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Can a closed-source research software be published as a journal paper?
I have been developing a piece of software related to my PhD research. My field is bioinformatics and molecular simulation.
The reason being that my supervisor's software has been written in a hapazard manner over the past 17 years or so, and the source code is so low in quality that I found the source code to be not only impossible to refactor but also not worth refactoring.
Another reason is that I am developing my software in a programming language that I adore. It is fully object-oriented and truly platform-independent.
However, the catch is that I don't want to make my software open source. I only want to release the binary files and libraries for public use.
I was wondering if I could publish my software as a research paper in a peer-reviewed journal.
Can I?
Related:

Can open-source software be peer-reviewed and published?

Can I publish a piece of software as a research paper?

This is going to vary from field to field. @RicardoCruz notes that in Machine Learning journals/reviewers do not generally push for code to be made available, whereas in my field (bioinformatics), most journals do have a policy that all code must be made available, and quite a lot of reviewers will highlight if its not.
This does vary by the type of paper. The majority of journals publish software either where it is part of a paper reporting a methodological advance, or where it has been used to demonstrate a new piece of science. Where the science is the focus, rather than the method, it is easier to get away with just supplying exes.
There are a few places in my field where you can simply publish a software tool even if it is not a methological advance, or a used to demonstrate a new piece of science. Many of these places are the sorts of places that do prioritise open-source more than other places. E.g. JOSS (Journal of Open Source Software - the clue is in the name) or Bioinformaics, who state:

The Journal requires all authors, where ethically possible, to publicly release all data and software code underlying any published paper as a condition of publication ... The review of manuscripts describing new software, or where novel algorithms, code and/or data are central to the manuscript, includes peer review of the algorithm/code and underlying data. We therefore require that all relevant software and/or data are made available to the reviewers during the review process.

Of course making the code available isn't the same as making it open-source. It is possible to make it available with a restrictive licence.

My software is related to bioinformatics and molecular simulation.

There are no engraved rules about this, but in my experience (in machine learning) reviewers (unfortunately) usually do not push for source code to be released, nor do journals/conferences AFAIK demand it. While there has been some push for reproducible research, in my experience, these practices are not yet well entrenched.
You do not specify what the goal of your code is, but here are some general tips:

Simulator used to generate synthetic data: Reviewers are usually satisfied by only having the generated data published and explaining how it was generated (or reference whatever paper was used to implement it).
Implementation of existing or proposed algorithms that perform calculations necessary for your experiments. Again, make sure the algorithms are well-documents, either in your paper or existing literature. If a reviewer insists on having code published (which is rare), you could publish an MWE (minimal working example) with the part that the reviewer is concerned about. For example, if it is a predicted model, you can share the parameters and inference code (keeping the optimization part closed).
User interface to help automate some tasks such as data labeling. I doubt reviewers will care about such software unless the paper is specifically about the software.

All that being said, I would make sure to have your supervisor's consent (and whoever contributed to the existing code) before proceeding: is your motivation to eventually monetize from your software? You say that "the source code is so low in quality"; therefore, you had the opportunity to go through the existing code. I am pretty sure your code is now considered derived work. Courts have ruled that even inspecting binary code (called reverse engineering) is considered derived work (see clean room design), so I would expect no less from reproducing existing software after looking at its source code. (But that's the topic of another stackexchange.) Furthermore, since the software is produced as part of your studies and (I guess?) from a publicly funded PhD, you should have a look at whether you will need university or funding agency permission if you commercialize it (see this question about that).
If your goal is not to monetize the software, you should consider if giving back is not to your benefit -- others will use and build upon it, which implies citations, collaborations, networking opportunities and improve your curriculum vitae.
EDIT: As the other reply said, there is confusion in the title of your question. Open-access journals mean that the paper is publicly available (author pays). Closed-access journals mean the paper is behind a pay-wall (reader pays). It is a completely orthogonal topic to your question about source-code.

1. Simulator used to generate synthetic data --- this is my case.

therefore, you had the opportunity to go through the existing code --- his code is open source.

I am pretty sure your code is now considered derived work. --- absolutely not! I have studied his code to understand the theory, not for copy-pasting or translating the logic.

I did not accuse you of copy pasting. :) I am just calling attention to the fact that the standards for derived work are lower than that, but IANAL.

An open-access journal simply means that its content is accessible for free.
You are asking what kind of content can be published in the papers of open-acces journals.
Depending on the specific journal policy, you may be able to present a closed-source software there. There is no "general" mutual exclusivity.
Repeatability of the results presented in a scientific paper is a requirement for both closed and open-access papers (at least in theory).
So publishing your code in a closed-source paper would not be that different (probably it will be much cheaper, unless you are publishing on diamond open-source journal).
If you look for software in the academy, you will find plenty of examples of "only-exe" downloads, with non-commercial usage licenses. Have a look at them, then check the history of publication of the authors.


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Can privately administered colleges and universities in the USA successfully run without government funding?
Can privately administered colleges and universities in the USA and the UK successfully run without government (either state or federal) funding?
By "government funding," I mean any kind of money coming from a US state or the federal government that hinders the institution from implementing its own set of rules.
Related:

https://law.stackexchange.com/q/101381/32068
https://law.stackexchange.com/q/101491/32068

Just the first site on Google: https://usafacts.org/articles/what-do-universities-do-with-the-billions-they-receive-from-the-government/ - in 2018 about $100B was for student aid (scholarship, work-study, loans), then grants (NSF, NIH, etc.), and a bit for contracts (I have contracts with universities from my national lab group).

Short answer is yes for the USA. I've provided a list as my answer. A great follow-up questions is why?...

Define funding. Many U.S. colleges, very famous ones among them, are private institutions. Many of them perform research for the government, like for any other entity (but could likely survive with only private research). Do you consider that federal funding? Many students receive federal aid; do you consider that federal funding? Most (even private) colleges are tax-exempt; do you consider that federal funding?

@Peter-ReinstateMonica I took this to be any federal funding. But, yes, it is unclear.

@RichardErickson For me, there is a huge difference between a private institution (of which there are very few in Germany) and one that is actually government-funded (and run) (the vast majority in Germany). The difference between accepting public or only private research grants is much lesser. And finally, I would not consider student aid "funding" at all, and the idea that a college would not accept students who receive government aid for fear of undue government interference seems extreme and ludicrous to me. What about food stamps? Public transportation? Streets?

@Peter-ReinstateMonica, ah, you have a German perspective. I have a US perspective. Most "private" US schools fit your definition. However, there are some schools that do not want ANY federal funding i nthe US. And yes, these people want to get rid of food stamps, public transportation (e.g., city busses, Amtrak), and at least decrease funding to street (some libertarians want all roads to be toll roads). In the US, there are some schools that forgot any federal funding to avoid federal rules that happen to include anti-discrimination laws.

@Peter-ReinstateMonica for example, https://www.cbpp.org/blog/house-republicans-snap-amendments-would-take-food-away-from-more-than-1-million-low-income https://www.wpr.org/transportation/republicans-vote-cut-public-transit-funding-milwaukee-madison and  https://www.lp.org/blogs-staff-lp-monday-message-toll-roads/

@user366312 thanks. that's what I thought you meant, but there was some confusion in the comments.

@user366312 It would be helpful if you would include that in the question ("any federal funding as defined in the Civil Rights Act of 1964". I am still unsure whether student aid is contingent on the institution complying with that law (after all, it's the student who is funded, not the college). I'm still not sure whether being tax exempt is contingent either. "Being tax exempt" as a non-profit scientific organization is not the same as "funding" in my book. (Let's assume the college is properly licensed as an educational institution.)

@user366312 I asked a question over at law about that.

@user366312 Funding from the state would not be "federal," so if that's what you mean, you should say that.

Yes.
There are some colleges/universities (in the US, I do not know about the UK) that do not accept federal fundings due to their belief and principles.
These institutions are the "counter-example" that proves the rule of why most institutions do accept federal fundings.
Dean Clancy maintains a list.
Here is his list as of March 2024:

Aletheia Christian College (Idaho)
Bethlehem College & Seminary (Minnesota)
Boyce College (Kentucky)
Christendom College (Virginia)
Crown College (Tennessee)
Faith Bible College (Maine)
Grove City College (Pennsylvania)
Gutenberg College (Oregon)
Hildegard College (California)
Hillsdale College (Michigan)
Mid-America Baptist Theological Seminary (Tennessee)
Mount Liberty College (Utah)
New College Franklin (Tennessee)
New Saint Andrews College (Idaho)
Patrick Henry College (Virginia)
Pensacola Christian College (Florida)
Principia College (Illinois)
Southern Baptist Theological Seminary (Kentucky)
Southwestern Baptist Theological Seminary (Texas)
Weimar University (California)
Wyoming Catholic College (Wyoming)

If you browse this site, you can gain insight into the common belief system of these colleges.
They are mostly fiscal and religious [Christian] conservatives who do not want a large federal government nor federal influence on their education.

The list you provided includes just colleges (and seminaries) are there any universities, as in larger institutions that also have consistent research output, that do not accept federal funding?

@jDAQ My guess is not for the US. Almost all researcher in academics obtain (or at least try to) federal funding. Plus, there are private research foundations that do not accept federal funds. so, why have a non-federal research university? A college can teach and private research institutes can research. If you can find anything, I'd be happy to edit it in.

I'm most familiar with Hillsdale, where there is research output on the level of peer liberal arts colleges.  Faculty can receive funding from private foundations.  In some cases they gain an affiliation with an independent research corporation and receive federal funding through that entity.

@PaulT. thank you for that insight. Makes sense. Also, would be interesting thought experiment if the rest of higher ed operated that way.

One bit of context is that the main reason why these US colleges refuse federal funding (including federally backed student loans) is to avoid complying with Title IX of the education amendments to the civil rights act, see e.g. Grove City College v. Bell and the Civil Rights Restoration Act a.k.a. the Grove City Bill.

@PaulT. I agree with the context, it's just not part of the OP's question. I even suggest it as a new question in another comment. I was being diplomatic with my suggestion into looking as to why.

The situation in the UK depends on your definitions of public funding and public/private universities.
In the UK all universities are non-governmental institutions (the most common corportate form is a schedule 3 charity, which replaced royal charter as the most common form recently).
However, most universities in the UK are publically funded, in that the government issues loans to students to pay for tuition, and only about 50% of students actaully end up paying these back. In addition, most universities recieve a small amount of teaching grant and a larger (although still relevitively small) quality related research block grant (a grant awarded on the average quality of the research, not for any particular project). The balance of funding usually comes from research grants, which again, mostly come from the government.
Universities that accept students funded by student loans must follow various government mandated rules and submit to regulation by the Office for Students.
There are a very small number of universities in the UK that don't accept government regulations, and therefore can't accept students funded by government loans. This is what is called "private" universities in the UK. There are 8 such institutions, and mostly they are small specialist institutions, such as "University of Law", only two are "general purpose" as far as I can tell: The university of Buckingham and Arden University, and even these specialise in vocation and professional degrees rather than the usual academic subjects.

This seems a broad question as there are a great variety of institutions and programs. Some might, but many important ones could not.
Regardless, the status quo is that federal funding for research is extremely important (it has always been). Quoting from an NSF source:

Institutions of higher education in the United States spent nearly $90 billion on R&D in FY 2021, the highest amount reported to date. Most of that spending (55%) was financed by federal government sources.

I don't think it is guesswork to state that simply doing away with this source of funding would thoroughly alter  the nature of education in the USA. Look only at what has happened to the social sciences and humanities as their funding has shrunk in favor of STEM. Most European universities also rely to a large degree on government funding  to sustain research.
Government funding is important (I would say essential) because research carried out in universities is to a large degree an educational experience, typically with no direct financial return but producing highly educated graduates.

This doesn't answer the question.

"Can privately administered colleges and universities in the USA and the UK successfully run without federal funding?" @AzorAhai-him- Of course it answers this, it depends on your definition of "successful". According to my answer, the answer for many universities (private or not) is no, because research and associated educational activities would be severely compromised (truncated by 50+%, although admin would take some of the hit) and they represents an important part of the mission of many universities.

I agree the last paragraph might be superfluous. I merely tried to explain why Universities bother with research at all.

In the US, very few colleges and universities, even public ones, receive direct Federal funding. Or, at least, no substantial contribution to cost of operation. Public universities in the US have support from individual states, not the federal government. Some colleges (community and junior colleges) have local governmental funding (city, county, ...).
There is indirect support, however. Students are funded through loans and some grants. But those loans and grants can be used at any accredited place, public or private. Research is partly funded through competitive grants from the Federal government, but those are also available to faculty at both public (state funded) and private institutions. Private organizations (IBM, Google, ...) also provide grants.
And, most research grants, while they go to individuals and groups of faculty, do provide funding to the institutions through "overhead" which consumes a fairly large piece of a grant. This is to support the general infrastructure of the university (buildings and such) as well as labs, computing infrastructure, and similar things. But the flow is technically Government -> individual -> institution, rather than Government -> institution -> individual. The institution also incurs costs in administering the grant so as to assure compliance with regulations and proper use of the monies.
The current administration (Biden et. al. 2024) is trying to forgive a lot of student loans. That money is Federal and benefits the individuals directly. It does, of course, represent funds previously paid to colleges and universities, both public and private.
Many universités, public and private, do work on behalf of government, both Federal and state, and that is funded.
Private institutions (and to an increasingly large extent public ones) are funded by student tuition and gifts of donors, often graduates of those institutions. Both my undergraduate and doctoral institutions are continuously (daily emails) begging me for contributions. Harvard University, for example, has a vast endowment that comes from past contributions over its long life and careful investment of the funds.
As for success, my old undergraduate place was then a small private liberal arts college with about 2000 students. It is now listed as an R2 and has been in operation for about 175 years without federal funding. It is successful in sending people into academic careers as well as business and the sciences.
The Federal government has a role in accreditation and in assuring fairness of treatment through regulations. The states also take such a role, as do private organizations.
See https://www2.ed.gov/about/overview/fed/role.html for the federal role in education in the US.
I suspect that the UK answer is quite different. And, I think that the US usage of "public institution" is different from that in the UK. Here it implies creation by a state government and some institutional control by a state, such as New York. Private institutions, OTOH, are created by private entities, sometimes church units, and funded mostly independent of government other than as mentioned above.

I disagree with your first sentence. See this article that would suggest they receive direct federal funding from a legal perspective: https://www.nationalaffairs.com/publications/detail/the-strange-evolution-of-title-ix

@RichardErickson, that article is about regulation, not funding.

Yes and the regulations apply to universities because they receive direct federal funding.

@RichardErickson, hmmm.. Actually they apply because we have regulations about lots of things without funding. It's the law, not a quid pro quo.

Generally, you are correct about laws and regulations applying to everyone, but in this case you are wrong. Title IX applies to universities that receive any federal funding. No federal funding, no Title IX (and some other federal regulations). The linked article describes law was snuck in as a rider.

Also, you overall answer is correct but how universities are functionally funded (i.e., not from taxpayers at any level as the primary source of income), but any federal funding causes extra federal regulation.

I believe your chain of funding for research is wrong. Federal grants and contracts are always made to an organization which administers the funds for the proposed and approved research by an individual. If a researcher wants to go to another institution, they have to get approval to move the funds to that other institution. Approval is rarely withheld.

To my knowledge the only Federal colleges and universities are the Army, Air Force and Naval academies and the lesser known Coast Guard and Merchant Marine Academies. In addition, Gallaudet College (for deaf people) was founded by the Federal Government but I do not know if this is still a Federal institution. If there are others I would like to know.

@DavidSmith thanks for the input. For trivia sake, BIE directly operates two post-secondary institutions as well https://www.bia.gov/bie

There is also the Uniformed Services University of the health sciences in Washington, DC, operated by the Defense Department.

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What should be the standard procedure for covering the expense in the case of independent research publications for a PhD student?
I am preparing an independent research paper to publish in an open access peer-reviewed journal.
Independent means: my PhD supervisor doesn't have any contribution in this. Since my supervisor doesn't have any contribution in it, I cannot request him to cover the expenses for this paper.
What should be the standard procedure for covering the expense in the case of independent research publications for a PhD student?
N.B. Last time, when I sent an email to the dean's office inquiring about funding a GPU-enabled laptop, they forwarded that email straight to my supervisor. So, this time, I am not sending any emails to them.

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The SOP is to go through the chain of command, one link at a time. First speak with your advisor. If they say no, then ask your advisor if it would be OK to ask the dean. If the dean says no, then to the research office (or "development" office, or whatever). Then to the Provost's, etc. Your university may have funds to pay for publication fees.
From the comments, I gather that you don't have a good relationship with your advisor. That's never a good thing. So keep in mind that even if you get funding from the university administration, they will probably ask your advisor to sign off, and if the advisor refuses to sign, then you will get no money. Unless your advisor has a reputation for being vindictive and/or unfair, in which case the admin might override him/her. But this would be an exceptional case.
If all else fails, you can ask the journal for a fee waiver. It's not uncommon.
What you did with your previous request is considered bad manners, often referred as "going over my head" from the perspective of the advisor. The dean replied appropriately by routing it down to your advisor. Higher-ups do this to discourage students from just sending all requests to the top without first going through the appropriate channels.

Do OA journals ever waive fees? Traditional journals will for students in some cases, I know.

In my field of Biology, all of the OA journals have a fee waiver policy. They often require proof that you have explored all channels at your own institution. I've never gone through the process, choosing to publish in traditional journals when the admin will not pay the fees.

I gather that you don't have a good relationship with your advisor. That's never a good thing. --- My relationship is not bad. I just don't trust him.

@user366312 If you don't trust your supervisor that means the relationship is bad. It can be bad in different ways and to different degrees but lack of trust definitely counts as a form of a bad relationship.

@quarague, Okay, But, that is his fault, not mine.

@user366312 It may not be your fault, but it's certainly your problem (also, nobody said that it's your fault to start with).

Somewhere before going up the chain of command I'd also check if the university library might have some agreement with the publisher/journal for discounts or covered fees.

@DanielHatton It's not an idea, it's how things work in a bureaucracy. Deans and provosts are inundated with student complaints about homework and other minor things. Those complaints are always bumped down. You can't create a culture of "I want to speak with the manager". Now, if your supervisor is harassing you, you don't go ask them permission to complain to next level up, but for everything else, and that very much includes funding requests, you are in for a learnin' if you try to go over your supervisor.

@DanielHatton, I think you are reading too much into the answer.  Don't view this as saying that it's never ok to go over your advisor's head.  The answer never said that.  View this as saying that it's rarely a good idea to go over your advisor's head -- and this is clearly one of the times when you shouldn't go over your advisor's head.  There is no "accountability vacuum" in expecting students who are looking for funding for publication fees to start by talking to their advisor; that is just normal procedure in academia.

The answer never said that "people have to ask permission".  It said that what the student did is considered bad manners.  This is my experience too. It also said that "standard operating procedure (SOP) is...." to speak with your advisor first.  That is also my experience -- in my experience it is indeed the standard procedure for most circumstances, especially funding, and it doesn't mean that "people have to ask permission from their intermediate supervisor/manager to talk to anyone more senior".

A publication doesn't need to be OA to be useful for your CV or for the profession as a whole.

The standard procedure "should be" that the university, or at least the department, have a stated policy on paying fees for doctoral student publications. If they insist that you need publications for the degree then they should be willing to pay the costs of that.
Open access fees are another matter, however, since they are high. While the principle above still applies, I doubt that many places would pay the full fees for student publications, whether "independent" or not.
A typical faculty member will seek grants that provide funds for publications under the grant. Some faculty members will have funds for publication that are more broadly based and less restricted.
But the choice to go open access is yours. You understand the costs involved. If you aren't willing to ask the professor directly or indirectly then you are probably stuck with those costs.
I'd actually recommend, in your situation, that you publish in a more traditional venue. There might still be page charges, but much less than open access and with a higher likelihood that either the university will absorb the cost (a good policy) or that the journal will forgive the fees due to the fact that you are a student (independent or not). That is fairly common in publishing, or was when I was still active.
Save OA publishing for later in your career when you have the opportunity to develop funding sources for such things.

In some cases the funder can even have a stated policy (in places where funding a studentship from a single source is common and where they consider open access is desirable).

Based on your question and replies, fixing your relationship with your advisor should be your top priority, before being concerned about publishing. Your advisor will have to support you in order for you to finish the program. If you can't trust him to help you publish then you certainly can't trust him to help you successfully finish the program. With that said, whatever work you are doing should be a part of your dissertation, so by design nothing you do should be independent of your advisor. If you are doing independent work you are undermining your success in a PhD program. Doing your proposed dissertation work shouldn't leave room for pet projects, especially any that don't include your advisor.

@DanielHatton In what location would that not be the case?

@DanielHatton Although I am happy it worked out for you, I wouldn't suggest anyone make a decision based on your personal anecdote. Your advisor is suppose to help you, so having a poor relationship with them is counterproductive. In general a student's access to funding, supplies, instrumentation, and collaborators is severely limited outside of their advisor. The OP's dilemma demonstrates that. They may not be almighty but the support and advocacy of your advisor is irreplaceable.

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Is it ethical to submit papers under a false identity and affiliation to avoid peer review bias?
According to Huber, J., Inoua, S., Kerschbamer, R., König-Kersting, C., Palan, S., & Smith, V. L. (2022). Nobel and novice: Author prominence affects peer review (August 16, 2022):

We invite more than 3,300 researchers to review a paper jointly written by a prominent author – a Nobel laureate – and by a relatively unknown author – an early-career research associate -, varying whether reviewers see the prominent author’s name, an anonymized version of the paper, or the less well-known author’s name. We find strong evidence for the status bias: while only 23 percent recommend “reject” when the prominent researcher is the only author shown, 48 percent do so when the paper is anonymized, and 65 percent do so when the little-known author is the only author shown.

The same effect was also replicated in 2006 and 2017, so it's not just one paper making this claim.
Given such a significant bias, would it be ethical to submit one's papers under a false identity? I.e. if you're Maria Ivanova from Moscow State University you might be worried about bias against Russian scientists, so you submit your paper as John Smith from MIT instead to make sure it gets a fair review. Or you might be working for the University of Alabama and worried that your papers won't get reviewed fairly due to the low rankings of your institution, so you instead pretend you work for Cornell.

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As you keep suggesting to use MIT as your false affiliation, I suggest you change the title of your question to "Is it ethical to submit papers under a false identity and affiliation to take advantage of peer review bias?". This seems to be what you are actually after.

@wimi peer review bias isn’t supposed to exist though, right? So any reviewer who complains could be pointed out they weren’t supposed to think about the affiliation in the first place.

"Things are unfair. How can I cheat to make them in my favor." Don't be surprised if people who care about academia are not interested in helping you with your plan.

@JonathanZsupportsMonicaC You assume that people from MIT get preferential treatment. I assume that they're getting baseline treatment and people in lower ranking colleges are getting discriminated against, so if anyone's "cheating" it would be the actual employees of MIT. But in any case - how is it acceptable for such bias to exist in the first place?

No one is saying it is acceptable. But your question is not about how to eliminate/reduce it, but how might one take advantage of it. "The works is unfair, therefore no one may be judged" should be covered in your Phil 101 class.

"I assume that they're getting baseline treatment" But you know they're not, because your reference tested vs a control group (all names hidden), and found a distinct difference vs the control group.

@BenVoigt that depends on whether you think the control group is the Nobel prize winner or the grad student. To me it’s the Nobel winner who’s getting a fair treatment, not the other way around.

@JonathanReez: The control group is the anonymous one (which I said in my last comment).  The Nobel winner is getting special treatment.

@BenVoigt that's your interpretation. Mine is that the Nobel prize winner is the true control.

As a preliminary observation, I will just note that this phenomenon is a good reason that academic journals should practice blinding of papers sent to peer reviewers.  For journals that practice effective blinding of papers, this whole situation cannot arise, so we are really just talking about the journals that don’t use blinding, or don’t do it effectively.
I think some of the answers here are being a bit uncharitable to your question, by making the assumption that deception of the peer reviewers in the process must be coupled with some broader deception of the journal, or even ultimate publication under a false name or affiliation.  Ethical problems arise in those latter actions, but they are not necessary for what you want to achieve here.  One can imagine an approach in which an author submits a paper to a journal (that does not use blinding) using their correct name and affiliation in the submission system and with correspondence with the editor, but giving a false name and affiliation on the actual document that will be seen by the peer-reviewer.  In this case the submitter would presumably be open with the editor about what they’re doing and why they’re doing it.  If this were drawn to the attention of the editor, it would then be up to the editor to make a decision on whether a deception of their peer reviewer is justified or not.  (In practice I doubt a journal editor would agree to this, since they can achieve the same results by blinding papers, without any use of deception.)  If the editor is willing to go along with it, one can even imagine further safety protocols being added, such as disclosing the true author of the paper to the reviewer after the review is complete, and giving them some debriefing on the deception and why it occurred.  And obviously if the paper were to be accepted and published, it would be published with the correct author name and affiliation, not the one used for deception in the peer review.
If such an approach were to be proposed, it would be quite similar to a number of experiments in academia where a subject group is exposed to a temporary deception to affect their behaviour and then they are debriefed on that deception at the end of the experiment.  Ethics panels at universities routinely examine proposals like this to determine whether or not they meet ethics requirements.  Typically, such actions will be allowed so long as the deception has a bona fide research purpose, is not too harmful, and so long as the people being deceived are debriefed at the end to be made aware of the deception and its purpose.  In the case of a submission of a paper to a journal the difference here is that this is not an experiment, and the only research purpose is to shield existing research work from an adverse peer review effect that is not being dealt with adequately by blinding.
While such a proposal might not be looked on kindly, I’m not convinced that it would be impossible to do this ethically, and certainly without distortion of publication statistics.  Nevertheless, the whole idea is somewhat undercut by the fact that it is simpler to just give a blinded paper to the peer reviewer to achieve essentially the same goal.

Unfortunately double blind reviews are not practical in fields where publishing pre-prints is the default norm. And you'll need triple blind reviews to avoid editor bias, as the editor can make or break a paper by choosing which reviewer to assign to review the manuscript or just reject it outright on their own, so the editor's bias plays a role here too.

@JonathanReez But pre-prints are optional... if a field chooses en masse the convenience of pre-prints over the justice of (say) double blind reviews, then surely they should be held accountable for that decision, rather than it being used to justify foisting dishonesty upon the rest of us?

@LouKnee: There might be some practical issues in holding the field of [insert academic speciality here] accountable en masse.

Also note that in some cases (say when publishing in a non-English language, or when the research is of limited geographical interest), the scientific communities are small enough that reviewers can sometimes guess who wrote given article, just by writing style and implicit biases evident in the papers. No amount of blinding is going to make up for that.

@Arthur I would it is fairly easy to guess the author from a blinded paper just from who they are citing. Even in very big fields and without doing any detective work.

@Arthur in those fields I imagine it would be perfectly ethical to mimic the writing style of a different author to trick the reviewer into thinking the paper was written by an another person.

@Arthur: I'm at the intersection between a particular type of measurement (vibrational spectroscopy), data analysis (chemometrics) and applications (medical, agriculture). Also there double-blinding would be highly ineffective: groups specialize on subtypes of measurements and particular applications (e.g. disesase) over long times. The combination of measurement technique and disease alone would usually narrow down the possibilities to very few (if not one) group. Plus of course, the paper needs to refer to previous work, and IMHO should point out what is previous own work and what is not.

@Lee Mosher If the field of [insert academic specialty here] gets a reputation for propagating bias in the review process, it may then struggle to get the best people. So there is a little bit of leverage... certainly, publicizing the issue is a much more constructive step forward than the OP's proposed web of lies.

It is ethical to submit papers under a pseudonym, see for example this question. Journals do not require you to use your legal name.
But stating an affiliation that you do not have is unethical because you are misrepresenting. It associates your paper with an institution that may not want to be associated with it, and it distorts the publication statistics of that university.
Failing to state your actual affiliation may also put you in breach of contract, because institutions and funding agencies often require you to mention them in the publications made using their funding. Breaking a contract (i.e., committing to do something and then not doing it) is not only unethical but may also get you in legal trouble.

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No.
(Edit: this refers to using a false identity, that is, pretending to be a person that doesn’t exist but with the pretense that the person does exist. This is different from using a pseudonym, that is, hiding your own name but not making the misrepresentation that you are a specific other person with an institutional affiliation that you have no right to claim. As @wimi says in their answer, using a pseudonym is perfectly ethical.)
You are describing a Matthew effect (aka “the rich get richer”) in the context of academic publishing, where the notion of being “rich” corresponds to having a good reputation, being employed by a prestigious institution, etc. Your premise is that once a person is “rich” in that sense, it becomes easier for them to get “richer”.
Now, this premise may well be true (I personally believe it is), and it’s even something to be reasonably concerned about. Where things get problematic is when you cite this effect as your rationale for why certain behavior to compensate for the supposed “bias” associated with the effect should be considered ethical even though it involves clear dishonesty.
The thing to keep in mind is that such effects are not unique to academia, and exist in pretty much any industry and walk of life. Having a good reputation, whether it’s in academia, on academia.se, or elsewhere, will often translate into certain advantages and favorable reception for your ideas compared to people who are unknown in the field they are operating in. (Indeed, it's precisely these advantages that are the reason why the notion of "reputation" even exists as a meaningful concept.) And yet, as a general rule we do not condone dishonesty as a means of dealing with the supposed bias of reputational effects. E.g., would it be okay for me to claim to have won some prestigious writing award when I pitch my novel to a publisher, or to state nonexistent work experience on my résumé when I apply for a job? Obviously not. Dishonesty as a solution to the problem (even if it is a real one) of reputational bias is a case of the cure being worse than the disease. So no, it’s not ethical.

when I pitch my novel to a publisher => this is unethical because book readers aren't supposed to be impartial and are more likely to read books by writers than won a prestigious award. state nonexistent work experience on my résumé when I apply for a job => this is unethical because past performance correlates with future performance, so your employer is correct to demand the truth about your past.

Scientific papers are different because each paper is supposed to be evaluated on its merits alone, regardless of who wrote it, why, and whether or not you've had a beer last week with the author. It's not comparable to job interviews or book publishing.

I'll be happy to accept your answer if you can quote an official journal's policy (or a statement by an editor of a reputed journal) confirming that reputation is indeed important and it's completely acceptable for it to be taken into account during peer review. This would invalidate my initial assumption that this is not how peer review is supposed to work.

@JonathanReez the “merit” of a paper is not a precisely well-defined concept, and suffers from some of the same reputational biases you’re worried about. In pure math for example, a paper solving an open problem that was posed by a famous (=high reputation) mathematician will often confer that paper with a high degree of perceived “merit”, compared to a paper solving a conjecture of a less well known mathematician. I cannot produce a journal statement of the type you want, but my point is that reputation is somehow “built in” at many different levels to the entire system of evaluating …

… scientific work, in a way that makes it impossible (and not even necessarily desirable) to eliminate. Moreover, all the people who participate in this system understand that this is so, whether or not it is made explicit by statements from journals. Perhaps some of them are unhappy about it at some level, but I think most understand that this is an imperfect system but the best one that we’ve come up with to deal with the practical issues of publishing a large quantity of scientific work being generated by many people, while also sorting out the wheat from the chaff.

Interesting... so sounds like everyone understands that there's a ton of bias but it's simply not said out loud? That's sad to hear but also explains a lot about academia...

@JonathanReez I wouldn’t say “a ton of bias”, and I’m not even sure the word “bias” is completely accurate to use in this context, although it’s probably okay as an approximation. “Bias” suggests unfairness, and I think your view that taking reputation into account is automatically unfair is a bit naive and unrealistic. But yes, I think most people understand that this sort of “bias” does exist to some extent. But it’s neither a secret, nor the reason for outrage and cynicism that you seem to think it is.

@DanRomik I think that is much better now. I'll delete my prior comment.

My two cents
I do not think this question has anything to do with ethics. Unless you want to conceal your identity for some reasons, it just does not make sense to publish a paper under a fake identity just to be treated fairly. What will you do after that? Telling your colleagues that it is your work but you want to be treated fairly so you have to use the alias John Smith? I think reviewers care more about the quality of the paper than the nationality of the author.
As for the study you mentioned, from my personal perspective, it is not a bias because if someone gets a fast-track peer-review just because they are prominent researchers. They deserve that because their "conditional" (probability of) error will be lower than that of other authors. They have earned that privilege. If they are wrong, it is the job of other researchers or even themself to show that, but in this comment, I implicitly assume that their papers are high-quality.
Also, why does a prominent researcher want to risk their reputation by publishing a low quality paper and hope that it will be  accepted as a "high-quality" paper because of his/her reputation?
It is also an UNFAIR experiment to give reviewers the same paper that half of reviewers get the paper with the correct author name and the other half receive the paper with the fake alias John Smith. The average quality of papers written by a prominent professor should be better than a random unknown scientist.
Of course, it does happen sometimes that someone wants to conceal their identity for a valid reason. In my field, the most famous example is probably the Student t-test. William Sealy Gosset published the paper about t-test and t-distribution in 1908 under the pseudoname Student to conceal his identity as his employer does not want him to publish the finding.
It may be the case that someone wants to use a fake identity to publish something controversial that they also want to conceal identity, but generally, it just does not make sense to publish a paper under a fake identity.

If you read the linked paper you'll see that the paper was actually written by Vernon L. Smith (2002 Nobel prize winner) and Sabiou Inoua. You can find said paper here. The reviewers were either told the paper is by Smith&Inoua, by Smith alone or by Inoua alone. No fake pseudonyms were used.

What will you do after that? => if your institution doesn't object to this approach you can use the fact that your paper got into (say) Science as a data point for a future promotion. And of course your paper would now be seen by more scientists and will help your discipline move forward.

it is not a bias because if someone gets a fast-track peer-review just because they are prominent researchers => is this a publicly stated policy of any major scientific journals? As far as I can tell the official policy is that every paper is judged on its own merits.

Wait a minute!
If you use a pseudonyms, wouldn't you fall under the category of "the little known author is the only author shown"? which results in worst chances for acceptance?
It seems like the only way to improve your chances is by choosing a name of a well known researcher as your fake name. In that case, doing so would be extremely unethical and probably also illegal.

The linked papers from 2006 and 2017 have also shown bias towards famous institutions, so putting down MIT instead of Moscow State University should result in a pretty major bump in acceptance rates.

@JonathanReez I think that lying about the institute is also illegal, but I am not a lawyer. To me it seems unethical


text:
How can I politely decline a request to join my project by a free rider professor
I've been working on a project with one of my co-authors. The prep stage is done. We're about to get to the experiment stage. A senior professor in my group, who I know doesn't have the skill for the project, and has been pretty much a free rider on others' papers, insisted to join this paper. Not only the free rider problem concerns me but also it can make my other co-author (who is important to me) pretty mad. He is senior in the department. How can I politely say no?

Are you faculty or a student? Same for your co-author.

I am junior faculty and he is very senior

Is your co-author at the same institution as you and the senior faculty ?

@Marianne013. Good catch. I've edited my answer.

@Marianne013 Different institution actually

"He is senior in the department" is ambiguous.  Are you talking about your co-author or the faculty that wants to join?  What is the status of the other?

I'm not sure we can really give a good answer here, because it's going to depend on how generally corrupt (in a broad sense) the culture you're working in is.  I expect a good answer for Germany will look very different from a good answer for Nigeria.

This is hard, especially if the professor is willing to act unethically to force his will.
One approach, that is "polite" is to say that you are sorry, but you already have the necessary skills and background in the current group and time constraints argue against expansion of the group (assuming that is true). To sweeten the deal, you could suggest collaboration on a future, perhaps related, project depending on their interest.
You may have to depend on your co-author, whom you say is also senior, to protect you from any fallout and, perhaps, to make an appeal to the head of the department to relieve any pressure or blowback. This might be possible even if they are at a different institution. It might conceivably carry more weight - or not.
If you are tenure-track, you might, however, need to yield in order to protect yourself, assuming this person has power over your advancement. Don't get in to fights that are impossible to win. One paper isn't going to make or break your career in almost all cases.
I was once in a department (as a student) that had a few factions, constantly at war. Luckily those factions had different math specialties so the problem was manageable and didn't affect students. But factions happen.
Caveat: Your description doesn't suggest this, but in some cases such a request could be an honest appeal for collaboration and a desire for a person to learn something new as a "junior" partner, even though they hold a senior position. But that wouldn't involve coercion.

Practical advice, but not always nice to hear.  A good answer to a tricky problem.

I disagree with: "If you are tenure-track, you might, however, need to yield in order to protect yourself, assuming this person has power over your advancement." Need to in what sense? Science is more important than one person's tenure case. It seems quite simple to me to simply do the right thing and not list their name, and contact the journal if they escalate. It seems more likely the department would be supportive.

@CalebStanford, you seem naive about what a senior faculty member could do to affect the career of a very junior member. Lots of posts here suggest that one needs to protect oneself from vindictive members. Fighting with a senior member is seldom productive.

@Buffy Protect oneself, but at what cost? I don't feel that I am naive about it. If it is a question of giving up my integrity or losing tenure - what a sad decision to make! - perhaps I should choose to lose tenure. That's a high price to pay for a small boost with a colleague, however serious the possible consequences.

And I don't think I said anything about fighting with a senior member :)

@Buffy What do you think about placing the blame with the external collaborator? (assuming they agree to "take the fall") Still too dangerous if tenure track?

@CalebStanford Prioritizing the greater good doesn't always simplify decisions. In this case, making a decision based on scientific integrity that ends a person's career might seem like the more noble choice, but we can't know ahead of time what would have resulted from that career if it had not been ended early. Sometimes the greatest good is done by choosing to serve a smaller number of people in the short term to improve the outcomes for a larger number of people in the future.

@ToddWilcox I agree, but to be totally honest with you I find the outlook I'm seeing on this particular case to be quite disheartening. It's a hypothetical scenario that seems quite absurd (to me), but if the rest of the department would really take the senior colleague's side on this matter, then I'm not sure academia is worth fighting for. Maybe you can help me see why that's not the case.

Frame change: You do not have to say yes/no to him joining the project. Say that you welcome his contributions.
e.g.

Dear Senior Professor,
We are happy to hear you wish to contribute to our project. We are
currently in the experimental stage and expect to collect volumes of
data soon. My colleague is going to follow analysis technique A. Would
you be able to contribute with analysis technique B? Results from two
methods would greatly strengthen our paper and set a foundation for
cooperation on the project.

After this, he could return with an actual contribution, and there should not be an issue with including him. Or the problem solves itself.

I guess the problem is going to be if the senior professor comes back with a proposal for a "contribution" that's either virtual or not useful to the project. Then you are back to saying no to them and their expertise.

I'd push for specific asks, here - basically make it clear that if he wants in, there's specific work that needs to happen. It's a diplomatic way of saying no, and then for gods sake log conversations/meetings/etc, so when he agrees, then does nothing, you can make sure he doesn't end up an author.

We are lacking some context on this question. For instance, we don't know if you have previously met with this senior department member, or whether they have made contributions to a similar area or had prior discussions with you in some way, even if those discussions don't merit authorship, or whether their insistence is just a way for them to try to gain a collaboration which they deeply want and see as valuable, and in their eyes, would help both your research and theirs. It would be odd for the professor to just insist to join for no reason at all (presumably they have some reason which they would claim, however wrongly). It seems likely there is some additional context about your department culture, university, and field that would be helpful.
Nevertheless, the core of the question is about how to proceed if the professor has made no contribution whatsoever to the paper and still insists on joining, and I will answer the question on that basis.
In short, I think that you should weigh the small benefit to your career that might come from this unmerited authorship with the cost to your integrity and broader moral judgment, and the cost to the field itself. I outline seven factors to consider below.
First, in terms of the benefits, @Buffy is absolutely right that your relationship with your colleagues is critical to your success as a professor!
But I do have to wonder whether this is really the best way to achieve that.
I don't know the culture at your department, but if this professor is really as pushy as you say (and has pressured other department members similarly), it is likely that others in the department are unhappy with him for similar reasons. Tensions in departments sometimes go far back. You don't want to anger your colleagues, but is it possible you would also anger your colleagues by including this professor?
Second, there is the question of your other coauthor, who you say is senior.
An additional unmerited authorship will equally affect them, so what is their stake in the matter? Ideally, your senior coauthor should be your best ally here. In fact, they are the one who should (again, ideally) do the work of standing up for your case. If you haven't yet, please ask for their advice. If at all possible, the polite decline should come from them and not you.
Third, while it is likely this could anger your colleague, there are ways to do so more politely and pragmatically, to cover your bases, so to speak. I think that @Buffy and @Eriks have given very good advice about pragmatic approaches. In general, never argue or fight with a senior colleague; be firm and stand your ground, but never be rude, intense, or insulting. All you have to do is politely state your reasons to decline and how you will proceed. You could even give them a gift (for example) to express your disappointment that you were not able to collaborate for reasons X, Y, and Z and you sincerely regret that.
Fourth, we get to the more serious issues of your moral status of the decision. Your own sense of ethics has no small part to play in this matter! It would be my worry that if you throw away that sense now, it will only be a guilt that you have to bear later on, a painful grudge that works away at your inner conscience and may even hurt your belief in the progress of science itself and your own academic integrity. Which is more important? I would be very careful before throwing away that belief and integrity away for a short-term gain with a colleague.
Fifth, what you decide is highly visible -- not just in your department, but also in your community and in your field. I wish to point out that, should you go against your own better moral judgment, you are implicated in this too, not just the senior professor. You are guilty of misrepresenting your results and it is to the detriment of the journal and of your field. Depending on this professor's reputation, if there are many such similar cases, this could even later come to light, and this could even lead (in an extreme case) to a paper retraction.
Sixth, there is absolutely a risk of escalation, but then, we come to the the pragmatics of what to do in that case. I wish to point out that, at the end of the day, the path to proceed is really quite simple. You are the one who has the paper login to submit (and no one else does!) With this power, you have both the ability and scientific duty to submit the paper with the correct list of authors and follow the correct scientific process. The professor can counterclaim authorship over your paper, if they choose to do so; but in case of a dispute, this is also something you would work with the journal on. You may even need to be prepared to retract the paper rather than include their name, in case of a serious dispute.
Seventh and lastly, we come to how to proceed in case of a further escalation which affects your tenure case. In this worst case scenario, you do have some options. Document everything; communicate solely in writing, by email; and make the status of the paper and its contributions clear. Communicate with the journal and the editor early on to let them know about the situation; communicate both with your department chair, and with higher ups if necessary, about the situation in advance. If everything is documented, the department may see your side of things and support your case. Fortunately, people have received tenure under much worse departmental disputes. (And if they don't, is this really a department you want to be tenured at?)


text:
Why is it disadvantageous in graduate admissions to have a higher degree?
JeffE's answer here indicates that holders of a master’s degree are held to higher standards when it comes to graduate admissions. The stated requirements for some graduate programs (example from UC Berkeley) also outright exclude applicants with doctoral degrees. These seem to be saying that holding a higher degree prior to application is a disadvantage (a fatal one in the case of a PhD).
This also applies to private universities: Stanford apparently has the same restriction (at least in computer science); same goes for MIT.
I don't understand why:

If there are two applicants, Alice and Bob, who have achieved largely similar things, it seems logical that both should have a roughly equal chance of being admitted. However, based on JeffE's answer, if Alice has a Masters degree while Bob does not, it's Bob that gets admitted instead of Alice. JeffE's answer even indicates that if Alice has achieved slightly more than Bob, it's still Bob that gets admitted.
If graduate admissions is looking for students that are capable of succeeding in its program, then Alice should be more likely to succeed than Bob since she's already had some experience of graduate study. This should be even more the case if Alice already has a PhD – if she can do it once, she should be able to do it again.

JeffE's answer indicates that since Alice has had more opportunities than Bob, she should also be held to higher standard. However it should also be true that Alice has already achieved what Bob has yet to and in fact might not be able to achieve. Further, JeffE's answer seems to be saying that Alice should do the academic equivalent of financial engineering and pass her graduate-level courses & thesis without getting a master’s degree even if she qualifies for it, which sounds silly.
As for applicants with PhD degrees, my first guess would be that this is because multiple PhDs is not a good idea, and the university is acting in the applicant's best interests. However if this is the case, then this is effectively telling the applicant "I know what you want better than you do", which also sounds silly. UC Berkeley's requirements also seem to be saying that if someone with a CV worthy of a tenured position were to apply for a PhD student position, the university will say "no" even though it's clearly better in their best interests (in terms of research output) to say "yes".
Presumably I'm misunderstanding something because if this behavior were irrational, it would already have been changed. What am I missing?
EDIT: I wonder if things are different in programs where the student is involved in research directly without spending time on coursework?

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What we are looking for, or at least I'm looking for, when talking about graduate admissions is your potential as a researcher.
I'll touch on the PhD portion, which I think is actually more obvious, and then move onto the Masters.
PhD: As Nate Eldredge notes, one of the concepts behind a PhD is that you should have learned how to engage with a field, interact with the literature, learned new methods, etc. And you should have learned how to do it beyond what's taught in classes. Applying for a new degree program, unless it is in a vastly different field, suggests that you have tried to move into a different area and have failed enough that you think you need to go back for coursework and supervised learning. That's not a good sign.
Masters Degrees: The thing about a Masters is that, in some ways, you've already taken a "swing at the bat" - which means that you've had the chance to show your potential - so you need to have done so.

If there are two applicants, Alice and Bob, who have achieved largely
  similar things, it seems logical that both should have a roughly equal
  chance of being admitted. However, based on JeffE's answer, if Alice
  has a Masters degree while Bob does not, it's Bob that gets admitted
  instead of Alice. JeffE's answer even indicates that if Alice has
  achieved slightly more than Bob, it's still Bob that gets admitted.

In this case, they actually haven't achieved similar things. If Bob has gotten the same output despite not having Masters level coursework, access to faculty at the graduate level, etc. then they haven't achieved the same thing.

If graduate admissions is looking for students that are capable of
  succeeding in its program, then Alice should be more likely to succeed
  than Bob since she's already had some experience of graduate study.
  This should be even more the case if Alice already has a PhD - if she
  can do it once, she should be able to do it again.

"Getting through my degree program" is not actually what I'm looking for. For some reason, if Alice is reapplying to a PhD program, she has gotten through with all the tools she needs...and then wants to go back for more tools. That's not a good leading indicator of her potential as an independent researcher in the future.

However if this is the case, then this is effectively telling the
  applicant "I know what you want better than you do", which also sounds
  silly.

They probably do. If nothing else, UC Berkeley is working with a much larger experiential data set.

UC Berkeley's requirements also seem to be saying that if someone with
  a CV worthy of a tenured position were to apply for a PhD student
  position, the university will say "no" even though it's clearly better
  in their best interests (in terms of research output) to say "yes".

An extremely unlikely edge case that might prompt an exemption to their policy, but policy is not written for once-a-generation savants.

Wow, and my first thought if someone with a PhD applies for another PhD student position would be that he/she has failed to get a job, and although PhD positions aren't well paid, it's better than nothing.

@Allure Failing to get any job at all is a bad sign in and of itself. Not necessarily one's fault, but at best then we're talking about paying them for another 5+ years to take another go at it, and at worst, paying them just long enough for them to find another job and leave.
To be blunt, "I gave you the tools and you didn't get a job" should be evaluated with a much less lenient eye than someone who hasn't had those tools yet, which is what the OP's question gets to.

Well perhaps the applicant wants an academic job, couldn't find one, and is willing to take a lower salary to stay in academia; perhaps he has a two-body problem; perhaps he just likes the university work environment (cheap food, free internet, flexible hours ...). Besides even if you don't approve of his motives, as long as his CV checks out, you are effectively getting a postdoc for the price of a PhD student, which should be a great deal. I can understand the reasons, but the premise seems rather misguided to me.

@Allure In all of those cases, they should have talked to me about the potential of being a staff scientist, or perhaps a postdoc. Because I'm not getting a postdoc for the price of a PhD student - I'm getting a PhD student whose likely to quit. Just because one has a PhD doesn't mean they get to skip the course requirements - I'm not going to get useful work out of them for several years while they cool their heels and look for jobs. I'd rather pay more for an actual postdoc.

Clarification about the last part: when I wrote about someone with a CV worthy of a tenured position applying for a PhD position, I was thinking of something like, a professor is denied tenure, so he applies for a PhD student position. He has a CV worthy of a tenured position (a PhD, papers, even grants ...) and he's competing against people who aren't nearly comparable, but his application would be doomed from the start. You have already answered this, but it was what I was thinking about when I wrote it.

@Allure A professor who was denied tenure - but could have gotten it under different circumstances - whose next stop is starting over as a PhD student is both a really small edge case, and in and of itself sets off all kinds of warning flags.

Well, it's a warning that there are too few academic jobs available =/ Are you familiar with the case of Douglas Prasher? Without this kind of policy, he could've sustained himself as a PhD student after losing his job; with it, the next best option is to drive shuttle buses which is not just a waste of talent but also massively depressing.

@Allure While an unfortunate example, trying to turn PhD studentships into a general purpose jobs program and social safety net for academics is really stretching them beyond their purpose.

Berkeley offers the following rationale for their policy:

The Graduate Council views academic degrees as evidence of broad research training, not as vocational training certificates; therefore, applicants who already have academic graduate degrees should be able to take up new subject matter on a serious level without undertaking a graduate program, unless the fields are completely dissimilar.

Although this is rather vague, it does suggest that they believe that when one already has a PhD, it is pointless to enter another graduate program in a similar field, as one has already demonstrated "broad research training" and shouldn't need more.  And since PhD program spaces are a limited resource, and involve a considerable investment of faculty time and university resources, they don't want to spend it in ways that they consider pointless.
That's my interpretation, anyway.

Yes it is reasonable that a finished MSc could more easily start taking PhD courses on their own than a finished BSc could, but the PhD programme is not just (not even mainly) about the coursework. It is about learning to become an independent researcher.

If there are two applicants, Alice and Bob, who have achieved largely similar things, it seems logical that both should have a roughly equal chance of being admitted.

Not at all.  PhD admission is primarily based on potential for future success as an independent researcher.  Between two people with identical research portfolios, it is natural to judge the person who built their portfolio faster and with fewer opportunities to have stronger potential for future success.

If graduate admissions is looking for students that are capable of succeeding in its program, then Alice should be more likely to succeed than Bob since she's already had some experience of graduate study.

You've moved the goalposts.  If Alice produces more concrete evidence of research potential than Bob as a result of her graduate study, then she meets the higher standard expected of applicants with graduate-school experience!  On the other hand, if Alice does not produce more concrete evidence of research potential than Bob, despite her experience of graduate study, then Bob is a more attractive candidate.
Merely having been a graduate student is not by itself evidence of research potential; research rarely resembles coursework.

Thanks for the answer. Do you mean that if Alice meets the higher standard expected of applicants with graduate-school experience, she is also the more attractive candidate than Bob (because her graduate-school experience means she should be able to get into research sooner)?

@Allure Maybe.  Maybe not.  It depends on how much more evidence Alice has accumulated than Bob.  As a general rule, at least in strong US computer science departments, PhD applicants with master's degrees need to have publishable research results, if not actual publications, to be taken seriously.

Whether it is made explicit or not, I would imagine that most graduate programs try to evaluate candidates on the basis of future potential. Probably most programs should be more clear about this.
So, for example, if one has been allowed to take qualifying exams endlessly, for 20 years or so, and eventually passes all of them... what does it mean?
It's like age or weight classes in various sports. The possible fact that a 30-year-old can bat 1000 in T-ball aimed at 5-year olds does not earn a spot on a major-league team in the U.S.
Although there's very little age-ism practiced in the U.S. in PhD admissions in mathematics... the point is not "maxing out on prelim exams", or anything similar. It is infinitely more about people on an upward trajectory...

If by "succeeding in its program," you only mean finishing a PhD, then your premise that a graduate program is looking for students capable of succeeding in its program is quite flawed.
The impression I got from my graduate program is that they consider outcomes like mine failures, and I have a tenured position in a department with a PhD program, albeit a low-ranked one, and publish a paper or two a year.
If they had a choice between Student A, whom they thought was 100% likely to end up in a position like mine, or Student B, whom they thought was a 20% chance to end up in a top-30 research department with an NSF grant and an 80% chance to drop out after 2 years, I'm pretty sure they'd take Student B.  In fact, if there was Student C, whom they thought was a 2% chance of eventually winning the Fields Medal and a 98% chance of dropping out in the middle of their fifth semester, dropping the ball on their teaching duties, I'm not sure they wouldn't prefer Student C to both.
If you have already had graduate studies and did well but not brilliantly, you've proven that you won't be a disaster, but you've also shown you are less likely to be wildly successful.

I don't agree with this comment, but I upvoted it because it expresses clearly a perspective that may be useful to consider.

(+1) especially for the last sentence, which agrees with my experience in math in the U.S. -- 4 different graduate programs (admittance strategy for last program, if interested) and much advice from people looking out for me along the way. Besides what you said, for a student who already has a masters degree, but fails their Ph.D. exams and has to leave the program, it's more likely they won't bother trying to get a "charity masters degree" from the department, and thus won't contribute to the department's degree count.

PhD students do useful research work.  Supervisors will want a PhD student who successfully completes a project.  A candidate who already has a PhD may be more likely to quit prematurely.  I've seen it happen.
When I did my PhD, a new colleague PhD student joined.  He already had a PhD from a developing country, from a university that is perhaps not very well known outside his home country.  He considered that a PhD from a more established university in a more developed country would be more valuable.
Fast-forward two years, he suddenly left when to take up a postdoc position in yet another developed country.  His supervisor was not happy, and I expect will think twice before accepting again a PhD student who already has a PhD.

Thanks for answer. Follow up question: why is his supervisor not happy? After all, he got two years of productive work out of the postdoc-masquerading-as-PhD-student for what was presumably the lower pay of a PhD student.

@Allure Good question. I prefer not to go into detail on a public forum, for lack of anonymity, but the way in which it happened did not help.

In addition to the other excellent answers (from people who have infinitely more experience with the process than I), consider: It seems to be the case that for successful researchers, there is unique academic credit/prestige assigned to the PhD awarding department and advisor. Examples: (1) Richard Lipton's blog. (2) Joel David Hamkins' blog. If a person has multiple PhD's, then who gets that credit? At best this credit would seem to get split and diluted. At worst, one or the other is at risk of being forgotten entirely.

I don't see why that is worse than any successful person having lots of different adult teachers and inspirations around when they were kids. Who helped him the most to become that great? Well, who knows..? Probably does not even know that himself.

@mathreadler: I added the word "unique" and links to examples if you wish to confirm what I'm saying. Other teachers or inspirations are not cited in the academic research culture.

Ah so you are worried about the academic credit and not who actually helped the guy (wanting) to become a great scientist. Okay.

@mathreadler: Mind that Daniel R. Collins’ is not describing his own concerns but those that others may possibly have.

@Wrzlprmft yes I know, what he really wonders is who of the professors should get the credit for pitching the student on to his corporate masters.


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"Full" versions versus "Preliminary" version of result/paper. Are they considered different?
This is a common pattern in publications, not exclusive to my field (TCS):

An author submits a paper to a conference (as preliminary version). Then, after acceptance to a conference, virtually the same paper (modulo some modifications, etc mostly in length but rarely in any conceptual level) is submitted to a journal, possibly with a different title (but not always). The latter is called full version. In many cases, the two versions are indistinguishable and in most cases epsilon away (for a small epsilon).

At the end, the author has two publications (conference+journal) from practically the same technical result.

Is this considered as one or two publications? (technically of course are two different publications, but how people perceive that?)

From what I have seen, this is generally considered as 2 publications. So, an author with 5 results that follows the above pattern will have 5 conferences + 5 journals = 10 publications. Another author with again 5 results that are submitted only directly to journals (for one reason or the other, for example lack of travel funding from the institution) will have only 5 publications and, subsequently, will be ranked lower than the first author/candidate.

My question is:  How do academic people perceive the same publication that has been published in a conference as a short version and, subsequently, in a journal as a long version where both versions contain virtually the same text/results. How can someone evaluate this when sometimes these two publications appear with a different title?

What do you mean by "count" here?  "Count" for what purpose?

@AlexanderWoo I mean exactly what I write in the following paragraph. Technically it's two publications but in scientific terms it's just only 1 result.

@AlexanderWoo OK, I changed my wording. Hope it's clearer now.

Are they considered difeerent by whom? Speaking personally, as a theoretical computer scientist, I do not consider them different papers.

@JeffE I am also in TCS, and not everybody considers them as different papers. (sample, and personal experience, example: "look this candidate has 3 FOCS/STOC AND 3 SICOMP" no matter that the journals are the same as the conference papers)

By whom and for what purpose?  An award committee?  The dean?  A hiring committee?  A hiring committee for a research university or a liberal arts college?  Which university specifically?  In what country?  It's very possible that someone has x publications for purpose 1 and y publications for purpose 2, where x and y are different.  I also don't know of any sane reason for someone to compare raw counts of publications without further context.

@AlexanderWoo I was mostly asking how people in academia perceive such situations. For example grant proposals, or hiring committees. I've seen, even in TCS, some times decisions to be justified by raw counts as you say (looking at pub list, and comparing the names of the conferences/journals), thus the question.

I edited the question. Now it should be clear what I am asking.

I don't think this question has a universal or near-universal answer.  Different people, or even sometimes the same person in different contexts, will count differently if they need to count at all.
More generally, I don't think anyone actually makes decisions based on raw counts of papers, though plenty of people try to justify their decisions to others based on raw counts.
Two versions of the same paper count as two if the person doing the counting wants to make you look better and count as one if the person doing the counting wants to make you look worse.

I also think the "justification" of decisions could definitely lead, sadly, to different metrics.

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How can I do well with an unpredictable boss as a postdoc?
My current postdoc advisor is an expert in my research field. He is head of research center and has huge amount of experience in this field.
The poblem is, he is a bit whimsical. Sometimes he is happy in one day, but he become very unhappy the very next day when discussing exactly same topic. I think he is a...  bit emotional. It is not always the case, but if it is his unhappy day, a meeting on that day 'usually' goes bad. If he is happy, usually the meeting flows in good mood.
As you may imagine, he changes his mind frequently, and sometimes he changes his words. Sometimes I wish if I could record his voice and listen together next time. He is old, and he is controlling numerous projects from a moderate sized research center, so he may forget about my work. He can forget, that is OK, but sometimes it makes me really sad, feels like he doesn't care about my work at all.
Oh, and he is really skeptical. Skeptical attitude as a scientist is a good in general, but I think sometimes he asks too much. I achieved the research target last summer, and presented in conference back in September. But from then, I couldn't publish this paper because he is keep asking for more validation and validation over and over. He is a very experienced researcher, so I respect his decision. But I never saw such amount of validation from other papers in this field... To me, it seems enough, but to him, it is not.
So, I'm really demoralized. It is just one year after joining this group, I didn't even have a chance to show my full potential to him. But as I lose morale and will to pursue, I'm also losing my interest in this topic. This influenced my productivity, and he is not that happy about me recently.
What should do? In general, what is the best way to deal with such a boss?
Does his behavior mean that he doesn't like me and my results, and he expresses it in such way? I really have no idea how to satisfy him and publish this work.
Also, I wish to find a new post-doc position, but he will not write a good recommendation letter for me, so I feel like I'm trapped in here. Should I still try to find a new post-doc position, without his recommendation letter? Is this possible?

Should I still try to find a new post-doc position, without his recommendation letter? Is this possible? This is a separate question, and it probably has been asked before on this site.

@henning Thank you, could you give me a link about that question?

@Monika Thanks to share your experience. Yeah, it seems that I need to look for another position soon. I have at least 3 other people who could write a letter of recommendation so that should be good.

Try these: https://academia.stackexchange.com/questions/635/how-to-handle-not-having-my-phd-advisor-as-a-reference https://academia.stackexchange.com/questions/80702/what-to-do-when-expecting-a-negative-recommendation-letter https://academia.stackexchange.com/questions/58652/i-cant-trust-my-supervisor-anymore-but-have-to-have-his-letter-of-recommendati https://academia.stackexchange.com/questions/100404/professor-refusing-to-write-recommendation-letter-to-make-student-work-longer If this doesn't help, make it clear how your situation differs when you write a new question, so it won't be closed


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Convert Spanish grades to English scale?
I'm a English citizen which has been living in Spain for the past 7 years (I'm currently 15 years old in case you're wondering) and I plan to move back to England at the end of this school year.
Can anyone tell me what's classified as a C in percentage? And a B? A 50%? A 60%? In Spain the grade scale's from 1-10, 5 is classified as the minimum pass and 10 is classified as excellent. Thank you guys for helping me.

I'm voting to close this question as off-topic because it is about school and not about academia.

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Is the ETH Zurich part of the University of Zurich?
I'm wondering if the ETH Zurich is part of the University of Zurich. Not only are they build close together, according to Google there are famous graduates of the ETH that are also listed as graduates of the University of Zurich(for example Einstein). I couldn't find an answer on neither of their websites.

No, it is not. Actually, UZH was forked off of ETH 100 years ago. In practice, there is substantial collaboration between the institutions, though.

Some quotes from Wikipedia:

ETH is a federal institute (i.e., under direct administration by the Swiss government), whereas the University of Zürich is a cantonal institution. […] In the beginning, both universities were co-located in the buildings of the University of Zürich.
[…]
Events of the neighboring University of Zürich are well-attended by ETH students and vice versa.
[…]
The amicable rivalry between ETH and the neighbouring University of Zürich has been cultivated since 1951 […]


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Are professors generally straight forward about admission decisions?
I had applied for a PhD to some colleges in the US, and am waiting for admission results. A professor at a college that I am hoping I am accepted at has responded to my queries of "Is my application likely to be accepted, or should I just accept school B's offer?" with the same answer "your application will be considered in the second round, so you should wait for it. However, I cannot make any promises".
I feel that if the professor thought I had a good chance of getting in, he might have stated so in his replies. "I can't make any promises" seems to be a polite but safe reply, indicating I might be accepted, but thechances do not appear too bright. Should I just accept school B's offer?

I would imagine that 'I cannot make any promises' could mean anything from 'I really really want to have you, your application is really strong, and I'm annoyed and confused as to why they haven't accepted you yet, please don't go elsewhere' to 'you're on the list still, but near the bottom and there's not much chance we'll get enough funding, so you only have a chance if lots of people go elsewhere'. In between there's things like 'could someone please just decide how much funding we have so we can make decisions?' and 'grad applications? I forgot about those; could someone fill me in?'

I take "I cannot make any promises" to mean ... I cannot [i.e., I won't] make any promises.  Behind that door could be anything.
In other words, it added no information to your decision about whether to respond in advance to School B's offer.
I wouldn't recommend asking the same professor again, but a more informative question for you to have asked would be when (with specific reference to the April 15th deadline that most graduate programs operate under) you would hear back.
Your best bet is to wait.

Should I just accept school B's offer?

Probably not -- at least not yet.
In the U.S., at least in my discipline of mathematics, deadlines everywhere are coordinated to be April 15. If you decide where you would like to accept an offer beforehand, it is good manners to let everyone know of your decision immediately. But in your situation, where you are waiting on an offer you would prefer, it is fine to wait until B's deadline.


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Quitting a PhD program and starting another one: who is the legal owner of my research?
I am at the late stage of a PhD program. For some personal reasons, I have decided to quit this program and apply for a new PhD program in a different country.
I have presented one part of my research in an international conference, and I am about to submit it to a journal. Beside this paper, I have prepared 3 other papers but I have not presented them anywhere. I am the sole author of these three un-published works.
Now my question is whether it is possible to bring these researches to the next university and publish them afterwards? I am the legal owner of these researches? copyright-wise I mean.
I would be more than glad if anyone helps me in this tough situation.
PS: I would have no problem for getting recommendation letters.

Depends on the country and university, but you are likely not the legal owner of research performed using university/grant time or resources.

Sounds like you could just finish up your PhD. With good recommendation letters go get a post-doc, not another PhD program with who-knows-what hoops to jump through.

@JonCuster while that might be true in some sense, OP has unstated personal reasons for not going that route. Presumably they have weighed to pros and cons about making such a move.

@JohnColeman - True, but once one starts weighing other additional factors (like who 'owns' the research) then it is high time to re-evaluate the entire decision.

Is there actually such thing as legal ownership of research?  Copyrights and moral authorship rights for research papers, of course.  Research equipment, sure.  Research data, maybe.  But research per se?  What exactly are you supposed to "own"?

According to the Berne convention, authors automatically own the copyright to anything that they write.

Thanks all. What I meant is exactly the research papers. There are three papers that I have almost finished, but never presented anywhere, except to my supervisor.

I have considered finishing phD and going for a post-doc, the problem is exactly finishing the PhD. There are a lot of costs such as conference attendance, proofreading for publication (the university is in a non-English speaker country and all faculty use proofreading grant except me!), cost of submission of the thesis and so on that the department does not want to cover, while it is covered for other grant-holders. I am fed up with the discrimination, and actually I don't have saving to defray all these costs. I though somewhere else would appreciate my research better.

Within limits, you most definitely can bring the old research with you and publish it. Unregulated digital data stored on a standard computer should be fine, but for example, there may be limitations on moving human subject data (even de-identified data) depending on what the IRB protocol said. If the research involved samples (e.g., chemical compounds) moving these may also be regulated.
You may or may not be able to use this previous work towards your dissertation. You will have to check with your new department.

all my research is based on public data, I have only used University grant which I have done teaching and supervision in compensation. Thanks for the reply


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One of my former professors no longer works as an academic, Can I still ask her for a recommendation letter?
I am applying for a graduate school which has a special reference form to be filled. On the form, the referee should write his/her name and position. Does that mean all referees must be current academics?

Yes, you can ask your former professor.  No, it's almost certainly not required that all referees be current academics.  There'd be no sensible reason for a graduate program to require that.
Your professor can use her best judgment as to whether to fill the form with her current position or something like "Professor (former)".  In the letter, she should explain what her position was at the time that she worked with you.


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Is it worth enrolling in a Ph.D. program without employment?
As I understand, European universities offer two types of Ph.D. programs:

Ph.D. without employment
Ph.D. with employment

As far as I understand, North American universities do not work in that way.
Is it worth enrolling in a Ph.D. program without employment (#1) careerwise if someone wants a job in academia in future?

In several French universities you practically cannot enroll on a PhD on computer science without an employment contract (e.g. CIFRE)

The question in the title and the question in the post are wildly different. What are you asking, exactly?

Being in a PhD program with work contract does not mean that you will teach. Your working obligations may be exclusively research related.

As is this question is extremely unclear. Can you focus on what exactly it is you would like us to answer?

Even in the U.S., Ph.D. study in many subjects is without employment.  Most subjects in the arts and the humanities, for example.

Europe is not a country but a continent. The links you gave are from the university of Vienna, and the example of employed PhD students refers to a special program from the University of Vienna, so that is not even Austria-wide.
Enrolling in a PhD program without employment can mean many things, for example it could mean you get no financial support what so ever, i.e. you are self-funded (but even there is variability depending on how much tuition you pay). Being in a PhD program without employment could also mean you receive a stipend instead of wage (which has consequences for your eligibility for social security, pension, health insurgence, etc. This varies to a huge extend from country to country).
In general a PhD degree is a PhD degree regardless of how it was funded. It may be that some programs are more prestigious than others, but that is country specific: It may be that in some countries particular stipends are very prestigious, while in other countries employment is so rare, that getting it is considered prestigious.
I would be weary of self-funded PhD programs, but otherwise stipends and employment contracts are both fine.

+1 for "Europe is not a country". I do not know how often one must say this on Academia.SE.


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Does failing in a different program affect graduate admission application?
Suppose, someone failed in a STEM grad program 'A', and hence it is incomplete.
Then he gets acceptance in a non-STEM grad program 'B', and completes it.
Now, if he applies for a position in a funded Ph.D. program related to 'B', would he face hard-times in getting an acceptance because of his previous failure?
Why or why not?
Kindly, explain.

Potentially yes, this is really subjective (based on the grad program, your portfolio etc)

@Spark, it would be good if you expand that a bit to an answer. You have the key elements here.

@Buffy, how can I edit this question to make it reopen? Coz, I need more answers.

@Buffy, is the edit good enough?

@user366312 When you edit a closed question, it goes into a review queue where users with a certain level of reputation can decide to reopen it or not.  Moderators do not usually unilaterally close or reopen questions unless there's a clear cut case, but instead leave these kind of decisions to the community. Closures can be also discussed on [Meta].

It might.
First off: there is no record of you failing the program so it’s unlikely that anyone will know unless they actively try to find out. So, I wouldn’t highlight it. If they do find out, I strongly recommend telling the truth, it’s easy to find out whether you we’re enrolled. From now I’m assuming that the committee somehow finds out, or you tell them.
You have tried to get through one grad program and did not succeed. Taken on its own, this sends a negative message to the admissions committee, especially if your prospective topic is relevant to your past CS experience.
But grad applicants are humans, and humans make mistakes. You need to tell the grad committee what you learned from that experience and why do you think it won’t happen again. Don’t make it the focus of your application (again, they probably won’t know). You need to tell them what your strengths are and how you’d fit the grad program. As with every case, it’s hard to say how they’d react, because we don’t know what your portfolio is like.

there is no record of you failing the program so it’s unlikely that anyone will know unless they actively try to find out. So, I wouldn’t highlight it. --- not listing all academic program I attended and receiving money from the university at the same time, is a punishable offense, I believe. University reserves the right to revoke my degree in case of a fraud.

These details vary, so in that case see second part

I have emailed a professor in the USA regarding my situation. He told me that my abandoned STEM background is really not an issue and he doesn't care. So, for the moment, I am happy. But, I don't know about others.


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Is there any unwritten rule in the academia regarding the rate of paper publication during the PhD?
Is there any unwritten rule in the academia regarding the rate of paper publication by a PhD student?
I.e. how many paper publication per year is considered as a good performance for a PhD student?
How does that vary from 1st to last year?

See https://academia.stackexchange.com/q/34581/72855

The answer to this is dependent on too many things for any reasonable answer. In some fields it is unusual for a doctoral student to publish anything before finishing the dissertation and even that might be published after the degree is awarded, if at all.
In other fields it is common for the dissertation itself to be a summarization of some set of already published papers, but even then, the expectations will vary with the field and with the individual university. They might even vary with the advisor.
Of course, there are papers and there are papers. When publications are required a larger number of less significant papers may not outweigh even a single significant contribution.
The situation is complicated by normal practice in some lab sciences in which papers have a large number of authors and each contributes differently. In such fields, precisely where you are listed in the list of authors can be significant and can indicate the "amount" of contribution. There are many questions on this site that come from fierce disagreements over author placement. Again, however, having lots of minor placements might not get you very close to completion.
Number of papers produced is a terrible measure of productivity. Citations of those papers by others is a better measure.
But to get an answer that applies to yourself, ask your advisor or some other professor(s) in your field and at your university. That will yield the only meaningful expectation of your progress.

Computer science.

I agree with much of what @Buffy writes. I'll add: PhD students can compare themselves with their supervisor's other PhD students. Possibly using  publication venue as a crude means to determine paper quality.

But what kind of computer science? Publication practices in algorithms, architecture, and artificial intelligence differ significantly, and that’s only the A’s. Expectations also differ by county, by university, and even by advisor.