my mind, but I'm voting to reopen for now.

Significantly revised the post, tried to clean it up and remove the rant-y aspects. @MKB - feel free to roll back the edit if it's too significant.

Short answer while the question is still closed: Switch to a more ethical research area.  (I have never experienced any of the situations you describe.)

There is not a lot that you can do change the system. However, there are certain things you can do in the various instances you describe:

being asked to include a particular new author in order to be accepted

If the person has no good claim to authorship, I would politely refuse such a request and explain why this person is not an author. If they refuse to publish your paper, then submit elsewhere.

being asked to cite articles with no apparent link with my article

If there is no apparent link, then you can't cite it. I would respond with something like "We do not see how this article is related to our work. If the reviewer wishes to explain the relationship, we can include a citation."

being told by the conference TCP (one of the top conference) to reject all the articles I review

There is little point in reviewing the papers if the decision has already been made. You can politely refuse the review request.

In one unique case, I reviewed an article and recommended strong rejection, it was subsequently accepted without revision. Reviewing the authors profile and handling editor, I found one of the author is an Associate Editor for another journal. It appears that both help each to publish articles in their journals.

It's up to the editor to make the accept/reject decision, not the reviewer. Sometimes reviewers get it wrong and the editor has good reason to ignore their recommendation. However, it sounds like you believe this to be a case of corruption. There is little you can do about this other than refusing to have further interactions with these journals. You can tell others about what you have witnessed. Presumably others have witnessed it too. If news of this spreads, then it will (deservedly) harm the reputation of the editor.

All the above experiences were observed in well-reputed journals and conferences.

This is unfortunate. Such behaviours should bring journals and conferences into disrepute.
On the individual level, you can choose where to submit your articles and which review requests to accept. There are many factors to consider when choosing where to submit. Of course, prestige is a big factor, as publications in prestigious venues helps advance your career. However, you can include reviewing practices as a factor. You can also refuse review requests from venues that you believe will ignore your reviews. And, if there are venues that you believe are doing a good job, you can support them by submitting and reviewing.
If enough people begin to avoid venues with questionable practices, then that will have an effect on them. Likewise, if people support venues with good practices, then those will go up in the prestige rankings.

I am putting my answer here and will like to hear from community members as well. I hope there are people out there who will like to take practical steps as well.
I my opinion its hard to change the people but we can change the system. To assure fairness of review process it should be mandatory to publish article along with whole review process, including reviewer's comments, author's responses, and identity of handling editor.

Do you suggest revealing the identities of the reviewers as well?

I think only revealing the identity of handling editor is enough. it will push editors to have better review process. However, revealing reviewers identities after the completion of review process is also good suggestion.

No problem :) you provided with example. To be honest the quality of research papers 25-30 years ago was way better.

I have seen journals where the handling editor is named with each paper, so that part of your suggestion is already being practiced in some journals.

@JoelReyesNoche could you please name those journal? In my major is computer science. I will love to publish in those journal.

A search for "handling editor filetype:pdf" yielded results like this paper from Acta Societatis Botanicorum Poloniae which lists the handling editor of the paper at the left column of the first page.

@MBK - Please take advantage of the Markdown formatting. Two returns makes a  break. You don't need to manually add  tags. You can click "edit" to see my changes and see how it works in the live preview.

This does not answer the question.  OP describes their "short career", which means they likely don't have the influence or seniority to enact the changes you propose.  This is just not something OP can do (at least, not yet).

I agree with JeffE. "It should be mandatory" is not an answer to "What can I do".

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


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What style questions should I ask potential graduate students interviewing for positions in my lab?
As a converse to this question, as a professor, I find it difficult to conduct a useful interview. What types of questions should I ask which would give me a good idea as to how (1) productive and (2) self-sustaining of a student the interviewee may be? If different questions are required for each parameter, please mention that in your answer.

I underwent an interview recently from a prospective adviser, and I found the questions he asked of me to be pretty insightful - hence I'm sharing them here.

Why do you want to pursue research in this specific area?
This would highlight the candidate's motivation in wanting to do research in a particular field - and would also tell the professor more about the candidate's exposure to this area.
What made you apply to this lab/university, as a continuation of the previous question?
The answer would tell you whether the applicant had simply browsed the rankings list of universities, or did he/she actually go through the research publications of the lab - and the application was done due to an intersection of the two!
What would you like to be doing post Ph.D.?
There is no "right" answer to this, but it also tells a lot about the candidate's motivation in pursuing a PhD.
Finally, you can ask the candidate to discuss any problem that he is familiar with in that field - doesn't have to be anything fancy/complicated, but that would serve to highlight the clarity of the applicant's reasoning, communication skills, and level of exposure to the field.

I wish I could mark both yours and @aeismail correct... both excellent answers!

In addition to the questions that shan23 has mentioned, I ask candidates for my group a few other questions:

What kind of advising style do they like? How "hands-on" or "hands-off" do they want me to be? If they want someone whose style is vastly different from mine, that's going to be a problem.
What is your preferred working environment? (When?, Where?, etc.) I just want to get a sense of what they're going to be like to work with.
What kinds of projects do they like? Do they want a methodology-driven project, or are they more interested in applications.
Have you spoken with members of my group? I want future group members to have an interest in who they'll be working with.

Ask them about their expectations out of their coming 3-5 years as a grad student!
I find that a significant portion of the frustration that I (and those others around me) have experienced is due to severe disparity between expectations and reality. Note that this is as much for the benefit of the prospective student as it is for you as the PI.
Specifically things to consider regarding expectations:

The amount and style of supervision the student expects. My expectation was that I would "do science" and not "paperwork", in reality my PI knew less about the paperwork then I did, so I typically ended up needing to do a bunch of paperwork regarding employment (like salary raises, progress reports etc) and always late too...
The abundance and lack of relevant competencies in the lab, for that proposed project. I was confident that the lack of computational competency at our lab wasn't gonna be a problem for me. I couldn't be more wrong..
The workplace interaction with colleagues. I was under the impression that we'd be a team of intellectuals, tackling problems together, from our own angles. Again I was dead-wrong... Here, everyone's buried under their own pile of... Similarly, I can imagine that if the student expects to be a lone-wolf, forced team-work might be frustrating in the long run.
How to handle getting stuck/frustrated. This is quite self-explanatory I guess..

This is my favorite question to ask in interviews:
Can you tell me about a problem you encountered in the laboratory, and the process you went through to troubleshoot it?

I think a good general question to ask is what motivates them to do their research. The answer should give you a good idea at least for the latter and depending on the level of detail maybe also for the former.


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Self-endowed chair in the US and Europe
Endowed professorship is very common, but the financial endowment normally comes from external sources. Is it also common that a professor/research endow his/her position to establish a research group in the target university?
It should be an excellent approach for mid-level professors/researchers who can establish a research group in a top university (where it is normally hard to get that position) and get research fund from external sources such as industry and funding agencies.
This is of mutual benefit for both the university and professor, but I have not heard about such positions. Is it uncommon or just through private contracts?
UPDATE: Apparently, I confused endowed and named chair with research professor. I asked the question about research professor here. However, I still do not see a contradiction between research professor and self-endowed professor. Does a endowed chair must be necessary result of a huge donation to university? or a foundation can merely fund a professor position. If it is the latter case, one should be able to fund his own endowed position too.

As for your update. An endowed position must by definition be based on an endowment. Technically, one could create an endowed position with many small contributions (I think I might have a go at crowdfunding an endowed chair).

Endowed professorship typically are the result of a large donation of money to the university that allows them to fully fund a position in perpetuity based on the earnings on the initial donation. This is generally much larger than what an individual can bring in from external sources. If you manage to bring in that type of income, you will likely have little problem obtaining a permanent position.
I am aware of one independently wealthy individual who made a large enough donation to establish his own professorship. Basically he spent a small fraction of his wealth (which would be a large fraction of the wealth of most academics) to become a full professor with minimal teaching and service duties. His research was funded from his charitable foundation and I believe the foundation paid the standard overhead rates. He was reasonably productive throughout his entire career and probably could have obtained a professorship without using his personal wealth, but given the competitive nature of the job market and limited availability of positions, probably not at the institution of his choosing.

Oh, I interpreted the question differently (due to “get research fund from external sources such as industry and funding agencies”).

Regarding “one independently wealthy individual who made a large enough donation to establish his own professorship”, I think it creates somewhat of an ethical dilemma for the university…

@F'x I read it the same as you, but think it is a misuse of the term endowed chair. As for the ethical dilemma, it presents a big one, but individuals with a reasonable publication and teaching records and an outstanding record of bringing in grant money tend to be looked at favourably.

@shane I'd be very surprised if any reputable university would accept an endowment gift that comes with a stipulation that a particular individual be given the endowed chair, independently of the university's normal criteria for faculty appointments. (Indeed, if a university did allow such a stipulation, I'd probably stop thinking of it as reputable.) In other words, if I had a few million dollars to give away, I could endow a professorship, but I couldn't endow a professorship for myself.

@AndreasBlass but that is what the professor I know basically did at a top school. How much more "grant" funding does an applicant need to offset a poor teaching and publication record? My guess is an order of magnitude or two would cover it. In the Humanities, I am guessing $10 million would cover it and in the Sciences I cannot imagine a department turning down someone with $100 million in funding.

What you describe sounds like a research professor in the US system:

A professor who does not take on all of the classic duties of a professor, but instead focuses on research. At most universities, research professors are not eligible for tenure and must fund their salary entirely through research grants, with no regular salary commitment from internal university sources. In parallel with tenure-track faculty ranks, there are assistant and associate research professor positions.

The obvious drawback is that it puts enormous pressure on grant finding, with no tenure and thus no job security.

This is exactly what I meant, but I was thinking that research professors have institutional salary, but the university does not allocate fund for their research. Instead, they need to earn it externally.


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Different types of publications
During the literature review for my Master thesis, I have got in touch with many different types of scientific publications, meaning papers, working papers, conference papers, seminar papers and so on.
I have seen many discussion about sub-categories of these main objects but never one being at this higher level of grouping.
Thus, I was wondering which are the main difference among them in order to do some kind of hierarchy of content reliability when I read them. And clearly if there exist other types, please add them so we can build a complete collection.

Do you have any reason to believe there is a consistent hierarchy to find at that level?

In which field?

@PatriciaShanahan Computer Science

There exist a lot of standards for document/publication types. Here are some examples:

ORCiD work types
Endnote reference types
RAK WB, see chapter 1.2 (a system created for German libraries with a hierarchy for document types)
DRIVER used by DINI (repositories)
...

As stated here, each database might have its own definition, i.e. there are a lot of standards. Before creating a new one, I'd check if one of the already existing standards fits your requirements.
Note: Please feel free to edit this question to add more standards for document/publication types.


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PhD thesis - Names of appendices
I'm writing my PhD thesis (math) and struggling to find titles for the appendices. The thesis has three main chapters and for each one there is an appendix that contains some proofs that did not belong in the chapter itself (e.g. proofs of lemmas and technical details). What should I name the appendices? Currently I'm thinking about "Missing proofs for Chapter X" or "Omitted proofs of Chapter X". Any suggestions?

Do they share a common topic?

Chapters 1 and 2 are related. Chapter 3 is independent.

In a mathematics paper or thesis, the most common practice is simply to include all proofs in the body of the document, each one immediately following the statement of its corresponding theorem or lemma.  So you should seriously consider just doing that.
Placing proofs in an appendix might be appropriate if they are really ancillary to the main thrust of your thesis.  For instance, maybe there is a result that is not really relevant to the rest of the thesis, but you've included it simply because it is interesting.  Or you state a result that is well known, but you have written your own proof as an exercise.  Or you have multiple proofs of the same statement; you might want to place one of them in the body, and move the other(s) to the appendices.
But in any case, I would think there would not be more than a few proofs that would fit these criteria.  As such, it would be most natural to place each proof in its own appendix, rather than to group them by body chapter or any other criterion.
You could give the appendices names like "Appendix A.  Proof of Theorem 1.2.3".  Or better yet, something more descriptive like "Appendix A.  Proof of the Snargleberg–Veeblefester Theorem (Theorem 1.2.3)".  Of course, you will want to use LaTeX's \ref to produce the theorem number.
It would be a convenience to the reader if in each appendix, you repeat the statement of the relevant theorem before giving the proof.
If you feel the number of lettered appendices A, B, C, D, etc are becoming excessive, you could move down the hierarchy.  Most thesis templates are based on the book document class, in which the top-level text element is the chapter.  So if you want, you could write
\backmatter
\chapter{Additional Proofs}
\section{Proof of the Snargleberg--Veeblefester Theorem (Theorem \ref{snargleberg})}

Blah blah blah.

\section{Proof of the Dumbledore Lemma (Lemma \ref{dumbledore})}

Expecto Patronum.

Producing something like:

A. Additional proofs.
A.1.  Proof of the Snargleberg–Veeblefester Theorem (Theorem 1.2.3)
Blah blah blah.
A.2.  Proof of the Dumbledore Lemma (Lemma 2.3.4)
Expecto Patronum.

I disagree with Pete L. Clark's suggestion to just leave the appendices with non-descriptive titles like "Appendix A".  Using descriptive appendix titles will help keep the reader from getting lost.

The chapters themselves contain the main proofs so I feel like "Proofs for Chapter X" is not accurate. Perhaps "Other proofs of/for Chapter X".

I see, then maybe "additional proofs"  or  "supplementary proofs"?

@Johannes: After thinking some more, I have rewritten my answer.

After thinking some more, I agree with you rather than me.

I would think twice about including these results in appendices at all.  You have one appendix for each chapter and each "contains some proofs that did not belong in the chapter itself (e.g. proofs of lemmas and technical details)".  Why doesn't that belong in the chapter itself?  That sounds like exactly the sort of material that I would expect to take up space in a math PhD thesis.  You may want to organize things so that the most technical bits can be quickly identified and skipped by the uninterested reader, but putting them in appendices doesn't sound quite right to me.  Appendices should contain material which is ancillary to the thesis, not the technical core of the thesis.
Anyway, if you decide to go for the multiple appendices: I would call the Appendix "The Appendix" if there is one of them, and if there is more than one "Appendix A", "Appendix B", and so forth.
Added: After more thought, I agree with @Nate Eldredge's disagreement.  If there is more than one appendix, you should probably give some help to the reader by saying what is in each one.  Now that I seriously contemplate this possibility though [not that seriously; I still am not convinced that this is a good use of appendices at all, but whatever...] I find the question a bit weird: in that the OP can see his thesis, he is in a much better position than we to make the titles.  But a simple, descriptive title should be fine.

Thanks. I have to use a standard template and the appendices are ordered A, B, C,... but each one needs a name as well.

In most LaTeX classes, appendices are like sections or chapters, so they have a descriptive title in addition to their number or letter.

@Nate: They can have a name, but they don't need to (in LaTeX, or in mathematics generally).  Johannes: I can only repeat my advice above.  The fact that you are having trouble thinking of a name other than "Missing/Omitted Proofs From Chapter X" strongly suggests to me that this material belongs in Chapter X.  Unless you're saying that your template requires every chapter to have an appendix?

I'm not, but this material definitely belongs in an appendix. It's tedious derivations that don't require any intuition or ingenuity, but have to be there nevertheless.

"I'm not, but this material definitely belongs in an appendix. It's tedious derivations that don't require any intuition or ingenuity, but have to be there nevertheless." How many PhD theses have you read?  Over 2/3 of the theses I've looked at (let's say, a few hundred) devote a substantial amount of space to showing mastery of routine material.  I cannot recall ever having seen material relegated to an appendix because it does not require ingenuity.  Have you talked to your advisor about this?  What does she advise?

Thanks for your helpful comments. Yes, I have talked to my advisor and he agrees, but I will see whether I can restructure things to some extent. Some of this is already published but in the paper I could simply use "Appendix A'. I guess it's hard to explain why these things should be deferred to an appendix without actually seeing the thesis, but, for example, in chapter 1 I derive some asymptotic expansions. Then in a remark I mention that the coefficients can be rewritten in a certain way, but leave the details (2-3 pages of glorified integration by parts) to appendix 1.

I suppose it's a question of style now, but I wouldn't move a proof to an appendix merely because it's tedious. The real question is: is it important? Would a reader need to check it to be convinced that your main results are correct and correctly proved? If so, leave it in the body of the paper, no matter how tedious it seems.


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All my papers have alphabetical author lists, but an award application asks for author lists to judge contribution
I am a graduate student in pure math, namely graph theory and combinatorics. I have recently been nominated by my department to be the math department candidate for a university-wide research award. In the award application materials, it asks for my CV and is very specific that the authors names need to be in the same order as on the published paper so that the level of my involvement can be judged.
I am in a field where the convention is to put all names of co-authors alphabetically, regardless of input. It is clear to me that I need to mention this on my CV, but I am worried that if I just say that that the order of the authors is irrelevant in my field, the people judging my CV will be unsatisfied because then they won't have any information about how much I contributed to each paper.
Is there a tactful way to deal with this issue?

AFAIK, the authors are in alphabetical order because the contribution is expected to be equal by all authors, right? Can't you mention that somewhere?

If they are actually judging research contributions from a CV by people not familiar with each field, this sounds like a horrible way to assign an award. Authorship order is only one of many things that vary across fields. Some fields publish primarily peer-reviewed journal articles, others conference presentations; in some fields 1 paper gets you a PhD, in others you might be expected to publish several. In some fields you publish as sole author, in others you have dozens or hundreds of authors.

@AnderBiguri I worked in a field that used alphabetical author ordering, and the contributions of different authors to papers I worked on were often very unequal. My understanding was always that we used alphabetical order precisely to avoid fights over the first/second/last author position, although to be fair I never got any "official" confirmation of that.

Do you have the possibility of explaining what your actual contribution was to each paper on the CV? When listing employments, it's very common to include what your specific responsibilities were within the team - and not just write "Researcher at X" - it might be possible to do the same here.

If you are concerned, you may want to include more information about the culture of coauthorship in mathematics.  For instance, you could enclose the following updated AMS culture statement.
As a mathematical "lifer," I want to be honest: the way that we handle coauthorship in mathematics does sometimes obscure the individual contributions of the authors.  On the job market, this is often circumvented by getting letters from one's senior coauthors describing the contributions you made.  You might consider doing that here, or that may be too heavy-handed for this case.
You could also talk to a mentor in your department and see what they think.  They may have more experience with what happens at the university level.

I appreciate the input. Unfortunately, the award application only allows for the submission of my CV and a short letter from my mentor, so this either needs to be clear from my CV or from the letter. The letter we have is already too long just detailing the required points from the application, so conciseness is important.

@Sean: In that case, you should just be clear about it in your CV, and you can include a link to (e.g.) the above culture statement.

Unless the CV has a fixed, required format, such as in an NSF proposal biosketch, you are free to include any additional information you judge to be pertinent.
Since they require the author order to match what's in the paper, then you should preface your list of publications for this CV with a quick note stating: "Mathematics publications use alphabetical order when listing authors because [reasons]." That will allow you to explain the issue concisely.
(Note that a number of other fields have similar issues—such as economics.)

I worked for more than a decade in a field where authors are always listed alphabetically, and the typical author list includes 500+ names. Individuals do get awarded in this field.
As it has been suggested, the contribution of a single author in such a paper is not officially recognized on a paper in this case, but it is unofficially recognized by the community. Most people in your field will know the work of somebody worth an award, either through letters of recommendations and word of mouth, or presentations, posters or seminars on the same topic of papers you published.
As you can afford only one letter for this award, all you can do is to highlight the public talks you have given related to the papers you list on your CV, and count on your reputation in the field. Good luck.

Another idea is to include something like an annotated bibliography for you papers.  Included in your annotation will be a description of your contributions to each paper.
Doing this will have the added benefit of helping prospective employers understand what roles you played in each paper.  It will also help if you are in academia and are going up for rank advancement.


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What are the pros and cons of multidisciplinary research?
Does doing multidisciplinary research enhance one's employment opportunities compared to doing a degree in "basic" sciences?
For example, is a Ph.D. in Nano-science/Nano-technology in any way better than a Ph.D. in Physics or Chemistry, considering employment in India or in Asia? Would like to hear perspectives from other regions as well.
(In India, the basic qualification for employment in universities or affiliated colleges, as Assistant Professor is M.Sc. with UGC-NET or a Ph.D. in the relevant subject. Multidisciplinary research is available only in major research institutes and a limited number of universities.)

I suspect that this may be an overly broad question. Multidisciplinarity versus "basic" sciences is a huge question that would need a books to answer it.

@EnergyNumbers The question details also suggest that? Thought, I cannot go specific than this. I am not seeking a detailed exposition of each and every multidisciplinary research arenas or all benefits/demerits of multidisciplinary research. My specific query is about employment opportunities; Am I sounding otherwise?

This does not fully answer your question, but it is certainly one consideration.
Multidisciplinary theses are often examined by multidisciplinary committees.
Examining such theses is difficult, especially if the committee has no experience examining multidisciplinary theses.
 A consequence is that you will often be forced to conform to the conventions of different communities. In addition, the chemistry committee member may not see the thesis as a chemistry thesis and the sociology committee member may not see the thesis as a sociology thesis, because it lies somewhere in between the two fields and cannot be a complete thesis in both fields.

I am a PhD student in Computational Science, which is an interdisciplinary major spanning mathematics, computer science, and engineerning.  We are often pegged with the label "jack of all trades, but master of none" because we are a relatively new major with out well-established guidelines or rules judging the merit of work.  Often, we are required to accept a "home department" whose quality judgment rules dominate.  I'm not sure if this is the case for all interdisciplinary programs, but it helps alleviate the grey area and ensures that the work is evaluated according to a well-established criterion.