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Mixing primary and secondary references
Suppose paper 1 establishes that roses are red, and cites paper 2 for the statement that violets are blue. Apart from the blueness of violets, no other results from paper 2 are relevant for paper 1, nor for my own essay.
How should my essay refer to these two assertions?
I see three possible options:

Citing the primary source for each statement: Roses are red.[1] Violets are blue.[2]
Citing each relevant source for each statement: Roses are red.[1] Violets are blue.[1,2]
Downgrading the second statement to a secondary citation: Roses are red.[1] 2 had earlier established that violets are blue.[1]

Is there a generally accepted preference for one of these?

I'd go with 1. Why complicate things?

Normally you should cite the primary source. The only reason I would prefer to cite a secondary source is if it is more readable than the primary source, in which case I would cite both.

It really depends on the context and the reasons why you feel that sharing such assertions contributes to your own essay.
Generally, the first option you mentioned is best, which is citing each assertion according to its original source: Roses are red.[1] Violets are blue.[2]
In some cases, if you have no access to source 2 cited in 1, it may be acceptable to cite only 1, particularly if 1 is a meta-analysis or a review of existing assertions: 1 notes that roses are red and violets are blue.
Similarly, if you are using a direct quote that was itself directly quoted in source 1, it is generally acceptable to simply explicitly make note of this if it is difficult to track down the original source 2: "violets are blue"[2, cited in 1]
Your second option could falsely imply that both source 1 and 2 independently demonstrated that violets are blue (which they do not in your example), and your third option misleadingly cites 1 when you have already cited 2 in the sentence, which is confusing to the reader.

Thank you @electroducer for your comments

It really depends on the context and the reasons why you feel that sharing such assertions contributes to your own essay.

What I'm trying to convey is, "The credit for the research on violets goes to [2], but if you want to read more about either of the two assertions, [1] is the place to start."

(Sorry for the garbled markup in the comment above; it seems that I don't have permissions to use newlines and blockquotes in my comments.)

Honestly, @tyomitch, I think what you have written in the above comment is similar to what I would write if I wanted to convey that.

@electroducer answer is good because it also deals with the related  issue of how to handle not having adequate access to assess the sources. In option [1], the reader must assume you either read both, or that you are comfortable that secondary source did not accidentally or willfully mis-color their interpretation.


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How to be efficient with large blocks of time?
I'm currently a graduate student in engineering (working toward my Master's). Over the summer semester I'm taking three classes in addition to researching at my adviser's lab.
The lab is located off-campus (about a 30 minute commute), so it doesn't make much sense to fill in all of my gaps between classes with research time.
However, after making my schedule, I realize that I have these awkward 2-hour breaks in the afternoon. I also have 30-minute breaks later in the day, as well.
Given that I can't research in these times (the commute is too long), and given that I'm generally a nocturnal person and like to work on problem sets at night (from the comfort of my dorm), what is the best academic use of my time during these breaks?

As far as I can tell, many of these apply to your situation. Maybe duplicate?

Keep a to-do list, and glance over it to see if there is anything you can do easily (i.e. without needing to commute)

Maybe this is just me, but 30-minute breaks are a perfect opportunity to sit down and plan out the rest of your week: when are you going to get the problem set done, when are you going to finally finish that Netflix series, when are you going to go grocery shopping, etc. Depending on how in-depth your "weekly plan" is, it might take the whole thirty minutes to plan it all out, and I feel really relaxed afterward knowing that I have dedicated time slots for everything for the rest of my week. (:

ff254's comment has a great list of links and I think reading papers is the best academic use of that time time. But I also recommend using the time to relax so your don't get burnt out from work/class. Two hours is perfect amount of time to grab a meal, read a book, take a nap, or hit up the gym. Remember to invest in your mental and emotional wellbeing as well as your academic education.
(This was originally a comment, but it got a little long so now it's an answer. I'm sorry it's not directly answering the question.)

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Eternal Doctoral Thesis
How can I help a friend who is working on a doctoral thesis since about 10 years?
It seems to me that achieving a doctoral degree is close to impossible at that point. I am sure that there is no actual progress on the thesis out of a lack of motivation and too little motivation to try something else.
He evades questions about the thesis, but at least tries to pretend that work progresses, if slowly.
I think there is no gain in helping him in the short term. By that I mean that currently my friend seems to be happy enough, and it does not feel like he just pretends to be. Also, he gets financial support from his family.
But my judgement might be off, since I only know him since about five years, and I heard an other opinion stating that he changed significantly. Also, when I try to put myself in my friends position, I would likely be devastated to the core. But try as I might, I don't think that I could repress my problems and veil them to the outside for long.
Putting that aside, I suppose that he will suffer social and financial insecurity in the long term, when his parents will not support him any more. So in this respect, it seems to be a good idea for him to get a job, except that he would need to face that he failed at his academic career to a larger extend. Even though it seems to be a rational choice to me, assuming that I manage to convince him to apply for a job, it might have psychological repercussions and damage our friendship.
Nonetheless, I would still like to push him to get a job if it can be done. So instead of asking about other options or more insight; Do I have a chance to nudge him into getting a job and if so how can it be done?
There is no fail-safe formula or instant solution to this problem, but if you have advice apart from the actual question please leave a comment/link.

The tricky aspect of this question is that you don't seem to know for sure how much progress he is actually making.  Ten years is a long time to spend in graduate school, but not unheard of.  If he is slowly making progress and supporting him isn't too much of a burden on his family, then he might be better off finishing in eleven or twelve years total, rather than quitting after ten.  (Finishing may feel much better than quitting, even if he doesn't get an academic job at all.  There are also different sorts of academic jobs: he might benefit from the degree if he ends up in high school or community college teaching, where having a Ph.D. could mean something and they might not care if it was a long, slow process.)
If he is making no progress at all and will most likely never complete the degree, then doing something else with his life would be a better choice, but of course that's a very difficult conversation to have.  If this is the case, then his advisor should already be dealing with this issue, but it's possible that the advisor is avoiding the topic.
Another difficult case is if he could complete the degree, but nobody wants to support him for long enough, or if his plans for what he'll do with the degree are unrealistic.
My recommendation is that you shouldn't intervene unless you have an exceptionally close relationship (romantic partner, best friend, etc.).  Otherwise, it's really none of your business and I doubt you'll have a productive conversation.
If you do have a close enough relationship, then the first step is to have a honest conversation about how things are going, what his hopes are for the future, what's realistically possible, what the trade-offs are, what his fallback plan is, etc.  Without that, all you're doing is guessing.  Merely having this conversation could be a useful way for him to clarify his thoughts, so I'd start with that rather than focusing on making changes.  Discussing potential changes can wait until you have reached consensus on the situation he is facing.

Some people take upwards of 4 decades to complete their Ph.D. ;)

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Is the adoption of IS0 9000 principles, or even actual ISO certification very common in universities?
I'm not sure if this is on-topic but nothing seemed conclusive that it wasn't in the help center, so let's see what happens.
The ISO 9000 family of standards has been adopted by well over a million organizations in the world, most of them are of course businesses with customers, but not all of them are.
I'd like to know if the adoption of IS0 9000 principles, or even actual ISO certification is very common in universities.
The two areas I'm interested in are

Large science efforts that handle substantial funding, where the standardization of procedures might improve efficiency of use of funds and project completion
Universities of no particular size or areas of research, but where the procedures are of a departmental nature i.e. paperwork, human resources, departmental budgets and management, etc.

My guess is that there may indeed be some adoption in the first category and only small, scattered or isolated instances of the second, but it's only a guess.

What are you trying to achieve?

@AnonymousPhysicist I believe that the purpose of Stack Exchange is to work in a collaborative way to generate good answers to on-topic questions. By asking thousands of Stack Exchange questions I hope to do my part to facilitate that. Thank you for doing yours!

Universities have to go through a periodic accreditation process, which has roughly the same function. See for example https://sacscoc.org/ for an organization that performs accreditation audits.

Where I was doing my PhD, Tyndall National Institute (an Irish research institute associated to a university), I remember admin circulating emails about some inspection related to ISO certification. I don't know if they got it or already had it, but they were certainly striving to be certified.

@DanielHatton Don't you think that students are customers? Don't they provide cash and expect something of value in return? What about agencies that provide funding for research (equipment, travel, staff salaries, etc.)? Don't they expect that the funds are managed well, spent in appropriate and accountable ways to further specific, stated goals? Modern universities are more than just places to further the "ethos of independent, self-governing scholars" these days. They're not just hotels for smart people to sit around and think independently and express themselves whenever they see fit.

@DanielHatton anyway, just because some aspects fo ISO standardization might require customer-specified standards doesn't mean the adoption of some ISO principles (as asked about here) is impossible. For example, one aspect might include 1) standard procedures for doing things exist, that 2) these procedures are documented, that 3) they are followed, and that 4) there's a mechanism to verify and ensure they are followed. How would those, applied to things like money, record-keeping/privacy, human resources, etc. run counter to  the "ethos of independent, self-governing scholars" these days?

I know of one university which is ISO 9001 certified.  Most universities are not.  I have not been able to discern any benefit to the certification.  I am not aware of any "science effort" that is certified.

Various DOE national labs (US) have a range of ISO certifications.

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Is it okay to cite a supplemental attachment when referencing a previously published technique or method? (advanced materials and surface science)
The thorough answer to Roadmap and possible pitfalls for a first-time software author to publish a paper on a Python package? covers the issue nicely, and it's not yet clear if in my case this paper still needs to be published stand-alone. The reason is that the mathematics behind it will be sufficiently described in a supplemental materials document associated with a (hopefully forthcoming) publication in the general fields of advanced materials and surface science.
Now my question is if the supplemental section of a published paper in a well recognized journal will sufficient to use as a citation in subsequent papers e.g. "coefficients were extracted using the same analysis as previously described in X et al." (or something with less awkward cadence) where the bibliographic item will mention the supplemental section to that paper.
Question: Is this a generally acceptable way to do this, or are supplemental materials not considered to be "real" references, either because (perhaps, just guessing) they are not as thoroughly peer-reviewed as the main paper to which they are attached, or don't appear in the print version and so are not considered as accessible, or for reasons I can't yet imagine?

Maybe there's variation in this, but I've written citations like "following the method described in the Supplementary Information of Ref. [X]".

@Anyon this might turn out to be a simpler question to answer than I'd originally thought, and that might be a well be the well-received answer to it!

Why wouldn't you be able to cite this?  Citation just gives credit, it doesn't attest that it's been peer reviewed.

@ScottSeidman the goal of citing the supplemental material is to provide a source where the  "...mathematics behind it will be sufficiently described ...", not to assign credit. It's achieving that goal that I'm asking about. Rather than a "Why would you think it wouldn't be?" comment, if you think it will be okay then please feel free to post that as an answer. Thanks!

(Converting my old comment to an answer.)
Maybe there's variation in what is acceptable or commonplace, but (in physics) I've written and read citations like "following the method described in the Supplementary Information of Ref. [X]". To me this is not particularly different from referencing specific parts of a paper, such as a specific page, equation, theorem etc. The supplement is obviously less central to or integrated with a paper than such specific parts, but since it's usually published along the main paper, I consider it to be associated with it.

Yes this certainly seems to be okay now that "published" pretty much refers to the electronic rather than just the library-shelved bound journal version of a paper (from my previous academic incarnation).

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Second bachelors needed to transition from math to engineering?
If I have a BA in math and want to transition to mechanical or electrical engineering graduate school, is it better for me to complete a second BS in MechE or EE and then apply to grad programs, or is it enough to take some undergraduate prerequisites and then apply to graduate programs in engineering? Does it look "credible" to have a math undergrad and engineering grad degree, or will people assume I am missing the fundamentals without the BS on my CV?

What do you envision studying in grad school and what applied math classes have you taken? Some subfields, e.g., controls or the theoretical end of fluid dynamics, are strongly aligned with mathematics; others, e.g., experimental material science, will be much more dependent on engineering principles and other domain knowledge.

Nobody really cares about your undergrad degree once you have a PhD (broadly speaking). The bigger issue is convincing an engineering PhD program to admit you. That will depend on their concentrations and your other courses (physics, chemistry, some engineering).

In which country or countries do you hope to study?

To expand on Buffy's comment, in countries with a "short" PhD programme, the natural route from a very  pure maths undergraduate course to an engineering PhD would be through an appropriate masters degree (in the UK, a taught MSc). It's unclear from your current question of this is an option you're discounting or haven't considered.


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Can I use a Stack Exchange answer post as references in journal articles in the physical sciences? Should I include precedent so editor doesn't balk?
While this Mathematics SE answer might (or might not) be a straightforward exercise to a number theorist, to an experimental surface scientist it seems new, as-yet unpublished (in this field) and really helpful and enabling.
Queries in comments don't seem to indicate that the author has a keen interest in recognition for it (it's hard to ask direct personal questions of users in SE) but nonetheless I would like to cite it in a paper that might be destined for Physical Review B or Review of Scientific Instruments or similar in the scientific modeling/computing field, depending on how the paper finally fleshes out.
I'm curious how often SE answer posts are cited in scientific journal articles, and if there are (perhaps notable) precedents in the Physical sciences I could cite in an effort to put an editor (or reviewer) at ease who might otherwise balk at such a nonstandard reference format.
Question: Can I use a Stack Exchange answer post as references in journal articles in the physical sciences? Should I a priori include a mention of precedent along with the submission so that the editor doesn't balk?

Q: Why not just do as the post author suggests "Maybe their authors would know some good text for you to cite?" and avoid citing Stack Exchange

I'll be implementing this specific algorithm exactly as written, hints and caveats and all. (go have a look - it's quite complete and rigorous!) Other references will be less complete and applicable.
This is like a standard, named "private communication" except that it's public and less-named. We do this in the academe - we give credit where credit is due, we acknowledge the individuals who contribute even when not at the author level.
Personal reason: I'm a Stack Exchange enthusiast, and raising awareness that solid, useful, and yes citable material is available in mathematics and the sciences is good for the academe.

@BryanKrause Thanks, hopefully someone will and post it as an answer so that each future reader of my question won't have to repeat the same process. However some folks here are pretty close tot he editorial and review processes and many have some personal experience to draw from as well.

@BryanKrause I've adjusted the title so that "just google it" is less applicable, thanks!

I've had the same kind of experience (mathy result that seems somewhat easy for mathematicians but that I could not have come up with by myself). I ended up citing the post in my J Stat Mech article without issue. See https://doi.org/10.1088/1742-5468/ab0c12 I did not write anything to the editor, who did not seem to care

I just did a quick Google search for stackexchange site:journals.aps.org and found out that one of my answers on the physics site has been cited in a Physical Review B paper.

@Anyon congratulations and Q.E.D. :-)

Interestingly enough, pubs.aip.org has more hits than aps.org...

@Anyon: I just did a quick Google search ... --- Being curious, I tried this google scholar search and found 3 papers that cite answers by me on the math site (I looked at each paper to make sure), although none of the papers rises to the level of yours. For that matter, none of my cited answers are anywhere near what I would consider to among my best written and/or most most mathematically significant answers.

Can I use a Stack Exchange answer post as reference...

"Can" is not the right way to phrase this. You must credit sources for the intellectual content you use in a paper.
I think you should do some due diligence to make sure anything you use on Stack Exchange is actually original. It's not too hard to plagiarize here, and though there's rules against it, it isn't easy to enforce systematically. You really want to cite the original source and not a plagiarized copy (of course, this is relevant for things published in other places, too). You also need to be diligent that the content is correct: for math, hopefully you understand the content well enough to feel confident it is correct and verify any proofs the way you would if you were a peer reviewer. For other content, it may be more tricky and depend on how you intend to use the content and also whether the Stack Exchange post is itself drawing on cited sources.
Generally, I would say academics are more familiar with other sources, so if the same author has posted the same content in a preprint or paper, I'd prefer citing those. But, if not, you have to credit where you got the idea.
If you want to look for precedent in your research area, Google indexes the full text of papers, including references; if you search "stackexchange.com" you would discover papers that have cited something on Stack Exchange (likely also other uses, of course). Don't forget some content is on other domains like mathoverflow.net. But, if you've used content from any of these cites, you need to cite it, whether or not your colleagues have done so.

As the other answer mentions, as a matter of principle, you must cite your sources.
There is no need to mention to the editor that you cite Stack Exchange.  They do not care.
As a matter of personal experience (not the same thing as a matter of principle or good practice), if you submit your manuscript to Physical Review, the editor and referees will not check your reference list (unless I am the referee).  I usually observe that authors forget to cite important sources even if they are written by the same authors.  The other referees do not notice, though it can be discovered with a brief Google Scholar search.


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What are some innovative techniques that new professors use to populate their new laboratories with students and postdocs? (besides advertising)
In cases where new professors at universities or research institutes are given laboratory space and budgets for new equipment, graduate students and postdocs, but assistance in recruiting those graduate students and postdocs is not provided, what are techniques that they use to populate their labs with students and postdocs?
I'm interested in nonstandard, novel and innovative techniques beyond advertising in applicable academic newsletters and conferences.
Experimental physical sciences would be a good context for me (note: I'm literally "asking for a friend") but answers that address this more generally might be more valuable for future readers. So for the purposes of this question I won't be getting into any specifics so as not to unnecessarily constrain answers.

I don't know if the ideas below count as innovative, but they are things that go beyond advertising in applicable academic newsletters and conferences.

Social Media. If you have, or can build up, a following on social media, within the community of people interested in your subject area, this can be a good avenue for recruitment. Being active on social media can help create awareness of your lab and what you do and if you have an active, interesting and well-followed account then when you post a job ad, relevant people will see it. Building up a following takes time, of course, so if you need to attract applications right now and don't already have a social media presence it won't help much. But over the longer term it could be part of a recruitment strategy.

Professional network. Anyone who has got far enough in research to be setting up their own lab will surely have a substantial network of collaborators and former colleagues/bosses. Those people have students and postdocs who want to find their next job. Ask around your network if people know of promising candidates who might be interested.

Seminars and conference talks. Try to get invited to give seminars in places with big labs in your specialty. Attend relevant conferences, hopefully with the opportunity to give a talk. Mention, at the start of the talk, while you still have everyone's attention, that you are setting up a lab and hiring and that people who are interested in joining should talk to you afterwards or send you an email. Then, hopefully, give a really engaging talk about your recent work, creating the impression that you are an interesting and inspiring person with lots of good ideas.

Head-hunt. Look at recent preprints and papers in your field, and find ones that you really like where the first author is someone you've never heard of. It is likely that that person is a PhD student or junior postdoc who's going to be looking for a job in the not-too-distant future. Invite them for a seminar + discussion. If they make a good impression, offer them a job. Since the question implies a situation where the lab is not at one of the top-reputed institutions (otherwise there would be no need for special effort to find applicants), it probably isn't worth trying this with people who are already at top institutions, or where the paper in question is a very splashy, high-profile one. Those people will have lots of other offers. Instead, seek people from non "top-tier" institutions who've produced high-quality work that isn't necessarily getting the attention it deserves.

I guess you are talking from one of the not famous institutions, so that you do not get flooded by applications as soon as you open an internship position of 1 month to perform a task that requires 6 months of qualified work from a professional.
Quite simple: offering funds for a 3 or 6 months stint at the top facilities, leaving to the applicant complete freedom (and burden) to get the contact/advisor at the top facility.

I think all ways already have been found. Any HR work is time-consuming. So the best for a professor is not making it all only his job. Hand out a big chunk of it away. Make a net of trusted helpers - PhD students, students who already finished their Masters and so on. Make a Net of trustees. Send trustees to missions: schools, universities, conferences. Not just to present you, but look out for people to catch. Continuous and distributed search is the only option.
Also, people who qualify, already probably doing something else. Which does not mean that they will reject your projects. People often decline money bump for additional intensity in their life, so they can go with you for the freedom science can give.
Also, people who qualify, often have less then ideal papers. It does not mean they can't grow more to overcome themselves. You should be careful about looking into papers and citation numbers. It is just a number, nothing more. Humans are not numbers. Einstein had effectively zero citations because he was not a scientist at all, he was worker at patent office and was declined a chance to work in all major universities.
Also, don't look at formal side. Ramanujan had no formal education at all. And nobody could ever vouch for him, at all. Same with hundreds of thousands of people who were declined a few times because of formal documents they were lacking, and it halted their progress.
What to look at, then?
Initiative. People who initiatively nest in specific places, who make their move first. If somebody writes to you, and you never even heard of, ask the person's name and what he is interested in. People who are interested in your works, will continiously generate ideas and constantly handle at least a few at any given moment. At the very least if person is interested in other areas, you can redirect him to other professionals.
Self-sufficient. Sufficiency is the very basic stage of scientific person.
Language-rich. People who speak at least four languages are better choices. And you cannot know how much a person can speak until somebody actually speaks with him. For physics field, it would be: 1 computer language, 1 mathematical language (ability to work with CAS), English (for writing papers, obviously), some other language (Russian, French, German etc etc).
Positive-feedback versus Negative-feedback personalities.
Look for positive-feedbacked personalities for scientific works. These people are generators, able to bootstrap themselves, their ideas and their equipment from the given initial conditions. Emotionally unstable, often depressed, positive-feedback personalities require careful handling and additional work on polishing their personality. Most of them are rejects by the society, including scientific society. Nicola Tesla and Thomas Edison, most likely both did NOT recieve Nobel prize, just because they did hate each other.

There is certainly a lot of good advice here, but I feel much of it will get read once it is added as an answer to a different question that perhaps still needs to be asked. I've asked only "...innovative techniques that new professors use to populate their new laboratories..." and new professors without anybody working for them yet may not have any way to make a "net of trustees".

@uhoh A lab is a just a tool for facilitating the research logistics. And creating an empty lab is, by large, pointless - unless you specifically have funding available for equipment and want to start housing it somewhere. Even then, those labs typically do not last for too long. To start a lab, one needs some initial human capital; usually it is done by reassigning people or creating a roadmap which includes new hires and/or students by the time you create it. This way, one can at least hope it does not fizzle immediately (or after completing a grant or two).

The existence of Ramanujan and Einstein can be safely ignored in the academic hiring process. At least to first, second, third, and fourth order...


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Do academic researchers generally not worry about their work infringing on patents? Have there been cases where they wish they had?
My Law SE question Instrument builder in a scientific lab w/ academic funding using a technique described in a patent for research, and for developing new technology covers both

Basic academic research that might employ some device, design, algorithm or process that is arguably covered by some patent held by someone else
Academic research that pursues something that might be patentable, that for a short period of time only used something like that described above.

The answer surprised me. It seems that at least in the US, the only situation where a patent holder can not sue someone for using something that is covered by a patent is if it were solely for amusement, to satisfy idle curiosity, or for strictly philosophical inquiry!
When one carries out research, it can sometimes be complicated, the realities are that several things need to be done in order to get a desired inquiry to yield meaningful information. We build gizmos, implement algorithms, procedures, etc. sometimes gleaned from colleagues or accumulated knowledge or by spontaneous ingenuity and invention, and to my personal knowledge, nobody runs every single thing through an exhaustive patent search and vets it as liability-free.
And yet, if the answers in Law SE are to be believed, there are probably zillions of infringements, many may be trivial, some might even be egregious (from a patent prosecution standpoint).
There are of course several reasons why viable patent prosecutions against academic researchers might not happen.
This is all new to me, so I'd like to ask:
Question: Do academic researchers generally not worry about their work infringing on patents? Have there been cases where they wish they had?
And if so, are there certain fields where it's extremely rare or much more common? For example, a Physics vs a Molecular Biology?
note: I'm focusing on academic research and let's further constrain this to publicly funded research through governmental agencies. Things get murky quickly if it is funded via industrial contract or the researcher is starting a company on the side.

The question is ambiguous as it stands. Even if they WERE "worried", how would a worry necessarily produce a better outcome? They have to submit the paper, do they not? Academia is a balance of worries and successes. My point is that whether or not they had a worry about it, it doesn't necessarily mean they won't publish anyway.

@Snared it seems  that the authors of the three well-received answers are able to draw from both shared experience in academia and what the question is getting at and come to a common-sense understanding of what "worried" means here. Nonetheless, the following gives an example of what someone who was (particularly) worried might do. "...and to my personal knowledge, nobody runs every single thing through an exhaustive patent search and vets it as liability-free". Based on everything on this page, it's pretty clear the question, as-asked, is just fine.

In molecular biology we'd generally assume we were covered by "solely for amusement, to satisfy idle curiosity, or for strictly philosophical inquiry".
There are places however, where we do worry about intellectual property slightly, and that is when a supplier produces a product, covered by a patent, specially designed to be used by researchers in their research.
For example, a common protocol used in molecular biology is the Polymerase Chain Reaction. The patent on PCR itself expired long ago, but a key part of a the protocol is the use of a thermostable DNA polymerases. Companies continue to isolate and produce better, faster, more reliable and more accurate polymerases, and patent the use of them in PCR. These are then sold at a high price - the average lab will use thousands of dollars of polymerase in a year, and every lab uses them.
Once the DNA sequence of the polymerase has been identified, making the polymerase yourself is really not that difficult. As every lab uses such things, you could even imagine departments making it in bulk for all the labs in a department. But most labs don't because they worry that they might land themselves in trouble.

Nice example.  Note though, that their are licenses implied when you buy those polymerases, and if you discover, say, a drug using one of them, the patents on the polymerases don't necessarily encumber the drug that was so developed.  Similarly, lets say production of that drug used a patented machine.  Buying the machine probably gives license, and if it doesn't the drug company would need to negotiate the license, so simply encumbering it does not mean the drug will never see the light of day.

@ScottSeidman - Yes. The worry is not that we use patented products in our research, for which we have a licence. But rather we'd be in trouble for infringing a patent for the act of making our own version of the kit itself, not for the consequences it would have on our own downstream IP (we very rarely have any downstream IP, we are not, in general, IP driven).

For most jurisdictions, patents grant the holder only the right to exclude commercial use. I try to answer using US law, which allows the patent holder to exclude any use of the patented invention.
Since most academic research is not for profit, the question is usually moot. Patent infringement can be constituted using a patented method, but there needs to be some tort. If I, by accident, re-invent a patented method, I can also argue that the patent is invalid because it is obvious and lacks novelty. This means that the patent holder is not incentivized to proceed with a lawsuit that might draw the patent holder's competitors into a fight to invalidate a patent.
In academia, I am not worried about patent violations. In industry, as I was told repeatedly, researchers are told not to  worry about patents in their development of products and methods while they are researching and developing, because they might interpret an existing patent too broadly. Whether their proposal is violating a patent will be decided at a later time by vetting a potential product or procedure with patent lawyers. They are under more restrictions, as companies are worried about them using something licensed under a GNU or similar that disallows the company to claim patents.
Historically, there was an issue with product licenses. There was a famous case (I am quoting from memory so details might be wrong, but I was told this by one party) in which a U Wisconsin (Madison) group compared the performance of several databases. Oracle objected to the publication because publishing performance measurements was excluded according to the Oracle license and because their product did not look very good. This lead to a change in federal law that limited the right to exclude performance evaluation by researchers who had NSF grants.
Another related area, where we do need to worry, is non-disclosure agreements, which we enter often without the advice of a lawyer. A NDA can be very one-sided without being obviously so.
So, in short, in Computer Science and at a university, we tend to not worry about accidentally infringing on a patent, until we start thinking about creating a start-up and commercially using the product of our research.
I would be very interested to know what excluding others from "using" an invention actually means. The goal of the patent system is to prevent others from commercial exploitation, which means that there would be plenty of room for allowed use.
Let me make up an example. Assume that someone holds the patent for "database equi-joins by hashing" (It'a a thing). I think I have an even better way of doing it and to show that this is the case, I implement equi-joins by hashing and my new method and then evaluate both of them with many test-cases. Would this constitute "use"? I would argue that this is not the case, as I am not creating an artifact that relies on equi-joins by hashing, I am merely testing it. Of course, the patent holder in my ficticious example would want to argue that by using the patent I created great harm to the patent holder, because my publication makes the patent useless and might want to sue me for damages. I hope that if this were to succeed, federal law might be changed.

"In industry ... researchers are told not to worry about patents in their development of products and methods": my experience is the exact opposite. My legal department would like me not to read any scientific publications, not to do reviews, not to talk to people at conferences, for fear that our product development could infringe on someone's IP. No, they couldn't tell me how this was supposed to work in practice.

That's not what I meant. I edit.

OK. I will leave my comment up, though, and add this: we are told by our legal department not to look at existing patents, again out of fear we might be contaminated. I guess my bottom line is that life in industry can be quite hard, depending on how far internal enforcement goes.

That is my impression as well, but I think it is more about getting scared by patent claims than about contamination. Of course, your experience is more valid than mine, which is indirect, so by all means, keep your comments.

We were told not to look at patents because the legal damages are different for accidental infringement than for intentional infringement, if you never look you can never knowingly infringe.  If we thought we had something that might be patentable we tossed it over the wall to legal for investigation so we would stay 'pure'. This was at a large computer company 20-some years ago so it might also have just been the culture there.

I believe patents exclude for most uses, not commercial uses.  When people tend to get caught infringing is when they try to commercialize.

That's US law, but not e.g. German law.

are there certain fields where it's extremely rare

I work in sociology, and as you can imagine patents just aren't a thing there...

Sure you missed the patent on logistic regression.

"Method for inducing person A to engage in behavior X..."

This actually makes me curious if facebook and google have filed patents over their specific methods for A/B testing features over a wide audience.


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Do PhD admission committees prefer prospective professors over practitioners?
I am about to submit my application to a PhD in Statistics and I was wondering whether writing in the SoP about being willing to work in the industry to make a tangible impact would downgrade my application with respect to writing that I would enjoy being a professor in the future.
They already make clear that they prefer recommendations from academics rather than practitioners but I do not know what figures they expect to train (professors vs. practitioners).

Who can predict how individuals make such judgements. I doubt that it is much of a factor. Every judgement will be different in the absence of some stated institutional preference or rule. But it is better to be honest in your SoP than otherwise.

For anyone reading this with a general-sounding title, it's important to note that the answer will vary widely by what field you're in.

I doubt it, as probably 1% of PhD students will go on to be professors.

The idea that people should commit to Academia before the PhD (where they learn how research, academia are and how the general "academic spirit" is) sounds wrong to me. However, I talked to many profs (in and outside my department) who would never give a chance to someone who openly prefers Industry over Academia (my experience is the more famous a prof is, the more of this biases they have).

This is country specific.

"willing" is an odd word to use - it makes it sound like you're saying that industry is the compromise you're happy to make, which in turn makes it sound like you're expecting to settle for second best. If you want to work in industry and have it as your preferred outcome, then you might want to consider a different phrasing.

It is useful to let people know your preferences. It can be useful in defining the topic of the PhD, some can be done in collaboration with a company (and funding this may actually be easier) while others are completely abstract, etc.

Yes (but it's usually an unconscious bias, and not openly stated).
Many academics consider failing to become a professor actual "failure". An academic career is supposed to be a vocation. PhD students are supposed to be passionate about the topic, so much so that they'll want to continue to work on it after graduating. The best graduate students go on to become professors; the not-so-good ones are eliminated and "get a job" (because being an academic isn't actually a job!). The belief is pervasive enough that many academics who quit felt compelled to write blogs about why they're quitting and why they don't consider themselves to have failed.
Viewed this way, a prospective PhD student openly states they want to work in industry is a red flag. They've already ruled themselves out of being the best, they're likely to fail. Admission committees might not think this crassly, but they'll come up with the closely-related reasons "not passionate enough" or "applicant is not motivated by the subject, therefore when things inevitably go badly in the PhD they might drop out", both of which stem from the idea that the only way to be sure the applicant is passionate/motivated enough is for them to want to be a professor.
Granted not all academics think like this, but unless you are certain otherwise (e.g., you are applying to work under Phillip Greenspun, or the program description explicitly says they have an eye on preparing students for industry jobs), I think you should err on the side of caution and say you will consider an academic career even if you are almost certain you will join industry, or at least be non-committal about your future plans.

Comments are not for extended discussion; this conversation has been moved to chat.

Nearly all PhD students will never be professors.  Some PhD programs might prefer to recruit PhD students who intend to become professors, but sensible PhD programs will realize that students who wish to work in industry are students capable of making a realistic plan.  That is a good thing.
Stating your intent to work in industry is unlikely to hurt your application.  If it does, then you probably applied to a program that will not help you reach your goals.

PhD admission committees are made up of people, and people are notorious for having individual opinions that vary greatly from one person to the next. So: some people may care; others won’t care; and some people will care, but in the opposite direction from what you think. (For example, if I were to read your SOP and got a sense that you want a PhD because you have a passion for changing the world through groundbreaking industry applications of statistics, I would regard that as a wonderful motivation to have, and one that is much better than the generic “I’ve always dreamed of becoming a professor” line I see in every other grad school application I look at. Disclaimer: I’m in pure math, not statistics.)
For that reason, personally I feel it’s a fool’s errand to try to game the admissions system by trying to guess what the admissions committee “really” wants to hear and then give it to them.
Of course, I am confident that now that I have publicly posted this bit of wisdom, grad school applicants everywhere will stop these silly guessing games and just write the honest truth about who they are and why they want to do a PhD.
Anyway, best of luck with your applications, and my apologies for this non-answer.

I am faculty in a Biostats department.  In my experience, there is a small premium placed on students who are likely to remain in academia (doesn't matter what fashion) in that they are more likely to publish components of their dissertation.  As these papers often include substantial contributions from their advisors, this means more senior-authored papers for the advisor.  However, a PhD is such a winding road, students who claim to be dead-set on acquiring a faculty position will not seem so credible in a personal statement.
My advice: do be honest with what sort of problems excite you, and why they motivate you to pursue a PhD.  But perhaps do not spend much time describing your eagerness to enter industry per se.  After all, a PhD is a poor time and money investment for an industry career in statistics / data science right now.

this generally seems to be the case in econ. not sure how it is in stats. my advice is to say that you want to be in academia and don't hint that you'd rather do something else even if that's the case. i agree with others that it's very hard to get a job in academia and that you should have a backup plan as a result, but for the sake of maximizing your chances of getting in, please keep those non-academic plans secret.
phd programs are for producing academic researchers. the thing about getting recommendations from academics instead of practitioners for this purpose is that academics will generally be far better judges of your ability to survive a phd program and become a successful researcher than someone who has never taught in one or even been through one.

The researchers I know who are or have been at IBM, Google, Sun Microsystems Bell Labs, Oracle, Honeywell, etc. all have PhDs. Are they all just failed "academics". Oh, and they all earned about twice or so what I did. The summers were mine, of course.

@Buffy i wouldn't call anyone who goes into industry instead of academia a failure. the job market is how it is and we all have to make a living. phd admissions committees should be more realistic about what their students can do given the scarce supply of academic jobs across fields.

All of them chose industry. It wasn't forced on them. If you were in CS you would recognize many of the names. And the OP here suggest a preference for industry.

well, if that's what they really wanted, then i'm happy for them. nevertheless phd admissions committees generally have this narrow way of thinking.

"phd programs are for producing academic researchers"  This does not reflect the reality of what PhDs do after their degree, so I consider it false.  In reality PhD programs mostly train students to be nonacademics who are capable of research.

"ability to survive a phd program and become a successful researcher" the (appropriate) choice of words explain why the recent wave of professors are appaling, but they are very proficient at getting funds and working extra-hours: they survived that way, or even worse, the phd is a path designed to give a prize to the ones that can do such a thing. For the losers: plenty of consolation prizes. Burnout, anxiety, depression, etcetc ...

I think it's difficult to answer this question universally.  However, you can look at the placement record of the institution of which you are applying.  If many previous graduates go on to academia, then you might be hurting your chances at that particular school in stating a desire for industry.  If it's 50/50 or even more-so weighted on industry, then it probably doesn't matter.  Of course, applying to grad school is always a crapshoot, but this is a way to get some 'data'.
Generally speaking, however, I would be honest with yourself and your application.  I'm currently a PhD student in a statistics department, and a good department and good faculty/adviser (both of which can be hard to find) will help you reach your goals.  It's going to be a long 4-5 years if you're working towards a goal you don't really want.

This is a great answer because it points to the fact that this is rather department (read rankings) dependent.

Actually, if I were teaching at a department with a high industry placement percentage, I would want applicants to say they wanted to do research in industry to make sure I was admitting people who were a good match.


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I think my TA winked at me and have developed feelings. Should I ask her out after the semester ends?
TLDR: I have feelings for my TA, think she winked at me, and would like to ask her out after the end of the semester.
So my eyes do this weird thing sometimes when I'm sleep-deprived or stressed where it can look to an observer as if I might be winking. This can sometimes lead to problems for me for obvious reasons. However, a few weeks ago in class on a day when my eyes were particularly acting up I believe I might have received a first-- an unexpected return wink. My TA, turning around from the chalkboard momentarily, smiled and gave a very clear wink towards the direction of the room where I was sitting. I had been looking her way over the course of the class since she's the instructor, so it seems quite possible to me that she thought I was winking at her.
However, this was the final day of class before we transitioned to Zoom lectures due to coronavirus, and it's been really difficult to explore my suspicion that she's interested in me through online communication alone. I feel like the odds are low that she was winking at someone else. There were only about 15-20 students in the room, around 40-50% of whom are men. The seating arrangement meant that only about 5-7 people were seated in the direction of the room I was seated in. I wasn't really sure what to make of this when it first happened, but in recent weeks I've noticed myself developing feelings. When I contacted her with a question about an assignment, she responded by inviting me to toss some ideas around over zoom "for fun." I did a few days later, and she also made a point of asking me how I'd been doing with all that's going on and whether I'd be staying in town over the summer. I notice her tone of voice changing a bit when she talks to me, as well.
I really do enjoy talking to her and feel like I would genuinely like to get to know more about her academic passions and interests. As a 24-year-old re-entry student, I feel that the age gap isn't all that intense. In fact, I think I would probably have more in common with her than I would with most undergraduates. The area her work is focused in is also one of my intended majors.
With only two more weeks of instruction, I feel pressured to act before she loses interest. I was having trouble falling asleep most of the night last night due to my mind being so preoccupied with this, so I don't think I could feel alright with doing nothing and letting this pass. My plan was to continue to ask the occasional question during and after class and maybe schedule an office hours appointment for an assignment I genuinely have questions about, wait until the semester is over, and email her 1-2 weeks into the summer asking if she might be interested in getting coffee once social distancing restrictions begin to lift. Does this sound like a reasonable idea, or could it be that all the quarantine and social isolation is just getting to my head?

There's a lot going on here but...regardless of any other advice you get, please, for the good of anyone involved, do not under any circumstances say anything until the semester is over and grades are in. And after that, also just, given what I've read here...probably best to walk away.

#1 question: does she have influence on your mark? Will she be a TA of yours in the future? If any of these answer with "yes" - be very careful. You can utterly damage her (and possibly your) career. If she still has to grade you, she is strictly taboo, possibly even formally so in some unis.

She definitely won't be responsible for grading me after the end of this semester, as this is my last lower-division major requirement.

@BryanKrause Do you say that because of the department she works in?

This has been asked, and answered on here before - worth you having a search.

I say it because your intentions seem in conflict with that of a student, which is a big warning sign.

As long as you wait until after the semester is over and final grades have been assigned before asking her out, you are on clear grounds ethically. Personally I find the idea no less reasonable than the idea of asking anyone else out. You are both adults. She will either be interested or not. You will never know unless you ask her.
A good friend of mine started dating his former student back when he was a TA. They waited until the semester was over. They are now happily married with two kids.
Good luck! And don’t pay attention to the downvotes. Your question may not be the most pressing one the world of academia has right now, but it’s a valid question and is important to you.


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Publishing a plot based on numbers in another physics paper's supplemental material; do we need permission from the publisher or authors?
Our simple calculation reproduces and explains the behavior shown by a much more elaborate calculation that's been published in a physics journal. The supplementary information published with the paper contains a table of x, y, z coordinates of atoms from that calculation.
We'd like to compare our numbers to these numbers to these by comparing plots of both.
Do we need permission from the other paper's publisher or the paper's authors to publish our own plot using these numbers, assuming we already cite their source clearly?
I don't know if it matters or not, but there are only of order 100 numbers, a few digits each; something one can simply retype.

You are free to plot those published numbers (with credit, of course). Reproducing graphics from a publication would need permission.

Could you say why or under what circumstances? eg, numbers that are further analyzed is a fair use or numbers can't be copyrighted?

I can't speak to legal issues. My answer is  about   common practice. The point of publishing is to make ideas and data available to the public, in this case for the advancement of science. That's why you can use the data to learn more. That might even mean correcting their analysis. If you are really worried you could contact the editor of the journal where the data appears.

@DavidSmith It's always been common practice in the physical sciences since.. forever probably, and this is the answer that I expected. The whole point of making the raw data available should be for others to use it or build on it. But in recent years, shifts in what "academy" even means, and with the advent of electronic publishing and the "big business" models that publishers use, I just wanted to double check that what has been true for centuries hasn't gone by the wayside in these norm-breaking times.


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Preprint to arXiv before submission to an AIP journal, how exactly to modify it after 1) submission, 2) acceptance?
From AIP's Web Posting Guidelines for Journal Authors:

For noncommercial free-access preprint servers (e.g., arXiv)

You may post the preprint prior to submission and/or acceptance, using the credit line formatting below
You may post the accepted manuscript immediately after acceptance, using the credit line formatting below
You may update with the VOR 12 months after publication, with the credit line and a link to the VOR on AIP Publishing’s site

and

Format for credit lines

After publication please use: “This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in (citation of published article) and may be found at (URL/link for published article abstract).
Prior to publication please use: “The following article has been submitted to/accepted by [Name of Journal]. After it is published, it will be found at Link.”
For Creative Commons licensed material, please use: “Copyright (year) Author(s). This article is distributed under a Creative Commons Attribution (CC BY) License.”

Perhaps it's just me, but the second bullet in the "Format for credit lines" section doesn't seem clear; there's sort-of an infinite half-space of time "prior to publication", where several things can happen.
Assuming I've posted in arXiv first, does AIP say I need to add "submitted to [Name of Journal]" upon submission, then change it again to "accepted by [Name of Journal]" assuming that happens? And if it's ultimately rejected, must I then add a "rejected by" or just repost with any mention of submission removed?

In my non-lawyer's opinion, these clauses are silly.
Their "format for credit lines" do not substitute for the license the work is released under. Any of the licenses you choose to post on arXiv for are more permissive than that clause, and that clause has no weight over someone using the version of your paper posted on arXiv. It's silly.

Prior to publication please use: “The following article has been submitted to/accepted by [Name of Journal]. After it is published, it will be found at Link.”

This is even sillier - a preprint doesn't belong to anyone but the authors. The clause "after it is published, it will be found at..." would only possibly apply once the article is actually accepted. Are they implying that they accept all work that is submitted? That's not a mark of a reputable journal. I don't feel like a reputable journal should ever want this statement on a submitted article, as any submitted articles deemed not suitable will not and should not ever be found at "Link". A submitted article could be some crank perpetual motion paper, or, worse, some screed against a particular ethnicity.
The part that doesn't seem as silly is this part:

For Creative Commons licensed material, please use: “Copyright (year) Author(s). This article is distributed under a Creative Commons Attribution (CC BY) License.”

The "For Creative Commons licensed material" implies to me that they're perfectly fine with you releasing your stuff with a CC-BY license, and no other add-on restrictions are going to fly if you've already labeled your work with a CC-BY license, so if you're using CC-BY it seems like you can just ignore that. Personally, I'd probably choose not to use this publisher based on the level of silliness, but if I was then I'd assume that the other silliness only applies if you didn't use a CC-BY license and just comply with this one clause. Giving them the benefit of the doubt, maybe they really only meant for those other statements to apply if you choose to submit a preprint without a CC-BY license.

Interesting and illuminating, especially never having been a submitting author before and no experience submitting to arXiv. It seems I need to do some reading on the arXiv license options now.

Note that use of a CC-BY license will likely mean that you also have to select an open access option for publishing in the journal, which usually comes with a fee.


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Disadvantages/risks of publishing new raw data as one of a group of instructive examples while planning to publish a full analysis of the data later?
We have a few 2D low energy electron diffraction LEED images (field is Physics/Surface Science) that are currently not yet published, the analysis is not complete nor their implications fully explored.
But they would be really nice to include within a larger group of images in a paper I'm writing now about how to analyze these kinds of images, because they represent special cases - they're "edge cases" so to speak, and honestly their patterns are particularly intriguing. One might consider using one as a first or "lead" image for the current paper.
I think the main and most obvious reason not to include them at this point is to avoid being "scooped" - somebody (with plenty of time on their hands) figures out what it is, how to make it, then publishes a full "first" paper before we do.
Besides that what would be the biggest disadvantages and risks of publishing new raw data as one of a group of instructive examples while planning to publish a full analysis of the data later?
note: the necessary information for the description of the image is minimal, essentially "Depositing X atoms on Y surface sometimes produces the following diffraction patterns."

different but perhaps slightly related:

Why don’t researchers publish their raw data for the advancement of science?

I think the other main potential disadvantage to consider would be that the data/diffraction patterns you include in your how-to paper could be considered previously published when it comes to the submission of the full analysis paper. Whether this is a big deal or not can depend on the publisher, journal and what percentage of the full data is included in the how-to paper. In physics I wouldn't be particularly concerned unless the goal is to submit the full paper to, e.g., one of the Nature-branded journals. I don't know if surface science has a different publishing culture as parts of it are closer to chemistry.

Good point! Indeed Nature Scientific Reports (editorial-policies) is a potential target for the full analysis paper while (depending on how it fleshes out) the how-to would be more suitable for Physical Review B. (authors; content) or even Journal of Applied Crystallography (authors) or Review of Scientific Instruments (AIP author instructions).

So this disadvantage bifurcates into the challenges associated with reading, understanding and interpreting published policies, extra time associated with proactive communicating directly with editors of targets for the full analysis paper explaining a hypothetical, and delays associated with resubmission if an editor upon reviewing a manuscript with either a notification of raw-data reuse, or perhaps a letter of permission for reuse from how-to journal's editor. All for a few additional black-and-white thumbnails that looks "cool" plus a few extra data point on a graph. Hmm... :-)

@uhoh Well, if those data points improve the paper it might be worth the effort... Don't spend too much time on interpreting editorial policies. For the journals you mention, I think you can probably just obtain approval for reuse of any copyrighted material as appropriate, and then make data sources clear in both the text and cover letter of the analysis paper. The concern I alluded to in the answer is rather in regards to acceptance if it was a submission to one of the top impact factor journals (by Nature-branded journals I meant e.g. Nature Physics, not Scientific Reports et al.).


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If someone reads my manuscript, makes helpful suggestions and I thank them at the end, have I now removed them from the pool of potential reviewers?
There's a senior researcher who literally "wrote the book" on the topic of a paper I'm writing. I'll draw from and cite the book but introduce some new things.
As I am new to this long-established field of physics with a strong mathematical component, I'm certain that I may be missing some perspectives and references that will be important to include, and there could be some important points I fail to recognize.
I'd like to ask1 this senior to read my manuscript, and I will mention to them that while I would welcome any suggestions in the areas outlined above, if they see some real room for improvement and would be interested, we'd also be happy to welcome them as a co-author.
Assuming that doesn't happen and I end up thanking them at the end of the paper for helpful suggestions and insight, if I then submit this to a journal which asks for suggested reviewers, have I now excluded this person from the pool of potential reviewers by involving them in the process and thanking them in the manuscript?
I don't see that as necessarily a bad thing -- other reviewers, seeing mention of the person who "wrote the book" on the topic may feel more comfortable about the work and results  -- I'm just curious how all of this works.
update: ...but I do not necessarily want to exclude them. I'm only asking if this would have that unintended effect. That completely differentiates this question from Acknowledging the discussion with someone in the paper but excluding this person as a reviewer: how to do this? As far as I can tell, this question is also not answered in Acknowledgements and reviewer selection.

1We're not strangers; we've had some basic and helpful discussions already

different but somewhat related: Ethical standards in asking a professor for reviewing a finished manuscript and publishing it together

Related: Acknowledgements and reviewer selection and Acknowledging the discussion with someone in the paper but excluding this person as a reviewer: how to do this?.

@Anyon Thanks, I've now added links to both of these in my question and explained why this one is different.

You are not necessarily removing the acknowledgee from the potential reviewer pool, but you are reducing the likelihood of them being invited.
Editors seeking impartial referees would be disinclined to invite reviewers who are perceived as close to the author or invested in the fate of the manuscript. Presumably there is somewhat of a spectrum of disinclination, depending on the nature of the acknowledgment. Thanking someone for pointing out Ref. [50] may be perceived differently from thanking someone for providing substantial help and feedback, for example. Personally, I have been invited to referee a couple of physics papers in which I was acknowledged for discussions.


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How Important is the rank of a school in a certain specialty?
I am interested in applying for PhD programs in discrete mathematics, but one of the schools I'm looking at isn't included in the top 10 rankings of discrete math programs (at least not according to US News: https://www.usnews.com/best-graduate-schools/top-science-schools/discrete-mathematics-rankings). The school I am looking at is an overall top 25 school in math, but just not in the top 10 for the specific area I am interested in. They do have several people (about 5) researching discrete math, so it is not a non-existent research area in this school.
The part that I am especially torn about is that if I were to go to this school, then I wouldn't have to move (and incidentally the city I currently live in is my favorite city), and I could likely keep my current job and just work at my job half-time. I figure that if I'd have to likely work 10-20 hours a week as a TA, it might be worth it just to do 20 hours a week at my current job with better pay. Also I should mention that so long as I do 20 hours a week at my current job, I will get tuition payed for, health insurance, 401k etc (all the benefits I currently have). My goal isn't to stay in industry, but to go into academia, and so I would need a really stellar dissertation since academia is so competitive. My question is therefore if you want to take the academia route, how important is (in shaping how good of a mathematician you will become) the ranking of a school in a certain specialty if its overall math ranking is good (top 25), and there are still several people doing research in that specialty?
EDIT:
I wouldn't be able to live in the same city as the school is located in. I'm in a city that is close by. How important is it to live near the campus when doing a PhD?

A small warning: it's possible that the TA position includes some tuition reduction too (as well as insurance benefits). Depending on what the department charges, your current job may be less beneficial than it seems at first. It's something to take into account.

@Anyon Good point, I have made edits to my question.

A big warning: Don't put all your eggs in any one basket. Competition for admission at any high ranked school is fierce. Have a backup. Have several. And not all clones of each other.

Do you think it is feasible to do 20 hours a week at my current job plus a PhD program? That is the main thing I am concerned about. My current job doesn't require all that much mental effort, so I don't think it would cause too much of a mental drain when I go to study. It just pays so much more than what a TA would be, and I think that the hours are comparable right? From what I hear most TAs work 10-20 hours

Don’t trust the US News grad school subfield rankings at all.  They’re based entirely on surveys and most people don’t actually know a lot about things outside their speciality and their university.  So you infamously end up with high ranking places that actually don’t have anyone in the subfield.
If you want to know how good a school is in a subfield you’ll have to look into it seriously yourself.  Ask people you know in that subfield, look up the research interests in the department, find out whether their have been grad students their recently, after you get accepted visit the dept and ask questions.
That said, I think in the US in math it’s a mistake to narrow down to a specialty before you go to grad school.  You have a year of grad school before you have to pick an advisor, and you’ll learn a lot in that year.  Plus you’re more likely to find a good advisor match if you are picking between 20 potential advisors and not 2.

I disagree with the last part.  The sooner you start your research the sooner it's done.

I agree that you shouldn’t put off starting research, but in math in the US no one does research their first year.  If you find an advisor early your second year you’re already ahead of things.  This is very specific to math in the US.

The general math rankings are better.  I wouldn’t take small gradations very seriously, but just about everyone will agree that the 5th ranked one is clearly better than the 25th ranked one, which is clearly better than the 45th ranked one.

My school is ranked in the mid-30s, and I’d generally agree that the schools above 20 or so are better, the schools below 50 are worse and the schools between 25 and 45 are in a comparable tier.


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What should I do if professor grades unfairly?
Background:
I take the required course through another university in order to graduate earlier, and that is how my nightmare starts.
From the first few weeks, everything was going fine; however, after the mid-term, the professor approached me and said she needed to talk to me.
When I went to see her, the first thing she asked me to do was read aloud of the instruction of the exam (which I felt being insulating because English is not my native language). The instruction is basically said this exam contains the answer key, do not take them with you or take any pics and hand in back as same as it is.
After I read it, she asked me "where is the answer key"? I immediately realized that she thought I took her answer key. I told her that I did not take your answer key, because when I reviewed the exam, I thought the scantron was the answer key. She said it's fine and she would take me out of the report (What report!!??) Per my understanding now, everyone should have an answer key, instruction guild, and scantron on the exam when she hands back for us to review. However, what the hell would I know it as we just had a few mins to review our exam back at that time?
BTW, I remembered when she handed in the exam, I saw my classmates do not even have instruction paper being stapped on the exam, meaning that it may be a simple mistake that she forgot to staple the answer key on my exam.
After this incident happened, she kept giving me lower grades. I compared my papers with my classmates. Most of them got full points without following her instructions or writing properly. She makes comments saying I did not answer questions, but I did answer all the questions in my paper. My friends reviewed my papers and all agree with me, so the professor may not even finish my paper.
I am so upset and I really need to pass this class. What should I do? Go to talk with deen or persons with higher positions? I just felt like because I am not coming from the school she works, so she treats me differently. However, ironically this course is ethics. She was not supposed to accuse me of things I have never done and based on her bias to treat me differently compared with others. I really don't know what to do...

Escalate. How to do that depends on the country/culture.

"because I am not coming from the school she works" - she may not even know that you're coming from another school. When I teach, I don't know who in my class is matriculated at my university and who is a visiting student.

She knew because she did not add me to a group, so I told her that I was added a few ago because I came from another university.

"I told her that I did not take your answer key, and when I reviewed the exam, I thought the scantron was the answers" I can't make any sense of this sentence.

I am sorry about my sentence. I was trying to say that professor stabled another sheet of answer on the exam, but I did not know it bc I thought that scantron is the answer key.

"Answer key" means the list of correct answers, something that typically only the professor/TA/etc would have. Do you instead mean the sheet where you write your answer choices? So this test had 3 pieces, A) a list of questions, B) an answer sheet, and C) a scantron page, and you were never given (B) and then accused of removing (B) from the test room?

She handed the exam back to us for review and took it back after the class. She stepped on (a) answer key (b) scantron (where we wrote all answer). My exam does not include an answer key while I was reviewing it, because I thought a scantron was the answer key as it lists up all correct answers on it, so I did not raise any concerns at that time. However, the next thing I encountered in the following week was being accused of stealing her answer key. After this, I have never gotten good grades no matter how hard I worked.

I am not sure if I would trust your friends to give you good objective information in this case!

Honestly your story sets off alarm bells. Students struggling with language skills often fail to follow instructions, and not even be aware of the fact, believing they did follow instructions. Students also tend to not understand why they lost points versus other students, since they didn't understand how to get the right answer in the first place. I'm also wondering about the mix of scantron tests and writing. How big is the class? The professor may not even be the one grading your writing.

Two steps:

Ask her for a meeting in her office where you can talk in peace and
phrase your concerns in a friendly but clear way. First say that
your feeling is that there is a problem but you are not exactly sure
what it is and why it is there. Then ask what you can do to improve
the situation. Don't make any accusations ("You grade my papers
worse!!") and dont get personal  ("You don't like me!") that will just make her defensive. Rather say
things like "I feel that something in our communication is not quite
optimal and I am here today to ask what I could do to improve the
situation.".
If this meeting does not improve the situtation then you will need
to go higher up in the food chain and talk to whoever this is.

Can I ask her to review my papers again? If she refuses, will I fail the final?

You should ask her to go over your papers with you and explain what you needed to do to earn full points. Frankly you should have done this after the first bad paper. Then you could have improved!

I asked her about how to get full points before the incident took place. I followed her guilds but I did not get good grades. So, I went over my classmates' papers, and make me realize that she graded me unfairly on purpose. My classmates did not follow her instructions and it could tell that they were wrapping up the papers in the last minute. But, They still got full points..... what can I say :(

@user106838 You should NOT ask her to review your papers again because you would ask her to indirectly admit to misconduct (graded your papers worse than they are) and she is not going to do this. But yes, you can follow Dawn's advice.


text:
Referee did not fully understand accepted paper
I just got a paper accepted without revisions in a prestigious journal. This is of course nice. Reading the referee report makes me a bit worried, though. It is clear that the referee has gotten the basic ideas of the paper, and has identified what we also think is the primary contribution. It is, however, also clear that quite a lot of details regarding the implications of the primary result, were not correctly understood by the referee.
What actions should I take from here? I of course want the paper published, but I am worried that people in general will misunderstand the parts about implications. Should I contact the editor and ask for another reviewer? Should I ask permission to re-write that part of the paper? Or should I just shut up and be happy to be accepted without revisions?

Were there other reviewers who did appear to understand the part you think may possibly be unclear?

No, this journal only uses one reviewer. This is quite common within my field.

In our field it would be very strange if a prestigious journal used one referee only, and even more strange for a paper to be accepted in such a journal without revisions.

I would really rather not go in to more specific details about the journal or my field, as I don't want the referee to find this question...

Your concern is that other people might misunderstand the paper as well. This is a valid concern, but at this moment, you have little data to support that it actually applies: the reviewer might just be an exceptionally bad/hasty reader. To be sure, you could have additional proofreaders from your network of colleagues read your paper and let them comment on it.

@nabla: The referee probably thinks they have fully understood the paper. They are unlikely to assume a story about a referee who did not fully understand the paper is meant to refer to them ;)

@FedericoPoloni Some prestigious journals use only one or two referee(take for example Phys. Rev. D).

@Federico: I thought we were in the same field, but in the last two years alone I have had several papers accepted by what I think of as prestigious journals with only one referee: Comptes Rendus, Math. Z., Crelle.  I wonder what is the resolution here?

@PeteL.Clark Maybe it is a pure vs. applied math difference? Anyway, that is my (limited, I admit) experience; I might be wrong.

@FedericoPoloni: From my own limited experience (and mainly as a referee in the case of applied math journals), it is indeed true that applied math journals tend to use more referees than pure math journals.

I mostly agree with the answers that with respect to the journal, you do not need to do anything. With respect to the content of the paper, you could give it to a colleague in your department who isn't directly familiar with your work to get their perspective and check that their understanding matches yours - if not, you can make an effort to clarify at future conferences/next publications. Otherwise, they may show your concerns are unfounded.

May I ask if you are a big named prof? Accept without revision is so rare.

@HighGPA - I certainly am not.

As is the custom on this site (or at least it should be) let's assume the premises of the question are correct - that is that it is indeed a prestigious journal.
Do nothing.
In fact no: celebrate acceptance in the way you find most appropriate.
The fact that some people misunderstand what you're trying to say is not a basis to act after acceptance. It might indicate that you presented your results in a not so clear manner — which would speak in favor of refining your writing for future articles — but that would not be an exception in the scientific literature. At any rate, edits (other than very minor ones such as typos) after final acceptance are generally not allowed.
If you see errors in your article that are not trivial and you feel need addressing, the appropriate way to handle this is to publish an erratum. I imagine most journals have a standard procedure for that.

"At any rate, edits after acceptance are generally not allowed." - really? I'm more acquainted with conferences than with journals, but there, the camera ready version often does include edits in response to the reviews. Granted, there usually is no second, third, and so on, review round for conferences, so it's more customary for the "final" accepted version to still receive a few minor changes for clarification in response to the reviewers' comments before becoming the camera-ready version.

@O.R.Mapper well if there are still edits to do in response to reviews I wouldn't consider it accepted. I'll specify "final acceptance" in my answer.

Ok, never mind then. It's indeed different from CS conferences, where "accepted" (as in final acceptance; inclusion in proceedings more or less guaranteed and no more reviews to come) usually means "accepted without any substantial changes to content or structure", which does not exclude the possibility of some minor improvements in wording or visual presentation between the accepted and the camera-ready version.

I had a paper through peer-review and then was allowed to change a few sentences, even at the camera stage

@henning I'm sure there are variations between journals and practices, hence the word 'generally'.

@Cape Code, for sure.

Celebrate the acceptance, but rework the sections that were apparently poorly understood.
You will want your readers to fully understand and appreciate your contribution. A clear paper is not only more useful, it is also more frequently cited. If a reviewer, who more closely looks at your paper than the usual casual reader, misunderstands, this is a warning-signal.
In practical terms: You could approach the reviewer (via the editor, to be sure) with your concern that parts of the paper were not as clear as they could have been and politely ask whether she might explicate which passages could be improved in terms of their transparency. You could also ask other colleagues to have a look at your paper, focusing on the clarity of your writing. Also signal to the editor that you would like to make some minor stylistic revisions before submitting the final manuscript, so the editor knows what to expect and when.

Risks making the referee change their mind. Present the work at conferences and write a pedagogical proceedings

@innisfree It depends on how you approach the reviewer. You could write something like "Thank you for the constructive feedback etc. We were happy that you found our article convincing. As you know, a transparent paper is cited more often and in general more useful to the reader. We believe that some sections of our paper could be written in more simple terms. Therefore, we would like to improve the paper's clarity. You would help us a lot if you could point out briefly which parts you found least transparent, presuming an expert but casual reader".

Do you know for a fact that a transparent paper is cited more? Depends on whether insights or mistakes/weaknesses become apparent.  Don't open up a can of worms. Just be happy it's accepted.

I don't. It just seems plausible, since I can only cite what I understand. 2) I'm not sure if that is maybe the prudent thing to do, but it's certainly not the right thing to do.

It often happens that referees have no time to understand the papers they are supposed to review. It's a systematic consequence of the imperfection of the current peer-review‒system. At the moment, not so much could be done about it. Said that,

there is no reason for celebration, since you are not sure whether your paper was intelligible,
there is a reason to feel satisfied since the paper was accepted,
but actions as you mentioned are neither required nor
expected.

If you really wish to do something, you can improve the text at the earliest point the reviewer had a problem with.  Of course, you could ask the editor to issue a request to the referee to tell you this earliest point, but the editor or referee may choose not to answer: it goes beyond the usual duties of their roles.
Too many improvements could be regarded as deviating too much from the accepted part.  Typically, improvements are regarded as acceptable only if they address the concerns raised by the reviewers.

I can't comment due to newness, but wanted to support Cape Code's answer with additional thoughts:
Do Nothing. As the author of a paper, you cannot prevent any reader from forming their own conclusions. Any reader, like the referee in question, will have variance with the precise point you would like to drive. Also, when a reader sufficiently internalizes the material, his/her own way of expressing the idea will be quite different than your own.
If it were me, I would first examine the referee's comments as though he/she wrote the paper. Does the conclusion seem compatible with the point I was trying to make? If so, I personally would leave it alone. If it does not seem compatible and I had such recourse, I might reach out to the referee and ask for deeper feedback regarding his/her unexpected response.
Only if the reader's conclusion were totally incompatible with the one I was trying for and such erroneous conclusions were contrary to the furtherance of the discussion would I request to retract or rewrite.

If I were in your position, if I could infer from the referee's report the nature of the misunderstanding, and if that misunderstanding could be alleviated by adding just a few clarifying sentences to the paper, then I'd add those sentences. I'd tell the editor exacty what I had done: "I added sentences at page X line Y, to clarify a point that the referee might not have completely understood."  I would also tell the editor that, if (s)he doesn't want me to add these sentences at this stage of the process, or if adding them would lead to the inconvenience of another round of refereeing, then I'd be willing to remove those sentences.
If, on the other hand, I can't tell what the referee misunderstood, or if alleviating the misunderstanding would take more than a few new sentences, then I'd leave it alone and just hope that not too many other readers join in the referee's misunderstanding.
In the preceding paragraph, "leave it alone" refers to the version of the paper that will be published. If you're in a field like mine (mathematics) where there's a good preprint server that just about everyone uses (the arXiv), then I might, if I can find the time, make whatever revisions, even substantial ones, I consider appropriate in light of the referee's misunderstanding, and I'd post that revised version on the arXiv.