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Why should I format a citation manually without bibliographic software?
During a lecture (and a separate presentation) my instructor told us about bibliographic software, how it composes references automatically and is able to correctly cite articles in many formats. The software is freely available to everyone.
However, many others did not use it and were penalized on incorrect formatting when the assignment was due. Why would one not use software to compose references and citations? Is there advantage in learning how to cite articles manually?

Why wouldn't others use it? They probably didn't think it was important to have the references in a perfect style.

All bibliographic software has a learning curve.  You have to invest time and energy up front to learn the system and set up your database, and only reap the benefits later in the decreased amortized cost of maintaining correct citations.
If somebody doesn't think the tradeoff will be worth it (e.g., thinks they "aren't good with computers" or doesn't think they'll write many papers that the software would be useful for or is in a rush and isn't thinking about the long term), then they may manage a bibliography by hand.
For example, I'm a devout LaTeX/BibTeX user and would never consider doing something by hand---except that I have done so on a few occasions when forced to use an incompatible format where it wasn't worth setting up a new toolchain (e.g., putting a few citations at the end of a PowerPoint deck).

@Superbest but the fact that there were many people that didn't do that must mean that it must have been a bit more complicated (but not in my mind).

@alexy13 What is your null hypothesis? You are reasoning from a logical fallacy.

@Superbest What, exactly, do you disagree with?  I'll say, as somebody who's been using LaTeX for preparing paper for nearly 20 years now, I'd never even heard of JabRef before.  I'm always up for something to make life easier, so I figured I'd try it.  I got as far as downloading and launching JabRef.  At this point, the application announced that it was damaged and could not run, and I decided I couldn't be bothered to try to debug  it and deleted it.

@jakebeal My point was that the learning curve is trivial for many programs, and not using any citation management is a universally bad decision as opposed to a legitimate tradeoff. With regards to not hearing of JabRef, the second google result for free citation manager is a Wikipedia list including JabRef, and result #13 is jabref.sourcefourge.net. However, since you say you found the program to be broken, I retract my comment - I guess it's not so easy to use after all. Granted, JabRef is hardly the only software or the best one.

We are speaking about two different things here. There is Bibtex, which automates citation formatting but is still a text-only format, and there is a second layer of abstraction/UI provided by Jabref and the like. While I can vouch for the great utility of Bibtex, the advantages of Jabref are less obvious to me.

Yes, this is a standard cost-benefit relation: everybody working as a researcher and publishing for two years or more '''does''' use a citation database (my bibtex file now has 1.2 MB of text, for example) whereas people (students, engineers) do not see the benefit.

I can think of at least three real-world advantages we gain by learning how to cite articles manually:

It compels us to become familiar with the syntax and form of citations, which makes references to articles easier to read and parse ... something that we all still have to do manually.
If you only need to jot down or reference one article you can do so without troubling with software tools.
By knowing how citations should be formatted, you are in a position to recognize errors and correct them (i.e. you can tell when your bib software malfunctions).

Pocket calculators are cheap, reliable, and widely available. Why do we insist on learning addition? The answer is, there are a lot of times you might want to use addition and you don't always want to depend on a calculator for that.
Of course we should take advantage of software tools for compiling references and bibliographies, but this is not always viable or always necessarily better than doing it manually unless we can assume that bibliographic software:

correctly cites articles in the desired format.
composes references with little effort (automatically).
is freely available to everyone (i.e., at no cost).

In my experience, all three of these assumptions break down much more often than one would like. For instance, it might be difficult and very frustrating to make a small change to a standard format in your bib software, which is required by the journal or funding agency you need to work with.

I think assumption #3 isn't really necessary. If I'm writing an article, it's still advantageous for me to use bibliographic software that is available to me, regardless of whether it is available to anyone else. Once the article is prepared, nobody else needs the bib software to read it.

@DavidZ I would be inclined to agree, except that the point of references is collaboration. If I need special software to work with citations it can be a headache and an obstacle when I try to work with another researcher, dept., etc. to prepare a paper or a research proposal.

@DavidZ also, keep in mind that the cost mentioned here isn't necessarily measured in dollars and cents.

Re Assumption #3: I have met lots of people that thought they could be faster and more accurate doing a repetitive task by hand rather than using a computer. Most of them were wrong.

Point 1 is not so relevant since the arrival of DOI.

@FedericoPoloni I think you missed the point of #3. The point is that if you don't understand the format, you won't know when something is wrong. dionys points out that this helps you if the software does something wrong, but it also helps you when you do something wrong. For example, if you type some information in the wrong field, you won't catch it being out of place unless you know what to expect. To dionys' point about the software making errors, this might be more likely if you're trying out new, immature software.

@jpmc26 I see -- you are correct, I was missing the difference between doing it manually and learning how to do it.

@Davidmh I agree that DOI's are nice, but they don't provide much information if they don't resolve, and they aren't very robust to typographical errors. So, I see them as a nice complement to references, rather than a viable replacement for full citations.

A very important point from this post: "(i.e. you can tell when your bib software malfunctions)." I realized just before I submitted my paper that my bibliographic software requires that you if start a sentence with a citation then you have to click on a different button in order to get the citation to format properly. It usually autocorrects any citations that I move around or cite twice in one sentence, which led me to believe that it would fix a citation's format if I were to start a sentence with one.

I think is the type of things you need to do by hand once, in order to know the basic idea of it. After that it should be left for computers to do, just like determinants or matrix multiplication.
Doing it by hand is extremely time consuming and prone to errors. There are too many citation styles for anyone to master them anyway, even within a specific field.
This is just another thing better left to automated algorithms.


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Where can I borrow books that my own university's library doesn't have?
I need a book for my teaching and/or research, but my university's library doesn't have this book.  I don't think I'll use it enough to justify spending money out of my own pocket to own it.  What other ways should I try?  I searched Internet, there is no "free" (in whatever sense) PDF of it either.

If you need it for your work then it should be justified to ask your department to purchase it and charge the cost on its budget. I did this with a book I needed a couple of months ago.

Ask your university librarian.
Usually universities libraries collaborate with each other. They can look whether the other universities have the book (I know this happens within Canadian universities)..

This is is called inter-library loan and most academic libraries participate in an ILL network.

Depending on the school, they may have access to both ILL and a more specialized network, like BorrowDirect (http://library.columbia.edu/find/request/borrow-direct.html)

Usually I try to

Aks to profs. at the university. Most are happy to lend them for a short time.

Public libraries can be nice, but for some scientific literature I must admit they are not optimal

A somewhat grey area is buying them used books online. A online interface to physical 'used books' shops is use often is abebooks.com. Buying them a tenth of the price with shipping from Asia most of the time in comparison to the price at the university bookstore does feel like cheating but meh.

The last option could become illegal in the US depending of this court case, but for now it seems legit.

Kirtsaeng v. Wiley, the court case you cite, was decided 6-3 in favour of Kirtsaeng: in summary, if you are the legal owner of a copy of a copyrighted work (e.g., a book or DVD) in the USA, you have the right to sell it, just as you do everywhere else in the world. Buying second-hand books online is in no way "grey".

@DavidRicherby The problem is that a few publisher don't sell used books but print new copies and sell those as used book, this is where the grey area comes from.

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If a journal publishing an article about a software tool requires the software to be freely available, must the article be open access?
I am interesting in publishing a Bioinformatics software as a paid access article in a journal where they have open access as well as paid access options (Oxford's Bioinformatics).
But it stated at the journal's website that

Software If the manuscript describes new software tools or the implementation of novel algorithms the software must be freely available to non-commercial users at the time of submission, and appropriate test data should be made available. Availability must be clearly stated in the article. Authors must also ensure that the software and test data is available for a full TWO YEARS following publication. The editors of Bioinformatics encourage authors to make their source code available and, if possible, to provide access through an open source license (see www.opensource.org for examples). Authors should make every effort to use URLs that will remain stable. At the minimum, authors must provide one of: webserver, source code or binary. The name of the software should be included in the title of the paper wherever possible.

Does that mean the article publishing that software must be an open access article?  or can it be a paid access article?

You seem to be using "open source" (which refers to the source code of the software) and "open access" (which refers to the journal article) interchangeably. It's therefore difficult to tell what you're asking. Can you [edit] your post to correct this and clarify the question?

The software itself should be open source, e.g. freely available without licensing. Whether or not the article is open access doesn't matter.

Nari2, can you clarify whether you are aiming at publishing your software as an article, or whether you want to publish a tool paper on your software. Perhaps you are confusing the two. The sentence from the journal seems to refer to the latter approach. With it, you would first publish your tool by setting up a web page and then write an article about it that you submit to a journal.

@MarcClaesen: Thats what I wanted to know, thanks for bearing my mistake.

The two are entirely independent.

The journal does not require you to make the software open source. It merely requires you to make it free for non-commercial use for at least two full years from the day of submission of the article.
It however recommends that you make the source available, preferably via an open source license. But it states that it is even acceptable to simply provide the compiled binary to the editors. (Presumably to verify that the software does what you report it to do.)

The requirement is only applied to a software if you wish to publish a paper describing a new software tool or a new implementation or algorithm. (Which seems to be your case as you want to write about a new bioinformatics software.)

The OA publishing option is something else entirely. The default publishing format in the journal is subscriber pays. With payment of additional fees you can purchase the option to make your paper open access, but that is not a requirement.

I note that the condition described in point 1 would be evaluated at the time of submission by the editorial board, whereas the possibility of publishing the article open access will not generally be discussed at all until after the paper is accepted.

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What is the actual process by which academic ethics change?
Some of the answers to my question Are academic ethics global or local? indicate the possibility that academic ethics themselves (rather than just laws and policies affecting academics) may change over time.
What is the actual process by which academic ethics may be altered? More specifically, is the process:

Top-down, in which regulatory agencies, funding sources, legislatures, etc. push down new rules onto academics, who are expected to internalize them as normative? (e.g. "Please take note that fooing the bar is now against our Code of Ethics. If you do not cease all bar fooing activity by the end of the fiscal year, your grant will not be renewed.")
Bottom-up, in which written codes of ethics, laws, funding guidelines, etc. are modified as time goes on to match popular consensus? (e.g. "According to our recent surveys, 95% of academics and 82% of the general public Agree with the statement 'It should be considered unethical when academics foo the bar.'. For the 2020 fiscal year, we should make not fooing the bar a requirement for funding.")

The question can alternately be phrased as asking about the nature of academic ethics themselves - whether the "true state" of what is ethical and what is not is part of written rules of academia (and thus reflected in applicable policies, laws, procedures, etc.), or part of the unwritten rules.

Slowly, reading some of the questions posted on here about « my supervisor published my work without my name included »...

@SolarMike perhaps, but what is the "endgame" for such a scenario? Is this going to be solved by tougher laws, or will only a popular movement solve this?

A « scenario »? So you think it does not happen? Under the carpet then ...

@SolarMike I think you need to look up what the word "scenario" actually means.

@SolarMike no sorry, perhaps that wasn't the best term to use. I meant to ask what the real solution for the problem of supervisors omitting the names of junior researchers - is this a problem that will be solved by imposing tighter regulations or harsher penalties on supervisors who "unethically" omit names, or is this more something that would be affected by a grassroots movement or uprising against "unethical" supervisors?

@TobiasKildetoft ?A scenario basically a story ie fiction... so you don’t seem to think it happens...

@SolarMike Sometimes, you need to look past the first definition in the dictionary and look at the others (as well as how terms are generally used in everyday conversation rather than their "official" definition).

Perhaps using words more precisely is better in the first place...

I'm sure both processes happen.
The latest Common Rule for human subjects is a great top-down example.  https://nexus.od.nih.gov/all/2019/01/07/nih-implementation-of-the-final-rule-on-the-federal-policy-for-the-protection-of-human-subjects-common-rule/
This process reinvestigated human  subject ethics in the context of modern-day genetics.  It almost required specific informed consent for the collection of deidentified tissue, with periodic renewals of consent and the ability to yank consent.  Picture what that would do to say, developed perpetual cell lines used for research!  MANY universities were waiting anxiously to see what would come out of that process and there were very large discussions on how such requirements would be met.  We even modified our CLINICAL operations to accommodate anticipated changes that never happened!!
I say this is a great top-down example because the ethics are, and still remain, hard to figure out.  Stakeholders had to get together and form consensus.  Nobody knew what the outcome would be when the process started.
As an example of bottom up, there is the example of neurosurgeons that now require sham surgeries before adopting a new procedure. This fell out of human fetal tissue transplant attempts. ncbi.nlm.nih.gov/pmc/articles/PMC1733639  There is no relevant reg, but I'm sure this is now incorporated into RSRB discussion.

Can you give an example of the opposite process, where changes in ethical rules existed informally for some time (but represented "real" norms with real enforcement, even if only through social pressure) and were only later codified as official rules that could easily be looked up by anyone? E.g. "In the late 1990's, there was a wide-scale movement that wearing blue hats was unethical. Although this rule was never codified in any formal Code of Ethics or similar document until 2015, there is ample evidence that blue-hat-wearers frequently got their tires slashed and rarely received tenure."

@RobertColumbia -- that would require some real research, but off the top of my head, some of the bigger ethical failures were well-recognized as ethical failures at the time, but codifying them as regs was not always easy.  Nazi human studies, Tuskegee, Milgram,....

Another one that springs to mind is a population of neurosurgeons that now require sham surgeries before adopting a new procedure.  This fell out of human fetal tissue transplant attempts. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1733639/  There is no relevant reg, but I'm sure this is now incorporated into RSRB discussion.

Top down makes little sense. Regulations are independent, generally, of ethics. Some regulations embody ethical principles and some don't. On the other hand, behaving ethically shouldn't require regulation.
Bottom up, as you state it, makes little sense. I isn't "consensus" that makes a thing ethical or not. At one time, in the US, there was (somewhat less than universal) consensus that slavery was appropriate and necessary to the well being of the country.
Ethics itself derives from principles and from theoretical concepts of the nature of humanity and our world. These principles are debated by philosophers and others and only evolve slowly. Very slowly. Most of the ethical principles at play today are very old.
Applied ethics, however, is a bit different. Applied ethics needs to apply the ethical principles to changes as they evolve. The rise of automation, for example, has caused rethinking of some of the economic principles used to organize modern society. What is right in this context, derives from fundamental principles of what is right.
But new thinking about applications of ethics only permeates through a society slowly as there are vested interests at play that may be (relatively) disadvantaged by new thinking. I don't know my history well enough to know when plagiarism, for example, became an issue. But far enough back, I doubt that anyone thought much about it. But when new knowledge started to be associated with individuals, and those individuals depended on it for their livelihood, it became more and more of an issue. I doubt that Aristotle, for example, gave a thought to it. That implies a sometimes bottom up (permeate) and sometimes top down (recognize and codify) process. Not a dichotomy, but also, only applicable to applied ethics not ethical principles.

To give an example, the Tuskegee Experiment was unethical, though there were, apparently, no laws or regulations at the time to prevent it's being carried out. Afterwards, laws and regulations were created to make it obvious to everyone that it was wrong. But it was still unethical and immoral in the absence of any such regulations. It isn't the laws and regulations, later passed, that made it unethical.
What the laws and regulations did, however, was to make it easier for others to make proper judgements without actually considering the ethics and making their own determination. "Do this, and you will avoid an ethical trap."
Had those who carried out the experiment done a proper ethical analysis they would (or at least should) have realized that it was unethical.
But, again, those rules and laws are just already existing ethical principles being applied.

Maybe my experience is atypical, but IME 99% of actual "ethics" discussions have really been about regulatory or funding compliance ("the agency won't allow us to do X while receiving their funding"), not about "what's right" ("doing X is wrong because of the following timeless reasons unrelated to who is formally in charge of what").

But those aren't ethics discussions. It is just a different realm.

Perhaps if someone wants to tell you it is an ethical requirement, they are trying to avoid telling you that you are just being required to do something due to an imbalance of power or authority. They are trying to give you the responsibility rather than taking in on themselves. There is, for example, no ethical consideration in crossing the street against the light or in the middle of the block when it is safe, but there are still regulations.

There are many universities closely examining policies related to international collaborations right now because of an NIH mandate, so top-down could work.  In fact, most RSRB policies in the US are in place to make sure NIH compliance is met.

In fact https://nexus.od.nih.gov/all/2019/01/07/nih-implementation-of-the-final-rule-on-the-federal-policy-for-the-protection-of-human-subjects-common-rule/ was largely about the reapplication of ethical principles to research carried out in the modern genetic age.  EVERY university I know was waiting with bated breath to find our what was going to be in this policy, so they could adhere to it.

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Has a journal ever switched between being a predatory journal and a reputable one?
There are a lot of questions here on what predatory journals are, and how to tell if a journal is one or not.
Are there known cases where a journal has "switched" camps, or where substantial evidence has been presented that they have? That is, has it ever occurred where:

A journal developed a strong reputation for being predatory, recognized this, and engaged in a good-faith process of reform, eventually gaining at least a non-trivial amount of scientific credibility or impact?
A journal with no history of predatory behavior suddenly started showing signs of becoming a predatory journal? For example, a publisher may have fallen on hard times, or been scooped by wealthier journals, and decided to lower their standards to such a level as to become predatory in order to survive.

For example, if someone has claimed, "The Podunk University Journal of Advanced Best Practices in Intermediate Spline Reticulation used to be a low-impact but serious journal, but after Podunk U was rocked by a cheating scandal in 2003 and there was a gradual movement away from Spline Reticulation toward Spline Retransmogrification from about 2005 to 2010 with a corresponding drop in the number of serious papers on Spline Reticulation being submitted, they started becoming a 'pay for play' publication and nowadays mostly publish incomprehensible screed written by rich patrons who want to increase their publication count.", that would count.
As the definition of a "predatory" journal is somewhat vague and based on professional judgments rather than 100% objective criteria, I would consider any of the following to "count" as a determination that a journal is or is not "predatory":

The journal's practices or policies are so blatantly predatory or non-predatory that a conclusion is self-evident.
A large-scale consensus exists on a journal's nature, even though there may be a minority that has raised a legitimate case for the opposite conclusion.
A substantial, notable professional opinion has been released concluding that a journal is/was or is/was not predatory at a specific time. Inclusion on Beall's list would count as a professional opinion that the journal was predatory at the time it was added.

Very cool question. I am looking forward to the answers. Journals have lost quality, but turning to the dark side entirely would be really interesting...

@CaptainEmacs right, I'm talking about a light side/dark side-type switch. Simply gaining prestige over time through hard work or losing it gradually due to laziness is just life.

Hindawi has shoddy practices.  Example: the text sent by my colleague for a call for special issue was plagiarised by Hindawi's staff for a different special issue.

Upvote just for the Spline Reticulation joke... and it's an interesting question.

I really want to give trolling answers about journals that used to be run by scientists and were purchased by predatory multinationals like Elsevier.

This question isn't really answerable because what's predatory and what isn't predatory isn't well-defined.
If you define "predatory" as being on Beall's list, then the answer is yes: MDPI was on Beall's list in 2014, and then removed in 2015 (there are a few other publishers that bounced back and forth on the list too, e.g. Hindawi). However if you believe that MDPI was not predatory to start with, or if you believe that MDPI is still predatory, then saying this publisher has switched from being predatory to reputable makes no sense.
The same goes for the other bullet point you mentioned (of a reputable journal becoming disreputable). In 2016, OMICS - a publisher generally held to be disreputable - acquired two Canadian publishers Andrew John Publishing and Pulsus Group, as well as their journals. You can see from the Wikipedia page that this "led to a decline in publishing standards". However if you read the quoted source, the objection is:

Rose Simpson, the former managing editor of the Canadian Journal of General Internal Medicine, said that after the OMICS deal was announced in January, she went on the company’s website and immediately noticed red flags as she started browsing through the journals.
“There were all kinds of typos, the grammar was wrong,” she said in an interview from Ottawa. “In medical journals, everything has to be accurate -- every comma, every word -- so that was my first suspicion.”

In other words, the decline in publishing standards is based on poor copyediting. Does poor copyediting make these OMICS-acquired journals predatory, given that poor copyediting can happen even in reputable journals? You'll have to come to your own conclusion. Rose Simpson clearly thinks so, but not every reasonable person will agree with her.
Edit: to further illustrate how much of a grey area there is in what's predatory and what isn't, consider a journal that doesn't perform peer review. Say this in a vacuum and most people will immediately assume the journal is predatory. If this is your definition, then there has indeed been a predatory journal that "reformed" and started implementing peer review: Medical Hypotheses.
The problem is, as you can see from the "Peer review debate" section of the Wikipedia article, this journal was started by a reputable academic (David Horrobin) and published by a reputable publisher (Elsevier). David Horrobin's stated reason for starting the journal is that peer reviewers tend to dislike ideas outside the scientific mainstream, which makes it hard to publish new ideas. His solution was to not perform peer review, and to worry less about whether the paper is true but whether the paper is interesting. Ironically, when put this way, there are people who agree with this sentiment too.
The upshot of this policy is that in 2009, Medical Hypotheses published two papers arguing that there's no proof that HIV causes AIDS. There was a backlash, the media got involved, Elsevier investigated and subsequently demanded the journal implement some level of peer review. The then editor-in-chief Bruce Charlton refused and was subsequently sacked. A couple of years later, 198 academics published an article in another journal defending Bruce Charlton and Medical Hypotheses' original peer review model.
Is Medical Hypotheses predatory? It didn't perform peer review and published pseudoscientific papers! Is Elsevier predatory? It fired an editor that didn't do what it wanted! Again, you'll have to come to your own conclusions. There's no clear answer.

“This question isn't really answerable because what's predatory and what isn't predatory isn't well-defined.” — sure, the difference is a spectrum not a hard boundary, and is in many instances debatable. But at any given time, plenty of journals are either clearly legitimate or clearly predatory, so it’s easy to imagine what a clear-cut answer to this question could look like, and the two other current answers (FuzzyLeapfrog and iayork) both come pretty close.

@PLL Very few journals start from "haha academics are so gullible I'll just charge them to publish". Instead it's a long slippery slope all the way to the bottom, and at each point the odds are the journals think they're acting with good intentions. That's why Beall's list generated such controversy even from people unaffiliated with publishers. FuzzyLeapfrog's answer for example is fine if you believe Frontiers used to be predatory but no longer; on the other hand some people will argue that Frontiers is still predatory today, or indeed that it was never predatory to start with.

I agree with basically everything in your comment, especially the problems with Beall’s list.  But I don’t think that contradicts that there could be a clear-cut answer (a journal going from “most academics feel its practices are predatory” to “most/all academics agree it’s legitimate”).  Reading up further on the Frontiers situation, though, I agree it’s a bad example.

"Rose Simpson clearly thinks so" The passage you present says, in their words, that they were "red flags", and then quotes Rose Simpson as saying that they were her "first suspicion". That suggests that this prompted her to look into it more and find more evidence. Your passage does not at all support the conclusion that Rose Simpson find typos by themselves to be conclusive proof of a journal being predatory.

@Acccumulation right, but if the source says Rose Simpson found more evidence, it didn't go into details on what that evidence is. The only other detail mentioned is that OMICS moved the publishing operations to India, but that's quite reasonable since India's labour costs are cheaper than Canada's. By argumentum ex silentio I'd guess that she didn't find anything particularly clear-cut. At most, it's guilt by association because of the FTC suit.

Did Medical Hypothesis actually charge authors to publish? That's a rather critical part of the equation and the wikipedia page didn't mention it.

@ASimpleAlgorithm no, but the question of whether only author-pays journals can be predatory is a controversial one too. See e.g. https://en.wikipedia.org/wiki/Talk:Predatory_open-access_publishing#Requested_move_24_April_2019

@Allure I skimmed that discussion and it seems mainly over whether to restrict the term to open access or include other publishers which also charge the author a fee.

The Publisher Frontiers was - and, since there is no further development, still is - listed on Beall's List. Starting from scratch and with problems and therefore seen as predatory in the beginning by some researchers, Frontiers is now a reputable publisher with their journals listed in Scopus, Web of Science and the Journal Citation Report. The whole story is even included in Frontiers' Wikipedia article.
Regarding the question of what is a predatory publisher/journal and what is not, there is no clear answer or dividing line. There is a recent publication (still preprint) trying to gain further insight by analyzing the publishers/journals on black and white lists and comparing their characteristics.

That's what you get by fighting Beall's list: it's now "final" and there's no way to get one's name off. That said, the misadventures of Frontiers are far from over.

@darijgrinberg Unfortunately, the term predatory is limited to open access publishers or those who claim to be one. Looking at the practices of "traditional" publishers, like Elsevier or OUP, that ask for color charges (like 500 USD for one color figure ... in the 21st century where most people only use/have the electronic version of a journal) and letting authors pay for cover images and for re-use of figures and ... and making up to 37% profit be reselling our own reseaech back to us ... this limitation is kind of ... let's say ... unsatisfying.

Yep -- the list was useful for picking open access publishers; picking an established subscription-based one is a much simpler problem (just look at where others in your subject are publishing). Researchers have been faulting Frontiers for firing editors who didn't accept enough manuscripts; I haven't heard about this issue ever getting resolved, so the extent to which Frontiers is considered reputable is questionable.

@darij-grinberg Picking a publisher based on where others in your subject are publishing or which journals you typically cite applies to all publishers, not only to the traditional ones.

Has Frontiers really made improvements?  Leaving Beall’s list aside, it seems like the accusations of (arguably) questionable practices have continued into the last couple of years just as much as in previous years, at least going by what’s listed/linked on their wikipedia article; e.g. “In 2017, further editors were removed, allegedly for their rejection rate being high.”

@PLL Frontiers makes questionable decisions and produces controversy as other "traditional" publishers do, e.g. the entire editorial board of Elsevier's Journal of Infometrics resigned recently due to Elsevier's commercial control of scholarly work. After all, Frontiers is still a publisher. Nevertheless, it seem to have a proper peer-review process (based on feedback from authors and reviewers I know) and a robust publishing/payment process, i.e. you get what you expect. But still, predatory is a not very well defined phrase, e.g. compared to OMICS most publishers seem non-predatory.

This is an example of either a predatory journal taking over a legitimate one, or of a predatory journal trying to become legitimate, in 2016:

OMICS International, a “predatory” publisher of fake and low-quality research, has bought another Canadian science publisher — its third this year.
OMICS has acquired Intellectual Consortium of Drug Discovery & Technology Development Incorporation, of Saskatoon. Jeffrey Beall of the University of Colorado, who investigates the shadowy world of fake science publishing, discovered OMICS has expanded the group from three to 10 journal titles, all of them operating only online.

--Predatory publisher expands control of Canadian science journals
At least one person believed that the purchase of his journals was an attempt to go straight for OMICS:

One of the world’s most well-known “predatory” publishers has bought two commercial Canadian publishers of about 16 medical specialty journals ... When Robert Kalina decided to retire after running Pulsus since 1984, he said he searched for potential buyers, but could find “no other takers” for the remaining journals. ... He stated that he believed OMICS bought Pulsus in order to “start anew” as a legitimate publisher.

--Alleged predatory publisher buys medical journals
However, OMICS continues its predatory practices in general since buying these journals, and the expansion from three to ten journals is very suspicious. Several of the journals that were bought have terminated or attempted to terminate their relationship with OMICS. For that reason, among others, I can't really tell if the new ownership has been outright predatory, if the journals are still above board, or if they're somewhere in between.

So is this an instance of a predatory publisher raising its content standards and going legitimate, or respected journals getting taken over and becoming predatory, or are they meeting somewhere in the middle (shoddy scientific practices but not outright misconduct)?

You know, I assumed it was the former (journals becoming predatory) and I am still morally sure of it, but now you ask I suppose it's possible that OMICS is trying to become legit. I'll edit the answer to clarify.

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


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Will students without a Gradescope submission be able to see the test after grades are posted for the others?
I have a class test graded, and want to publish/post the grades.
However, some students are expected to makeup the test, and I don't want them to see the test yet. Will a student with

This student doesn't have a submission

be able to see the test, after the grades are posted?
My Gradescope is linked to the course Moodle. The test is currently hidden on Moodle. The test is normally handwritten and then uploaded by TAs.

I do not know the software, but isn't the integrity of the test compromised if you release it to part of the students, and only later to others? Independently of software?

Ask the TAs/professor/school.


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Doing a (Math) PhD abroad vs the same university
I am a math masters student at an university in Germany, almost finished with my degree. I want to do a PhD and have the following options:
Option A: Do my PhD at the university I am doing my masters right now. I also did my bachelors here. The university is not considered very strong (it's not Bonn) but the relevant department got a lot of money from a grant for 8+ years and my advisor is a very renowned researcher in his field (which I am also interested in). He advised my bachelors thesis and I am doing my masters thesis with him. I get along with him very well. Also my support system (friends and family) is here.
Option B: Apply for a PhD abroad (in Europe). The obvious cons are that I probably have to learn another language, I have to put in time to find a new social circle and I may find myself with an advisor I do not get along so well. The pros would be expanding my network within math and do my PhD at a strong institute, which could be good for my career.
Some more information about myself: I don't have perfect grades but they are very good, my math grades are mostly perfect (it's my minor which doesn't have very good grades). I am not 100% determined to stay in academia after obtaining my doctorate but I want to give it my best and decide after.
I have trouble deciding which option to take. Obviously Option A is more "comfortable", but I am also unsure how important it is for a career in academia to do your PhD abroad. To me it feels a bit like a gamble, since I could land in some insitute, where I get a bad advisor and I am basically alone, abroad doing my PhD.

"The university is not considered very strong (it's not Bonn)" That sentence is a bit weird.

@JochenGlueck this was more meant as a joke, I feel like in germany only bonn is really regarded as a strong institute (as a whole, not just one department)

Depends what you are asking. Purely from an academic perspective, B is better. But you are a human first academic second, and if you human needs are better met by staying where you are, that it's okey and a reasonable and smart move to make.

At the PhD stage, the chances are you can get away without learning the local language, especially in Universities with a lot of international PhD candidates

Other than the professional aspects, as an expat from Germany myself, I can unambiguously say that moving abroad (more than once) and getting to live in other countries has been among the most enriching parts of my life. In fact, most people living abroad will say that.
Of course, it's also hard in the beginning. You have find to a new social network, and learn to live with a different social system in which some things are done differently than at home (for example, in Germany I bet you never wrote or received a check, but here in the US people do all the time). But in the long run, it is enriching to your life, in addition to perhaps being good for your career.

This "personal development" aspect has been the main argument to consider option B

Unless you plan to leave Germany eventually in any case, everything you say points to the current university and supervisor. It is not only more 'comfortable' but the other is risky as well.
The main reason for changing universities (my view) is that the current faculty no longer has much to teach you since they have already done what they could. Meeting others (home or abroad) has some advantage. But mixing language study with a doctoral research program doesn't sound optimal.
And not everyone gets to work with a renowned researcher with whom they get along well. Just an opinion, of course, but you have made the case yourself.

"But mixing language study with a doctoral research program doesn't sound optimal." May I remark that this sentence probably has a bit of US bias to it? For instance, the European Union has a population only slightly larger than the US (450 instead of 335 millions) but has 24 official languages. If you want to do a PhD as a, say, Slovenian, than your options are to do it at one of the three universities in Slovenia or to go abbroad. Learning a language during a PhD is quite common in Europe.

In addition to @JochenGlueck, it is often quite possible to get by with English only, especially in university towns. This depends heavily on the country.

@Jochen, I think other language refers to non-English. Of course science in almost all of Europe is done in English and you will get by at work only knowing English. If the local language is used for "Science" to for example the extent that papers are not written in English you should seriously reconsider whether what they are doing is really Science. The hard part of "getting by" is of course the personal/social life. There you're options might be severely limited by not speaking the language.

... Oops didn't have space for the thing I was actually going to write. I'm from Europe. I moved to a country where I didn't speak the language for my PhD. And I agree with "mixing language study with a doctoral research program doesn't sound optimal."
I made some effort to learn the local language during the whole time I was there (as in a few hours a week). I never got to the point where I could use the language well enough to get by in a social setting. Learning a language can be quite hard and and so can doing a PhD be. Be prepared that you might not be able to do both at the same time.

@Kvothe: Please note that I didn't say doing a PhD and learning a new language at the same time were easy. I only said that it's rather common (which does of course not mean that everybody does it). No offence intended, but when you say that one will "get by at work only knowing English" you seem to be overextrapolating your own experience. Whether English suffices at work heavily depends on the group/lab. Some groups do a lot of their daily work in English. Some don't but are willing to adapt if one or several team members don't speak the local language. [...]

[...] Again others  might reluctantly agree to speak English to you all the time during your PhD, but will have most of their conversations in the local language, even if you are present (hence, you'll miss a lot of opportunities). I also know several German professors who insist that their international PhD students immediately start learning German. They simply enforce it by speaking more and more German and less English with the PhD student as time passes.

@Kvothe: Another thing is that some PhD students have teaching duties. Undergraduate classes are often taught in the local language.

I completely disagree with the suggestion that learning a new language while doing a PhD is a bad thing. Learning a foreign language while in the country where it's spoken is an excellent life experience, and although this takes daily practice, hours which are always scarce, I'd say a PhD is about the best point in an academic career for it: the time frame is just enough, but not so much that you can just keep postponing it; PhD candidates are typically neither too tied up in family nor side job; and it's a great concrete motivation for social interaction.

That said: it is very common for foreign PhDs in Europe to always and exclusively talk English (or else to cluster together with others with the same country of origin and then talk in their native language). IMO this is a shame.

If you seek an academic career in mathematics in Germany, it will be very useful to spend some time abroad. However, there is no particular need for this to be for doctoral studies, it could be as a postdoc instead.
Advantages of going abroad as a postdoc over going abroad as a PhD student in your case include the following:

You can only be employed on temporary contracts at German Universities for 6 years post PhD. Doing a postdoc abroad makes the ticking clock for getting a professorship less harsh.
A postdoc position is typically significantly shorter than a PhD, and leaving early isn't necessarily failure. This mitigates the risk that you could be miserable abroad.
You have more time to built a professional network first, so that you know the mentor you'd be working with, rather than jumping in blindly.

Going for your PhD abroad (Option B) seems like a great choice. Yes, it's a bit scary to move, learn a new language, and find new friends. But, it's a chance to study at a top university, meet new people, and really boost your career. Sure, you're comfortable where you are, and you have a great advisor. But stepping out of your comfort zone could lead to big rewards, not just in work but in growing as a person. It might feel like a gamble, but taking this step could really pay off for your future.
In fact, many of the PhDs (in math) I met did a PhD precisely because they could have the chance to move to another country to experience a new life. And as an academic, you may find that you have to go to where works are instead of staying in your home country. Doing a PhD abroad is a good practice for living abroad.

Two aspects:

As mentioned by others, moving to another country will always be beneficial. You learn new ways of doing things. And it's particularly "easy" for something like a PhD: in the worst case, you know that 3-4 years later, you can head back home.
In general, I recommend that students change universities or at least supervisors. Especially if you have already been supervised by the same person as both an undergraduate and an MSc student. We all have different ways of doing things and the same way as going to a different country will help you grow on a personal side, going to a different university or at least changing supervisors will help you grow mathematically.

2 is important, from personal experience. I did my two first year of undergraduate in one university, next two in another, my fifth year in another and my PhD in a fourth. All in the same European country. Then moved to another continent and did two postdocs in two different institutions. Altogether, worked in 6 universities (7 if we include my current one) and had 5 different advisors. All (unis and people) did things differently and I think that this makes me a more versatile academic and (I hope) a better advisor.
And I should point out that even if you are not considering an academic career, seeing different ways of doing things, supervising people for instance, is also useful in a professional environment: as a PhD, I imagine you would quickly end up having to supervise people even if working in a company. Work habits also change from supervisor to supervisor, etc.
One last point that may be worth considering. In math, more than one place have a "soft" (as in "unwritten") rule on not hiring their PhD students, precisely because they are looking for people that don't have the local institutional biases. So if you think you may be interested in a position where you currently are, it's a good idea to go elsewhere. (Not saying your university does this, but it happens often enough that it is worth bearing that in mind.)


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Impression of field have worsened after applying to and accepting PhD programs
I was accepted to a STEM PhD program. But, my impression of this field have worsened, starting from interviews and campus visits. Maybe I have bound myself to a dying area, and I can’t imagine what can I do in my 5 years PhD to stand out myself.
Maybe the programs I applied for are not the places I truly want to go to. If I applied to some other programs, I think I would get offers based on my application's strength. (Everyone I met during the visits said that my application is very strong.)
It has been 3 weeks since April 15, and I accepted an offer. I think maybe I made a wrong decision, and it would be better to reject the offer and apply again next year. Or maybe I should go to a master's program first.
But if I want to switch my direction, the school I accepted is not the best fit. Maybe the result has been destined since I submitted applications last December. Maybe my decisions were based on stereotypes and biases, or a small sample size, or failing to explain my thoughts, so I changed my mind after receiving more information. There were so many things I didn't know when I applied. Quitting the program (which is a top program) doesn't seem so feasible, I will lose everything.
I don't know what is a clear question to ask now. Maybe someone has some suggestion?

As you probably realize, there is not very much for any of us that we can provide in terms of an answer. I suspect that perhaps having a therapist may be useful to talk through some of the confusion?

This question is just the PhD-centered version of  "Why do we always feel that the other queue moves faster?"
Doing a PhD (and research in general) is an extremely boring task, where it takes forever to reach a minimally tangible result. Yes, even if you were to be Bohr looking for the H2 atom.
Just think of the technology that went into something as powerful (for the good or the bad) as a smartphone: it is decades of research, but no researcher was "there" to see the process from the inception of the R&D to the blossoming of the product.
Maybe the scientist creating the A-bomb had some "not-boring" times, and similarly the people working today at the intersection between AI and nanorobotics... maybe.
But for the vast rest of scientist time is slow. And rightly so, the brain works well at a relatively slow pace.

If you let go of the romanticized version of the PhD, which many people hold, and instead view your PhD as what it is (see below), you will be happier.
The (sub)topic or even (sub)field of your PhD is not so important. This is a time where you will be learning how to conduct research, write papers, present at conferences, and grow professionally both in skills and network. If you are in a solid program (regardless of how trendy), with a good advisor, your PhD will set you up for success.
Of course, if your dying area is phrenology, then perhaps yes, find something else to study.

Happiness during a PhD seems to follow a bimodal distribution. And a top predictor of being on the sunny side of it is intrinsic motivation: being super curious about the topic you work on. If what keeps you up at night are the ideas bubbling in your head - regarding that last paper, experiment or model, then you're at the right place. If it's strategic doubts about the field, I'd say you aren't. My advice: don't do it, drop out now, rather than later. A masters may be a good way to find out whether there is a (sub)field exciting you in this way.

You must define your goal first: are you after a title PhD for better chances? Or can you create your own chances in your own business? In which case you must test your talent for academic study in that field, in which branch can you do outstanding studies, create something new, which new thing can be done differently to help others.
Your passion for the specialization that you choose is the energizer for the long study, so check if you are passionate about doing it and bear whatever obstacle. Besides, having a trusted advisor in the field or making a quick online survey around the pros and cons of that specialization can help you decide well.  On the other hand, you should also build up your own business project to keep working on, in case you withdraw from that academic study, you will find a shelter to encompass your talent and let it grow more and more.

After getting a PhD after five years in Biochemistry, I can say don't do a PhD. It's not worth it unless you need the comma PhD in your LinkedIn to be a better candidate for a job position. There are clever ways to make money than a PhD. A lot can happen in five years. Don't waste your time because that is more precious than any STEM scientific research program can give you. Most people who have a PhD regret doing it. Don't regret starting a program; you can always quit anytime. Worst case scenario: you start and reach your comprehensive exam. You can either continue or fail out with a masters, and not pay tuition for it as it is typically covered in STEM PhD programs. Just check and see if your tuition reimbursement comes with a not quitting in 180 days into the semester. Best wishes on your decision.

"You can either continue or fail out with a masters"
This is country dependent.

Yeah very true, and program specific as well. However most in US follow this so that is my assumption based on the question asked

I do not believe the statement "Most people who have a PhD regret doing it". Not only do I think that you cannot back up this assertion with actual data, but I actually think that it is not true.

There are clever ways to make money than a PhD This is one of the worst reason not to do a PhD (and there are plenty good reasons not to do a PhD).


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Can I use the notation A:=B in a humanities assignment?
Currently I am working on a sociology assignment. Can I write A:=B (A is defined as B) in this assignment? Is this notation general in humanity assignments?
In STEM assignments, I frequently use ":=" to define things: for instance, "Pr:=probability" or "A_{i,j}:= ith resident is j years old".

I would guess that "=" is enough and more common.

Explain your notation. I think that "=" notation is evil, and a very bad practice introduced by C programming, because that equality notation confounds definition or even variable overwriting with equality established through proofs, or equality being checked for validity. Other people use a different explicit notation for definition, but as long as you introduce it, I think it is fine. ":=" is a nice notation.

What is commonly used in the literature? Using new, non-standard notation is not going to make it easy to get your point across.

For what it's worth, your A_{i,j} example strikes me as awkward from a STEM perspective. How is it supposed to be read? "A_{i,j} is defined as ith resident is j years old"? Would probably flow better if written out as a sentence using 'denotes' instead.

It's a course assignment? (You tagged it homework.) The person you should be asking is the person who will evaluate it.  I can't assign a grade to the assignment, so my opinion is pretty much value free.

No, A:=B is not acceptable for a sociology; you want to use natural language, and simply use words instead of notation, in a written piece. Honestly, as a mathematician, I would say it isn't even proper to put := in the middle of a paragraph in a mathematics research paper---a lot of people, including myself, prefer to use natural language and full sentences, with logical signs such as $\forall, \exists, \Rightarrow$ reserved for within equations.

If you want to use a notation that isn't common in that field, then you need to define it at first use. There is nothing wrong with the notation, but you can't assume that a reader will know that you mean it as a "defining" relationship rather than something else.
Moreover, in a non-technical paper, if you are only going to use such a notation a small number of times, it might be better to avoid it altogether and just use natural language to express your intent.
Note also that ":=" isn't universally used for a definition even in STEM fields. For example, in some programming languages it is used for a variable assignment and a reassignment may be permitted, depending on the language.
Even mathematicians define any new (to the field) notations.


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Are academic ethics global or local?
This question is inspired by this recent answer that mentions that whether downloading articles from 'questionable' sites is legal (not ethical) may depend on local law. That is, law is local.
Are academic ethics global or local? Clearly, legal principles and conclusions vary from place to place, but does the same apply to academic ethics, or are academic ethics the same no matter where you go? That is, while there may be (and may continue to be) genuine debates on various ethical matters in academia, do these debates and disagreements apply fully to academics everywhere in the world, or are there "local" ethics?
At first, I figured that getting large numbers of people scattered throughout the world to agree on anything is so remotely implausible that there must be local ethics, but then I realized that I couldn't think of any rational set of circumstances where I would advise a colleague that they could solve their ethical issue not by changing their behavior, but by crossing a border, e.g.,

Dude, while fooing the bar does not violate any specific statute in the Civil or Criminal Codes of Florin, it is near-universially considered academically unethical here! Have you considered a transfer to our branch campus in Guilder? You can foo the bar all you like there - they even have a Department of Fooing the Bar and award annual scholarships for the most bars fooed that year. Just take care that Guilderian ethics requires that you disclose your blood type to research subjects before you ask them to fill out a survey - people who don't are not charged in court per se, but their names get published in Guilder's Most Annoying Unethical Jerkfaces Quarterly and are rarely, if ever, allowed to return to academia there.

FWIW, I have intentionally avoided mentioning specific places or specific issues as I do not want to have the question derailed by frame-challenging ethical debates (e.g. "No, Stem Cell Research is wholly ethical, it's just these stupid regulatory regimes that keep asserting it isn't.... Your question is invalid.").

The question is also inspired somewhat by my own experiences with people treating ethics and law as more or less the same thing, citing legal requirements as thought-stopping "ethics" conclusions. E.g. when speaking about "ethics", someone will say, "Here are the statutes, case law, administrative regulations, university policies, etc. that cover what we are doing. We've got to obey them, get to work.", and I can't remember the last time someone formed a circle and asked, "Forget the law, is what we are doing (or planning to do) really right? Let me read my favorite passage from Kant...."

Another way to consider the question is to consider how legal questions ("Is X legal?") must usually have a jurisdiction in order to get a "real" answer ("Is fooing the bar legal in Pakistan?"). Does this or a similar rule apply to or make sense for asking questions about ethics? E.g. "Is fooing the bar ethical in academia?" versus "I know fooing the bar is ethical here in the Czech Republic, but I just got a faculty appointment at FSU and I want to continue my research there. Is fooing the bar ethical according to the standards of academics in Florida? A lawyer told me it's legal."

If you have a specific example where two regions have come to different conclusions about one of the "big" ethical issues of our day (stem cell research, human cloning, not wearing clean underwear during thesis defense, etc.), that can be an answer, as long as it truly reflects ethical considerations rather than differences in what is permitted by applicable laws or administrative regulations.

Your ethics vs the ethics of your community
It may well be that your personal ethics differs from the dominant ethics of the society where you happen to live, the society which is also setting the rules that influence your research.
While for many cases there's more or less a worldwide consensus about what's acceptable and not, there are genuine debates where multiple options are plausible, and in the case of such debates it's feasible that the IRB's of different countries would have contrary opinions.  One such factor where it's obvious why there are differences (and also obvious why some people may not consider the other's arguments as binding or even relevant) is religious influence which has some impact on medical experiments (e.g. stem cell debate or certain aspects of sexuality in some parts of the world), other factors of medicine include things such as research on certain recreational substances and euthanasia. There are also topics (or findings of fact) that are highly unpopular for political reasons, which again are local.
It may well be that the IRB considers a particular type of research unethical and unacceptable (i.e. it wouldn't be minor adjustments to do that thing properly but "your goal is taboo"), it's not a fluke and every IRB around them would consider it unethical, but the researcher, taking all the arguments provided by the IRB into account, still finds that they personally believe this action to be ethical. In such situations, a reasonably valid option would be to move to a location where the locally dominant ethics matches your own - and which would likely not have objections to that research.

It's difficult to draw a clear line between ethical and legal restrictions, since of course lawmakers are influenced by what is generally considered as ethical in a certain community. For instance,
according to Jewish law, the soul does not populate the body until 40 days after conception,
whereas Christian theologians will tell you that this happens immediately at conception.
This theological difference leads to very different laws concerning the use of human stem cells and embryonic tissue
in Israel compared to most of Europe.
(As a result, there are European stem cell researchers who move to Israeli research institutes because their research would be considered as unethical and illegal by the authorities of their home country.)

Could you elaborate on the European perspective? As far as I can tell, having such a strong influence from Christian sources on what is considered ethical in research is mainly an American thing.

Not on the European perspective as a whole, but at least on the German one: The German Ethics Council  had 26 members. According to this page, 6 of them are delegates of religious communities (1 Jew, 1 Muslim), 2 are teaching at Christian schools, and at least 9 more members have a strong Christian background. That's 15 out of 26, including the chairperson. And don't forget that the CDU (Christian Democratic Union) has been ruling Germany for decades. Occasionally, it feels the need to stress the "C".

I see. A quick glance at a few other countries seems to suggest that Germany are by far the most restrictive in this regard (though I may have missed some, as I only checked up on a few).

The Declaration of Helsinki attempts to define medical research ethics. Over time debates, often local, have occurred leading to alternativesee like Good Clinical Practice and the Common Rule. Each ethical guideline is slightly different and research that might not be allowed in one locale, could be permissible under a different set of guidelines.

Ideally, ethics are universal, based on fundamental principles that don't differ by place or time. Nor by profession, actually. Ethics may be applied a bit differently in different professions, but only in the sense that different issues arise there.
But there are two other considerations. One is what is considered to be ethical in a place might be considered differently somewhere else, but this is a mistaken judgement. There was a time, and certainly places, where slavery was considered to be ethical, even meritorious, and some still do (sadly) believe that. But such considerations are based on faulty analysis.
The other consideration isn't really about ethics. It is about what sort of behavior people in a place or time expect of other people. It is about regulations, whether formal or not and whether sanctioned officially or unofficially. Your example of barring foos is of this sort of thing. One place celebrates it and a neighboring place forbids it. This has nothing to do with ethics, nor with law. It is all about social pressure which can be intense. Such social pressures can lead to shunning or even killing. I think the other examples here also fall into the social pressure or community expectations framework, rather than being ethical considerations.
But this question is one for philosophers rather than for academics per se.
And note that my first word here was "Ideally". There are philosophers who believe differently about the very nature of ethics, leading to different conclusion.
You can, for example, study situational ethics which comes to a different conclusion.
However, I don't think that we have discovered all ethical principles and so are in a bit of a muddle.

Vaguely remembering Dr. Seuss: I do not like them Sam I Am. I do not like green eggs and ham. I do not like them here nor there I do not like them anywhere. Etc.

I would argue that, while agreeing on them to a certain extent is required for a functioning society, ethics are inherently personal, and depend in no small amount on what the individual researcher believes to be true. Due to their socialization as well as the necessity to get along with one another, people will tend to form localized groups with similar beliefs, and thus ethics. It follows that where a person learns and works is likely to influence their ethics, but just crossing a border will usually not. In other words, if your hypothetical colleague is themself unsure whether a certain behaviour is ethical, moving them around the globe shouldn't alter their (or your) perspective on the matter.
However, if they are in disagreement with the majority in their location, I could think of a few scenarios where, while impractical, moving from one place to another might resolve the issue. Others have pointed out religious differences, and closely related to that are (e.g. professional) codes of conduct, but for the sake of simplicity I'm going to point towards the issue of intellectual property and, by extension, plagiarism. I'd posit that, on average, Chinese researchers have a different outlook on that than US based ones. Perhaps not even in principle, but certainly in terms of relative priorities.*
The relationship between law and ethics is an interesting one. Not only will a society's commonly held beliefs influence its legislation, there is also a certain pressure from authorities, via propaganda, law enforcement etc. in the opposite direction. While the academic community as a whole emphasizes communication and critical thinking, and might, one would hope, be less affected than the "average" citizen, I do not believe that we are entirely immune to this effect. At the very least, research ethics have changed with time, but they have not changed at the same pace in every culture.
* No judgment intended either way.

Can you think of a specific example where crossing a border would solve an ethical issue? I'm not talking about moving to an area where one is likely to get away with ethical violations due to less-well-funded watchdogs, but to an area where the substantive ethics are different. E.g. "My research proposal is clearly unethical here. Instead of editing it according to the suggestions of my IRB, I'm going to go to Ruritania, where patient privacy ethics is notably different! "

@Robert Columbia I'm trying to think of something that's not too politically charged. A lot of what's commonplace in some countries would tend to feel like "getting away with something" to someone with "western" ethics, e.g. animal rights considerations. Genetics/cloning/stem cell research come to mind as well, but I don't feel qualified to state hard facts concerning this area.


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When does coming up with an idea constitute sufficient contribution for authorship?
To what extent does coming up with a research idea, without contributing anything else to the actual work, constitute a sufficient contribution to be an author?
As a hypothetical, suppose a five year-old child tells me one day that he wonders if banana peels can be used to cure leukemia. I am intrigued by the idea and go and write a research proposal. The proposal gets funded (!) and I get positive results (!!). In this case, does the child deserve authorship for coming up with the idea, which I might never have considered?
One obvious problem with this is that while "coming up with an idea" might involve deep theoretical knowledge, wisdom, and intelligence, it could also be the academic equivalent of buying a lottery ticket. For example, I could pick a random chemical name out of a reference manual and declare that my idea is that this chemical cures cancer. I've essentially made a bet on this chemical. If some later researcher who is actually competent in biomedical research manages to get a positive result on this chemical, I've won. My "jackpot" payment is authorship on their article. I'm now a famous, published biomedical researcher even though my actual field might be art history or French literature.
Ideas:

Coming up with an idea always deserves authorship as long as the idea was novel.
Coming up with an idea deserves authorship only when the idea-maker establishes a sufficient foundation for the idea. For example, randomly proposing a cure for cancer by picking random chemical names out of a dictionary and hoping for a jackpot cannot result in authorship, while providing a theoretical basis for why a specific chemical might work does, even if the idea-generator leaves it at that and does none of the actual experimental design, lab work, etc., or quite possibly is not even qualified to do so.
An idea is never sufficient for authorship. Proposing an idea, without doing any of the actual work, merits at most an acknowledgement or a citation ("Thanks to John McWhatever for coming up with the idea of solving the Closeability Problem by applying hyperparallelized matrices across the transverse manifold.", or "On an online Question and Answer site, Columbia (2019) proposed the use of banana peels in curing leukemia, but did not provide a theoretical basis or a practical methodology. In this paper, I demonstrate a clinically significant benefit of 10g banana peel topical tincture daily versus placebo in the treatment of leukemia....").

To be clear, you're asking about authorship of an academic paper, not of any subsequent patent?

@smci right, I am talking about academic authorship.

I will give an answer that applies to mathematics and maybe some other things. It isn't quite your second point, but close. Background first.
Newcomers to maths think of it as a bunch of facts. You learn some of those facts in early schooling but don't get a wider view. If you study maths at a higher level you think of it as proving theorems. Some facts and a bit of logic let you derive other facts. But if that is as far as you go, then you really aren't yet a mathematician. A mathematician is a person with enough insight into the workings of the thing that they can propose things that might be theorems if they could only be proven. But this isn't, to a mathematician, just making random statements. There has to be a reason why something is suspected to be true. Things that are likely to be true.
So, if the kid just randomly proposes a connection between bananas and leukemia, then it isn't worthy of authorship. But if a person with deep insight into the workings of the disease and the properties of bananas proposes it as a topic of study then, yes, they could/should certainly be a co-author of the study even if others do the actual proof of the concept.
It is the insight into the likely connection that has value.
Otherwise, you might just be sent off on a random quest without any hope of success.
However, in mathematics, if an advisor suggests a problem to a student, having the insight that the student hasn't yet developed, it is still pretty rare to demand co-authorship unless there is more of a collaboration in the development. But this is just the custom. Certainly it is worthy of acknowledgement, and maybe even co-authorship. It isn't even necessary in this case that the advisor have an outline of a proof, or even any deep insight into how to develop it. It is just insight into a problem worth pursuing.
But if it is, in mathematics, not an advisor-student relationship and one proposes an idea to another, I suspect that co-authorship would feel more natural, but probably with an acknowledgement section in the resulting paper that details the contributions. But in this case, also, it is more likely that the work would be developed cooperatively, so the authorship question would be obvious.
Other fields than mathematics have different views on authorship, of course, but it is, even there, a question of insight. Among an infinite number of roads, someone proposes one as worthy of following. If you follow that you owe them something for putting you on the path. How you acknowledge it is a matter of custom that varies from field to field.

You seem to imply that insight, seniority or experience are a factor in authorship, rather than contribution.  A random thought doesn’t count if it remains random - we agree on this - but if someone can expand on this thought, defend it, and show how it fits into the logic of the process, then surely it doesn’t matter the level of insight or experience of the thinker.   Granted: this occurs very rarely in 5yr olds.

Even if someone with considerable experience proposes a problem and leaves it for someone else to develop, the person proposing the problem should not be a co-author:  Riemann should not get author credit for proof of the Riemann hypothesis.

@ZeroTheHero, nor Landau for solution of the Landau Problems. But I think it is different for living people who actually correspond in some way with the authors and pass on the insights directly from hand to hand. But I think you misinterpret a bit. I tried to focus on insight alone, not seniority or experience, though noting that others do value those things. Seniority alone doesn't make you a mathematician. But insight does.

@ZeroTheHero Insight is a contribution!

@ZeroTheHero you may be right, but your example is certainly flawed. To be considered for co-authorship in some paper, someone must make some significant insights into whatever is novel in that paper. In the case of a paper that suggests a new, interesting theorem and proves it, coming up with that theorem (Buffy's example) is a significant insight leading to the paper and deserves co-authorship. On the other hand, a paper that proves an existing theorem (Riemann Hypothesis) no new ground gained by that paper is do to the insights of the person originally proposing that theorem.

To what extent does coming up with a research idea, without contributing anything else to the actual work, constitute a sufficient contribution to be an author?

This really depends on what you mean by "coming up with a research idea".  A "research idea" can be very general, or very specific, and the idea could potentially include substantial progress towards solving the research.  If the "research idea" is merely a broad idea for a topic of research, then that would never be a sufficient condition for authorship of a paper.  However, if the "research idea" means coming up with a novel method which in itself constitutes a major research contribution, then that might be sufficient for authorship of resultant work.
Probably the most extreme example of this would be in a field like mathematics, where difficult research problems can be "cracked open" by a new insight.  As an extreme example, suppose Researcher A comes up with the idea to "try to prove the Riemann hypothesis using Fourier series" and then Researcher B listens to this and goes away and figures out a way to do this, and actually succeeds in proving the theorem, leading to a major paper.  Notwithstanding its success, the "research idea" of Researcher A is much too broad to constitute an actual contribution to the research of Researcher B, let alone a contribution worthy of authorship.  If Researcher B were feeling generous (and why wouldn't he be after such a great success!) he might thank Researcher A in an acknowledgement, for steering him towards the solution to the problem.
On the other hand, if Researcher A instead comes up with a much more specific idea "to prove the Riemann hypothesis by using this particular application of Fourier series (shows some sketch working to give an idea of what he means)" then that idea might constitute the major breakthrough towards the actual result.  If it turns out that this idea is the key to breaking open the problem, and Researcher B then grinds out the details, that would probably be a case where joint authorship is appropriate.
In summary, a "research idea" would be sufficient for authorship if that idea is sufficiently novel and clever that it constitutes a substantial contribution to the work in its own right.

I do not think we can have a general answer here. It will always depend on a lot of factors; mostly because research is, unfortunately, not only ideas, but work and resources. Let me tell you my point; if a Professor (or anybody else, let's call it the proposer) has some insight like the one about bananas and cancer and proposes the topic to some PhD student or postdoc or Assoc. Prof. or whatever (let's call it the worker), the latter will probably have a need of resources in order to carry out the researcher. If the proposer can also provide funds, lab or resources, I think she should be a co-author of the paper, patent, whatever. Also because this is a cycle and the proposer with more papers in the new subject will have more chances to secure funding and therefore provide with them to the worker. So at the end this is a symbiosis and the proposer should be on the paper, where of course, she must at least read it and give feedback. And this should be ethical as well. Why not?

I think this question fundamental misunderstands how the collaboration process and coauthorship decisions happen.  You don't typically finish a paper and then decide who the coauthors are, you decide the coauthors and then finish the paper. If someone suggests an idea to you, you should keep them in the loop if you work on it, and you discuss whether you're collaborating or not.  (Otherwise you run the risk of scooping one of their students.)  So one of three things happens here:

You decide early on that you're not collaborating.  Then they are not a coauthor but you give a generous acknowledgement thanking them for suggesting the problem or the idea.
You decide early on that you are collaborating and they do more work on the paper than just suggesting one idea (how extensive will vary).
Occasionally you'll decide to collaborate and then the person will not end up doing any work on the project.  In this situation that person should ask to be removed from coauthorship.  If someone isn't actively collaborating, you might also inquire whether they want to stay a coauthor.  This can be slightly awkward,  but it's somewhat unusual and the best way to sort this out is to communicate during the collaboration process.

This answer seems to be most relevant in practice while the others make good points too.

No.  Ideally a co-author should know the contents of the paper, the methodology, and be able to defend this contents and methodology.  In practice, a co-author should have an identifiable contribution to the submission, not just an idea.
Ideas are cheap; most ideas are wrong and it is the process of checking that an idea is right that elevates a contribution to the author or co-author level.  How much checking depends on the topic, but just shooting the breeze is not enough.
The OP gives the example of a 5yr old, but it’s easy enough to imagine a conversation with a colleague at a conference or a seminar generating an idea eventually developed in a research paper by one but not the other participant to the conversation, even if they were both involved in the original conversation.

I second all of Buffy's eloquent answer, but I think I can provide a slightly different perspective that is of value. For background, I do some academic work in law and my undergraduate degree was in mathematics.
I think that merely coming up with an idea is never enough to deserve co-authorship by itself. Though, like Buffy, I think it does deserve an acknowledgement in some form. In most law journals, the first footnote would be the appropriate place for something like that.
However, I would argue that your second example goes beyond merely putting forth an idea. Someone may provide a solid basis for their idea based on thought and experience without doing the work to write it out or research the background to properly develop it. At that point, they have given the primary author something more akin to a roadmap than a mere starting point idea. At that point, it is appropriate to offer the person who provided that kind of foundation a co-authoriship if they agree with the ultimate conclusions.

In practical manners, many advisors get co-authorships just for proposing projects versus doing work on them.  This probably doesn't really cross the threshold for a real contribution.  And it seems to be very different in how it is applied to PIs versus fellow students or even people outside the lab group.  (I could write 50+ great projects to do...should I get co-authorship from whoever does them?  Even if I transmit the list to people?  Not really.)
But I think at the end of the day, you have to realize that the idealistic vision of coauthorship does not really apply.  At least in experimental R1 science with big lab groups.  It hasn't for at least last 50 years.  And the professors actually need to collect the co-authorships to keep writing grants, get tenure/promoted, etc.
You're better off just figuring that it is a tribal custom, like wearing clothes, that you have to deal with.  Plus, they're at the back of the bus (stereotypically) in terms of the byline name order.  So don't let it bug you too much, man.

This is quite interesting reading some of the commentary. There seems to be a pervasive call to ignore initiators of potentially great ideas.
So then I would ask: If you accidentally come across a great solution to a problem that was mentioned to you by someone is this to be ignored? This is effectively the same problem, but as we all well know, many great ideas have come through this process.
So does it matter if there is a un-attached instigator of the idea, or if that input comes during development of an idea?
In my opinion - Any contribution, is a contribution. How you weight that contribution reflects on you, and not others.

The problem is that word "potentially". Yeah some idea are really valuable. The overwhelming majority are not. In industry you can't really get a job selling ideas alone. There's always something else of value you need to attach to it to remove the risk. That should tell you something.


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What should I do if I cannot afford a journal Article Processing Charge?
I would like to publish an article open access, but I cannot afford the article processing charge (APC). I am based in the UK, so I do not qualify for some of the available fee reductions or waivers. I also do not have grant funding to coverage the fee. How can I obtain funding to cover the publication fee to make my research open access?

For EU, there were also OpenAIRE funds to cover APC: https://postgrantoapilot.openaire.eu/ Over 1300 articles have been funded by this "post-grant open access pilot": https://blogs.openaire.eu/?p=2917

Where are you based? If you're at an institution, I'd get in contact with your library. They usually have funds of some sort to cover APCs these days.
Depending on where you're submitting, it is still possible to get a fee waiver if you can provide financial justification (which it seems like you should be able to do). I don't know how well this works at most journals, but those like PLOS ONE and PeerJ are well known for providing fee waivers for researchers with OA support (apart from a couple of incidents).
Alternatively, you could pursue the 'green' route of OA. Submit your paper, but don't make it OA (via the 'gold' route), and self archive the pre-print, post-print, or whatever the options available for your journal are. You can check policies here: http://www.sherpa.ac.uk/romeo/
Try playing with these options a bit, and then report back if there are further complications or details to add.

Publish in a reputable, subscription-based journal.
Self-archive the preprint on your institution's website or public repository.

Even subscription based journals want money now.

@Euler....IS_ALIVE some subscription-based journals have article processing charges and it's not new. The majority don't.

@Euler....IS_ALIVE: also, subscription-based journals usually charge a lot less than common open access journals.

Alternatively: Publish in a reputable open access journal that does not charge author fees.

@JeffE sure, but these are very rare for obvious reasons.

They're only "very rare" in some fields; in others, they're quite common.

When preparing your manuscript, you could also approach the journal editors and ask for their policy on waivers.  I would do it before finalising the manuscript according to the journal's style.  Even if the journal does not offer waivers, journal editors should be interested in finding out how often APCs are preventing people from submitting to their journal.

You could co-author the article. Authorship will be shared so does cost. Perhaps co-author could have such cost free options. That will not only minimize your cost but will open you to collaboration. Of course there is a trade off in such a scenario but better than delaying the publishing or even not being able to publish.
Please look at my comment below. I did not mean it something unethical.

I did not mean to do it unethically of course. Look at the word "colllaboration" please. What is the unethical ground to include a new co-author if co-author both shares cost and his academic background to make the article happen?