text:
How do academics in humanities such as philosophy apply mathematics or physics in their discipline?
(I am from an engineering background and know very little about liberal arts
and humanity programs, so I apologize in advance if my question sounds condescending or ignorant.)
I am often puzzled as to how academicians in the humanities (<- corrected) such as philosophy or religious study or in other branches of liberal arts, apply or integrate what we usually think of as "hard sciences" such as mathematics or physics into their studies. This is partially motivated by the plethora of questions on academia stackexchange asking about the feasibility of switching between from one to the other and vice versa, such as,
Teaching philosophy with a PhD in math
Changing field from Computer Science to Philosophy
I have two main questions:

I am not certain as to the difference between, for
example, a computer scientist like Stephen Cook, versus a philosopher
of computer science (there is certainly no shortage of philosophizing computer science, see
https://www.scottaaronson.com/papers/philos.pdf). In particular,
could your average researcher or a student studying the philosophy of computer science feasibly come up
with new results in computer science or theorems on complexity theory?
Are there well-publicized research performed by religious
scholars or philosophers that actually inform or advances or guides
the development of mainstream theory in say astrophysics, biology,
medicine, mathematics, etc.?

While I am aware that these titles are not mutually exclusive, i.e.,
   a student of philosophy may well have a background in mathematics and vice versa, ultimately I am not certain about how subjects such as mathematics and physics can be made relevant to philosophy (or other areas). This has kept me wondering about the hypothetical questions: what would Kant say about string theory? What would Spinoza say about ZFC?
   What would Kierkegaard say about neural networks? Or the other way around, in what ways can quantum computing inform phenomenology?

Mathematics and branches of philosophy like logic are very closely related. One could even argue that mathematics is a branch of philosophy.

Your second question reminded me of Georges Lemaître. He was a Catholic priest and also a famous cosmologist who came up with the idea of the big bang. If you will allow “religious scholar” to be interpreted as “scholar who was also a religious figure”, that would make a good answer to your question, but I doubt that this is what you meant.

Correctly, I hope... as a direct answer to the title question...

In the US, the term “soft science” refers to social sciences (economics, sociology, psychology) and sometimes biological sciences (biology, botany, zoology) but never to philosophy or religious studies. Those are almost universally classified as humanities.

See for example https://philosophy.stackexchange.com/questions/2304/what-are-the-philosophical-implications-of-category-theory

Note that both your examples refer to switching in one direction --- a person with a scientific formation who tries to switch over to philosophy.

First, a historical note: The idea that philosophy and mathematics are separate fields is a recent invention. A few hundred years ago, they were spoken of as one and the same. If you go back even further to the 16th century, physics becomes part of that same field, and even further back the term “philosophy” referred to any systemic investigation whose result was knowledge. For example, Newton’s great work was titled Principles of Natural Philosophy (in Latin) and while Aristotle more famously wrote on ethics and metaphysics, he also wrote on zoology, logic, physics, and biological taxonomy amongst other topics. Herodotus (primarily a historian by modern standards) and Hippocrates (a primarily a physician) were both considered philosophers. Herodotus wrote important religious theory in his history books and Hippocrates wrote important ethical ideas in his medical works (ask any western doctor about the “Hippocratic Oath”). These didn’t seem like digressions and interludes to contemporary readers. These were all works addressing topics of philosophy.

What is the difference between the Philosophy of Computer Science and Computer Science?

Roughly, science studies X and the philosophy of science studies people who study X, ideas about X, and the connection between X and other philosophical questions. Topics in the philosophy of X (for every science) include questions that define the scope and nature of the field, as well as its epistemic standards such as research methods and standards of evidence.
Three examples of questions along these lines are:

In physics, there is generally a preference for a theory that possesses “mathematical elegance” over one that appears to be more ad hoc, even when the two theories have identical observed evidence. Is having this preference legitimate? If so, can it be justified based on the practice of physics alone or does it require appeal to other principles (maybe ontological principles, or epistemic ones)?
In computer science, one studies computers and computation. Given an object, how do you tell if it’s a computer? What does it mean to solve something “via a computation” or “via an algorithm” as opposed to via other means?
In physics, one studies the physical properties of objects. Someone might be tempted to say that mathematics analogously studies the mathematical properties of objects. However, we are used to thinking of physical properties as being those embodied by physical objects that exists in physical space (that is, mass is a property of this ball that exists in the world). Is there an analogous sense in which mathematical properties are embodied by mathematical objects that exist in mathematical space?

Over the course of the investigation of these topics, topic-specific questions tend to crop up. Contemporary philosophy of mathematics is extremely concerned with ontological and epistemological questions, while contemporary philosophy of medicine is primarily concerned with ethical issues and the philosophy of biology involves questions about the precise nature of life and the implications of extraterrestrial life.
It’s quite possible that someone could be an expert in subjects like this and not be able to do cutting edge mathematics and physics, though answering these questions certainly requires a substantial knowledge of the fields of science you are analyzing.

Are there well-publicized research performed by religious scholars or philosophers that actually inform or advances or guides the development of mainstream theory in say astrophysics, biology, medicine, mathematics, etc.?

The answer historically is yes, even setting aside the historical note I opened with. Thales, Aristotle, Alhazen, Ptolemy the Second, and Jean Buridan are all famous people who would be considered philosophers by today’s standards who made substantial contributions to physics, astronomy, biology, medicine, mathematics, and other fields of science. If you’re looking for more recent contributions it’s more difficult.
There seems to be a historical bias in categorizing people as scientists when they did both science and philosophy (by modern standards). Although he’s far more famous for his work on calculus, Leibniz was also a very influential philosopher, and probably more influential as a philosopher in his time than as a mathematician. You’ve probably heard of his theory that we live in the “best of all possible worlds,” because an all powerful and all good god wouldn’t let us live in anything else. These ideas were so influential in his day that Voltaire became famous in part for attacking Leibniz’s philosophy, such as in his book Candide. Einstein, Minkowski, Turing, and Nash all did philosophy, but that aspect of their work is less well-known to the general public.
There are some people who are widely classified as philosophers who made substantial scientific advances in recent times. The work of the logician Gottlob Frege (1848 - 1925) was ignored in mathematics for a while, but the mathematicians Bertrand Russell and Giuseppe Peano would revolutionize mathematics by introducing axiomatic systems of logic and arithmetic grounded in Frege’s work. Linguistics is an example of a science that recently grew out of a field of philosophy, and so many recent philosophers have had substantial impacts on linguistics, such as Ludwig Wittgenstein (1889 - 1951) and Saul Kripke (1940 - Present). The philosopher of mind and philosopher of language David Chalmers (1966 - Present) is hugely influential in the development of fields of computer science such as artificial intelligence and human-computer interaction. Chalmers is one of those people whose ideas are used to benchmark and understand developments in AI, as he has written extensively on the concept of intelligence and coined the term “the hard problem of consciousness.”
David Hume (1711 - 1776) wrote a book called an Enquiry Concerning Human Understanding which is undoubtedly one of the 10 most influential philosophical works ever written in the West. Although it’s impact is most prominent in philosophy (Kant famously claimed that it woke him from his “dogmatic slumber”), it also was highly relevant to scientists and the sciences. Einstein had the following to say about it in a letter to Moritz Schlick, 14 December 1915

You have also correctly seen that this trend of thought [positivism] was of great influence on my efforts, and specifically E. Mach and still much more Hume, whose treatise on understanding I studied with fervor and admiration shortly before the discovery of the theory of relativity. It is very well possible that without these philosophical studies I would not have arrived at the solution.

This wasn’t one of your main points, but I also wanted to address this:

ultimately I am not certain about how subjects such as mathematics and physics can be made relevant to philosophy (or other areas).

They don’t need to be “made relevant to philosophy.” Anything that increases ones understanding of the world is something that is relevant to philosophy. However, one could wonder to what extent the technical details of scientific theories or scientific methods affect philosophy. Like any question about the interdisciplinary use of techniques developed in one field but applied to others, the answer to highly depends on the field of philosophy and the skill of the philosopher, but virtually every scientific advance gets used by some philosophers for something. There are ontologists whose arguments about the philosophy of time that revolve around technical details of Einstein’s theories of relativity, epistemologists who use category theory, philosophers of mind who use results from cutting edge neuroscience research, and ethicists and metaethicists who read and make extensive use of results from social sciences such as economics, behavioral psychology, and decision theory.

Newton's a great example.  In his own words, he saw his work as "philosophy", but today most folks would find it strange for him to be identified as such.  I think that social forces had philosophers who could do technical work identify themselves in such terms, such that "philosopher" evolved into a de facto label used only when someone couldn't claim a technical title.

The older meaning of "philosophy" as encompassing "any systematic investigation whose result was knowledge" survives in our times in the phrase "doctor of philosophy", i.e., Ph.D., a degree that can earned by work in any of a wide range of fields of knowledge.

A physicist focuses on physical objects, but a philosopher is not limited to that which is observable as an object. Mathematical knowledge is necessary for mechanical reproduction of a non physical concept. Theoretical mathematics is helpful in understanding something that is already physically manifest or in attempting to create something physical from a concept.
A philosopher can contemplate without the use of mathematics relationships that are not easily measured e.g. those that exist within and between the human species. Although, the more resources we expend to understanding and developing the human species the more likely we will begin to apply mathematics to human behavior. However, we currently expend more resources developing machines to the point of creating machines that mimic human behavior. Why, because we know that the creative capabilities of the human species far exceeds anything else physically that we have general access to.

Are there well-publicized research performed by religious scholars or philosophers that actually inform or advances or guides the development of mainstream theory in say astrophysics, biology, medicine, mathematics, etc.?

Philosophers, and religious scholars, have had a tremendous impact on these fields in a number of ways. The most obvious is bioethics - especially in medicine and related fields (public health, veterinary medicine, etc.) the advancement of science is accompanied by potential interventions on populations and individuals. These are inherently ethical and philosophical questions, and do not take place in a purely philosophical vacuum.
Whether a study is ethical, whether an intervention is ethical, and even questions like what is the cost of an intervention are often discussions that involve the humanities. As are things like understanding why people do what they do - I'd argue that medicine and public health have suffered from not paying attention to the social sciences and the humanities more.
Consider this quote from Neil deGrasse Tyson:

In school, rarely do we learn skepticism, and how political winds can
  influence it, morphing skepticism into obstinance.

It would be fairly straightforward to argue that this is precisely what the humanities teaches.
I'd also note that a year or so ago at a major conference in my field (infectious diseases), I noticed that every keynote speaker said something in their talk that betrayed a grounding in the liberal arts had influenced their work.

How do academics in fields like philosophy apply mathematics or physics in their discipline?

They usually don't.
Typically, being a "philosopher" is taken to disclaim one's ability to perform technical work.  Anyone who can do both Physics and Philosophy:

is a physicist;
is not a philosopher;

in mainstream terminology.  For example, Albert Einstein is a "physicist"; calling him a "philosopher" would sound strange to many, despite his powerful mastery of Philosophy and the fact that this mastery led to his greatest scientific achievements.
The thing is that you need to study the technical aspect of a field to be competitive in it.  The philosophical side is something that you do in your own time.
For example, Einstein studied "Physics" in school.  Through his personal studies, he acquired a deeper understanding of it than many of his peers; in some sense, he was a true physicist while many of his peers were more like technicians who worked the abstract machinery others had made for them.  But, since he got his PhD in Physics, that's how folks saw him.
Though I used Physics as a specific example above, the same applies to most technical fields, including math, computer science, etc..  In general, if you excel at a technical field, you're identified in terms of that technical field.
@StellaBiderman's answer covers a lot of great points, so I won't repeat them here.

Anyone who can do both Physics and Philosophy is a physicist — [citation needed] Not everyone who can do physics does do physics. — is not a philosopher — [citation needed] Now you're just being a snob.

@JeffE I'm not so into the personal insults thing.  I mean, if you'd disagree, I'd love to hear your perspective on it.  Just, if you're saying that citations are needed or accusing me of snobbery - not upset - just, what purpose does it serve, ya know?  In all honesty, this is my understanding of the situation.  If you have additional information that'd improve upon it, I'd be genuinely interested to hear what information you could provide.

@JeffE Oh, and to clarify, my point about "is not a philosopher" isn't meant as an insult to physicists (in case that's how it came off).  My point was that we don't typically call physicists "philosophers", not that physicists can't do philosophy.  I'd meant Einstein as a prime example of this - he was a great philosopher, but we don't call him a "philosopher".

What do you mean by “technical work”? Many philosophers do do technical work, by any definition I’m familiar with.

@StellaBiderman I meant "technical work" to refer to applied knowledge, e.g. I'd consider Physics to be technical work because it applies knowledge to describe the universe.  I'd meant to say that, when people apply their knowledge, they tend to gain a label other than "philosopher" based on how they apply it.

@Nat What country are you from? Maybe this is a cultural barrier that’s causing my confusion.

@StellaBiderman The US; I think that I mostly use "technical work" when talking in a business setting to hand-wavingly refer to the broad class of people who do STEM-related work, as business executives tend to see all such workers as "technical workers", in contrast to, say, managers, people who work in sales or with customers, manual laborers, etc..  (Just to link xkcd, business folks tend to see all such work as being qualitatively similar.)


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I feel like my research is stalled because of a lack of available mentors and my lab situation isn't conducive to research. What are my options?
I'm a graduate student at a top-20 research university in the US who's working towards their PhD in an engineering field.
My issue is that I feel like I'm making very slow progress towards graduating. It's the end of my third year and I haven't even chosen a thesis topic. While I'm sure that some of the blame lies with me, here are some other extenuating circumstances.

Few mentors. My PI is fairly busy and takes trips overseas often. As a result, their leadership style is mostly 'hands off, learn by doing' and they are rarely available on a day to day basis. My professor recently moved from another institution a few years ago and although they are highly regarded in the field, they weren't able to bring any of his graduate students with them. I joined the lab nearly when it first came to the school, so there really aren't any senior graduate students to give any practical guidance.
I'm self-funded. My first year I took loans out, every term after that I've been able to pay for tuition as a teaching assistant, which is a good gig that I enjoy but it does take a significant amount of hours per week. (15-20 per week) Some of the lab members are research assistants, but not all.
Lab projects can provide research funding but don't always contribute to graduating. My lab does a lot of short term (6mo-2 year projects) that can provide research assistant stipends. However, we have so many people that are trying to get in good with my PI that most times, people are volunteering to do the work for free. These projects tend to be pretty time consuming with close deadlines and high stress. I've joined a couple of them as a volunteer in order to be a bigger part of the lab but they ended up taking up so much of my time and energy that I couldn't really work on anything else.

The area that I'm interested in (robotics/controls) is fairly difficult to get into because you need to have some background in programming, electronics and mechanical design. I had an okay experience in undergrad which meant that I've spent a lot of time relearning/augmenting skills and theory. I feel like even after three years of grad school, I've barely gotten to the heart of what I need to know in order to understand current papers, much less advance the field of knowledge.
Should i stay/join another lab/leave for another school?
I've debated this ever since I came to the school. Initially I had just planned to do my master's here and then leave. However, I ended up staying because I felt like I had already made it pretty far at this school and have a way to provide for myself through TAing, have a good living situation, have been in the lab for a long time, etc. I'm hesitant to try and join the other professors' research groups because I'm not very interested in the topics they are focused on. I'm also hesitant to try and leave and go to another university because I don't have much to show for my time in grad school (I have a single conference paper that was recently accepted, no completed projects aside from classwork) and I'm not sure if I can get a good recommendation from my PI.
EDIT: No direct conflict with anyone, but possibly misunderstandings with the professor. I've worked on a few short term projects, most with middling success. In the first one, our lab didn't have the facilities to really make something well. The following year, I made a prototype design and later decided to pursue something else because I didn't feel like it was going anywhere. Most recently, we had a relatively large team project that I was heavily involved in but due to really short deadlines, it ended up being somewhat shoddily put together. I'm also working on a design project that's what my paper is in with a teammate but our work is being overshadowed by another lab mate who is taking a different approach.
I think the biggest difficulty making it hard for me to communicate with my professor is that I don't think he has a positive view of me/ how useful I'll be to him. Most of the face-to-face meetings I have with him he either doesn't seem to be interested in what I'm working on or doesn't think that I'll be able to contribute. As a result, I don't meet with him very much. (maybe once or twice in the past year)
EDIT2:
When I graduate I want to continue to work as a researcher, eventually leading a research group. As far as I can see, that could either be in academia or in industry. A teaching only position wouldn't be of much interest to me.
A minimum effort PhD isn't of interest to me because it wouldn't get me very far; I'm aiming to stay in this field and build on my work/knowledge afterwards. I'm aware that it will very likely be another 3-4 years before I can graduate.

TL;DR I'm willing to put in the work to graduate but I feel like it's been quite a while since I've made measurable progress and that I'm probably spinning my wheels due to a lack of mentors/people to learn from. What are my options, and what would you do in this situation?

"I'm sure that some of the blame lies with me". What have you done to contribute to this situation? (To answer properly): Any misunderstanding with the professor? Any conflict with anyone?...

With 15-20 hours of teaching per week and presumably taught classes on top of that, you aren't leaving enough time for research, imo.

If you are in robotics/controls, why are you self-funded?

@user2768: Maybe, but 15-20 hrs/week of TAing (half time) is quite standard, at least at many US universities. It's usually how departments pay for grad students' tuition and health insurance. I should add that most US grad students work 50-70 hour weeks, or even more when taking classes.

@jvriesem, that perhaps explains why US students take twice as long as Europeans.

@Llopis: added more information as an edit

@JonCuster: that's just how our department is. Also, I probably made the mistake of not applying to other schools when I was graduating, but I went straight from undergrad to graduate school, at the same university.

Are you actually paying for tuition as a TA, or are you getting tuition remission for being a TA and then getting paid on top of that, using those funds for living expenses? The former would seem very very unusual to me in the US, the latter is common, and I wouldn't really consider you "self funded" at that point.

@BryanKrause: It's the latter.

@BryanKrause - I think that either Jon misunderstood, or else Jon meant that OP is not an RA.

@JonCuster - Can you clarify, please?  (See comment directed to Bryan.)

oubliette, can you finish your sentence that started with "In addition, most of"?

@aparente001 What are you saying? My comment about self funding was to OP, who used that term in the question.

@BryanKrause - Oh, yes, I see, the "self-funded" description came from the question.  Okay, let me restate.  I think maybe what was meant was that OP is not an RA. //  I agree with you, "self funding" usually means no support.

Being an RA is not particularly different from being a TA - you are being paid to do a job. True, with a TA the specific job is not research. Depending on the department, many 1st-2nd year grad students are TAs, and move to being an RA once past their qualifiers. So, get better at everything, and follow @BryanKrause's advice below.

I'm concerned that you don't mention anything about what you are aiming to do after you get your degree. While this is very common, it's no less dangerous. Do you have a personally-compelling answer to the questions "why am I doing this?" and "what do I want to get out of this experience?"
The problem with just kind of going along with the flow is that you will only get where the flow happens to take you, and this generally has absolutely no consideration for what your personal preferences and values are. This destination could be "being flung off a waterfall and onto a pile of rocks", for all you know, if you haven't put in serious effort to chart a course and decide what you want to aim for.
From your description of the situation, I imagine that the analysis of you from your advisor's perspective might be something like this:

Nice person
Does at least non-objectionable work
Stays out of the way
Doesn't cost me much of anything (money or time)
Not particularly motivated
Not really sure how I can help this person

What do they do? Well, they just kind of let you do your own thing, because as far as they can tell you are fine with that. It's not exactly active advising and mentoring, but it's the low-energy response, so it sounds like what they are going for. Some students even want exactly that out of their relationship with an advisor, so I can't even say you have a bad advisor - just one who's extremely hands-off.
The real danger here for you is: what's at the end of this flow for you, based on your current trajectory? What is the value to you of a "minimal PhD" (you passed and got the degree, but you didn't really do much more than what you had to)? Do you have solid evidence to support that this is a reasonably likely outcome?
The Options Ahead
Once you'd done the probably-very-hard work of deciding what you want to aim for (which is extremely important, because every outcome requires a different technique), then you'll need to do the hard work of deciding how to make that happen before it is simply too late.
If you want to stay with your current advisor, you'll really have to light some fire under yourself and ditch the acceptance of the lab-hanger-on position. Make a provisional plan, make a meeting happen with him (anyone worth working with is busy - don't rationalize avoidance), and make it amazingly obvious that you aren't screwing around anymore. Have a reasonably detailed plan in hand, and talk about what you need to do as a next step to get things straightened out and headed in the right direction. Insist on being of value, and of being appropriately valued. You'll need to start to be assertive, no matter how uncomfortable it makes you, and see if your advisor is supportive of your new-found direction and goals. They won't be sending limos for you or anything, but they should at least be interested to see if you really do change your behavior of hiding in the background and going along to get along.
If you decide to seek out a different advisor, all of the above still applies. You are going to need to know at least somewhat about what you want to explore short-term and long-term, and be willing to start hard at work somewhere.
If your long-term goal requires more research, you're going to have to start trimming down the time and energy that goes into teaching and redirect it into research, either to get a research assistant position or just to get things done. If you've decided you want a teaching-only position - and you read up and explore what that really means in the real world of 4/4 and 5/5 course loads with no class buy-out or prep support - then you'll need to start pushing for being more than just a TA and find out what is necessary to start being an instructor of record, and any other professional development you'll need.
If you decide to switch institutions, none of the above changes. You'll be "starting over" only in the sense of having to bring a new approach, attitude, strategy, and energy to your work, or you can end up in the same place you are now in 3-years time. Most of anyone you'd ever want to work with will be busy advancing their own agenda, because that's just the reality of most modern University programs, like it or not.
If you decide to jump out of academia entirely, I would encourage you to still take the same attitude. I have personally never found life to hand out treasures easily, and going with the flow never seemed to take me anywhere I wanted to actually end up. I don't know if you would find the same thing - but I would strongly encourage you not to passively wait and find out.
Finally, I encourage you to consider the concept of sunk cost. The decision you made to be at this place for this period of time is done and gone, and absolutely nothing you can do will recover that. It isn't "invested" in the proper sense, and it isn't something you lose or don't lose - it's just the past. It's natural to try to use it to make decisions, but it provably encourages "throwing good money after bad" (or spending more time on a relationship that just isn't a good one, because you've already spent so much time on it) and other such bad decision making.
Do the hard work and soul-searching to make the best decision from this point forward, as considered from the perspective of you in 5-10 years. What is behind you is a very small thing compared to what is ahead of you. Good luck to you, regardless of what you decide.

I added more info under my question as EDIT2 to answer your question. Thanks, that's good advice in general. The part about having a really detailed plan is something I'm not sure how to do though. How am I supposed to come up with a through research plan when I still feel like I barely understand the state of the art? I don't even know the right questions to ask.

Excellent answer (+1); your assessment from the advisor's standpoint is spot-on, and a lot of graduate students could really benefit from reading this.

@oubliette That's actually a big part of why the plan is important, but realize the detail is an end goal - you just start with what you can do, and you progressively begin to replace blanks and question marks with more details. It can start high level, like "identify a thesis topic -> graduate -> find a job", but you just keep refining and filling in the missing pieces. It should start as vague junk - and progress towards something increasingly clear as you work. And I'd bet you know and understand more than you think - but only in sitting down and connecting dots does awareness appear.

@oubliette Oh, and based on your edits of interest in research, I cannot more highly recommend you check out the book "The Professor Is In". There are more details and specifics spelled out there than can fit in any answer, and while it was written from a humanities/social science perspective, it will still be largely applicable to you. If you wait until the end of your degree to develop a plan to get you the job you want, you are quite likely to be unable to attain it - and most people won't warn you, because they don't want to have hard conversations.

Good advice from a supervisor point of view. Hope the graduate students who are in the middle of their studies can understand the situation in a better way.

It's not clear to me whether your PI has made a commitment to be your advisor.  When you wrote "PI," should I take that as a synonym for "advisor"?
For the rest of my answer, I'll assume that he has made such a commitment, or that you go ahead and ask for clarification, and he provides it.
You need more regular guidance from your advisor.  Typically, a PhD student would have a standing face to face meeting scheduled with the advisor.  You can request that.  (Don't let yourself get defensive or offensive -- just ask.)
Apparently there are things you like about this professor.  In that case, it would be worth your while to bring the mountain to Mohammed, if you find that in practice, weekly meetings do not occur.
The way to bring the mountain to Mohammed is to use whatever mode of communication works for your advisor.  You can try email, fax, Skype or something similar, phone, recorded audio or video, powerpoint, etc.  You can ask him what would work best for him.  You can experiment and then ask his opinion.
You'll have to take the initiative to find things to ask and discuss.  For example, you can

write a weekly report, where you can write up things you've learned in coursework, things you've learned in seminars, summaries of papers you've read, project proposals, project progress reports, etc.
write an informal proposal about something you propose to do (either on the short term, or Some Day).
invite him to edit or comment on what you've written.
write up some questions.  (If he doesn't answer them, work on finding the answers, and then the following week, write up the partial answers or additional confusion you have discovered.)

Have you finished all your basic exams for the PhD?  If so, congratulations!  If not, you can report on progress made, places you are stuck.  (Presumably you are working from old exam questions....?)
If your advisor is unresponsive and uninterested after some time attempting these initiatives... then you'll know where you stand, and you'll know it's time to work with a different advisor and perhaps a different department.

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text:
Which set of results to cite when there are contradicting numerical results between articles
I am working on a literature review of various machine learning models doing the same general tasks, both to learn the theory and challenges involved and also to find the current state-of-the-art and average expected performance to compare the experimental result to. In my search, I found that some articles measuring the same model, on the same dataset, with very different final results.
Seeing as this is about machine learning, which inherently has some amount of result instability, not to mention that each lab will have its own model build, pipeline, and practice, some amount of it is expected. Furthermore, all the articles are from IEEE, and the authors are from famous universities, so they are about as trustworthy as it is going to get. It still leaves the question of which set of results to cite, however.
The way I see it, there are a few options:

Cite the model's results from the article it came from: The authors obviously know how to get the best performance out of their own work
Cite a model's results from the article it did not come from: Prevent any bias, however unlikely
Cite all results from unaffiliated review articles: Prevent bias, and also give a "neutral playfield" for all competing models. The downside is that such reports are almost always a few years behind current developments
Try to test the models myself: Unless I decided to write my own review article comparing the models, I highly doubt that will be approved. In addition, the limited resources and time I have for this may not allow for a good or fair comparison, nor is it going to be much similar to any current results available

Edit:
To give a simple example of what I mean by "contradicting numerical results" in machine learning (ML), assuming that the current standard performance is against a (sometimes not even an ML model, just a mathematical algorithm) with average error Ep = 0.6 (cited as [3]). A and B are 2 models from 2 different labs and follow different model families:
Model A paper [1]:

We have found that the newest Model A has an average error Ea = 0.5, ahead of SOTA B [2] with Eb = 0.8 and production model [3] Ep = 0.6

Model B paper [2]:

We have found that the newest Model B has Eb = 0.57, above industry standard [3] Ep = 0.6, and better than Model A [1] with Ea = 0.75

Assuming a lab C, which is not connected to either of the above, deigns to write a review paper about them, they might write [4]:

The tests conducted have shown that model A [1] has an average error of Ea = 0.7, similar to model B [2]

"To the best of the author's knowledge, the following results were obtained: 0.5 in [1], 0.57 in [2], 0.8 in [3]. While it is, to the best of the author's knowledge, not clear how the differences can be explained, all of them imply.."

Fair enough, but the problem with the machine learning model is that sometimes the difference in results is only ~1-2 %, and citing everything can lead to ridiculous moments of modern research less accurate than algorithms from 1993, or worse, not even as good as its own predecessor, which means its article should not have been published in the first place (?)

If there are really large amounts of different results, I would make a complete table listing the authors, paper, year, result and then, in the normal text, especially emphasize the "non-ridiculous" research and additional important things (eg that while some result doesn't improve the result, it gives some other perspective etc.)

Of course, it depends on the result but there are many reasons why a worse result should be published.

True, true, especially when the new model is the first of a new family. Due to the nature of many of the articles, though, there is rarely a non-Review Paper set of data that does not contain some level of "Huh?" to it. For example:
Model A paper [1]: "We have found that the newest Model A has average error Ea = 0.5, ahead of SOTA B [2] with Eb = 0.8 and 90s production model [3] Ep = 0.6"
Model B paper [2]: "We have found that the newest Model B has Eb = 0.57, above industry standard [3], and better than Model A [1] with Ea = 0.75"

Are they even testing on the same data?

Yes, same dataset (more like the only public dataset in that field), same name, and pretty much anything on the article itself is the same

Well, it has been over a week since the last answer to this question, and I would not be able to monitor this question in the near future due to work, so I will be accepting the answer I think to be the best at the moment, though don't be discouraged from further discussion

If you are reviewing a field, then you need to be complete. Picking and choosing is a form of bias, though you can explore whether newer results are an advance in validity over older.
So, you need to cover it all, or at least all of it post some reasonable date.
If you leave out a study you may be doing a disservice. Some models, approaches, etc, can be valuable in the extension if not done that way originally.
And yes, you can say that there is potential variability in results based on other factors than the models themselves. Those differences may actually be important - too important to leave out of a review.
Your last suggestion seems to take you beyond the realm of review, however.

Yes, include all (reputable).

The last suggestion is mostly so that people do not assume infinite time/resources for this problem by prefacing that "Unless it is the point of the project itself, that is NOT going to happen"

For covering all sources, feel free to check out my comment on the question, but the short version is: Just because everything is legitimate, does not mean everything makes sense

Of the options you suggested, only the first seems reasonable:

Just cite the model's results from the article it came from: The authors obviously know how to get the best performance out of their own work

A review is supposed to report what the literature says, with some intelligent commentary. So, for you, that would mean:

Report what the literature says. If there are contradictions in the literature, then report it as such. That is useful information to readers, rather than hiding that fact by selectively picking what you think are the "best" results.
Give some intelligent commentary. You should admit that you are not sure why there is so much variation in the literature, but try to intelligently suggest some plausible reaons. If this is quite an important issue, then it would be worthwhile for you to run the model yourself and see what you get. Although this should not be a formal part of your review, your experience could give you some insights as to why some results in the literature vary from each other. This would add value to your readers.

I do not think any of your other suggestions would be very helpful:

Cite a model's results from the article it did not come from: Prevent any bias, however unlikely

Maybe I don't understand what you are saying here, but I do not see any logic (or integrity) to citing results from articles from which they did not come.

Cite all results from neutral review articles: Prevent bias, and also give a "neutral playfield" for all competing models. The downside is that such articles are almost always a few years behind current developments

From the scenario you describe, how would you determine these so-called "neutral" review articles? You would be introducing a value judgment of "neutrality" that might be difficult to justify.

Try to test the models myself: Unless I decided to write my own review article comparing the models, I highly doubt that will be approved. In addition, the limited resources and time I have for this may not allow for a good or fair comparison, nor is it going to be much similar to any current results available

I did suggest that you run a quick model for your own understanding, but not for publication of the results. Any such models would not normally be publishable because they would have to be subject to peer review in order to merit comparison with the literature that you are reviewing.

By "neutral" review articles I mean Review Papers written by a different lab, without sharing any author with any of the previous research model articles, and not written to prove their own model. This normally means their result only includes a comparison between models, or showcasing their dataset(s)

@NamNguyenHoang, OK, I see what you mean. I still don't like the term "neutral", though. "Neutral" sounds to me along the lines of "scholarly objectivity", which I consider to mostly be a convenient fiction. (I think that scholars should strive to be self-critical, without presuming that we can be truly objective.) I would say something like, "research whose authors were not involved in the models that they review". But that's just my opinion.

How about "uninvolved" or "unconnected" then? Would rewording it that way make things more clear for you?

@NamNguyenHoang "Unconnected" sounds good to me.

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text:
What are the benefits of a poster award?
What are the benefits of poster awards? Is being awarded at a conference really useful for one's career (e.g. when applying for a PhD or a job) or is it just scene? In other words: Can I say that having such award on my resumé is better than just nothing?

Surely it is better than nothing. How much a poster award will help you is a bit dubios, but certainly any award at a non-scammy conference cannot be bad for you.

In terms of it being on your CV, yes it can help.  For positions that get lots of applications, even awards that don't mean much to you can help your application stick out to search committees.  (The extent to which it helps can vary greatly, depending on both the position and the particular award.)

You mean apart from the cash prize?

In my field the thinking is

It draws attention to posters from conference participators.
It provides encouragements to individuals (students) to make an extra effort
It encourages discussion about "good poster design"

The selection criteria is always focusing on good communication of good science, never one or the other.  Since such awards are given only to students and there ids usually also a similar student presentation award both selected by a set of valued senior scientists, the award should be and is seen as a merit.

Peter Jansson's answer provides a good description of the general benefits of poster awards mostly from the perspective of the conference organizer. My answer focuses on your latter questions.
A poster awards is definitely a positive signal of your quality as a researcher. If it was from a major conference (and perhaps even if it is not), it might do quite a bit to distinguish you from other prospective students in a PhD program applicant pool. Although its value while applying for non-academic jobs is more dubious, it can only there as well.
It is clearly better than nothing and you should put it on your resumé or CV.

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text:
Is it OK to have many graphs, tables, and images in a masters thesis?
I am writing my master thesis. In my document I have lots of tables. images and graph. Is this have a bad effect on any academic person when want to evaluate my  thesis.
I ask this question because I am afraid that they see my
document say "look at his thesis , he fills all his document just by picture" . But I am really take time and effort to draw them and I absolutely think they are essential. So what is your idea ?

Any answer you might get here is infinitely less informed and thus less helpful than advice from your advisor, his or her postdocs and senior Ph.D. students, and faculty at your department who can take a look at your thesis and are familiar with the norm and culture in your field and subfield relevant to your thesis topic; we don't know what your thesis is about or your field, and have no idea what your thesis actually looks like...

@PouyanRafieiFard If you like to answer this question, please use "Your Answer" button. Please do not use edit to enter your answer.

How much is too much? May be a thesis has lots of experimental data or simulation output; and the researcher has to present all the graphs and tables. On the other hand, in a literature, psychology or sociology thesis, there may be two or three graphs or tables. Even, in some engineering or science thesis, there may be no graphs or tables and in another there may be lots of graphs. I think that answers to your question hugely depends on the major of the student who is writing his thesis or report and type of research which is done. Nobody can give you precise answer. Just ask your advisor.

In my opinion, it is perfectly fine if you want to put so many original pictures in your thesis and if you are writing a thesis in natural science, you can even put some pictures from other papers/books in your introduction chapter. Just try to imagine you are a thesis reader (a professor) with so many other things to do. They would like to read less text and see more comprehensive figures. Of course, making a figure comprehensive depends on the quality of your graphics as well as your caption text.
So here's what I suggest: anytime you want to put a figure in your text, ask yourself: how this figure is going to help my readers understand the main point? Is it conveying the main message? And how the captions will help to understand this message?
Remember, other people also have limited time and sometimes limited interest in what you did or even the task of evaluating the thesis, so it is up to you to make your material concisely so that they can understand about your intentions easily.


text:
Impact of type of institution (public vs. private) on long-term tenure track career perspectives
I am curious about to what degree and how, if any, type of educational institution (public vs. private) has an impact on long-term career perspectives in academia (with eventual target of a tenure-track faculty member). For the purposes of this question, please assume we are talking mostly about educational institutions in the U.S. with a very high research activity per Carnegie Classification.

Are you looking for data and/or formal studies of this (if so, tag it [tag:reference-request]), or will answers of the form "In my experience, it makes no difference" suffice?

Could you clarify what you're looking for?  Are you asking how the chances of getting a tenure-track job compare for graduates of public and private universities?  (Or maybe for employees of such universities who are not yet on the tenure track?  I'm having trouble telling what you mean.)

Incidentally, this is an interesting theoretical topic, but it's worth noting that nobody should choose between admission/employment offers on this basis.  (If you want to know whether graduates of a given department have careers of the sort you'd like, it's far more informative to look into the actual track record in recent years, rather than trying to guess based on combining weak indicators like public vs. private status.)

What's a "career perspective"?

@ff524: I am mostly looking for answers, based on experience. However, if someone is aware of data and/or references that support (or don't) their experience or otherwise shed more light on the topic, such information is welcome as well. So, since references are not the main type of resources, I think it makes sense not to use that tag.

@AnonymousMathematician: My question pertains not to graduates of institutions of both types, but rather to postdocs and researchers, working at those institutions (that is, as you said, "employees ... who are not yet on the tenure track").

@NateEldredge: Well... For the purposes of this question, I would define the term "career perspectives" as progression paths and potential outcomes of a scholar (currently not tenure track), aiming for a tenure-track position, based on selected factors.

I think the public-vs.-private distinction that you asked about is essentially irrelevant to career prospects.  There are excellent public universities and excellent private universities, which lead to good career prospects.  There are also lousy public universities and lousy private universities, which lead to lousy career prospects. (Actually, that's an oversimplification, since there can be good departments or good individual professors in lousy universities, and vice versa.)

@AndreasBlass: Thank you for your thoughts. I agree with what you've said, but was hoping to get more information, based on people's experience, which would illuminate important factors and conditions, assuming the purely theoretical case of equal quality of universities, departments and professors.

It is often held that the strongest determinant for career is the strength of a university in one's particular sub-field.  We might then reasonably guess that we can coarsely evaluate the strength of "public" vs. "private" by comparing the ranking of graduate schools (bearing in mind, of course, all the well-known problems with rankings).
Considering a test case then, the current top 10 American engineering grad schools, according to US News, are:

Private: MIT, Stanford, Carnegie Mellon, Caltech, USC
Public: Berkeley, Georgia Tech, Purdue, University of Illinois, University of Michigan, UT Austin

Yes, that's 11 schools in the top 10, because they list ties in their rankings.  The breakdown appears remarkably balanced, and scanning further down the list it appears to stay reasonably balanced.  Amongst elite universities, then, it appears that public vs. private makes little difference in this case, and is likely to make little difference in others either.

Thank you for your answer (+1). While it is nice and makes a lot of sense, I am additionally interested in people's real experiences in terms of moving between very good public and private universities and illuminating important factors and conditions that affect such career moves, if any.


text:
Are there websites for hosting solely academic videos?
I have a video from my simulation and would like to add the link to my journal article. However, I do not want to post it on YouTube since I do not want my video next to some random video. Are there websites dedicated solely for this purpose?

The journal may usually include your videos, animations through hosting links. Ask the editor/contact at the journal.

@drN Thanks. However, I am looking for something like GitHub where I can share my code.

I don't understand the argument: "However, I do not want to post it on YouTube since I do not want my video next to some random video". Other videos are not science-related... so what? (BTW: video abstract of New Journal of Physics are on YT: http://www.youtube.com/user/NewJournalofPhysics). (That said, there may be other arguments against YouTube for scientific content - e.g. data preservation.)

If you post to YouTube you can set the visibility (public/unlisted/private). If you choose unlisted anyone with the link can see it but YouTube will not list it, which seems to be part of your concern.

Usually the journal will host the videos as supplementary material, but if you want to host it externally, there are options. For example, figshare (see also this blog post).


text:
I have found an error in a textbook. What can I do about it?
In the book Electronic Devices and Circuit Theory (10th edition) by Boylestad and Louis Nashelsky, I have found a technical mistake.

What can I do about this?
To whom should I send an email, the authors or the publisher? (Also, there is no email address mentioned in the book or on the Internet to which I can send my suggestions.)
I have never written an official email of this kind. If I should send an email, how should I write it?

Boylestad was born in 1939. I doubt very much that he is going to read every email. You may want to check the other author or the publisher. I also doubt that an error(if it is) in a book in Electronic Devices and Circuit Theory is applicable in Chemistry.

Googling [book name] + "errata" is always a good place to start to see if they are already aware of the problem (and you might find other mistakes too).

Note that the book has an 11th (2012) edition now. Nashelsky appears to work at a teaching-oriented college, so if you email him, he'll probably care.

@RespawnedFluff I had emailed to Pearson company last year, IIRC they said that they ensure they will forward my email to the relevant person. I will not email anything to anyone about this issue now.

@starsplusplus In case when more than one book have almost same name, it is hard to find errata for a particular book. What do you recommend in this case?

First of all, see if the book has a newer edition, and try to look at a copy and see if it corrects the error.
If not, then try to find:

The publisher's web page for the book
The author's professional web page, which hopefully has some mention of the book.
An unofficial errata list (google the book's title and "errata" or "corrections").

Check in both places for an errata list, which may already have a correction of the error.
If not, then it is worth trying to report it.  Writing the email is the easy part: just politely point out that you believe there is an error on page NNN, and explain as completely as possible why you believe it is incorrect.  If you think you know how it could be corrected, you could explain that as well, but it isn't strictly necessary.
The hard part is figuring out where to send it; publishers and authors should make this obvious, but often they do not.
For a major established textbook (which I assume this is), I would focus on the publisher, since the original author may well not be actively involved with the book anymore.  See if there is any contact or feedback information on the book's web page.
If you are a faculty member, the publisher probably has assigned a representative for your institution.  You may get a better response by contacting your rep directly and asking them to forward your report to the appropriate person.  If you are a student and this is your course text, you could ask your professor to contact the publisher's rep.
If there is an unofficial errata list, it should include contact information for the person who's maintaining it; send a report to them.
For a text or monograph with a smaller audience, you will probably do better to contact the author directly; look for contact info on their professional web page.
It's a good service to the community to report errors in books so they can eventually be fixed, so thanks for doing this.  However, if the publisher/author make it a huge pain to do so, that is ultimately their problem.  Make a reasonable effort to report it to an appropriate person, but if you don't succeed, there's no need for heroic efforts.

Note, that if the author is not actively involved with the book anymore, there may be another expert on the subject who has taken over maintaining the book and who could a better person to contact than the publisher.

The International ed. of 11th revised ed. was published 23. July 2013. (I did not find an 12th ed) The error is still present, along with some antique explanations.

@Martin: Oops, I was looking at a different book by the same author.

Sir, I have sent an email (in this email I further asked for them, where I can report the error. I have not reported the actual technical error yet) to Mr. Amit Phadhak and the same email to schooleditorial@pearson.com. There are many email id's mention on Pearson's official website. I do not know at which email I should report. Could you link me to the page which mentions the particular email to which I should report.

Recently I got their reply from schooleditorial@pearson.com . I think I did it correctly.  Btw thanks for your answer.

I was wondering how long (in years) after publication (of latest edition of course) it makes sense to submit errata. Could you include this aspect in your answer or should I just open a new question?

I‘m not sure if this answer is allowed, based on advertising guidelines of Stack Exchange. Either way: A friend and I have started an app for iOS and Android with the intention of making reporting, discussing and looking up errors in publications as easy as possible. If you want you can check it out at https://mistakey.com.
The idea is to provide a network for collecting reports on all kinds of literature (currently, anything that has an ISBN, ISSN, or DOI can be reported), while we’re also pursuing contact with publishers and authors to actually get the mistakes fixed.

Please note that this is not spam as per our rules as it addresses the question and comes with full disclosure. However: “Don't talk about your product / website / book / job too much.” – Do not post any further answers promoting your software before you have contributed to this site in another manner.

That being said, I do not think this software can solve any problems. If I contact the publisher with an erratum and they react, I will reach a far larger audience than your software, in particular if the publisher maintains public errata. Otherwise your software seems to hinge on the utopic assumption that almost everybody uses it, because otherwise the overlap of books read by its users would be almost zero.

If someone is interested in the conversation started by @Wrzlprmft, please refer to a related answer: https://academia.stackexchange.com/a/147588/122579

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text:
Is it okay if a student wears a mask to class to conceal scars?
Like a halloween mask to conceal injuries of a burn?

What sort of halloween mask did you have in mind?

I would make sure to notify the instructor of the class in advance if you're planning on doing this.

Have you asked your instructor(s)?

Of course. If there's a medical reason for it and the student can produce an appropriate doctor's certificate or what not. You would need to check the regulations.
It probably depends on what sort of mask it is. If the mask is distracting for other students  or plain silly, then I can imagine that it is reasonable to object to it. So, 'halloween mask' may not be the best description of an appropriate mask.

You will definitely need to check regulations regarding the wearing of costumes that conceal one's appearance. For example, in France it's forbidden by law to conceal one's face in public space, including in universities (and it's made explicit in universities' by-laws). While there's normally allowances made for legitimate medical reasons, there will definitely be limits. "Halloween-style" costumes and masks will probably be disallowed.
One additional comment not mentioned in Dave's answer is that in cases of laboratories and other "practical" exercises, such costumes may be disallowed for legal and protective reasons. You will need to talk with the appropriate staff about any accommodations that can be made.

@NajibIdrissi: Yes, you can do that.

There are mask laws in the United States, too.  In my state, Georgia, it was intended as a weapon against masked thuggery and might not be enforced in the case described.  However, "might not be enforced" is pretty thin ice upon which to walk.

In general, I second Dave's answer. There is one point, however. During exams students have to identify themselves, and this is commonly done by showing some identification document (e.g., student id) to the person in charge. Wearing a mask would likely be interpreted as a failure to identify yourself, unless identification is possible in some other way. As a rule, failing to identify yourself at our university means that the lecturer is not allowed to grade the exam. However, if wearing a mask is required due to a medical condition, the student can notify the examination board before the exam that can decide to deviate from the identification rule and oblige the lecturer to grade the exam.


text:
Is a description of product development work suitable for a journal paper?
I have worked on a project to develop a machine which is a end-of-arm-tooling type. I am thinking about bringing this work to a journal paper.
It means the content might include product design information, hardware & software and testing data
Is this type of work suitable for a journal paper? So far, in my field of computer vision and robotics control, I rarely see such direction of publication. I am not sure it is popular in elsewhere branch
There's also a wondering I have is that the review section of this journal mostly will have to mention available similar industry products instead of mentioning other journal papers (I haven't been able to find journals talking about product designs somewhere). And it's clear that citing company products is a weak citation I personally think because the source is the company's website which is providing advertising information

Can you tell us what Journal you have in mind? The appropriate of your submission will very much depend on that.

@Wilson: this project is actually a bit off-topic of the research I am doing, therefore, I haven't reviewed or even known the relevant journals. If possible, could you suggest me some related to design of mechatronics machines, robotics, end-of-arm-tooling journals? SCI ones? I am not even sure whether these journals exist or in which category such topics are popular due to limited  access to certain journal databases from my school

@Wilson: I personally think if I know some similar journals, or I can estimate the  publication potential of my project by its citation i.e. cite company products/websites or the way it is written i.e. written about product design for application. I believe that if a product design has some innovative ideas, it is worth publication. But what if it is a general product design? because some people might think that any product has at least its market value, some usage value, then is it also worth a publication?

Academic journals generally publish papers describing original research results that advance (or try to advance) a particular field of study.  Development of a product is not necessarily an original research result.

Does your design involve a new approach or technique that has not previously been used in the field? Does it represent a new way of thinking about a problem? Then it may be an original research result.
Is your design an application or straightforward extension of previously known techniques, possibly with some small tweaks and optimizations? Then it may be a great new product, but is probably not a research result.

Possible counterexamples:  Journal of Visualized Experiments, Review of Scientific Instruments.

@ff524: I'd rather say it's an application project integrating different known design and control techniques. The application sounds new but not yet verified through paper reviewing. And I likely believe such application can be provided by big industrial corporations as customized solution, kind of solution only known to the two parties. Therefore, it took me a great deal of time to search for it in Google Scholar, Engineering Village with very few and not convincing results

@ShawnLe If it advances human knowledge, it's a legitimate scientific result.

@jakebeal thanks for your comment! this extension is a broad and ambiguous notation for a young researcher. For example, he has to know a lot about the available pool of knowledge before knowing that his work has some new values or not. This is sometimes not possible for young researchers like me

@ShawnLe in order to publish a decent paper, you need to learn about the existing work in the field and/or find a mentor who is an expert in the field and can advise you on that. Part of writing a research paper (on any subject) is putting your work in the context of existing work in the field, and explaining how your work contributes something new.


text:
What to do after PhD?
I obtained a PhD in Microbiology. I have some papers and a competitive CV. I would like to continue in Academia or to try industry.
Is the normal path to find a postdoc job in naturejobs.com? I'm overwhelmed by the high number of jobs that are being offered, I just need one!

How did your PhD advisor answer this question?  You did ask your advisor this question, didn't you?

The normal path is that you ask your advisor or other trusted peoples from your university. This is assuming you have already gotten drunk or whatever other foolish thing people do when they get their PhD.

@JeffE, I have not asked yet since I even didn't know what to say. I'm information collapsed now. I want to continue doing research but collapsed by the large number of options on the internet and the lack of guide by my previous research centre (if I don't ask they don't say anything). There is no protocol for this, I assume I should ask my advisor from your comments.

@gfjhjgfhj Actually, the normal approach is to ask your advisor well before you finish your PhD.  I recommend asking in your first semester as a PhD student, if not in the first week.

In the sciences, it is almost expected if you want to go into academia that you will do at least one postdoc.  (In some disciplines like astrophysics, you might even do more than one!)  There are a lot of different job boards out there for finding a postdoc, but your best source (assuming you are still on speaking terms) is your thesis advisor.  He/she will likely have friends and colleagues looking for a postdoc.  Those folks will then know the background you are coming from and likely put you on their short list.  Good luck!

Biology graduates also generally do more than one postdoc. "your thesis advisor" <-- this is the obvious answer. Any thesis advisor worth their salt should help you find a job.

@cjsullivan: as always, this depends a lot on your country - in some, it is is perfectly normal to do more than one postdoc, in many it is not and you get promoted to associate professor and start a group.

In some disciplines like astrophysics, you might even do more than one! Actually, in some disciplines like astrophysics, it is normal experience to spend almost all your life on postdocs positions only.

@ChrisWhite That was exactly my point, as emphasising that it is very unlikely to only do one-two postdocs and then get a longer position. Having ahead of you people with already many more years of positions (and hence publications) that still do not get tenures, it is highly improbable that a new joiner in the field will get one (unless you are outstandingly good).

As Sullivan mentioned, it is very popular to rely on the help, support, and networking skills of one's supervisor when looking for a first postdoc. The pro's are quite clear:

You do not have to search for the job on the various job-boards --- your supervisor will find the post by asking his friends
You do not have to choose the most appropriate job among advertised ---  your supervisor will do the choice (or compose the short-list) for you
You do not have to engage in competition with other candidates --- the recommendation and influence of your supervisor works on your behalf
You do not take any risks associated with the wrong choice, poorly prepared application documents, poor presentation skills, tough luck, etc.

However, there is at least one major con of doing this:

By using your supervisor as a door opener you demonstrate a certain degree of dependence and lack of your own vision and responsibility. In other words, you do not put yourself on board as an independent researcher.

what if the supervisor does not help due to several issues raised during PhD work.


text:
From thesis text to slides. How to ease the process?
I spent a considerable amount of time to write my thesis. Now I have to create the slides for the defense. I thought it was going to be easier, but found important difficulties creating them. I would like to have a method to make it easier, at least the first draft. Starting with a section, I will try to create a slide from one paragraph, although they can be further divided in more than one slide. I thought about:

convert to bullets each sentence of the paragraph, or set of sentences of related topic. This slide may be further removed.
in a different slide, replace text from previous slide with images from cited references, and try to memorise the necessary part of the replaced text. This will be specially useful for the introduction. On the other hand, thesis results sections already have their own pictures, so they will be directly taken from thesis.

Do you think this method is OK, or maybe someone has a better one?

Basically, as @vonbrand said (+1), you will have a very limited time (in my case, it was about half an hour) to present your research, so, using painting terminology, you have to paint a decent picture, using large brush strokes. In other words, present only key elements (have additional slides for details, if asked). For more relevant advice, see this answer of mine. Good luck!

In my opinion you would be better to write the presentation text from scratch rather than try to painstakingly distill your thesis to a set of slides. With some more info about the target audience and time constraints one might be able to formulate some more detailed advice

Yeah, don't copy-paste from the  thesis, except maybe math environment stuff. It will be very dry/too quick otherwise.
Better, examples and pictures should be more abundant in a presentation, as well as motivation and general ideas.

About "create a slide from each paragraph": Even the shortest thesis I've seen has far more paragraphs than the number of slides in a reasonable presentation.

You have to cut down brutally. You will have a half hour or so to show the work of a year or more, that is hard.

Explain what this is all about. A short introduction/reminder (depending on your audience!) is probably needed.
State your objectives clearly. One slide for this should be enough.
Summarize your main results. You won't be able to cover everything, but make sure you show enough to cover the stated objectives. Perhaps highlight some tricky point, or a neat technique.
Summarize your objectives again, explaining how they were met.
If pertinent, point out possible future fruitful work building on your thesis
It might be useful to have a slide with publications resulting from the thesis, both already published or in the works (submitted and waiting for approval).

You might consider having some "spare" slides with more details, on which you can fall back when asked to elaborate.

I suggest "build up" rather than "cut down". That is, begin with an empty presentation, and start creating slides for each of the bullets.

Note that the following approach may not work for every topic and field.

Find out what prerequisites you can expect from your audience or how generally understandable your talk shall be. For example a guideline at my department is that a defense shall be directed at somebody who studied the same field (but did not necessarily specialise on the same subfield).

Take your most important result. This may be a plot, a number, a model or a hypothesis, but also that some approach that you found not to work.

Consider the minimal background information that your audience needs to understand and appreciate this result.
For example, if your result is a plot: Your audience needs to understand what quantities are depicted on the axis, how the data was obtained and what important steps you made processing it; it needs to understand why the plot was important to make and what major conclusion follows from it. You do not need to tell it about every detail though, e.g., that you rejected three samples because they were highly implausible (and checked thoroughly that this was appropriate).

Structure that information and make slides presenting it. This should contain an introduction and a conclusion.

Test how long you will need to present this talk. If you do not cram your slides (which you shouldn’t do anyway), a rough guideline is one minute per slide. Actually giving the talk in front of a test audience is a better estimator though.

In the rare event that you have time left, add additional details, interesting side results or whatever you seem best fit. Preferrably add something that needs little build-up, given the information that you already intend to present.

It is strongly advisable to talk to your supervisor and other peers, as they can better tell you what part of your work is most important, what guidelines and convention your field and university have and give feedback on a draft of your presentiation.

Do you think this method is OK […] ?

To be frank, I think this method is horrible for the following reasons:

What is a good structure for a thesis is not necessarily a good structure for a talk. And even if it is, your method restricts how you distribute content on your slides in a way that you will find hard to get rid off, even through intensive refactoring.
Not all information contained in your thesis needs to be contained in your talk. Moreover, it is pretty normal that certain paragraphs of your thesis are devoted to technical details (and should be only mentioned as an aside) while others deserve a whole slide.
At no point do you have the top-level structure in mind – which is most important.

Two basic rules for presentations: Think about who you are talking to, and plan top down.
Look at the convention in your university and your discipline and the time constraints imposed by the rules to decide how much time you want to give the different strata in your audience. There is general public, general scientists, scientists from your general area and may be two or three who understand what you did. If your work touches different scientific areas, decide how you want to split your time between them. After assigning a certain amount of time to each part of the audience ask yourself what kind of talk you would enjoy in an area which was similarly far from you. History usually works for experts and layman alike, unless it is commonly known (to the experts).
Top down means start with the large parts, break these into smaller parts and refine until you arrive at what you want to put on every single slide, then write the slide. You will have to cut down, do so by working backward. Decide which goals you want to present and don't fret about unrelated stuff. You don't have to be too precise, the audience will not be able to process all details in the short time they have for a slide anyway. "Under some rather technical condition" or "after some manipulation" usually works here.

It might be easier for you to escape from the pages of your thesis if you storyboard your talk initially.  In other words, start by choosing and inserting images, and then add text frugally.


text:
Differences between the introduction of a sandwich thesis and a paper
I would like to know what are the main differences between the introductory part of a paper and of a thesis. My thesis would be a sandwich type, so I would have to wrap everything there.
Some of the differences are:

Longer in thesis.
Deeper in thesis. Extended definition of key terms, concepts and methodology in thesis.
Clear definition of the whole goal in thesis, whereas paper smaller goal.

To narrow the possible answers, I do research on the molecular aspects of the infection steps of a pathogenic swine bacteria. Also develop strategies to block infection by using vaccines.

Note there is no much information about this, so would be useful for others.

Although there is a post with some guidelines about writing a thesis introduction, they are also common to paper introduction. What I'm looking for is for aspects that are more different between them. http://academia.stackexchange.com/questions/12170/how-to-write-a-ph-d-thesis-introduction-chapter

From a structural point of view, there is no major difference. An introduction should set the work in a wider context starting by establishing the wider context and showing the need for the work done and identifying the knowledge gap that is filled. What is different concerns the matter since a thesis introduction should focus on the thesis not the individual studies (articles/manuscripts).
If the articles/manuscripts all are very tightly tied, then it is probably easier to write the introduction. If the articles are more disparate, which is not uncommon, then trying to tie everything together can be more challenging.The stumbling block for most is that they have not thought about the wider perspective and some do not even manage well to include it in the articles/manuscripts themselves. So I would say that the difficulty does not lie with the fact that it is a thesis introduction per se but rather that many do not see the forest for all the trees while they write the articles/manuscripts to be included in the thesis.


text:
Shared office is messy to the point that I can't do any work, how to proceed?
Four months in my postdoc and I feel the mess, up to the point that I can't further do any, any work in my office. Nothing. My passion, bioinformatics, is gone.
An office with 12 students where just 8 should be, and plenty of disorganised stuff, people coming in and out, chatting, not very clean... I would say it's more similar to a bar than to a real work office. Almost all them work on the bench, so they come and go to the computer frequently.
I've been promised to get a new place in a 5 students office in about a month, but this has already a delay of 2 months since I should have moved there like 2 months ago. This is the reason to be in a limit situation.
What to do? My mentor knows almost nothing about this. He knows I'm waiting for the new place but thinks I'm doing well, when this is far from true.
I work in bioinformatics but seems my mentor thinks this is like kid games. I feel homeless moving through libraries trying to go ahead with my work.

talk to your mentor. why are you holding back? 2. talk to your department/faculty/responsible administrative office. what have you done so far on that front?

Thanks @marts. I'm holding back because seems I'm the only one feeling this. Everyone is doing well, they like the mess. I have a real problem, can't do anything. Since I have two mentors, the main one and a retired professor, I think I will tell to the retired professor to see what he advices me to do.

What do you think I can say to my mentor. 'Hey, I'm doing nothing! My bioinformatic stuff is stacked since 2 months ago?'. In fact, I already told him that I need a new place and he told me that the conditions I have are not so bad. I'm worried he will fire me.

Does your bioinformatics studies include wet work or information that can be compromised (including genome and other identifying information) or contaminated? As this can change "bad working conditions" to "working conditions that may compromise research" - which is a strong argument for change

I don't need data privacy @JGreenwell, and work is mainly bioinformatics, dry  lab.

"My office is noisy and crowded, I cannot focus" is a perfectly reasonable complaint.

Talk also to the others to find out whether they really do well. Also, knowing both the wet lab and the data analysis world, their needs may in fact be different. And the chatting may quite inherent: they have to be highly concentrated when in the wet lab. Coming to the office may be part of their "breaks". Plus office may be where they find the people with whom to discuss their experiments. Which means that you need to have some extra space where you can do the high concentration part of your work, this is not going to work in your current office. Is home office an alternative?

Something you all might find interesting: http://www.npr.org/sections/money/2016/06/03/480625378/episode-704-open-office     Personally, I find it very hard to work with any noise.

To add another perspective: You write that everyone else is doing fine, and in fact is doing productive work. I know that people have very different working styles (in our department, all office space is 'flex-space', i.e., no-one (including full professors) has an 'own' office and people have very different preferences whether they want to sit in a more quiet place or a more social stting), and it can very well be the case that you are not productive in a setting where others are.
Nevertheless, I think you should consider the possibility that it is actually you who has the problem, not the setting that is the problem. If there is no easy solution (i.e., a different space for you), then, in fact, I guess it would be unreasonable to expect 11 people to adapt their working style rather than you (1 person).
I do not mean this negative at all, but there are solutions to work in a busy place, like putting on headphones and the like. Have you considered such options?
Good luck!

Not to disagree with you at all, but to offer yet another perspective: If biotech were a wheelchair user, we would have no problem at all with the other 11 people accommodating his or her mobility requirements (and anyway, they'd be legally obliged!) It may be that biotech simply cannot adapt to the situation as it stands and that a minor adjustment on the part of those 11 people could yield large dividends in terms of biotech's happiness and productivity. We don't know this, but it's something to consider.

@RobSkelly that's a valid point, thanks for raising it! [I just upvoted the comment]

Yes, I admit I'm the special guy here @damian. Headphones? I would dream headphones solve this. Just the two girls I have one of each side are enough to kill any of my ideas. My elbows almost touch them! I certainly cannot adapt to the situation. Chaotic environment is not good for my productivity. It may be good for my colleague's creativity. However, minor adjustments are not a problem, never have been. In fact, I love change. I'm looking forward to see what this new office offers, just four-five people seems reasonable for my needs.

If the office is overcrowded and noisy, then I am sure this lowers productivity for almost everyone, whether it appears that way to the OP or not.

"I guess it would be unreasonable to expect 11 people to adapt their working style rather than you (1 person). " I disagree, if you have to work in the same environment then all should compromise.  It isn't fair to make someones working environment unworkable just because the majority are happy with it.

You are in a difficult psychological position, a problem that is not of your choosing and where you don't feel you have any control.  It is easy in such a situation to assume victim status and cease to exercise any motivation at all.
I suggest you check with your mentor and emphasise the importance of your new office.
In the meantime it is very important that you take some small actions to improve your situation (and empower yourself).  Take an honest appraisal and brainstorm actions that can help you.  Do them.  Be aware that your victim status makes you automatically reject any ideas, even helpful ones.  My thoughts:
Move to a different desk.  I suggest a corner near the back of the room.  Away from walkways and doorways.  Try for visual quiet space above your desk.  Organise this desk to your satisfaction, your own refuge of order.
Schedule your day for quiet times.  Come in early, at least two hours or so before the bulk of colleagues.  Eat early while the office is busy and you will have time over lunch when the office is quieter.
Use noise cancelling headphones to give yourself white noise.
Be friendly to your colleagues.  If they like you the are more likely to accommodate your wishes.
If it is appropriate organise a working bee.  Provide some snacks!

You said "Everyone is doing well, they like the mess. I have a real problem, can't do anything"....I believe you should talk to your mentor immediately about the situation and start cleaning the mess on your part. Slowly but steadily keep on cleaning it. I don't think the mess is NOT bothering others but the thing is that no one is willing to do anything about it. If you start cleaning the mess, (by cleaning what I mean is to start assembling and organising things) I believe this is how others are going to realise their mistake and they'll also start doing something about it. I think you need to take an initiative, which is not easy, but someone has to. And that someone is YOU :) Good luck!

The real problem is too much people.

This is why I have written in the answer that first you need to talk to your mentor then take the next step.

Reaction is not going to be good, everyone knows @Zeb

The reaction of your mentor?

Yes @Zeb, he will repeat that I'm going to have a new place soon. I already said I need a more quiet place. At least, I think I should state I'm doing nothing now but lie on library puffs.

If you really need a quite place and you are serious about it then you must talk to a higher authority about it. Don't be afraid of the consequence, as whatever you are doing is the right thing to do. So without wasting more time discuss the issue with any higher authority ASAP. The rest is your choice.

My experiences with a messy office are a) an astonishing part of the built-up mess being due to people leaving and leaving behind things where no place exists where they should be put (often things they should not have taken, e.g. lab books, books with sample slides, etc.; things owned by the institute, all kinds of paperwork belonging to projects). This lead to shelves being already populated when new people moved in and b) even less self-space compared to what is needed. In one office, we were allowed to buy a hanging folder storage which helped massively.

"If you start cleaning the mess" I'd very much recommend to talk with people first and then to clean only mess that does not belong to anyone else and is not in anyone else's space - not everyone takes it as friendly if you touch/shift their things. Particularly if you are the new guy and supposed to move out again soon... (I remember a new colleague giving approving opinions on the first day about the one place in our office that was neatly clean and in order - when everyone who had been there a bit longer knew that this was the place of someone who did not do any work to speak of...)

You are on a bad place. The main problem with things such this, that surely not you are the only one seeing this problem, despite that nothing happens.
In such cases, the System (this time: a system from people, from their wishes and customs) will probably behave on a way, that as you start an action to change it, it will try to attack you back.
You must be able to defend yourself. It is very important, that while you are trying to change it, you must be enough good to be defended by your productivity. If it isn't so, nobody will care if you had right or not. And the System will say things like: "you aren't enough well in communication", "you are not a teamplayer" and many similar. Nobody will say: "We hate you because you won't allow us to sit in a dirty office room", although it would be the truth.
Carefully try to look for people having similar problems as you have.
If you aren't significantly better as the others, you probably can't do anything.


text:
Is it better to present a bad paper at a conference or cancel?
I'm a PhD student who recently had an abstract accepted for a conference. It was based on a survey that was scheduled to take place before the conference, but external issues caused the survey to be delayed. I don't have the data I thought I would. I've tried to rework a paper that is more theory-based and introduces some descriptive data from another data set, but it's not a strong paper. Should I cancel late notice or just suck it up? It would be my first conference.

I personally dislike the idea of not publishing "low quality materials". As long as your abstract is humble and descriptive everyone who will read it will read it on their own risk. At worst, your work will keep few megabytes of disk space on some server.

When you say "a paper", do you mean that this is a conference that plans to publish an essentially unreviewed paper based on only its intended abstract?

No, it's just a presentation of a paper in progress. It wouldn't be published.

What does your advisor suggest to do? They are the one in the best position to judge: they know your research, the audience, and the customs of the field.

You don't mention your exact field, but it is very common in the humanities for conferences papers to be, in effect, works (of larger scale) in progress.
One of the really nice things about that is that when you present it, you will have a number of people with expertise in your topic listening and often times will provide very constructive comments or ask questions that ultimately help you deepen or extend or improve the paper.
So as you mention, moving it to be more theory based isn't a bad thing.  You can focus on the design of your survey, and mention the intended use, and you will undoubtedly get some solid feedback (it's also totally fine to be upfront and explain why your paper doesn't match the submitted abstract/title).
The end result will be an even better survey that, once you've done it and analyzed it, will lead to a more easily published article (perhaps with another conference paper along the way).  You may also get people to come up to you afterwards who are doing similar work, and that could result in collaborations down the road.

As it is an oral presentation go and do your best. This assumes that there is some novelty and your scheduled approach is of interest. You must decorate (verbally) it and gives to the audience the envy to proceed in the same way.
You can also represent related previous data and results.
I assume that you have a minimum of a solid base, as it seems from the question. I also assume that you have limited time, say 15 minutes max.
Otherwise don't go.