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I wasted six years of my life getting a PhD degree. What should I do, and how will I survive?
I struggled with low self confidence throughout my bachelors, masters and PhD in chemical engineering. After spending two years in Masters and six years in getting a PhD degree, I am lost at what I can do with my life.
Initially, my plan was to be in academia. Though I love doing research, I don't see that as a possibility anymore.
I did not do well in my PhD. I have only two first-author journal publications in ~2.5 impact factor journals. I did not acquire significant skills. I am bad at programming, and I have a 3.7 GPA. I did not learn to drive or learn any foreign language. I did not improve my health or developed a new hobby. I even did not spend time on having a relationship. In short, I have done nothing over the past six years.
My PhD supervisor has given me a postdoc position. And I feel extremely inadequate. I feel that I won't be able to do anything after my postdoc year, and I will just be a burden and disappointment to my parents.
I am an international student living in the US.
I don't know what I should do. What should I do?

I think your only issue is one of self esteem. I suggest you find a counsellor and discuss where you are and how you feel. Don't let imposter syndrome lead to depression. Your advisor can give you professional advice, but you should also seek personal advice. The future is brighter than you think.

Is the work fun though?

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

Is there anything in your past that is unresolved? I suspect your low self confidence stems from something else and not the PhD itself. For example you mention lack of relationship, so I suspect you have a non-existent sex life. Are you exercising and eating right? All of those things need to be in order for you to be happy doing a PhD. Otherwise all you'll have is a PhD which is empty and meaningless.

‘I have only two publications …’ to me, who has a grand total of zero from both the PhD project that fell short of its desired outcome and my first two years of postdoc in which the ‘basically already finished, just this’ project turned out almost impossible, this is quite a violet slap in the face.

Get wasted, you won't surive this life anyway - no seriously, the others are just as bad at their job. Use the postdoc as an opportunity.

In addition to the other comments and answers pointing out that you have in fact achieved valuable things during this time, I want to add that living in a foreign country is objectively difficult. It is much harder to find friends and form relationships, and family are not around to help with chores and life.

Seek counselling! The problems you describe have very little to do with academia, but very much with you. This website cannot provide adequate counselling in that regard (although some of the answers of course hit very relevant points).

It's never too late to start living.

Imposter syndrome. Look up the word if you did not hear of it before (Maybe you need guidance from a counselor?). I am in no way qualified to evaluate you, but one is not blind. You got a master, a Phd and you published papers, let alone having a good GPA. How can you say you are incompetent if your own advisor offered you a postdoc! This mean he believe in your abilities. If you love what you are doing, fight for it.

It looks to me like you did not do so badly as you think. Two publications and 3.7 GPA are not so bad. It might depend on the field, it might not be the best ever, but I have seen much worse. If your supervisor offered you a postdoc position after having you for 6 years as a PhD student, it means that they consider your work useful.
You might be suffering from impostor syndrome. Do read the question and the answers in that link and see if you identify.
If you are not sure now, you have plenty of time during your postdoc year to decide whether you want to continue in academia or get a job in industry. The pros and cons of both options have been discussed extensively, as a quick Google search for "industry vs academia" shows. I personally agree with this source.
And, in most cases, the answer to "I have wasted X years of my life because I did not do Y and Z" is "do not look at the past and do Y and Z now". Especially when, as  in your case, Y and Z can be done at any stage in your career life, such as learning languages, programming or driving.

Also, the field is chemistry, where the PhD is basically required for an entry level position in industry, so that is certainly not a waste of time.

@SimonRichter Actually, the field is engineering (chemical engineering) where a BSc is enough for entry level jobs industry.

Get a job in industry. The great part is, that at the end of the project/delivery/month, work is done and completed. At least for me, I never considered the results in science 'done'; also pace is probably faster, so you will get getting quite a few achievements under your belt quickly (since you are smart).

@Cell Where I've worked, a PhD is automatically hired into a position that it would take ~5 years to get promoted to from entry-level with BSc, and the PhD can offer more job opportunities and security in the right industry. If OP goes into industry, the last six years could be well worth it!

@Sam That's nice, but I never said getting a PhD is a bad idea. I was only correcting the previous poster. With that being said, unless you plan on doing novel research, a PhD may make you overqualified for many jobs that can be done by a BASc, or MEng. You also didn't say what your field is.

@Cell Wasn't contradicting you, just adding that I've often seen PhD's hired into level 3 positions where a BSc gets you into level 1 -- I hadn't seen anyone mention it, and I think it's relevant to the OP. My field is physics, but most of my coworkers are in chemical/materials/electrical engineering (MS or PhD, and a few BS) at large U.S. manufacturing companies.

I would upvote this a million times if I could. Imposter syndrome is... god... it's just real, that's all I can say without invoking profanity. It is very, very real... and the OP's problem sounds a whole lot like it.

To be honest, I'm tempted to agree with Buffy. It sounds like the biggest issue you have might actually be the one you identified at the start of your post - low self-confidence. Studying for a PhD, and working in academia in general, has a tendency to have that effect on people - you're far from alone.
If I were you, I'd be tempted to take stock of my overall life situation at this point, perhaps with some input from the people around me, and try to get an objective view of how things really are - they may not actually be as bad as you think.
For example, here are some plus points:

You finished a PhD. That's already a huge deal - lots of people don't even start a PhD, and of those who do, a proportion never finish. Of those who finish, lots of people feel like they didn't change the world with their PhD, and that's fine - most people don't, and that's not required. You've got the rest of your life to worry about that, if you want to, and it's not required even then. It's ok to just live and be happy sometimes.
You've got a postdoc position lined up, if you want to stay in academia. Your supervisor wants you to stay, which means you probably did something right during your PhD. Maybe your PhD didn't actually go as badly as you think.
If you've just finished your PhD, it's quite likely (in the absence of other evidence to the contrary, which I don't have) that you're still relatively young. That means you've got time on your side - there's still a whole lot of life ahead of you in which to do all the things you want to do (learning to drive, learning a foreign language, improving your health, developing your hobbies, having a relationship, ...). It sounds like you're unhappy that you haven't been doing those things, which means you'd probably be happier if you started doing them. Pick one and go start on it right now - hopefully you'll feel better (it's generally worked for me, when I've been feeling down). Starting on one of them sounds like much more fun than carrying on feeling fed up about not doing them, at any rate.

Best of luck!
p.s. For what it's worth, the fact that you've got a list of things you wish you'd been doing, and are unhappy that you haven't been doing them, is a good sign - there's an easy fix for that, which is go do some of them. That's much better than not having a list of things, and sitting there having existential angst and wondering whether life is pointless :)

The postdoc is with my PhD advisor. I don't think that's an achievement. Probably my advisor felt pity on me and gave me the position.

@AbhikTandon: Bear in mind that your advisor has something to lose from keeping you if you're truly not delivering (there's an opportunity cost - they could look for someone better). If they're keeping you, it's safe to assume you're at least above bar. Some advisors are kind, but few are so kind that they'll use their scarce funding to renew someone who has no possibility of being useful to them in any way. Advisors who pity you buy you a beer, gently tell you the truth, and help you find a job elsewhere; they don't generally commit £30k or more just to cheer you up.

@AbhikTandon Do consider that a PostDoc position often involves mentoring or teaching junior students, grading work, running tutorials, et cetera.  Given that your PhD advisor is judged and graded not just on their research, but also on their teaching methods/standards, it's a role they quite literally cannot afford to give out of pity.  You not being "up to standard" would put their job on the line!  (That said, finding a hobby - preferably something more physically active than mentally, such as a martial art, to contrast with work - for a couple of evenings a week is a good idea.)

You have:

the highest possible academic degree that one can achieve
a job in the field
a life in a developed country

You're faring really well.
This is not to say that what you're feeling isn't real. It is real, and there is a problem. It's just that the problem is not what you have, but who you are. What you have is a highly successful life, at the same time, you are depressed and miserable.
You don't need more things, you have it all. No Nature publication will take you out of your dark place. You need to learn to enjoy life and accept yourself.
I know the last sentence is useless in itself, because it only tells you what you need, but not how to do it. Unfortunately, that's about as far as a stranger on the internet can get you. Speak to friends, speak to a psychologist, speak to anyone willing to listen, speak to yourself and try to figure out where does this need for accomplishments comes from, so you can move on.

Technically I believe a DSc is a higher academic degree - but that usually comes at the end of a distinguished academic degree.

@MartinBonnersupportsMonica DSc is not universally higher than PhD. In some countries DSc is just what a PhD in biology/physics is called, while in other countries DSc is just honorary, while other countries don't use PhD at all and have only DSc, which are seen as the equivalent of PhD, in countries that have PhD.

You need to talk to someone – be that a counsellor (as @Buffy has suggested in the comments), a family member, a friend, or even (depending on your relationship) your supervisor. It does sound like a good part (if not most!) of the problem you describe may stem from impostor syndrome, and if that's the case, then it will be crucial to have others as a sounding board, to help put things into perspective. I have never known anyone in academia who didn't struggle at some point, somehow. Academia is tough, research is hard and failures are inevitable.
You mention you love doing research. Considering that you have also successfully turned that research into publications, it rather sounds like you do have what it takes to succeed. (Again, to put things into perspective, in my field it is normal for PhD students to graduate with 0–1 publications, and the impact factor of what's considered the leading journal is about 2.3. Different fields are different, yes. But you have definitely not failed.)
The other things you mention seem more minor to me. You say you are bad at programming. But you can always improve – programming, if anything, is one of those things where practice makes perfect. You mention you have neglected your health, hobbies and interpersonal relationships. But this is not uncommon: these things happen to many people who pursue a PhD, in various ways, and it is not too late to do something about them now. You say you have done nothing over the past 6 years. This cannot be literally true (you have earned a PhD, an enormous undertaking), but even if it were, the thing to do now would be to start doing those things you have neglected in the past.
But please do consider talking to someone. Having to verbalize your own thoughts and feelings is an excellent way of beginning to understand your thoughts and feelings, and of starting to see a solution.

Get your frame of reference right.
Achieving a PhD puts you in the 5% highest educated part of the population. That's quite significant. But you're comparing yourself to the smartest people in your direct environment - an environment set up try to get together all the smartest people.
If you don't manage to be in the top 1%, surely being in the top 5% is still something to feel pretty happy with?

They are marathon runners on arrival.
https://www.youtube.com/watch?v=xSZlSaPJAdQ
Do they look well? Can you imagine, how bad feeling could it be, being there, after 42km of running?
But believe me: it is uncomparably better to be there, than for us, watching them on the youtube.
Don't do any irrecoverable mistake now! Wait, at least some months, more ideally some years! Take some longer leave, if you can (probably you can), and do nothing! Only think.
For example, now you can learn to drive. Ask anybody having a driving license, but no Phd, would they switch to the other.

I know what it's like to feel like you "haven't been living" for years. Six years of my life disappeared by my being extremely sick.
I have 5 years of unemployment in my résumé, an unfinished PhD, a tiny professional network, and ongoing health problems which make many things impossible. But I'm living again.
Some people have been in prison for 10 years. Some have escaped war-torn countries. Some have recovered from drugs or alcoholism. It's very hard when you suddenly awaken from a world of constraints into a world of choices, seemingly at a huge disadvantage from others within it. (I am not saying you've got it easier than they do. I'm saying you have this in common.)
Some of them go on to do amazing things. They have a moment that will define their life, and they work and work and work and work to a level that others can't imagine, and do something great for the benefit of their fellow man.
Others are just happy to be alive, happy to have gotten away from a bad place. Nothing wrong with that.
The most important thing in life is not success or respect or glory. It is to make choices that keep you out of misery. Anything more is a bonus.
But asking the question you're asking proves you are ready to change your life.
Maybe you could go to your home country or a country in poverty, where your skills and knowledge could make a bigger difference. Remember you don't need to use your degree at all; you could enter a completely different field. It's better to do it by choice than by necessity. Doing a variety of menial jobs of different sorts can be really enriching, since you see life from so many angles.
Doing a PhD doesn't just teach you about your topic; it teaches you about being thorough, exploring the state of the art, problem-solving, organisational skills, and so on. These make you very valuable if you use them well.
I know what I want to create. And I know what's stopping me is not my 6 missing years; it's my unwillingness to confront my weaknesses (like networking and time management.)  Now I'm confronting these things, and I'm surprised at my success.
Go get 'em.

Two first-authored papers is not bad, I seen a lot of people getting phd for way less and still being full of themselves. You are doing good.

You don't think you did well during your PhD, but you stuck with it anyways. That sounds like a lot of PhD students. But, it also sounds like students that stuck with something, b/c their parents were back-seat driving their futures.
As others have said, your self-esteem issues stem from something. Something makes you feel inadequate all the time, and makes you compare yourself to others all the time.
Usually, that starts from overbearing parents constantly comparing you to other kids, chastising you for not being as good as some top-tier, stellar performer in your same grade or field, etc.
My dad did that to me my whole life. I was expected to get good grades. When I got them, I didn't get a "good job!" or anything. But, if I got bad grades, I got punished. As I got older, my dad would constantly compare me and my siblings against each other and to other kids his coworkers had. "So-n-so's kid is doing XYZ." (to insinuate it's better then what I was planning on doing, or was doing).
Even when I was an adult, my dad was trying to back-seat drive my career with "advice" that wasn't so much him trying to do what was best for me, but what was best for my career. He never took me, as a person, into consideration when giving advice.
What I realized over time (chatting with my dad extensively) was that he made decisions in his career... he gave up moving up the ladder or managerial positions, because he decided to start a family. He took a back-seat position at his job where he kept his head down and kept his mouth shut so he could keep earning an income and not rock the boat while supporting his family. He made one major career shift up the ladder to get more money, and in retrospect it was an awful decision that uprooted the family and set in motion events that pretty much tore the family apart.
What I realized as I got older was that he was trying to coach me to have the career he wished he could have; he was trying to guide his dream job vicariously through me.
He would push it in ways by either telling me exactly things he thought I should do, or package it as "I was chatting with kids at the gym and giving them advice, and this one kids doing XYZ" (again, to insinuate this "one kid" was doing something better then I was).
I got sick of it.
So, I stopped chatting with him about work, school, etc. When he'd ask or press, I simply told him that I was only going to speak with him like a member of the family, not someone I was seeking career counseling from.
I eventually had a blow-up with him, because I was tired of him trying to back-seat drive my life while I was watching his life implode around him with issues he wasn't staying on top of during a situation that basically forced me to take control of his responsibilities when he ended up in the hospital.
What I learned was ... just ignore him.
In 20 years time, my dad won't be around any more. But, god-willing.. I will.
In 20 years time, will I be happy if I had followed my dad's advice and done this and that? No. I'd be miserable, because he was pushing me to go in directions that were making me miserable.
So, why bother listening to him? Why bother trying to please him?
In 20 years time I can follow his advice and be miserable while he's dead, or I can ignore it and be happy while he's also dead.
Ultimately, I have to figure out what makes me happy, though.
But, when you have someone constantly telling you that you're not doing good enough, you need to do better, you're not doing as well as so-n-so over there, you should be heading in a certain direction, you need to do it all before a certain BS time limit... you know what, you eventually turn into a hot mess that thinks very little of yourself b/c you constantly have a devil on your shoulder that never thinks what you're doing is good enough.
Tell that person (or those people) to go screw off.
Since you're international.. and you're in a STEM field.. and you went through a PhD even though it sounds like you didn't really want to .. I'm going to assume you're Indian.
You need to have a moment of clarity where you decide to be your own person and stop having your family tell you what you need to do and where you need to go in life.
That can be hard if your family is paying the bills.
But, I may be making assumptions, but your story sounds almost identical to a ton of other folks I rubbed elbows with in college... all of them Indian. They were taking STEM when really they wanted to do liberal arts or whatever they were passionate about. Their family pushed them into an "lucrative career", b/c it's all about the money and status with them.
I had a couple of Indian folks tell me they had a massive weight lifted off their shoulders when they told their family to stuff themselves. They were dating people locally, and one was wanting to marry the girl he was dating. One guy dropped his STEM and went into art which is what he really wanted to do (and he was an AMAZING artist).
Ultimately, you have to figure out what makes you happy, and stop listening to folks constantly running you down and telling you you're not good enough.
I rented a room from a gay couple, and one of the guys had a degree in aeronautic engineering. You know what he did for a living? He was the director of a high school band. His parents pushed him to do engineering, b/c he was in the closet and just kept his nose down and did what they said. When he finally got older, he got tired of them, and came out of the closet and pursued what really made him happy: music.
People have to have that moment.
So, you're asking how you'll survive over here? I think you really need to ask yourself what will make you happy. And, you need to start ignoring folks that are running you down.
With a PhD in Chemistry, you don't have to be a great programmer. There are companies that will hire you to figure out some chemistry, and team you up with Comp Sci or Info Sys folks that will do all the coding and stuff for reports, data science, etc.
If you don't like what you have a PhD in, then go figure out what you do like. Maybe you like working on motorcycles or scuba diving or whatever.. find a way to make a career out of it.
It's better to live a modest life that makes you happy, even at the expense of others, then to be rich and f'ing miserable b/c you decided to make everyone else happy.. usually folks that won't be alive in 20 years time.. which just leaves you miserable while they're dead.

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Best way to find references for statements in the thesis
I am struggling finding proper references for the known facts that are mentioned in my thesis.
For example: foundation of Cartesian coordinate system introduced the grid system for data visualization techniques.
How can I possibly find a reference to support that claim?
What is your best method for finding references?

You might be able to turn this into a good question if you can edit it to be more specific.  As it is, there's no right answer to this.

@user1449456: I fail to parse your example statement.

@Wrzlprmft I think the answer the OP needs would involve finding out who invented the Cartesian coordinate system. Hint: all the required pointers are already there >:-)

Although the question is a bit vague, I try to give you an answer from my experience. There are often statements that you heard somewhere or which are "obviously" true, but you need a reference.
My best bet is to search google scholar for a variety of different combinations of the terms or suspected authors. If you find some source stating the claim (or something similar) you can often go back through the chain of citations to find a more accurate and reliable source.
Depending on the subject, searching google books is also helpful.

Another good starting point can be the references section of the relevant Wikipedia page (treading with caution of course).

"Common knowledge" are usually not referenced. Yet, what is or is not common knowledge is field- or even individual-dependent. A little investigation may help: look at some journals you think would be a potential home of your article, and learn about their points of view on common knowledge. Talking to your supervisors will also be a good method.
And just a side comments: I am not sure if I understand your example statement and if other problematic statements are like this you may want to talk this through with someone. The coordinate system was meant to project data/information, and one of the manifestations looks like a rectangular grid. But why does it have to be "introduced" again to data visualization when the means and motive were pretty much identical? Be it on a sheepskin map or on a hi-def flat screen, data projection is still data projection. (tl; dr: I humbly think that example statement is redundant. But I am not an expert in this field, sorry if this sounds naive or offensive.)

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Having trouble getting my "assistant" to put in work. How do I tell him to help out more without being rude?
I was recently asked to train a new undergrad research assistant in the lab I work in. I was then told this new lab member is my assistant. He has no experience working in the lab before this, but I had been there for about a year before he came in. We have been working together for a few months now, but I am stuck.
I did have the chance to talk with him more, and he told me that he is only doing research to get a paper published. After all, if you complete research and do not get published, what is the point? I was a little bit taken back when I heard this, though not surprised. Of course almost every researcher dreams of being published, but me personally, I truly want to learn. I am not boasting and trying to make myself look better, but I personally believe my experience as a researcher will serve me well in my future career. If I do get published, all the better! I do strive to have enough data for publication, but I put my learning first.
After hearing this, my opinion of John changed, though I try very hard not to make it personal. I try very hard to focus on the research, and put all of my energy towards making my project successful. He always mentions to me how his schedule is very full, that he is always busy, but at the same time, I also struggle in giving him work to do. I do not want for him to take credit for something I did (in the long run), but I am afraid that because I may appear weak to him, this will most likely happen.
We had a meeting with our PI a few weeks back, and though John had mentioned to me he would be available for work that morning... once our meeting concluded, and several alarms later (that the professor subtly hinted his annoyance with the constant going off of his alarms), he mentioned to me that he has to get going. He gave me one idea that we could do to improve our project, but then as he walked away, said that his schedule is starting to become busy. I am busy too, I am overwhelmed sometimes, but I simply cannot stand the complaining anymore. I would like to tell him in a nice way, that if we are to work on this project together, he must put in the same amount of work that I do. However, the professor has mentioned he is to be my assistant, so I am not sure if he does have to put in as much work as I do?
I am really stuck on how to stand my ground and not appear weak, but at the same time, I do not want to be mean/a jerk. I am also wondering whether I am just putting John in a negative light because I see him as competition? Any thoughts?

I think there is a good question here, but there is way too much text. Can you edit out the information about your personal research goals and remove some of the identifying information? Even with that, I don't think we can give you any insight into your personal psych and why you don't like your new lab mate.

Meet with the person and lay out ground rules and expectations.

Seems very related: http://academia.stackexchange.com/questions/75096/how-to-increase-the-productivity-of-undergraduate-research-assistants

"Of course almost every researcher dreams of being published" I don't understand this statement. Being published is a fundamental part of being a researcher but you talk about it it as if it's some lofty goal that's unachievable for all but the very best. "Almost every researcher dreams of winning the Nobel prize" makes sense; "Almost every researcher dreams of being published" is like saying "Almost every doctor dreams of prescribing medicine."

@DavidRicherby: Publications for undergraduates are not so ubiquitous, are they?

@BenVoigt The sentence I quoted says "researchers", not "undergraduates." If that was intended to mean "undergraduates doing research", it should have said that: to me, in the context of academia, a researcher is somebody whose job it is to do research (i.e., a grad student or upwards).

Disclaimer lable: 100% organic locally grown opinion
I think there are a few aspects you need to reflect on.
First, it's fine for different people to create a joint effort with different motives. As long as the motives move the main goal forward. In addition, just because he wanted to publish a paper does not imply that he does not value learning. If his saying made you assume that he is just on for a free ride, I think that can be too premature a conclusion.
Second, learn how to manage people. Don't expect them just to fit in perfectly with your schedule and work style. Set up ground rules, lay out tasks, and negotiate on the ways of reporting. A very good feature about this case is you know his Achilles' tendon (or hanging carrot if you're a glass half-full kind of person): Name on the publication. Lay out all the works or tasks or learning for him and demand him to complete them on an agreed time or his name will not be listed as an author, but in the acknowledgement. Be civil about it and listen to what he says.
Third, sort out your own conflict. First:

How do I tell him to help out more without being rude?

And then:

but at the same time, I also struggle in giving him work to do. I do
  not want for him to take credit for something I did

Actually do you need an assistant or not? If yes, then make sure the terms are clear and he followed through. If he did, and ended up in the paper, he will eventually take some credits of yours AND you will also take some credits of his. This is what collaboration entails, at the end we have a general idea who did what, but it's inevitable to have some shared credit. If you're completely possessive about your work, and you think that he is taking advantage of you, then you should consider if you need an assistant or if you should decline this responsibility assigned by your supervisor.
Lastly, strengthen yourself up. Listen to this:

I am afraid that because I may appear weak to him, this will most
  likely happen.

What about you that is weak? Why do you just label yourself weak from the get go? Personality? Physique? French? The only thing you need to be stronger than him in this case is your knowledge in this project. All others are side matters and you should not place yourself in the victim seat. An effective manager does not have to have strong personality, he/she just need to be fair, just, and remain clear and open in communication.
Lastly lastly, you should also talk to your supervisor for advice and tips. Work on it to create a happier collaboration experience.

Very nice answer. Mine would have been shorter if I had seen it before.

"French" as in Napolean? As in, has a nuclear stockpile? As in, Algerian War massacres?

I was about to comment but then it got too long and even as a post it is quite long.

Speak with your PI

However, the professor has mentioned he is to be my assistant, so I am not sure if he does have to put in as much work as I do?

I suppose this is the first time you have an assistant and in that case, it seems fair to ask your PI what is the scope of tasks and the amount of time you are entitled to ask your 'assistant'.
I know that the amount of work/time really depends on your country/university/field/department and lab.
Your PI should be able to give you at least general guidelines and what it is the minimum expected from an undergrad assistant in his lab.
Then stick to it at first and see how things go.
BTW,

Were you given an assistant for the sole purpose that you were too busy?
OR
This new research undergrad had to be trained and since you have taken care of it, you can now 'be paid back' by his work to compensate the time you had put in his training?

If you don't know you should also figure this out with your PI.

I do not want for him to take credit for something I did (in the long run), but I am afraid that because I may appear weak to him, this will most likely happen.
  I am also wondering whether I am just putting [him] in a negative light because I see him as competition?

This should not happen as long as you keep your PI 'in the loop' about what everyone has done.
Keep a log of everything he has done and the things you have done. In a matter of fact and professional way.
This is also good to find out what is the contribution of each author/co-author in the final paper.
It is a good practice to keep your PI up-to-date by e-mails (particularly if you have a busy PI) of the progression of the work. (CC everyone involved in those emails). Even if your PI doesn't really read these emails. The purpose, here, is to keep track in a more formal way.

Speak with your "assistant"
He is busy, you are busy, everyone is busy.
There are several points to consider here:

Is your assistant still studying?
Is he 'doing research' in your lab as a full-time job? As a side?
As a requirement of his curriculum?
As to gain more experience for later so basically for free and his own volition?
Is he earning some financial compensation or reputational one due to this position?

And same questions about yourself?
The way to handle this situation is going to depend on his and your situation.
In any case, you can ask in advance how many hours per week he can give you and when: even if he is very busy, he should be able to give that much information before hand. Make him then understand that not being able to keep his words on what he promised is very unprofessional.
However, do give him a bit of time to figure this out, he looks pretty disorganised to me, so he might need a couple of weeks before he can give you a proper figure.

I also struggle in giving him work to do

That would help you to figure out what to give him. Particularly as you seem to do wet-lab work for me (chemistry I would guess if there are many alarms going off). It is hard to plan on the spot.

I would like to tell him in a nice way, that if we are to work on this project together, he must put in the same amount of work that I do.[...] but I simply cannot stand the complaining anymore.

Depending on the amount of time he can give you, you should be able to tell him something like:
OK, based on your schedule, you can only work 10h on this project per week, while I put 35h and X is putting y h., which means that would be only 2% of the total work per week and then I was working on this project from XX months and X,Y,Z from MM months.
You do realise that won't be enough for a proper contribution to the paper
The guy might be truly very busy and just didn't realise what he was committing himself to. You don't expect the same thing from an intern and an assistant. You don't expect the same amount of work from the technician and the PhD student either. They also won't have the same priority on the final authors list.
Try to keep in mind that he is unexperimented and maybe he doesn't realise what is the normal amount of work he should be doing. And maybe he is not fitted for it. What you think about his opinion about research is irrelevant to the problem; how much time he can spare is.
You should also assess why he tends to trigger the alarms so often. If it is because he doesn't apply the best practices, ask him to do so.
Teach him again if necessary.
Safety matters are not a joke. These can also block you to land future positions.
(In a former lab I was working in, one of the post-doc was a real danger and wasn't carrying about anyone health and safety but himself; he created different bad accidents - at the end, he had to go to teach in one this 'after school' complementary school for high-schooler as nobody was allowing them in their lab anymore).
Alarms might be seen as a nuisance to some people, but in the long term (life long-term) there aren't.

Speak with other people of the lab/department
If you can't have a clear idea about what to do from your PI, look/discuss with the other people from the lab about general politics of the lab. No need to complain about your assistant to other as it might be perceived as unprofessional.
Just figure out what is an assistant suppose to do, and how you are supposed to manage them, if there was any other undergrad assistant, etc.

About the publishing part:
If you do science, it is sad to be the only one to know about something, so please consider publishing in any case. ;)
And when you are publishing a paper, everyone is not required (and most of the time they are not) to put the same amount of effort and time. However, the contribution of everyone should be clearly stated in the final paper.
As long as you communicate clearly with your PI, you will be fine.

The context in which the question used "alarms" suggests to me the sense of an alarm clock, most likely an audible reminder from a cell phone of a meeting/task/etc.  Maybe the notification of incoming email or text message.

@BenVoigt I didn't think about that. While I am working fully in silico now, I was working at the bench before and nobody was bringing their phone in the lab (too dangerous for the phone and the experiments). And as everyone was writing in the office, nobody would have even dared to have their phone even pinged. I remember several undergrads being frowned upon as their phone vibrations were strong! The apps that  change the led colours based on the notifications are very handy in such environment.

You need to tease him in a slightly edgy way, e.g.:
(Monday morning) Hi, Manny, how's it going?
(Answering your own question, pretending to be or speak for him, so you'll have to change your voice slightly) Spent the whole weekend working!  (Now speaking for yourself)  No rest for the weary!  Come, let's get started so we can get out of here in good time.  Do you remember ... [and now quiz him on some safety procedures you taught him last week.]  Do not humiliate him under any circumstances.  Just tease him in a friendly, cheerful way.
We want him to get the idea that complaining, and not doing his job, is ludicrous.
Edit: If you're a grad student, and he is an undergrad, then you can expect his number of hours in the lab to be much less than yours.  However, you needn't have to put up with constant bragging, complaining, whining, etc.  Deflate his airs of self-importance by poking fun.  Gently.

OP is in a difficult position, as a quasi-peer of the new undergrad assistant.  Anything remotely stalinesque is not going to come off well.

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Is it acceptable for a referee to suggest changing "theorem" into "proposition"?
In mathematics, it is usual to call terminal results "theorems" and intermediate results "propositions" or even "lemmas" depending on importance and place in the overarching proof. Suppose that one is refereeing a paper where the authors have decided to call almost all their results "theorems", making a paper with a large number of "theorems" that even emeritus professors don't usually reach by the end of their career. (Such theorems include computation that could conceivably given to as end of year exams to master students. Not to diminish the importance of the paper, the actual theorems are good, but the 20 others are not theorems. There are more theorems than pages.)
Would it be acceptable and well-received to suggest toning it down? Or would it be overstepping and rude? This is not just a philosophical question: I truly believe that it makes the paper harder to reader, because it is difficult to separate the wheat from the chaff, so to say. A reader does not know what is important and what is not.

When I was being taught how to proof I was told two things about a the definition of a theorem, 1. A theorem is an important and true proposition. 2. The distinction between a proposition, lemma, and corollary is somewhat fluid.  Recommending a change from theorem to proposition or lemma could legitimately be taken as a diminishing of it's importance, depending on their academic background.

I think we should begin by acknowledging that it is the author's choice whether to label results Theorem, Lemma, Proposition, Remark, etc., so a referee should not insist on changing this as they should insist on the correction of an actual error or gap.

Suppose that one is refereeing a paper where the authors have decided to call almost all their results "theorems", making a paper with a large number of "theorems" that even emeritus professors don't usually reach by the end of their career.

Don't say that to the author, by the way.  It's snarky and not really helpful -- you seem to suggest that the author is somehow cheating their way to "too many theorems."  That's not a thing.
Referees can make stylistic suggestions, of course.  How much they should do this is quite a judgment call. I think a good referee should make stylistic suggestions when these suggestions impact the readability of the paper or affect its appraisal by readers.  Will it look a bit weird to many readers to have multiple theorems on every page?  Yes, I think so, and perhaps the author deserves to know.  However, if by having "too many theorems" the author makes it hard for the reader to see what are the important results of the paper -- and, as a statement about human cognition rather than mathematical achievement, a paper simply cannot have, say, 50 important results -- then that's a much bigger deal.
If I were you, I would lead with the latter: explain that you had trouble isolating the important results of the paper because so many results are being presented in the same way, then suggest that changing some theorems to propositions or lemmas might be helpful in alleviating this.  (Then, if you like, say that having fewer results called theorems might make a better impression on the reader.)  I think this is putting things in the right order and does the best possible job at getting your concerns addressed.
But it is possible to address the main concern -- that the important results not get drowned out -- while still calling every result a "Theorem."  If the author pulls that off...okay.  Up to them, really.

It's also worth considering that the author is from a different discipline (e.g., computer science) where the word theorem doesn't have the same connotation. I've considered submitting some of my more general results to mathematical journals, and I was not aware of this connotation. As an author, I'd appreciate a reviewer bringing it to my attention (but as you suggest, without sarcasm).

@BenHocking which author are you referring to? I’m not seeing any mention of computer science in the question. And can you clarify what you mean about the word theorem not having the same connotation in computer science? As far as I’m aware computer scientists mean exactly the same thing as mathematicians when they use that word, but perhaps that’s not inconsistent with what you meant.

@DanRomik — computer science was an e.g. (i.e., "for example"). The author I'm referring to is the one the OP is referring to. We don't know the author's discipline. In the NASA PVS libraries, you'll see theorem occasionally used for properties that are not necessarily terminal, though they are typically higher-level than lemmas, but you'll also find terminal lemmas. PVS itself enforces no hierarchy between CHALLENGE, CLAIM, CONJECTURE, COROLLARY, FACT, FORMULA, LAW, LEMMA, PROPOSITION, SUBLEMMA, or THEOREM (all are PVS keywords). See also http://pvs.csl.sri.com/doc/pvs-language-reference.pdf

@BenHocking OP’s question starts with “In mathematics, [...]”, so I don’t see the relevance of talking about other disciplines - it sounds like both OP and the author they are referring to are mathematicians. But thanks for the interesting reference.

@DanRomik, I correctly read the OP's question. He states nothing about whether the author comes from the mathematics discipline. He states that the author is doing something unusual for the mathematics discipline. I posit that it's at least worth considering that the author is not embedded in the mathematics discipline, but could be an outsider so might not be familiar with the connotation the OP refers to. It seems to me to be worth considering. Cross-discipline scholarship is not that unusual. It appears to me that you feel very strongly that it shouldn't even be considered.

@NajibIdrissi: When an author fails to follow the stylistic conventions of a field, one very common reason is that they’re coming from a different field.  And considering the likely reasons for the author’s overuse of “theorem” here is very relevant for considering how the referee should respond.

@BenHocking you could well be right, but I guess my point is that from the referee’s point of view it’s completely irrelevant why the author writes in this unconventional way - this has no bearing on OP’s question of what the referee should do in response. Anyway, if you feel that it’s worth mentioning, that’s fine.

@DanRomik: it's relevant because the author might not be aware of the convention. Thus, politely explaining the convention is completely reasonable. As an author myself, I personally would welcome such an explanation.

@BenHocking As a computer scientist (algorithms, complexity theory, etc.), I don't see any difference in the use of the word "theorem" between field and that of mathematicians (combinatorics, graph theory, probability, etc.)

I’ll work my way to answering your question by going down in decreasing levels of generality.
First, at the most general level, it is acceptable to require the author to make any changes to their paper that you believe in good faith to be warranted to bring the paper up to whatever level of clarity and readability that is your and the journal’s standard for publishability. In fact, it’s not just acceptable - it’s your job as a referee to do exactly that.
Second, it is perfectly reasonable if some of those changes are purely stylistic. If the paper has horribly formatted equations, or uses highly nonstandard terminology or notation (e.g., using a swastika as a mathematical symbol), or any number of other stylistic issues are present, it is perfectly acceptable to make the author correct them to make the paper readable by the community the journal is targeting. Someone might object and say “but authors should get to choose their notation!” (analogously to Pete Clark advocating in his answer that authors get to decide how to label a mathematical claim). Well, yeah, they 100% get to choose that, and the journal gets to choose whether to publish their paper once they’ve made their choice. You can’t “make” the author do anything, but you can certainly set conditions for recommending acceptance of their paper.
Finally, on the specific matter that you bring up, it seems pretty clear from your description that the paper does not adhere to standard conventions about publishing in mathematics. “(x+y)^2=x^2+2xy+y^2” is not a “theorem” in any context other than a middle school algebra textbook, and calling it (or something like it) a theorem in a research paper obfuscates the content of the paper and makes life difficult and unpleasant for the readers in exactly the same way as any of the other weird stylistic issues that referees are tasked with calling out. So, in my opinion it would be completely appropriate to ask the author to fix this issue.
As for whether it would be well-received, that’s anybody’s guess.

For the final "well-received" remark, it might not be in the journal's best interest for a referee to require a certain stylistic change that the author may refuse to do. Then the poor editor has to sort it out.

@LeeMosher if the author refuses to do something to bring their paper to publishable quality, the paper should not be published. It is not in the journal’s best interest to publish papers that are not up to its standards.

Referees can be wrong, sometimes. I've had it happen that the referee's insistence on a stylistic change was just wrong, in my judgement. I explained why to the editor.

@LeeMosher of course. Referees can be wrong about more substantive things as well. In any case, if you are a referee, “referees can be wrong” is a reason to be cautious about anything that you are asking the author to do, but is not a reason to not ask the author to do things.

I think you are probably correct, but it is also a matter of style, not formal definition. I think, also, that the paper would be strengthened by more carefully separating what is supportive (lemmas) from what is fundamental (theorems).
The main difference (personal view) is whether a proved result has "legs" to prove many other things (a theorem) or is primarily just a support lemma for something that is more generally useful. If you can envision a "proposition" as being generally useful in itself, call it a theorem. Otherwise probably a lemma.
The term "proposition" is a bit more nebulous. Sometimes it is something that is the subject of exploration with no known proof or counterexample. The "Four Color Problem" was a proposition until it became the "Four Color Theorem", for example. Personally, I'd stick with "lemma" and "theorem" as described above unless presenting statements that might be provable (or not).
And, of course, a big part of a referee's job is to help an author improve a work. Some of what you say may well be subjective, but that doesn't make it invalid. The author remains the author, of course.

Just for the laugh: lemmata is the real plural of lemma.  :-)

@PeterK., ok, but not "nice" to remind me I failed Latin in HS. Oh the shame.

I have never encountered anything named as a proposition which was not as rigorous as a lemma or a theorem. To me (and everyone I work with), the difference is in "importance". A lemma is mainly of interest as a stepping stone towards another result. A proposition has interest on its own, but not as much as a theorem does.

@TobiasKildetoft It is certainly fine for you (and everyone you work with) to use it in that way. However, while I failed HS Latin, I didn't fail Mathematical Logic, where "Proposition" has a well known meaning that isn't equivalent to "mini theorem". I expressed a personal view. Your mileage may differ. See wikipedia: https://en.wikipedia.org/wiki/Proposition.

@NajibIdrissi, the only difference between "proposition" used formally and "statement" is that a proposition is a statement that can be taken as "true" or "false". The truth (falsity) of a proposition can depend on the truth of other things. The wikipedia article gives a good explanation.

@Buffy It is not Latin, it is Greek :-)

In the wide world the term "proposition" is of course used for many things, including the usage in mathematical logic (cf. "propositional logic") mentioned above.  But that doesn't make the usage of e.g. "Proposition 2.76: In a compact metric space, a sequence with exactly one partial limit converges" ambiguous in any way.  Such usage is extremely common in mathematical writing.  (In fact this is quoted from some notes of mine on general topology.)

@PsySp, I never tried to pass Greek, but would likely fail that too. However, I did an entomology check (yes that was a joke) on it and it said Latin, so that's all I know. Of course, the Romans were heavily influenced by the Greeks in any case.

Or see e.g. this paper, which concerns mathematical logic: https://arxiv.org/abs/1708.01828.  It calls several stated mathematical results Propositions in the usual manner.

@PeteL.Clark, are you suspecting that I'm arguing here? I'm not. The usage is fine.

Well, it's an argument in a teapot, but in your answer you write that calling mathematical results Propositions is "nebulous" (and give an example that is over a hundred years old).  I'm just mentioning that the practice that you advocate against is extremely standard in mathematical writing.  No big deal, to be sure...

The “Four Color Problem” was a proposition until it became the “The Four Color Theorem”. Citation needed. I don’t think that’s true.

@DanRomik, what don't you think is true. The statement of it was unproven, hence not known to be true (a theorem) or false. It was, however, in the Mathematical Logic sense, a proposition: A statement admitting a truth value - in this case previously unknown. "Any planar map can be colored with not more than four colors". When I was an undergraduate it's truth value was undetermined. In a Platonic world it turned out that it was true, even then, of course, but without a proof, just a proposition - worth examining.

Coincidentally I was reviewing a book on Discrete Mathematics for an upcoming course (Rosen, Sec. 1.7) and he specifically includes as a boldfaced definition, "Less important theorems sometimes are called propositions". (Relegating "lemma" to a later paragraph.)

@Buffy I don’t think the four color theorem/conjecture was ever a proposition in the sense mathematicians use that word at all times other than when they’re talking about propositions in formal logic. But I understand now that you meant a proposition in the formal logic sense, and I agree that it was (and still is) one.

There is a double standard here: If you use all terms as objects in logic, a theorem is already a theorem before someone found a proof.

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Statement of purpose addressing expected contribution and outcomes
I am writing the statement of purpose for a PhD application (applied math, in the US) and wondering about how to address these two questions:

What are your expected outcomes from the program?
What do you expect to contribute as a student and later?

The university I am applying to expects answer for these questions in the SoP.
I am confused because at this point, I do not know which professor I will work with. And more importantly, what the professor (And I) will work on during PhD. Of course, it is possible to write a general statements such as I will conduct original research and expect to gain deeper understanding of the matter being investigated, and I will acquire skills of publishing a scientific article, etc. However, I do not think these sentences add any value to SoP.
Can someone comment on how to address these questions?
Edit:
I have a clear idea about the professors I will work with and the area I will work on. However, it is difficult to decide on a single professor because of many reasons. For instance, the said professor may not be able to accept any new student etc. Looking at the group's website, I can get ideas what the professor is working on, in general. But, one cannot say what projects will be worked on in future.

because at this point, I do not know which professor I will work with. And more importantly, what the professor (And I ) will work during PhD. You seem to have no idea what this PhD program is about. May I know why do you apply for the program?

This is not what I mean. See my updated question.

Note: I am not in the field of Mathematics. The below reflects how I would address this based on my experience elsewhere.

It sounds like you have a very clear answer to both of these.

What is your expected outcome?

You're looking to perform original research, become more familiar with the process and responsibilities of the academic Mathematics field, and contribute to the broader community. You say as much in your post; write that in your letter! Furthermore, you added later that you know which sub-field you're interested in... write that specifically! "I'm interested in studying <field>, and specifically investigating <subfield>." That makes you sound even more promising, because you're coming in with an understanding of the literature and existing research.
The fact that you haven't identified an advisor is something they are unlikely to penalize you on, as its expected that you're still working on that. You should focus on convincing them that you have done your homework with respect to understanding what academic Mathematics is.

What do you expect to contribute?

You stated that as well; you want to do original research, publish, and gain expertise in a specific subfield of math. That's likely all they're looking for. They do say "...and later"; it may be worth mentioning that you're looking for a long-term academic position, as opposed to, say, banking. That will likely reflect well on you.

Thanks for answer! As I mentioned in the post, all these things sound too general. In fact, anyone who wants to pursue PhD will do original research, will acquire research and scientific publication skills. I believe SoP is place to write specific things. Can writing general stuff hurt instead of help?

Yes. That said, it sounds like you have specific interests that are beyond just "do research"... you've identified a field where you want to focus. I would play that card as much as I could. Hopefully one of the Math people from this site can give more specific advice...


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How to find a scientific review of a theme?
I'm trying to search for a scientific review article of determined theme. That is, I'm not searching a single scientific article containing an analysis of a determined theme, I'm trying to search a scientific article containing a review of many articles about the theme and its conclusion.
What are the terms which I should include in my search (using Google)? Example: "free trade revision", or "free trade paper review"... what are the recommended terms for this search?
Extra question: What are the best sites to search about this? (scientific reviews, scientific articles, papers, books, etc..)
Note: I think my English is legible, I'm brazilian.

Google Scholar: the name of the field + review. Maybe it will be a good idea to limit it to the past few years. Also, read recent papers in the field. Reviews are commonly cited in the introduction.

In chemistry we've publications entitled like "current topics of..." or even journals like "Chemical Reviews".  Thomson-Reuter's  "Web of Science" many university libraries subscribe is an interdisciplinary database (STEM and social sciences) where key word-based search may be narrowed by publication type "review" instead of "article".

http://www.annualreviews.org is usually a good start, if you are seeking comprehensive reviews on well-established themes. Unlike highly specialized reviews, those reviews are well accessible to people of different fields, and put different work into context.

I think the easiest option is to use Scopus (if your University has access) and in the title, abstract, etc, fields type your keywords and in the document type field just select "Review".

You may look into meta-analysis:
https://en.m.wikipedia.org/wiki/Meta-analysis

You can search it in the Google and use "main title of your interest" +"review" in your search.
Google scholar also is an aletrnative way to get the result after searching in google main site.
The third alternative is to search in journals in your field devoted to the surveys and review papers e.g. http://www.nowpublishers.com/MAL or http://www.journals.elsevier.com/computer-science-review in computer science.
Also see the recent published textbook to find probable context of your interest.


text:
Is submitting two papers with identical introduction and methods considered plagiarism?
Our research (me being one of the co-authors) consists of two main sub-cases which are too long to be in a single paper. So, they were divided into two parts--Part1 and Part2. Both of these papers contain the same text in many places (theory,introduction,procedure). The authors for both the papers are also the same.
If we were to submit this to two different journals, is it plagiarism?

If both papers are so similar, why not publish as one paper with 2 experiments? Doing so would allow you to shorten the entire document by reducing the intro and methods sections. If published as you describe, you would be committing self-plagiarism.

Don't do this, the self-plagiarism could cause retraction.

If we were to submit this to two different journals, is it plagiarism?

Reusing text from another paper (even a closely related paper) without explicitly saying so would generally be considered self-plagiarism.  Unless they have exceptionally permissive publishing agreements, you would be in violation of your agreements with both publishers if you didn't get explicit permission to do this.  Even if the journals have the same publisher, they would probably still be unhappy, because this is a violation of scholarly norms.
If you feel your particular case is reasonable and would be considered acceptable in your field, then all you need to do is to be clear about it.  Include a sentence like "For the convenience of the reader, Section 2.1 is copied verbatim from [citation to part 1]" and explain the situation to both publishers when you submit the papers.  If they are OK with it (and you are honest with the reader), then everything's fine, but you certainly shouldn't submit the papers in this state without comment.
For this to work, you'll need permission from both publishers.  In mathematics that would be an unusual request, and I doubt you would receive permission, but things may work differently in your field.  In any case, you may come across as naive or eccentric if it doesn't work the way you expect, but at least nobody will be able to accuse you of being dishonest or manipulative.

@DavidSchwartz: Thanks, I removed the "yes" to clarify.  I also added a paragraph to point out that the publishers may well not agree, but that's a different issue.

Plagiarism is the use of others' ideas or distinctive language without sufficient attribution.  Your question is about the amount of allowed duplication in your own work.  That should (I think) not be talked about in terms of plagiarism.  The term "self-plagiarism" is sometimes used for this, but I don't like it: the two academic crimes are inherently different because the victims are different.  In a case of plagiarism, the primary plagiarized party is the victim.  In a case of improper duplication, the victim is, in a more diffuse way, the rest of the authors' academic community: they are, in several different ways depending on the situation, "paying twice" for the same product.
So "Is this plagiarism?" is (I think) not the right question here.  (Answer: not if each paper clearly cites the other and duplicated content is pointed out.)  The right question is Is the decision to make two papers out of one project with a substantial amount of identical content serving the academic community well?  What aspects of this course of action are potentially problematic, and what else could we do instead?
I would begin with

Our research (me being one of the co-authors) consists of two main sub-cases which are too long to be in a single paper.

How do you know your work is too long for a single paper?  At least in my part of academia [mathematics], on the one hand the length of a single paper is quite variable: many papers are published each year which are under 5 pages and over 100 pages, for instance, and relatively few journals have strict length requirements.  I have heard that length requirements are more common and more severe in other fields, but I would ask whether you are specifically violating the length requirements of all the best fit journals in your field.  On the other hand, the length of an academic paper is quite fungible: in my experience, most papers can be compressed by up to 25% without a reader really noticing a change, and many papers can be compressed by up to 50% without ruining the core content.  That amount of compression could solve your problem.  Have you tried?
Sometimes people do have feelings that "this paper is too long," but that can be quite subjective.  (For me as an author, fatigue starts to set in somewhere between 30 and 40 pages.  After 40, the burden of keeping the entire paper in mind as any individual changes are made starts to feel significant.  My longest paper is about 50 pages and had a very energetic coauthor.)  If you are not actually violating length requirements or very clear norms of your field, I think it would be better to submit a paper which feels a bit on the lengthy side and see what feedback you get.  Sometimes referees and editors recommend splitting a paper in two -- if you get such a recommendation, you can be more confident that you made the right decision.
Note also that your choice of "splitting" seems not to be a very natural one: you are not splitting the paper into two parts which can each stand on their own, and because of that you are repeating a lot.  This makes me think that even if you have decided to write two papers and not one, a different way of splitting might make more sense.  If your paper is unavoidably too lengthy to be published as one, then that should imply that you have enough academic content for two papers.  What you have done so far -- repeating several sections verbatim for most papers -- is likely to create the impression among your readers that you do not have enough academic content for both papers but are trying to stretch one paper into two anyway.
Well, I hope this gives you some things to think about.  I can't really give you the answer without seeing your paper.  Among other things, it depends on the proportions of everything involved.  If for instance the "theory, introduction, procedure" occupies two pages, and each case occupies 20 pages,
then the amount of duplication is probably acceptable.  Even in this case though a different reorganization might serve you better.  In my experience, breaking something unnaturally in half and trying to publish each half separately can devalue your work: academia wants to publish "full things" rather than "half things".  However, this is ultimately quite subjective, and with sufficient reorganization you could probably overcome this.

This really seems like it's more a problem of giving two people copyrights over largely the same work, so, yeah, plagiarism it is not. I agree that a better term would be useful.

In my experience, some repetition from authors in methods/procedures between publications is often permitted, even if it is technically self-plagiarized (though the original should still be cited, without question), because some techniques will simply be the same and there are only so many ways to say the same thing.
Duplication of an entire methods section is different, however, and should never happen because the work should never be exactly the same to be unique.
Having the same text in other sections, even just copying a few sentences, however, is quite bad form, and yes, I would say that is self-plagiarism. You have found a logical way to divide the results into two papers: there should be a logical shift in emphasis of the theory and background to match.

You seem to be assuming he won't disclose the duplication. Nothing in the question suggests this.

The two subcases have in common the following:

theory, introduction and procedure

Pick one paper in which to explain these in detail.  I'll call that one TBE (for Thorough Background Exposition).
Then in the other paper, give a brief sketch of the theory, introduction and procedure, and refer the reader to the TBE paper.
If it helps you -- you could think of the dividing up you're going to do as modularizing.

My way of dealing with this situation would be:

in paper one: state that the problem will be solved in two parts and the second part is still in preparation and will be published as separate paper.
in paper two: in the intro and method section write a statement that the paper is the continuation of paper one, then cite the first paper.

Why even worry about whether it's technically plagiarism or not?
Simply have the introduction and the preliminaries refer to their own use in another work.
It's easiest for the preliminaries, where you could either add this at the beginning:

In this section we present same fundamental definitions and basic tools necessary for our exploration of Foo. It should be noted that these are also relevant in the context of Bar, in a line of research which the authors { are currently pursuing | have pursued in [citation here] }.

or at the end:

The observant reader may note that the definitions and tools put forward in this section would also be relevant, as-is to the study of Bar etc. etc.

For the introduction the wording can probably not be generic, and I would weave in the mention of both Foo and Bar saying that this article focuses on Foo, while the authors are pursuing parallel work on Bar. Or something like that. As in the above, if something was already published, do cite it.
For both sections you don't need to spend more than 2-3 sentences to make sure you're self-plagiarism-free.

No, it would not be. The gist of plagiarism is that you misrepresent the authorship or originality of a work. So long as there is no misrepresentation whatsoever, there is no self-plagiarism and no plagiarism. So long as the later paper properly cites the former paper, there is no misrepresentation whatsoever.
Note that avoiding plagiarism by being honest about the duplication likely won't help you. You'll still have problems with getting the journals to accept the papers. The first journal will not be happy that you plan to publish a lot of the same content through another journal. The second journal will not be happy that much of the content has already been published in another journal.

For lengthy prose that is duplicated from another paper (even one by the same author), a blanket citation to the other paper isn't sufficient; it would need to be said explicitly that the duplicated prose is a direct quote from the earlier paper.

@GregMartin Agreed. Honesty is essential to avoid plagiarism.

I'd appreciate if the downvoters would explain their downvotes. The question was whether this is plagiarism with no suggestion that the duplication wouldn't be disclosed. If you are honest about the source, it's not plagiarism.

@DSVA No, it's not "clearly self-plagiarism". Plagiarism and self-plagiarism can only exist if there's misrepresentation and nothing in the question suggests that there will be any misrepresentation. I agree that it will look pathetic and editors will not allow it, but that doesn't make is plagiarism which requires dishonesty and/or misrepresentation.

No.  Plagiarism is defined as:

the practice of taking someone else's work or ideas and passing them off as one's own.

There are two essential elements both of which must be present:
  1) it being someone elses work  ... (it's not, it is the work of yourself and the co-author).
  2) passing off ... again, you are not doing that either.
Plagiarism is in essence, breach of copyright, but in this case it is your work and you are free to re-use, re-pack and repeat as much and as often as you wish.
At worst, you are guilty of repetition.

Self-plagiarism is a valid and applicable concept. Discussing copyright is thoroughly inappropriate since this is very likely to be assigned to the publisher, and this is without getting to the ethics of reusing material which has already been credited.

Plagiarism and breach of copyright have almost nothing to do with each other. You can commit plagiarism without breaching copyright, for example if you claim something is a work of original authorship that you didn't author when its copyright has expired. And you can breach copyright without committing plagiarism, for example if you correctly cite another's work but take almost all of it. Plagiarism and copyright are two completely different and almost entirely unrelated concepts and understanding that is absolutely vital to know whether or not you're committing plagiarism.


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How to define a project/thesis for the Master level?
I'm doing my PhD in computer science, and as a part of the PhD program I need to co-advise at least one Master thesis and 2 small Master projects.
Of course I went to my supervisor in the first place, but he told me to find a proper topic to define a Master thesis/project that is related to my PhD and also possible to be carried out by a master student, then he will officially support me. Let's say that he is so busy all the time...
Anyway, I want to define 2-3 MS thesis/projects to see if I can attract students to any of them. But I'm not sure how complex or easy it should be!
Let's say that during my PhD I invent algorithms to solve data driven problems, should I define a thesis in which students should try to devise a new algorithm? or it is too much for them? Or just applying some already tried algorithm in some new data (plus data acquisition) would be enough as the MS level thesis/project?
Also if it is supposed to be related to my PhD, should it be the answer to one of my PhD questions?? then I should do it in the first place, not the student!
I'm a bit bewildered here!

You're certainly not the only PhD student in your program. Anyone else you could ask for help or ask how they did it?

Not much of a definitive answer, but here are some prep works you should start doing:

If you did not obtain the Master program from this institute, gather their program information and understand it first. Key information include course offered (with syllabi if possible), degree audit (to figure out what is required and what is elective). This will give you a general idea of the students' level and capability.
Most theses are submitted to the school's own libraries or at least to their committee members. Check out a handful that are related to your field for an approximated scope.
If Master's defense presentations are open to public, go to a couple and learn about them.
Download the Master's degree program handbook and, if any, a list of instructions and obligations for committee members and skim them for useful information. These documents usually detail the length and specification of the project and thesis, as well as general procedure such as meeting frequency and responsibilities of all parties, etc. Be informed about these details helps a lot on budgeting time and effort.
You mentioned you're co-supervising, and I do hope each student also has at least one faculty member in the committee. Schedule an informal meeting with the faculty chair and ask for guidance. Unlike your supervisor, they have the obligation to care.

As for topics, by the time you have done the above you should have a good idea on the length, size, and depth. But some other tips here may be useful:

Dig out other Master or PhD topics that you might have given up.
Cast a look at your work, look for possible branches that you do not have time to explore. Try not to be overly possessive about these ideas, as you may not have time to actually explore them anyway.
One way is to think about your own thesis's Introduction. Are there any particular matters for which you wish there is a piece of evidence?
Start the habit of jotting down random ideas on handheld devices or a paper note pad.
Be extremely clear and open about the ownership of the ideas and deliveries before the student starts working on it.

Ideally (and I'm speaking from biomedical), the student should be technically capable to carry out 2/3 to 3/4 of the work. Try not to make them learn everything new or they can have integration anxiety and tremendous amount of self-doubt which leads to unrelenting reliance on you or worse, withdrawal.
Do know that (and I am sorry to be blunt) this supervising task is i) not a major determinant of your PhD graduation and ii) is but a small piece of evidence on mentoring that can get you hired. So don't invest excessive amount of time in it. And to achieve so, you need to first establish a  sense of non-possessive attitude (the student is working on his/her Master, not your PhD). Second, the topic needs to be able to help you move along your study, but in the same time it should not be so crucial that if it failed your study will be held up. Third, the student should be able to do a good amount of it technically, and your job is to move them along by i) encouraging them to think and act critically and independently, ii) conducting meeting and communication regularly, iii) providing feedback and reasoned suggestions, and iv) demonstrating all the above three consistently.

+1 for checking the library. When I did my MS, I wasn't getting clear guidance from my advisor on how much work was appropriate for the project. I spent an afternoon reading recent MS projects in the same area, both from my advisor and others, and quickly got a good idea for what my scope should be.


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No data for masters thesis
So I’m having my masters in Italy. My thesis is on a project with an Italian organization sponsored by the World Bank in Burundi, East Africa.
I was able to collect the baseline data from my sample. However, there are issues with the local government who has banned any international organizations working in Burundi. I foresee this as a big problem and I may not be able to collect my post intervention data. How do I conclude my thesis? Can I graduate without the complete data for my research?

This is the kind of advice your advisor is much better positioned to give than people on the internet, since your advisor presumably knows the local rules about theses and graduation, and is more familiar with your research.

Just to let you know that this question may likely be closed due to being too specifically dependent on your institute's policy.
The best people to answer you are: i) Your supervisor and your committee (do they think there are enough "meats" from the baseline data to sustain a Master level analysis? Would there be other projects from which you can carve out an aim for your thesis?) ii) The academic committee overseeing the execution of the curriculum (how do they consider disruption due to unforeseen circumstances? Do they need a revised research plan?) iii) The funding organization (Are they fine with only having the baseline data report?, etc.)
In this kind of position, as a student, it may be easy to fall into panic mode and let the flow take you. But do think deeply and clearly about it, and voice what you'd like to achieve. If you want to get the follow up data collected, then talk to your faculty who connected you with WB and see if you can partner with/contract a local agency to collect the data for you (assuming your intervention was delivered somewhat to the plan). Your team may need to seek legal advice as well, but if you do have the will to get this finished, don't give up the first time just because you're told not to.
If it's not a go, or the intervention is unfortunately cut short or terminated, consider proposing a new aim, perhaps focusing on literature review, on the potential impact on outcomes (the ones you are working on) during political instability or other disruptions, etc. That's another logical next step you can consider.

+1, especially for the suggestion to try to work with a local organization.


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When no program is available in your country and all attempts to join foreign ones failed
Here's my problem. I'm a high-school student, from Africa, I will now have completed my last year there; However, the only choice available to me, in my country, are either engineering schools or medical schools. But my interests lie elsewhere, since I want to become a theoretical physicist, and that's obviously not possible with these two options. I've looked at foreign programs, in particular, undergraduate programs. I know beforehand that getting full scholarships is extremely difficult, but I thought that it would be a good idea to at least try. According to my limited knowledge on the exact procedures that are a necessity to get into a foreign university (either the US, or the UK, I didn't look yet at other possibilities), but one should make an application before applying for a scholarship. And to do so, one has to fit certain requirements, amongst whom are a set of standarized tests, the SAT/A Levels. I've spent nearly 5 months, going to the British and US councils, asking many institutions, but none offered the possibility to take either of these tests.
I now have exactly zero idea on how to proceed, which kind of gets depressing, and I'm worried that with the advance of my age, I may not reach my goal.
(Sorry in advance if this question possibly violates Academia.SE policies, but in case it gets closed, I ask the interested persons who want to provide some help [even an infenitesimal one] to send me an email which you can find in my profile)

Hopefully you've looked at a site like this -- http://www.internationalstudent.com/study_usa/application-process/ Is going to the local engineering school and then a foreign school for graduate work in physics a possibility?

I have closed this question because undergraduate admissions is, unfortunately, out of the scope of this site. Having said that: if SAT exams are the main barrier to entry for you for admission to US universities, try looking for some reputable colleges with test-optional admissions. (You should of course explain in your application that it wasn't possible for you to take the SAT or ACT in your current location.)

Theoretical physics is quite heavy on the mathematics. You may get on the right track by studying mathematics first, and then moving into physics at a later point. In this regard, you may be interested in the African Institute of Mathematical Sciences that may have something for you: https://www.aims.edu.gh/aims-network/

SAT testing now appears to be available internationally: https://collegereadiness.collegeboard.org/sat/register/international

@WolfgangBangerth I was thinking about that, my initial plan was to make a major in Mathematics and a minor in Physics, then to do physics at the graduate level. I already contacted the AIMS but I didn't have any response.

@ff524 Thank you so much! I never thought that it was possible to make an application without these tests, and when I contacted some universities they were very strict about that and didn't mention any other possibilit. So I will definitely take a deeper look at that!

@jakebeal In theory, yes. However in practice that's not quiet correct. After contacting the council, I was redirected to another institute, who also redirected me to another one, then I was asked to write my informations to an e-mail to register. To this day, I didn't receive any response.


text:
Commissioning artist to make a figure
I have the idea to commission a local artist to make an artistic version of a couple of figures I often use for presentations, and that I would probably use for my thesis cover. The figures does not present any numbers, but rather conveys the general idea behind the work (subject area is theoretical chemistry). The artist does not have an online portfolio, but a lot of his work is probably best described as "kind of abstract, bad for people who suffers from trypophobia".
I already know that most of the conservative seniors at my department would think it is a bad idea. Normally we go with quite bland figures and monochrome covers (there is nothing in regulations stating that we can't spice it up though). But I am interested in hearing what you would think, if you saw such a thing, a bit out of the ordinary.
I would, by the way, probably pay him out of my own pocket, as I don't think my grant includes art money. And I am perfectly fine with that.

"if you saw such a thing, a bit out of the ordinary" - I have seen all kinds of skillfully designed thesis covers, each in the author's individual style. Hence, it is difficult to say what would be "out of the ordinary".

Ordinary meaning "not artistic covers". We usually go with monochrome.

@nabla: You may want to include that in the question, maybe as a precondition for those who answer. Otherwise, answers (to a question that borders on an opinion poll, anyway) might be quite uncomparable. For instance, in my CS subfield at the universities I am most acquainted with, coloured, semi-artistic covers are the norm, and the one noteworthy aspect about your plan would be that you have not created the cover art yourself (which I might perceive as negative, albeit very insignificantly so). Evidently, this is not comparable with someone's impression who is used to monochrome covers.

Thanks @O.R.Mapper, I clarified that point in the question.

In Stockholm University I have seen a thesis cover with a hand stitched topographic map (I thinkg it was geology), and another with a painting of two giraffes (bigravity, theoretical physics). There is no rule nor expectation that you should be the creator.

It's your thesis, and so long as the work --- including the cover ---conforms to the requirements set down by your institution, then I see no problem with it. Yes, you might upset some of the more conservative of your colleagues, but if you continue in research no doubt you will in future perturb the status quo again.
The only concern I have is whether such an unconventional decoration would influence a grader. However, I suspect you are considering the final version of the thesis, after any corrections set down by your examiners, so this isn't an issue.
Naturally, you should give credit to your artist.

I see no problem when it comes to presentations (eg on the first slide to give the general idea). As long as the "corporate design" of the academic institution is still recognizable. Otherwise slide 2 or 3 would work.
Thesis cover might work as well, as long as it's within regulations (eg cover not nitpickingly specified). And as long as there isn't even a hint that you want to put style over substance. Also, conform when it comes to the spine. If the thesis is in a library as physical copy, it's the spine that counts (and should look the same way as the rest). The cover is invisible.
As for figures to actually convey data in the thesis, I'd stick to the convention. There are reasons -- beyond a departments preference -- why graphs look the way they do. Any fluff is clutter that has no place in a scientific diagram. The primary aim is to argue, not to entertain.
But yeah, go for the cover. Reminds me of Randy Pausch's ("Last Lecture") story about the color image in a article ("Are there allowed to do that?!?!").

If everything fine by the standards of your advisor, then it would be fine to include the artwork. Also consider including the artist in our acknowledgements section. It should be completely acceptable for your presentations.
Your thesis is graded for your academic content. Your figures are added to illustrate concepts. If the idea and the concepts behind the figure itself is yours then worry not for the critic of others. As long as those figures are not copyrighted or published by another author, it should be alright to include them in your thesis.


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Can I ask my adviser for a raise?
Due to the recently passed tax bill by the United States Senate, graduate students will incur more taxes on their income which is already small. This will certainly affect my academic performance and research productivity. One of the professors in the department promised his students to compensate them by supplementary scholarships or awards. Can I ask my adviser to do the same thing to me?

How did he "promise" scholarships and awards to his students?

@Mark he sent an email to his students, one of whom is my friend and informed me about it

FYI, the grad student changes are in the House bill, not the Senate bill. So this will be decided during reconciliation. Also you will get a larger standard deduction. If you have health insurance through university you may be ahead. So much depends on reconciliation right now. So lobby!

"This will certainly affect my academic performance and research productivity." How? Is your effort a function of your pay?

So your income is going to be taxed harder..., and you therefore want more income so that you have to pay even more tax..? I don't see the logic.

@mathreadler: The OP wants more income so that they will have more money left over after taxes.

@jwodder but there may be other ways to do that which are not punished as harshly as with the new taxes would make.

@chessofnerd I really can't imagine how could the payment and productivity be NOT related! I mean, seriously?

@mathreadler Given that you're a mathematician, if you don't see the logic here then I think you made the wrong career choice.  Either that or you have an unbelievably deficient understanding of how taxes work...

@J... If I was a mathematician it would still not matter as this we are talking about is not mathematics but economics. If you get your income from somewhere else you may earn more than in the particular place where the taxes were increased. Say you could do another job that pays more relatively speaking but which is not punished by new taxes the same way. Then you would be better off doing that instead, at least if what you care about is the amount of money you get each month.

@mathreadler  Income from somewhere else is not an option.  First you assert taxes paid is what matters and then what you take home matters.  Are you a hot question spammer?

@Paparazzi Income from somewhere else is not an option you say? But you are not the OP and the OP does not state that... The OP doesn't either state in the question what actually is important to him, which is why I consider both those options. You seem to get mad because I point out possibilities that you don't want people on here to even think about. Are you a hot question brainwasher?

@mathreadler You answered my question.

I thunk this question is based on a false premise. I believe they removed the tuition tax change before before the senate vote.

I want to point out that the proposed tax change only affects you if getting your tuition waived by the university is a result of being employed as an RA/TA.  If your tuition is waived for being a student, then it is a scholarship, and not taxable income.  The solution?  Departments pay your tuition for being a student and your stipend for being a TA/RA.

First, it is not quite a law yet as it still needs to go through conference and be signed by the president. Regardless, you can ask for a raise, but arguing for a raise on the basis that your personal situation has changed is not really a good strategy. Most people ask for a raise when they can make a case that they have been performing well.
Many advisors do not have spare money floating around. Stipends can be set at the department or university level. As I said in this answer graduate student tution is an odd thing. Universities may either automatically increase stipends or decrease tution. It is really too soon to know. Your best bet is to probably unionize and make sure the university begins treating students responsibly.
The issue, at least as I see it, is that advisors need to justify to funders why a PhD student is needed as opposed to a permanent RA or post doc. When PhD students are cheaper than the other alternatives, it is easy. In my field, the NIH post doc rate is about $40,000 a year. This means there is only a little gap in costs between a PhD student, after covering tuition and fees, and a post doc.
The problem is not really the change in tax code, but rather in the fact that full time researchers are being charged tuition. This is something, at least in my opinion, that needs to be addressed on a university/department level and not with the individual advisor.

OP isn't asking for a raise - they're asking to keep the same stipend and not to take a pay cut while remaining at the same level performance and responsibilities. One can argue whether this should be dealt with at the supervisor, department, or university level, but the first paragraph here simply isn't helpful.

Actually, not his personal situation has changed. The law has changed. He asks, whether this change may be compensated as done by other professors, as it seems.

I am not familiar with the American academic system. Is there currently a student union, with any kind of power? And if not, then presumably it's the same as other countries where students simply have no bargaining power?

@E.P. No, he is literally asking for a raise. He says it in the question title, and the description of wanting more money for the same work is generally what is thought of as a "raise". The fact that it is merely to maintain the same net income after tax does not make it not a raise.

@Matt You're certainly entitled to disregard any and all context. However, if your attitude towards student welfare is that something required to maintain the same net income is still a "raise", then I would warn any prospective graduate students to stay well away from taking you on as their adviser.

@E.P. Definitions of words do not change given the context. Its a raise no matter how it effects the OP's standard of living. For example, it is still called a raise if your employer increases your pay to track inflation. The word does not mean what you seem to want it to mean, and "student welfare" does not change that.

@E.P. the law changed, but not everyone will have the same marginal tax rate on the tuition so it is not easy to calculate. Further, I can assure you that a faculty member asking for a raise since their taxes went up would be laughed at.

@StrongBad I'm surprised you consider that comparison appropriate. As I'm sure you're aware, some of the potential tax increases would make graduate school entirely untenable for many people, with a disproportionate effect on students from less-privileged backgrounds. If a given supervisor's response to that change were to demand an exceptional performance increase from their students (as opposed to working with the students, the department, the university, and any relevant funders to find an appropriate solution) then my response would be an unambiguous "don't walk, run".

@E.P. I have a responsibility to both my students and my funders. In order to go to my funder and justify a raise for the student, I need to be able to make a case why it is worth it to them.

@StrongBad Indeed; a good starting point might be "this will enable the student to continue contributing to the research". The viewpoint you're presenting here sends a clear message along the lines of "this supervisor simply does not care about the student, or their welfare, beyond their usefulness to some pre-existing research programme", which I would take as an immediate prompt to start looking for a new supervisor. If you're OK with causing that impression, then I hope your research profile really is hot enough to offset the dent that that will make on your recruitment abilities.

good answer, but in USA you dont have student UNIONS?

"arguing for a raise on the basis that your personal situation has changed is not really a good strategy" Well, saying something like "If I don't get a raise, I won't have enough money to live and will probably have to quit or take another job which will hurt my research. And BTW, no other students will want to replace me either." (if demonstrably true) in a salary negotiation does sound like a good bargaining strategy.

@JiK see edit. My funders would say, so have them drop out and become an RA. They are only willing to cover tuition and fees because a grad student is cheaper than a similarly qualified RA.

Due to the recently passed tax bill by the senate, graduate students
  will incur more taxes on their income which is already small.

It is not law yet.

One of the professors in the department promised his students to
  compensate them by supplementary scholarships or awards.

They should not have done that. For something that affects literally every graduate student waiting for the university to figure out what they want to do before putting together some sort of patchwork solution is likely to be way more useful in the long term.

Can I ask my adviser to do the same thing to me?

You can certainly ask. But graduate student funding often comes from fixed pots of money, and lots of faculty don't just have piles of unallocated money sitting about. Further, many departments are aggressively opposed to having compensation in a department vary by advisor.
Beyond that, if you asked me, my answer would be "Lets wait and see what the university intends first."

Such a request is likely to go nowhere. Most departments have a "fixed" stipend system: people get a pre-determined stipend, although this can be augmented when needed. Usually, such "raises" are to "reward" students for bringing in outside money, or for moving from the master's phase of a program to the doctoral phase.
The better approach would be to organize with students across the university to see what can be done (perhaps lowering the amount of the tuition charge associated with the waiver?).

The people who run universities in the United States are acutely aware of this legislation, even though it isn't in final form yet.  There will be a reconciliation process, in which the House and Senate bills are merged.  (Kind of like making sausage!)  When that happens, possibly in the next couple of weeks, you and everyone else will know what will happen to grad students' taxes.  The bill still has to be signed into law by the President, and that seems very likely to happen.
Then it will be appropriate to ask what your university will do for all graduate students in your situation.  Be aware that it may take some time for them to figure it out, but they probably can't leave grad students in a position of no or negative income.