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Are religious invocations in academic presentations appropriate?
One thing that I have noted come up a few times in presentations in the US in the last few years has been that some speakers—usually graduate students and postdocs, rather than more established career professionals—have included religious invocations at the end of presentations in entirely secular venues. One presenter went so far as to have an entire slide devoted to it, complete with quotations to spiritual texts and illustration.
Is there any sort of protocol about when such sorts of invocations are considered appropriate? (For instance, at a student's doctoral defense, but not at a public seminar?)

Things like "Jesus that was a difficult problem, but by God our algorithm solve it"?

I find them to be always awkward, although I respect the presenter's beliefs. To me it's like thanking your mother, I understand it after a thesis defense but would find it inappropriate in a conference or seminar. Never heard of any protocol regarding this though.

If you have a brief and compelling argument for how this gets in the way of science, you should say it. (e.g.  "We're here to talk about science: The five minutes of religious references obscure the ideas in my respectful opinion.")  If all it does is introduce an awkward moment, etiquette should be to ignore it and/or comment privately afterward to the presenter about its propriety (e.g. "Doing stuff like that hurts your credibility and discourages scientists from coming to your next talk.")  Of course this is very field and culture dependent; make sure of your social footing first.

Regarding social footing, my (incomplete and nonscientific) impression is that part of American society is turning towards church to answer certain things that could be considered societal deficits.  If this introduces awkward moments in conferences and has no larger effect on such venues, perhaps we need to rethink about why it is awkward and change our thinking.

Could you give an example? I have never seen religious references in presentations in Europe or US conferences so far. Is this really a thing in the US?

An example, suppressing actual sectarian content: "And finally, I would like to recognize the almighty [Deity X], whose [wonderful and miraculous attributes] allow us all to [do other amazing thing Y]." Again, this has happened only a few times in many hundreds of presentations (mainly in the US), but the sample space is not zero.

Btw if the "wonderful and miraculous attributes" are "noodly appendages" then it's a joke. At least, I hope it is.

@SteveJessop: I specifically avoided making Flying Spaghetti Monster references for precisely that reason.

I think this is a good question.
Let me propose some guidelines:
1) A religious invocation should occur at the beginning of the talk or the end of the talk, but not in the middle of the talk.
People often begin talks with material that is unrelated to the topic of the talk itself, e.g. thanks to various organizers; comments about the weather, the venue or the town; jokes; and so forth.  It seems to be clearly asking too much for someone to speak only about their scientific field during the entirety of their talk.  However, at a certain point you get down to business and the "talk itself" in the narrower sense begins.  One should not (of course this is an opinion, but a strongly held and easily defensible one) mix religion with the material of the talk itself.
2) A scientific talk is not an occasion for proselytization.
To me whether religious material is appropriate depends a lot on the purpose one has in bringing it up.  If you include religious material as an attempt to convert audience members to your religion, I think that is really problematic and unethical.  If you include religious material for other promotional reasons, then I still have a problem with it, just as I would be with someone promoting their not wholly scientific company or product.  (Even wholly scientific promotion might not be so great, but that's a different answer.)
On the other hand, it is a totally standard thing to have the last slide of a talk give thanks to various people and institutions.  If you feel deeply grateful or thankful in the religious sense, then it seems natural to want to express those feelings, given that other speakers are thanking people and things (e.g. the US government) that, in your sincere opinion, have not helped you out as deeply or fundamentally.  At any rate, it does not bother me if someone ends a talk by thanking some theological entity.
3) One should not express religious sentiments in a scientific talk in a way that encroaches on anyone else's religious sentiments or lack thereof, nor which implicitly or explicitly invites or requires participation or complicity from the audience.
Thus "Alhamdulillah" is probably okay; "Now Thank We All Our God" is probably not.
In general, in (e.g.!) an academic context, one should be respectful of others' beliefs and views, and one should not be controversial or exclusionary in anything without a specific intellectual purpose for doing so.  One should also be respectful of others' time and realize that speaking in front of a group is a privilege.  On the other hand, academics are human beings and can choose to say things which are not strictly necessary.  In my calculus class last week, I had students identify a quote about mathematics being someone's worst subject followed by a careful and insightful consideration of the reasons for this.  The quote turned out to be from Malcolm X.  What calculus reason could I possibly have to quote Malcolm X?  None.  But I thought it was interesting and perhaps important in its own way.  I enjoy my freedom to do that, so it is not a hard sell for me to give leeway to those who want to make some kinds of religious statements, so long as they are in line with the above guidelines.

Now I wonder if there are people who consistently say, "We will prove Lemma 3 later, insha'Allah". Not that I think it would be inappropriate to do so, and it's less intrusive than "Lord willing and the creek don't rise".

So why was math Malcolm X's worst subject?

@Olivier: See http://www.goodreads.com/quotes/279036-i-m-sorry-to-say-that-the-subject-i-most-disliked.  This is taken from his autobiography (which I am reading), where it appears in context of a description of the high level of academic success he had in his seventh grade class.


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Ordering Chemicals for a laboratory on a Student or J1 Visa
I just wanted to ask, if any time, any of you have had any issues ordering hazardous chemicals in a laboratory located in the US.
Specially if you had any of your students or postdocs do it, since I recently saw that they run a background check on you for certain chemicals, so I was just wondering if this may backfire sometime in the nearby future.
I ask this because my PI had me order a couple of chemicals, but my Postdoc is in computer science, so not at all related with this, I wanted to know if this may jump in some future in a Green Card application? Perhaps I'm just being paranoid.
Do you have any experience in your laboratories with this kind of issues?
Thank you

How would the government know you ordered chemicals?

@Bitwise The US government would know it if the hazardous chemicals are in the import/export control list.

How could this backfire on you? You're going through all the proper channels, following all safety procedures, and not doing anything illegal... right?

I am not sure anyone here can answer this question unless he works for the related US government authority. People could have different experience. The issue had no impact on one person does not necessarily mean it has no impact on another person and vice versa. If you absolutely have to do it, take Moriarty's advice. Follow all procedures and do nothing illegal.

If you mean order as in "sorting the bottles", then you anyways shouldn't do that unless you have the proper training so you know what you are doing. If I should give a paranoid guess: getting the training would have been the point that got you listed as owner of a "hazardous chemicals certificate". That's much easier from a large scale administrative point of view than knowing who entered which lab to touch a bottle at a nation-wide scale.
If you mean order as in "administrative task to buy things": This type of ordering does not imply physical access to the substances. Lists of people who do that would be full of secretaries and administrative/procurement/bookkeeping staff.
If you're trying to be paranoid: the other thing that is much easier to know than who actually enterd a particular lab is who is working in that group/building. From that point of view, you may already be listed as "possibly had access to X" if anyone from your lab does the order.

(Disclaimer: I'm German and in Germany and not overly worried what types of US visa I can have. However, I'm chemist, so if they list people in relation to harzardous substances, I'd expect to be listed by profession [or by my publication list/affiliations] anyways - even though taking also into account the amounts the most important hazardous substances I usually handle are alcohol/bacillol for cleaning instruments and the lab table.)

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What do you do when you find yourselves with an unreadable/inaccessible paper?
Since I started my life in Academia, I sometimes found that there are some seminal papers to which I cannot get any access.
Either they are very old, and the journal that published them charges for it, or they are simply not to be found anywhere in the internet. I have to admit I never went to look for the physical copy in the library, but I'm not sure they would have it either.
When I asked a labmate about a reference he had in his paper and I could not find, and that seemed to be ubiquitous in any other paper in the area, he mentioned me he had never read it, but that reviewers usually demand that you should put that seminal reference.
How do you try and solve this problem?

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Is it important to list the merits of a research paper?
When we write a research paper, most of the times we need to describe in the introduction what is the merit of the present work (unless is a survey of sorts).
Many professors, tell me that is enough to write it within the sentences with some context. And is the way I see it in most papers.
Other professors, however, I've seen they especifically list the merits and innovations of the papers in the introduction, for example:

The present work presents cherries using A, which has never been done before.
We implemented the mix of berries and bananas, which has never been tried.

While I find the approach intuitive and way more explicit than the usual approach, It seems a bit condescending.
What is your suggestion, should I write a list of merits or not?

Related: http://academia.stackexchange.com/q/2791/675

More closely related: http://academia.stackexchange.com/questions/3007/is-an-emphasis-on-novelty-necessary-in-academic-papers

Somehow it is common to start an introduction with a general blah-blah, basically saying that a field is important and repeating some popular facts.
However, in my opinion, the most important thing of the introduction is to say

what is there,
what is the actual contribution

and said in a precise way, so reader will know if the content is useful for her. And in such a way as "we prove X1 and X2, under the assumption of Y, and conjecture Z" instead of "we investigate X1, X2 and Z".
Of course, giving the general context is extremely important, but not more that saying what's there.
Personally, I wasted a lot of time reading papers whose abstract or introduction left me believing that they solve a general problem, when in fact it was only n=2,3,4 case, or just something tangentially related to my research interests.
There is an incentive to write introduction in a big talk / general blah-blah style (because it sounds serious, because it may bait uninterested readers, etc), but (IMHO) it is very counterproductive, sometimes verging on the edge of scientific dishonesty (i.e. an implicit overclaim).

In the end, the strength of your paper is in a large part defined by its contributions. Therefore, I believe it is absolutely vital to clearly state them. A bullet pointed list is an excellent way to do so. Remember: papers are almost never read from start to end. Therefore, it is important to make your paper visually pleasing, by, for example, making the most important parts (like the contributions) easy to find. Bullet-points serve that purpose.
Excellent slides by SP Jones on how to write a great research paper (which also covers this question) can be found  here.
The link also contains much advice on academic research, for instance on giving talks.

It is fine in most formats to finish your introduction by stating your goals. I tend not to over-emphasize the list of innovations in the paper right in the introduction, usually because it is already made clear in two places: abstract and conclusion.
Also: if by “specifically list the merits” you mean use a bullet-point list, I'd suggest to avoid it. It's not the same as an oral presentation, where you might want to focus on nice simple messages for an audience whose attention is never to be take for granted. When someone has read your introduction ’til the end, they are interested in your work, you don’t need to resort to oversimplifying your message.

Using bullets doesn't man you're oversimplifying. It's a typographical device to make your contributions stand out. Given the plethora of papers sloshing around, I for one am gratefuly for clearly marked lists of contributions.


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How to write good Response Letters for the reviewers
I've spoken with many friends, and they all agree that response letters to reviewers should be written in the most kind, cordial and humble possible way.
Even if the reviewers are in an error, one should make no major strides to show it to them.
I wonder, How do you write your response letters to the reviewers?

Hi Leon! I think that this question is overly broad… it pretty much depends on what the reviewers said or asked, and what you want to write.

Even if the reviewers are in an error, one should make no major strides to show it to them. — What!?  Of course you should correct them!

@JeffE: Of course you should correct it, but you should also try to correct them "gently." Don't say "as it clearly states," but say "On p. X, we indicate. . . ." Unless the reviewer is being completely obnoxious, rude, or dismissive, starting a reviewing "flame war" isn't very useful.

http://www.phdcomics.com/comics/archive.php?comicid=581

If the reviewers are in error, yes you should show it to them, but you should often also take the opportunity to revise your paper, so that your readers don't fall into the same error.  For example, suppose reviewers say that you could use such and such an approach to get a better result.  If they are right, then you should either do it, or explain why you're not doing it.
But if the reviewers are wrong, then maybe you should address this idea in your introduction.  In one paper I wrote, we included in our introduction a false one paragraph proof of the thing we took 10 pages to prove.  Afterwards we pointed out the error.
For one paper we submitted, we got conflicting referee reports.  Essentially, the referees both wanted us to revise the paper, but in different directions (to oversimplify: one reviewer said "shorten and simplify" and the other said "lengthen and elaborate").  We agreed with one report, and disagreed with the other.  So in our response, we pointed out that we couldn't do both .  We explained why we preferred the choice we were making, and our paper was accepted.
You don't have to do everything the reviewers suggest. But if you don't, your response letter should explain why you have chosen to do otherwise.

You're lucky if reviewers give conflicting instructions: that means you can very easily motivate to discard one of them.

As DanC states, you don't have to do everything a referee suggests, especially when they are asking for the wrong thing. A response along the lines of the following usually does the trick for me.

We do not believe the referee's suggested approach is appropriate in this context [Explain reason why]. However, we accept that Section x.x.x could easily mislead a careful reader into thinking this approach was required, and have clarified the text as follows:

This addresses the issue, explains why you disagree with the referee, but  throws the referee a bone by saying how helpful they have been. I make a point of thanking the referee as often as possible in a response. After all, they are taking time to make your paper better with no reward.

From my experience, successful letters to the reviewer have been very objective--guiding the reader to a specific line number in your original manuscript and/or reviewed manuscript.
Often times the reviewer will say something like "the author failed to show that x is correlated with y," to which I usually write: "the authors wish to thank the reviewer for raising this issue. We have added a new sentence to clarify how x and y correlate (please refer to line 100 of the reviewed manuscript)."
Sometimes, the reviewer simply does not understand a passage of your manuscript. For example "the authors did not explain why the sky is blue," to which I commonly reply "the authors wish to thank the reviewer for raising this issue. We wish to bring the attention to line 200 of the manuscript where we say that 'the sky is blue because of xyz, as supported by Figure 1.' "
Sometimes the reviewer is just mean. Once, a reviewer wrote the following to me: "the author is encouraged to understand the basics of physics," to which I simply replied: "5 new references have been added on line 300 to support our claim that heavier bodies accelerate slower when acting upon an unchanged force, a direct result from [Newton, 1687]."
You can't be rude, but you must be succinct and show exactly where in the manuscript you address the issue raised by the reviewer.
You can then take 3 actions:
 1. add a sentence to clarify the issue,
 2. point to the reviewer that you have in fact explained the issue in the manuscript, or
 3. add references that support your claim and weaken the reviewer's concern.
Some times, if your response letter is objective and clearly addresses all the reviewer's concerns, the Editor will accept your manuscript upon reading your letter and not send back to the reviewer for another round of reviews (this has happened to me at least 2 times before).

I'd recommend just "Thanks." instead of "The authors wish to thank the reviewer for raising this issue." The latter starts to look very formulaic (and, therefore, insincere) if you write it more than once. And why would you "wish to thank" somebody instead of just thanking them? Also, adding five references to support an obviously true claim is a ridiculous way to respond to a referee. Every single person who reads that paper will be wondering, "Why is this person giving me five citations for F=ma? Are they an idiot or do they think I am?"


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Is it normal for PIs to change projects to unrelated research
As I asked in a previous question, I ended up with a project that is not nearly close to my interests or research expertise, and my PI is pushing me so I publish something in that topic.
But that made me wonder. Is it usual for this to happen in Academia? I'm not talking "Topic was A and ended up with slightly related topic B", No, I'm talking a topic about a whole different field (even) than topic A, let say Topic Omega (Different Journals, Conferences, etc)
I reviewed my CV and the Job posting of almost 2 years ago, and it clearly said the job was on building algorithms for Brain Machine interfaces using Machine Learning.
However I ended up building electrodes (heavily balanced toward doing electrode characterization) for Brain Signal Capturing, and the paper he wants me to publish is in this topic, that is not nearly related to Machine Learning. Also, nowhere in my CV I even stated that I had nor the expertise nor the experience to deal with these particular field. And at the end of the day, had he advertised it as a heavily experimental postdoc I would not have applied at all.
We are talking Postdoc level here, not a grad student who suddenly switched topics. I just want to know if this is normal, or just a bad situation.
Knowing that this is normal might reduce my level of frustration, but if it is not, at least I can speak up in the exit interview.

I bet the PI doesn't see it as a significant topic change because he sees it as a brain-machine interfaces project, not an ML project. It's a sort of shift that can only happen in a highly interdisciplinary field, where you perceive it as a field change and the PI perceives it as a focus change.

It's also possible the PI thought that the interface design problem was solved, and it later turned out that the signals weren't yet good enough to do any kind of learning on. Not your fault of course, but this can happen.

Regarding
"if it is not, at least I can speak up in the exit interview", I think you should know that in the working world in general it's not considered a good sign when you have a problem with your work situation and you don't take steps while still in the situation to address it.  Wherever you apply for work next is going to want to know what you do when conflicts arise.  If your answer is "build up resentment during my tenure there, then unload about it in the exit interview", that's not really very positive.  You might want to talk to the PI now about your concerns.

@msouth I actually disagree, there can be any number of reasons people do not talk up ahead of the exit interview, and it does not have to be a rant.
I've worked in several places, and exit interviews have been a great medium to give one last suggestion to the company or working group.
I'm on a working Visa, which means my PI has all the power to essentially send me back to my country if he wishes, that is an unfortunate position to confront people about not liking your work.

@Leonpalafox I agree that there are situations, such as the one you described, where it is not practical/safe for you to raise objections.  (Or where so much is at stake that you can't be sure if it is practical or safe.)  So, yes, there are exceptions, and it sounds as though you are in one of those exceptional situations.  But the rule should be that if there is a problem, you talk to your manager about that problem and try to get it resolved.

I would say, no, it is not normal for a PI to shift focus so radically.
In the normal run of things, when hiring at the PostDoctoral level (and lower), the PI will have:

Submitted a funding request with a detailed outline of the research plan.
Have received acceptance of that plan and a budget.
Advertised open positions accordingly to the budget looking for people with the necessary skills.
Hire people with the necessary skills for the duration/budget allowed by the funds.
Supervise execution of the research according to the initial plan.

... pretty much in that order.
Topic shifts would normally occur where funding for a project has run out (which should correspond with the end of the PostDoc contract) and the PI wishes to find funds from other projects to keep the PostDoc employed and to extend the contract.
Shifts might also happen if the PI is pooling sources of funding together, which can sometimes happen: they might decide to juggle resources between different projects on the fly. This, however, is far from an ideal situation, esp. for managing researchers on temporary contracts.
The questions I would ask in your situation are: in which of the PI's projects you are working on, has it changed recently, where the funding for that project came from, and what the original proposal was.

If you have moved project, you should ask why.
If you are in the same project, you should ask why the topic changed so radically all of a sudden.


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How can I address my career future with my current PI?
I'm currently midway through my first Postdoc gig, I got a 1 year contract and haven't heard a word from my PI concerning any possible extensions. I only have 6 more months left in my program, and I was wondering whether I should:

Ask him directly whether he is considering to extend my contract.
Start looking for other jobs without consulting with him first.

I know I'm under a grant that runs out shortly after December (my contract is due on February), and we might or might not have an extension for that. The answer should come around September's end, but I'm afraid it'll be too late to look for another postdoc then, I'm under a J1 visa in the USA, and I'm worried that the immigration process to extend it and the whole hiring process might take considerable longer than 5 months.
AS professors and more experienced professionals, what would you recommend to do, I'm also wondering whether asking him if I should look for another job might strain our relationship.

Whether he extends your contract or not, your PI certainly knows that you'll be moving on in 6 or 18 months, and would be insane to believe you're not at least thinking about your next steps now.

Ask him directly — YES! Sheesh!  Just talk to each other already!

Your advisor has the duty to inform you if you are meeting expectations, and to notify you in a timely manner if your contract will be renewed or not. Politely bringing this up at the end of the meeting should not cause conflict with your advisor—unless your advisor is a control freak (in which case it's not exactly a bad thing that you'll need to move on!).
However, I would have this conversation as soon as possible, as the end of your contract will be here quite soon. You should inform him, if you'd like to continue working with him, that such is the case. You should also politely mention that if the finances aren't secure for a commitment, that you will need to consider additional job opportunities to ensure that you are not "stuck" looking for a job without a current source of income.


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What is the best way to turn down a Postdoc offer?
I've been recently offered a couple of Postdoc positions, and I was wondering how you as professors would prefer to be informed if a candidate would rather work with another institution.
I know we are professionals, and these things are to be expected, and probably the professor has another candidates to choose from, but I just want to be as respectful and professional myself as possible, so how would you turn down an offer, or would like to be turned down.

It should look a little something like this

Keep it short and honest.
For example,

Dear So and So, thank you for your offer for a postdoc at Blah. It's
  an attractive offer, but I've decided to take a position at Foo-Bar
  instead. The work you're doing over at Blah is very interesting and I
  look forward to interacting with you in the future.

Of course if you have more than one rejection to send out PLEASE PLEASE don't do it generically. Tailor it to each place individually. It takes a little more time, but it's a fair exchange given that they took the time to give you an offer.

foo-bar huh,, nice..

I agree with the previous answers: short, honest, polite.  I'll add: prompt.  As soon as you accept an offer, let the other institutions know immediately.  That will let them move on with their search.

Just send a short but polite note telling them something like: you appreciate the offer but have decided to accept a different one. Maybe tell them (especially if it's true!) that you respect their research, hope to see them at a conference or visit their institution in the future, or something nice along those lines. Don't overthink it, just be polite.

First, I really like Suresh's answer. Short, straight, polite, and mentioning you would like to work with them in the future.
When I did my post-doc, I had the same problem: I applied for more positions than I could accept 8^)
Turning down the offers I could not accept was along Suresh's lines,  but with one major point added: I did not send emails/write letters, I called the professors and talked to them  personally.
And yes, I met all of them again during my post-doc. The world of research is very small.

That's a good point (about calling them personally). Of course this can be a little awkward, so it depends on your comfort level with the person.

It is a little awkward, yes. But pays out later on.

one additional thought: If the offer you reject is a good one (i.e. a lab you can see yourself work in), I really believe it is important to call the PI you turn down, confirm your interest in the research done in the lab, and make clear that it was a really tough decision for you to make. Being in similar situation coming out of my PhD, I ended up choosing lab A over lab B, and after a few months, I realized PI of lab A was a nightmare, so I contacted lab B again and had a productive postdoc there.


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Are papers entirely unrelated to my field going to hurt my chances in the future?
For the past year I have been doing a postdoc in a Neuroscience lab, the position advertised was for computer science.
For the first year, the work was mostly related to my discipline, but my PI's funding got cut and now he has been pushing me to write and do experiments in an area that is entirely out of my expertise or even my field (electrodeposition/ impedance characterization). To be honest, I do not like the area, and was not written anywhere neither in the job posting or the offer letter.
I got a postdoc offer in a different University, and have already accepted, but my PI is pushing me to delay my start date or even come back over the summer to finish these experiments and the paper. (Probably at my own expense, the position is in a different US state)
As I would like to apply for a Tenure track position after the coming Postdoc, I would like to know how much can this affect my chances, would a publication in a field that is not even remotely similar to my own (Machine Learning) can hurt me more than help me?
I've tried to think on ways to turn it around so I can come with a feasible explanation on how is a paper on that topic even going to help build my ML expertise, but so far I have come with nothing.

Related question specific to cstheory.

Perhaps you can add a follow-up, given that five years have now elapsed.

A legitimate scholarly publication can only help you (although it might not help much).  If you're really worried you can always just leave it off your cv.

You cannot leave a paper off your CV

@ArtemKaznatcheev: You can leave things off of a CV if you don't think they're relevant or helpful, but you cannot take credit for something that you didn't actually do. I don't list a bunch of technical reports I wrote at my previous job—but some schools of thought say those should be listed. But they're not relevant to anything I do anymore, so there's no point in cluttering my CV with them.

I agree that you can leave things off your CV.  As usual, there are nuances involved: if you are employed as an academic in subject X and a while back you wrote a paper in unrelated subject Y, then that paper is just not a part of your professional identity, and I think everyone would accept that.  For a clearly defined subject like mathematics which has a globally available database of papers, leaving a paper in your current subject off your CV seems shadier.  I think you can still do it but that it would be appropriate to mark the list as "selected publications".

You can leave a paper off your CV, but I do not see how it could help you, unless there is a length limit.

I agree with vadim's answer above:

A legitimate scholarly publication can only help you.

As for the concern about the 'helpfulness' of a paper in an unrelated field, I would tend to see it as a positive thing, showing that you are not restricted to working/thinking in/knowing about one area only. You have proven that you are capable of scholarly research in a tangential area; this should help rather than hinder your TT search. Of course, you may find that some possible positions will be unappealing to you if you really hate electrodeposition/ impedance characterization. If that possibility is a large concern to you, then you might consider leaving the paper out of your CV.
However, I do not believe that leaving the paper out of your CV would be a good solution, unless the paper is also of very poor quality, in which case the point above does not apply and you really don't want to use this experience when searching for tenure track jobs. If the current project is of poor quality, you may be better off moving on to the next, more compatible post-doc, and also politely declining your (current) supervisor's offer to continue/finish the project you are working on now.

Interdisciplinary research, especially at the interface between computer science and biology, is pretty hot at the moment. In that sense, a paper in neuroscience could even be helpful, especially if you later want to apply machine learning to that kind of area.1 The down-side is that doing these experiments takes time, which is time you could spend doing something else.
If it wasn't for the fact that you already have another job lined up, I'd say you should weigh up the possible advantages (increased experience of possible applications of your ML research) against the obvious disadvantages (time spent away from your core expertise).  However, since you do have another job lined up, just go for that. Tell your current PI that you appreciate his efforts to keep you in a job even after his funding got cut but that the work he has for you just isn't your cup of tea. You're under no obligation to come back and finish the experiments (and, hey, if push comes to shove, your new employer can't give you that much time off, right?) and, since you're not an expert in that area anyway, your current PI can probably find somebody who can finish them better than you could.

1 If even makes sense... As you can probably tell, I know next to nothing about machine learning and even less about neuroscience.

My feeling is that a publication in a totally different field will simply be ignored and certainly wouldn't help, unless the job you're applying for is specifically interdisciplinary and across departments.
A publication in a different subfield can help or hurt depending on its quality (and somewhat on how you're selling yourself).

I don't really see why a publication in a different subfield would hurt.  Could you elaborate on that?

To clarify: papers in another field probably won't help or hurt because it's likely that nobody on the hiring committee can evaluate them.  On the other hand, papers in your field, but a different subfield, could hurt if they are bad papers (just like papers in your own subfield).  Also, having papers in a different subfield could hurt you "sell" yourself as being in one area, when your publication record may say otherwise.  It of course should go without saying that a good paper in your field, but a different subfield, can and usually will help your application.

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How to manage lot of random yet potential ideas for research and startup?
I am a graduate student and planning to pursue a PhD. For one year, in search for a research idea, I have been reading random research articles and papers in many dimensions of Computer Science.
Suddenly, I have been blasting my advisor with various ideas. The ideas as per my advisor are possibly a new paradigm but do have great potential. Also, he says the complete idea may or may not be doable by a single PhD student. I also see those ideas converting into good startup ideas as well. (I was an entrepreneur before pursuing research in search of some challenging work).Most of the ideas are not very much related to each other but still concentrated to my specific field of study (Computer Vision).
I am concerned that pondering of so many ideas may prolong my research without results. My questions are:

How can I manage so many wavy ideas in a streamlined way ?
How feasible is it to focus the research so that the outcome may be a startup (since making it commercially viable would require some amount of research in other areas of Computer Science such as Data Mining, Large Scale Search etc. ) ?

(1) Write them down. (2) Utterly infeasible for me, but you and I are different people.

For your first question, here is the workflow I follow:

Write them down (as @JeffE mentioned)
Organize them in order of viability/ease
Take the most viable idea and do a (very) quick prototype
If prototype is successful, develop it. If not, iterate.

From the prototype you probably have a better idea of how much work it would take to fully develop the research idea. If it seems like you won't be able to handle it in the amount of time you have, or if the outcome is not worth the effort, I usually archive that idea for later. For a  prototype I usually try to do the bare minimum to produce the simplest result possible. A common trap is to start from the complex before you've mastered the simple.
The second question depends a lot on your personality, so don't take the following advice much too serious. Personally, I have a very hard time focusing on two things at the same time. What I would do is focus on my PhD. You'll surely get many more ideas as your work progresses. For every problem you solve, you'll generate 10 new ones. Be sure to write things down so that you don't forget them later on.
This is a very personal question and you have to see what works for you.


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Tools for managing and scheduling meetings with students?
My advisor has been very busy and a lot of us hardly get quality time with him. he also acknowledges this and says it is usually very difficult to manage appointments and other commitments. He has lately been suffering from health problems, adding to crunch in time for all of us.
Me and my advisor were discussing several ways to schedule and manage meetings with his students, preferably a web based tool so as to keep us informed in case schedule changes and also to let him remember which student met him and which didn't. (He has a lot of students with him including undergrads).
Google Calendar could be one such tool, but I am wondering how do people in academia schedule and manage meetings with students ?

Be careful when using external tools (as opposed to self-hosted web-based solutions), as requiring students to use them might be in conflict with the privacy regulations of your place. That does not completely rule out external tools, you just need to be aware of possible problems. (For example, we use Doodle, which is mentioned in damian's answer, a lot, but we never input (or require anyone to input) much identifiying information such as full names.)

Good point, @O. R.Mapper ! Yes, in all solutions and tools I suggested, I'm completely fine if people just put in their first name or an acronym or whatever they want.

Several of my colleagues use YouCanBookMe (https://gb.youcanbook.me/), which integrates with GoogleCalendar. You can specifiy "office hours" or the like, and then students can book a meeting with you.
I myself, however, discuss individual appointments per mail and then immediately add them to my digital calendar, which to me works better, as I do not have fixed office hours.
When I want to have a whole day of meetings (e.g., everyone from a class is supposed to have an individual meeting with me on one specific day to get feedback), I create an etherpad at http://www.titanpad.com , give timeslots and ask all students to put their names on it.
For group meetings with colleagues, I use http://doodle.com (or http://datumprikker.nl , which offers a similar service in Dutch) to schedule group meetings. I guess pretty much everyone at our department does so.


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What is the role of advisor in writing a PhD thesis?
I am about to write my PhD thesis. The process is to first write the synopsis which will be read by examiners prior to agreeing to read the thesis. Now, I provided my advisor with copies of the synopsis and thesis a few months ago for review. But he was not able to read either the thesis or the synopsis. Since time for conduction of synopsis and subsequently thesis submission has arrived, he is now asking questions like "have you written the thesis", "if I will proceed with the formal procedure, make sure you submit on time".
I understand that during the course of PhD I have written many good papers, yet the situation leaves me wondering what is the role of supervisor in writing the final thesis document?
Note: To be honest, I have not written many theses' (my bachelor's thesis was the most ridiculous document I have written till date). My university is in India.

Sounds like a communication problem to me. Talk to your supervisor (in person).

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


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Writing letters of reference for a faculty position in China?
Does anyone know how to write good letters of reference into a Chinese university? I have an awesome former PhD student who is looking at a position that exactly suits their experience.  Is China like the USA that you can write something that is all praise, or is it like some countries in the EU where you are expected to comment on both strengths and weaknesses?  How should the letter open?

Are you expected to comment on weaknesses for positions in the EU?

Yes–some countries. I had a student rejected quite recently for a Belgian postdoc with a comment that his letters were "implausibly positive", and I have heard of the same thing happening in the UK. Because I am an American working in the UK, I tend to say "In America I wouldn't bother to comment on this, but I know here it is expected to mention a candidate's weaknesses. The worst thing I can say about the candidate is [something not very bad] which will I expect benefit from working at with you because [some plausible reason.]" I've heard Austria requires entirely positive letters though.

Certainly it's well known that letters from Europe tend to be more reserved than from the US, and I assumed most people took this into account when reading letters, but I guess there are some stodgy old codgers who don't.

According to what I know about Chinese academic culture - do they even read LoRs? But of course I have no first hand experience with this and it definitely differs from place to place. A top place, like Tsinghua or Peking's process is probably closer to that of a US/Europe research university, but things might be very different at e.g. Hunan Normal University.

criticism in Asians cultures....big NO

I just crossed the hurdles to get faculty position. Few suggestions: a) need to focus on how the candidate can able to survive in diverse Chinese cultures b) long term career plan, c) as suggested, no critical discussion about candidate’s weak points.

Writing my comment as an answer, following a suggestion.
I’ve spent two years in China as a postdoc. I have never read a recommendation letter (LoR) but I’ve experienced the culture in academia. As someone else hinted I also do not think anybody will actually read the LoR in any detail, but just skim through it. The focus is on who wrote it (more precisely, what is the author's university ranking and impact factors).
About the contents I’d recommend just dropping cliche positive comments but without any exaggeration. The Chinese are extremely sensitive to any form of criticism, and will generally not appreciate outspoken, frank discussions. This will look particularly "serious" if put in written, from a "leader" and addressed to 3rd parties, and might be interpreted as a gentle warning against the candidate.

As a side comment, I'd recommend advising the student against pursuing a career in the Chinese academia, as my overall experience with different institutions in that country was discouraging, to say the least. I believe a strong pervasive culture of short-term gain has eroded quintessential local scientific standards and collegiality.

My recommendations:

Highlight the applicant's ability to publish, particularly if they have a large number of publications, and particularly if they have publications in journals with a high SCI ranking (SCI 1 or SCI 2 journals, especially; searchable from LetPub).  There's other ranking systems, e.g., in computer science, we also use the CCF index.

Highlight international collaborations that the applicant is able to bring to the university.

In my opinion, the above two items are far more important than anything else.  These are always the top priorities when we have meetings---who's lab published what, and with whom.

If relevant, highlight the applicant's English level, especially if they're a native English speaker.  If possible, highlight the applicant's willingness to improve the English on student papers.

If relevant, name the professor(s) the applicant is intending to work with.  In interviews I've been to, if the applicant can't name the professor, they're not taken seriously.

Highlight how the applicant has the ability to apply for grants reserved for international applications, such as the Research Fund for International Young Scientists.

Describe the ranking of the university where they obtained their PhD.

Explain how the applicant is able to adapt to life in China, e.g., highlight their Chinese-language ability, Chinese co-authors, and experiences travelling to China or living abroad.  Make the applicant seem less "foreign", a friend of China, and unlikely to stir up trouble.
(Although if they're from China, Singapore, etc. [anywhere where they speak Chinese and the culture is similar to China], I'd skip this---they might not seem international enough.)

If relevant, highlight how the applicant is from a "Silk Road" country (interpreted broadly), which is in line with the government's Belt and Road Initiative.

And, I concur, don't write about weaknesses---they'll almost certainly be interpreted unfavorably.

Do not write about weaknesses in a reference letter for China. Your candor and frankness will not be appreciated as a dialogue...or friendly critique.


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How to prevent being intimidated by juniors in your group publishing before you
I am working towards my PhD for 2.5 years now. A few of the students who joined after me under my advisor have recently published in top-tier conferences. Though I have worked pretty closely with them and mostly have been involved in troubleshooting their problems while they were conducting experiments or studying for those papers.
I am very happy for them and have nothing against them, but when I see that I don't have a single publication to my name, I get a bit depressed. Earlier, this used to give me motivation and my killer instinct just made me work harder. But as the time has passed, I feel demotivated. My advisor still considers me amongst his best students. Mostly, I didn't publish my work till now because I didn't find it doing justification to my expectations. And I wanted to send it to a top-tier journal which would require extensive evaluation and mathematical rigor, which I am still working upon.
Is it common to be intimidated by such such situations and what is the best way  to overcome the feeling that you haven't done anything.
Note:

I have a lot work but unable to overcome this feeling when every few months, someone gets a paper accepted to a conference.
I am reluctant in sending papers to conferences since I am a self sponsored student and also not full time. So I want to utilize the funds available to me judiciously. The conferences won't fund me since there's a rider of being a full time student.

Why do you think you're intimidated? Does it have something to do with ego? From an absolute perspective, you don't seem to think you're a bad student, and you say that your advisor thinks highly of you. So does it have to do more with comparing yourself to others?

@Potato I think yes, I am comparing myself.

You sound like a perfectionist. You might not be aware that perfectionism can be a problem, and it's an endemic one among researchers — it's a common obstacle to getting a PhD.

@Blaisorblade It's not endemic, but it's surely common.

@PiotrMigdal Thanks, I'll stop misusing endemic to mean just common.

perfection is the enemy of good enough

First off: if you are not a full time student, it's natural that you will take longer than others (who I presume are full time students). Don't feel too pressured by this.
Second, if you are involved with your colleagues' papers, should you be a coauthor on them? Especially if this took time you would otherwise have spent on your own projects?
Most importantly, have you discussed your specific problem with your advisor? It appears like getting a publication accepted would be helpful to your peace of mind. Your question has a faint whiff of perfectionism, which may prevent you from submitting and publishing. Your advisor would be the logical person to discuss this with. He should have a good understanding of the expectations in your specific field. If he considers you one of his best students, this is a good starting point!
I would recommend that you write your advisor an email along these lines:

Recently, some other students in our group got accepted in upper tier
  conferences. I am extremely happy for them, and this motivates me
  immensely to follow their lead. I would like to get something accepted
  in a comparable venue soon. However, I feel unsure of what level of
  quality is sufficient for publication - at what point do I stop
  polishing and submit?
Could we have a meeting in which we discuss some of my current
  projects and work out what I still need to do to get a manuscript into
  submittable form, ideally with a time plan? Thank you!

Finally, I assume you have already read and taken to heart this canonical question, right?

thanks. My advisor suggested me to keep publishing in the conferences since I am involved in a lot of cross domain intellectual activities. The primary work may go in a journal. It relieves me a bit. The only thing now I have to discuss is the funding :)

I assume you are in computer science, since you are talking about top-tier conferences. So, I am going to talk from a pure CS perspective, since in CS in order to get a PHD you need to have publications.
First of all, do not let your ego get in the way of you getting a PHD. For getting a CS PHD, you need a critical mass of good and solid publications. That means a sufficient number (not just one) of good to excellent papers. According to the CORE conference ranking:
Conferences are assigned to one of the following categories:

 - A* - flagship conference, a leading venue in a discipline area
 - A  - excellent conference, and highly respected in a discipline area
 - B  - good conference, and well regarded in a discipline area
 - C  - other ranked conference venues that meet minimum standards

I know many people who took a CS PHD and went to successful careers afterward that during the duration of their PHD did not have any A* conference publication. Instead they had 1-2 A publications, a couple of Bs and some additional workshop / demo / poster publications. IMHO this is the most realistic plan for actually getting a good CS PHD and get it relatively fast. So, although it is good to aim high, you should know that getting an A* conference publication (VLDB, SIGMOD, FOCS, SODA) is not simply possible for all CS PHD students (and certainly not necessary) during their PHD duration.
In this sense, aiming for that one perfect publication that would take 4 years to write is counter-productive for you, because:

If it gets rejected you start from null
It is not enough to get you a PHD, because you cannot have a CS PHD thesis of 30 pages
Everyone will assume that it is your supervisor's doing if you cannot follow through with equally good publications
If you are Mr. Nobody in single-bind conferences, it will be harder for your work to be accepted initially, since nobody knows you or trusts you
It is very difficult to do so, because writing a paper of this magnitude needs experience and this kind of experience can come only after writing many good papers and many rejection / resubmission circles for mere mortals like us (unless you are Terens Tao)
If the paper is that good, it really does not make that difference where it was submitted. I know seminal papers presented in B-conferences with 300 - 1000 citations and papers in A* conference that nobody cites.

Also, your plan of sending to a journal is even worse, since it might take a year before it gets accepted and in the meantime many other people could catch up with you. And even if you did write this excellent paper, it will take some time for that publication to take off and be known and until then what? You will have finished a PHD with a citation number of less than 10. This is also bad on all counts.
On the other hand, putting out consistently good-solid publications in respectable A or B conferences on a frequency of 1-2 papers per year, means that in 3-5 years of your PHD, you may have 4-8 good publications and:

People will know you for you (and not your supervisor) because you have
proven yourself consistently by producing good papers on regular intervals
You will have gained better experience on how to actually write good papers and sell your ideas better
You will have a better citation index, due to your citing your work
and other people citing it because the related community knows and respects you
You will get review requests that will inform you faster on the current state-of-the-art
You will find faster external collaborators which means even more good papers for you.

In a nutshell, my advice is: If your work has produced good-solid results, wrap it up and publish it, instead of aiming for perfection. Once your first work is out, everything else will be on its way.

I'd like to add that top-level journals in CS tend to count less than top-level conferences (it's certainly so in programming languages, and I don't know CS fields which are exceptions) — so usually, you submit to journals extended and improved version of conference results.

thanks for core rankings. And listing out the specific points to shape my thought process

As other have mentioned, you sound like a perfectionist. This probably won't surprise you.
You might not be aware that perfectionism can be a problem, and it's an endemic one among researchers — it's a common obstacle to getting a PhD. The pattern matches your description: you set yourself excessively high standards, you miss them so they make your life worse, yet you keep attached to those standards, and ultimately you achieve worse results, both for motivations problems, and because you for instance self-censor your work, or work too much, or both.
I've had the same problem, and I've been recommended reading this self-help material. Of course, it's up to you to decide whether you recognize yourself in this pattern.
http://www.cci.health.wa.gov.au/resources/infopax.cfm?Info_ID=52


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Is there any difference between journals and conferences which charge money vs those which don't?
Some journals and conferences charge money before/after paper acceptance, similarly there are some which don't (like Open Access Journals). Does money matter in judging such journals/conferences before sending paper ? Unfortunately my organization is on a cost cutting and isn't funding for any such activities. Is there a list of journals which do not charge fees or charge modest fees, so that I can publish there on my own ?

I think this might depend on the field. In my subpart of computer science, if the journal asks for money, you don't publish with them.

agreed. if there are page charges, you do not publish, usually. (field: information science/HCI)

Is there a list of journals which do not charge fees or charge modest fees, so that I can publish there on my own? — If a journal charges to publish, it's probably a low-quality venue that nobody reads or cites.  So conversely, the journals that you read and cite probably don't charge to publish.

I do not agree with your characterisation of open access.  Open access means that there is no charge to access a paper.  There can still be a charge to publish a paper.  For example, open access journals by the European Geophysical Union charge for publication instead of for access.  Either the money comes from publication charges, or from subscription charges, or a combination thereof.

This might be useful: http://www.doaj.org/doaj?func=byPublicationFee&uiLanguage=en — Directory of Open Access Journals / Browse by publication charges.

Generally speaking, whether a journal charges money for publication or not should not be a criterium for judging the quality of one journal compared to another one. Use other means for that, for example checking where good papers are published, the academic reputation of the editorial board, opinions of colleagues, and, yes, even numeric factors such as the impact factor of the journal.
There are very high-quality open access journals, for example the PLoS series of life science journals, but also no-quality open access journals, for example the ones produced by most of the publishers on Beall's list. Some very high-quality non-open access journals ask for page fees (or even submission fees, as I learnt recently), others don't.
I am not sure whether there is a specific list of journals which don't require paying fees, or an overview listing publication fees for a range of journals. There is the quite well-known SHERPA/Romeo list, which distinguishes between different levels of self-archiving. I guess most of the green journals (highest self-archiving rating) listed there will be open-access journals and ask for publishing fees, so you could go and check the other journals in more detail, by looking at their instructions for authors.

The SHERPA/Romeo list is about the self-archiving policies of various journals. It is not a database of open-access journals. The "green" journals in the list are not necessarily open-access journals.

@JukkaSuomela you're right, I clarified this point in my answer. But I assume there will be a high correlation for a journal between being green in the SHERPA/Romeo list and being open access...


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How to show proof of publication?
I have just got my first paper accepted to a reputed IEEE (say X for generality) conference. Now, one of the authors have registered for the conference as a student member of X. I have applied for student membership, but probably won't receive the member card before registration deadline. In that case, I have been informed that only the author attending the conference would be getting the certificate.
So I have the following question:
1) Do I need the certificate to proof that I have this publication in future ? (My dept has procedure of submitting copies of all certificates that you earn during the semester, and my co-author would definitely be submitting his there.)
2) Is it worth to register without availing student discount so that I may get the certificate ?

Interesting, I never heard of someone being asked for a proof of publication. Has anyone encountered this before?

As the previous answer speaks about journal, I just wanted to clarify for conference.
The proceedings are prepared by the Programme Committee and submitted to IEEEXplore library. They can appear there before the conference or after the conference, depending on the arrangementes chairs made with IEEE. Once the proceedings are there, you'll be able to locate your paper and print a screenshot and/or the paper in case you need to proof the publication.
The e-mail from the PC you received should also serve as a proof of publication, as long as it mentions the authors of the papers.


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What are the advantages or disadvantages of using LaTeX for writing scientific publications
What are objective advantages or disadvantages of using the markup language LaTeX instead of a WYSIWYG word processor like MS Word or LibreOffice Writer?
Please use objective arguments to prevent a flame war...

In principle the question does not limit itself to only math heavy papers, although I think mathematical equations are one big advantage of LaTeX, so I suspect it will be part of a good answer

related: http://academia.stackexchange.com/q/3054/675

Back in my Uni day's (early 90's) I used TechWriter, on RISC OS, which offered the best of both worlds. Unfortunately there doesn't appear to be anything as functional today (unless you obtain an old copy, and run it under an emulator or Raspberry Pi), but there are LaTex export Wizards available for all the popular office suites, if you can live with the quotation editors (the one in word used to be very buggy, but haven't used it in years).

In 1994 I was asking myself the same question. FrameMaker was my final choice as it was WYSIWYG, decent cross references, ran under MacOS and Solaris, supported PS/PDF output, integrated color graphics and equation editor, etc. It's still way better than Word, IMO, but costs too much. Adobe bought the company and aimed the product at a niche market (SGML).

I find it ridiculously difficult to manage documents with a large number of figures in Word. Word seems to do its own thing when minor changes are made. With Latex, I get exactly what I want. Stopped using MSWord years ago. My advice would be to bite the bullet and learn LaTex. Steep learning curve, but the results are well worth the effort...and then some.

LaTeX has other advantages, mainly that a) it is deterministic, that is, the same .tex file will always produce the same output, with page breaks etc. in the same places, and b) the output generally looks better (the density of black versus white is fairly constant). LaTeX can produce output which can be printed as it is, whereas Word output will have to be put through a page layout programme. (Of course, you have to know what you're doing with LaTeX to do that). Donald Knuth, who invented TeX, spent a lot of time talking to printers in order to get it that way.

LaTeX is better at:

Dealing with mathematical notation. Layout and entry are generally easier using LaTeX than some other sort of equation editor.
Consistent handling of intra-document references and bibliography. As of a couple of years ago the major WYSIWYG editors still had problems with re-numbering cross-references and bibliography items. This is never a problem with BibTeX or LaTeX.
Separation of content and style. In principle this means that you can write your document without caring how it is formatted, and at the end of the day wrap it in the style-file provided by the journal publisher before submission to conform to the house style. In practice some of the journal publishers demand special formatting commands that partially moots this process. Furthermore recent versions of Word and LibreOffice Writer, when properly used, should be able to keep track of various levels of section heading separate from the body text, and apply uniform styling to each level. The gap is somewhat closing.
Tables and illustrations. With PSTricks or TikZ, one can produce high quality illustrations within the document (though the learning curve is a bit steep there). And I've found LaTeX to be better at preparing complex tables.

WYSIWYG (especially Word and Writer) is better at:

Collaborative editing. Without using an online site for collaborative LaTeX editing (such as ShareLaTeX), working collaboratively on a LaTeX file ideally requires some sort of separate revision control software. Word and Writer have very good comments/annotations and edit-tracking features. When a large number of authors are commenting on the writing of one file, this can be very useful.
Spell check. Admittedly most text editors one uses to edit TeX files also do spell check. But this is generally conveniently built into WYSIWYG editors.
Compatibility. Unless you work in mathematics, computer science, or physics (and sometimes even if you work in those fields), it is more likely that your collaborators will know what to do with a Word or Writer file than a LaTeX file.
Minimum barrier to entry. If you just care about getting the ideas down on paper, you can use a WYSIWYG editor just like a typewriter. Sure, it may be tedious to fix the formatting later on, compared to LaTeX where one need to first figure out how to setup a bare-minimum file before using, it may be an attractive point.

A wash:

Most journals provide templates for both Word and LaTeX, so there's no real winner there.

Suggestion: if you want to convince someone to start using LaTeX, start them out first in one of the WYSIWYG environments designed for LaTeX first (for example LyX). This will help somewhat to ameliorate the scary entry barrier.

+1 The separation of content and formatting is hard to get right in Word, and trivial in LaTeX.

In addition, if you have them using LyX, don't do collaborative editing with someone else not using LyX. LyX is idiosyncratic and LyX documents don't easily compile with other LaTeX flavors

good answer! Totally agree. and +1 here: it's fun to use LaTeX.

I agree, but I have a comment. LaTeX does not really separate content and formatting. If LaTeX is used properly, you'll practically get content and formatting mostly separated, but LaTeX does not enforce this. It's common to see "{\bf foo}" and numerous minor tweaks to get formatting look right, such as "\vskip{1ex}", in LaTeX documents. XHTML/CSS gets separation right at a conceptual level.

@Suresh: What are you talking about? LyX is not a LaTeX flavor, but a front-end. Just export its documents as LaTeX, and you can collaborate with others.

@KarsusRen I realize that Lyx is a front-end. I've had problem with the latex that gets exported from lyx.

@Jan: I agree. Hence "LaTeX is better at [it]" and not "LaTeX forces you to [it]". And for argument's sake neither does XHTML/CSS do it. There's nothing preventing you from defining a <div class=boldface> </div> that does exactly the same function as {\bf foo}. (Ever try reading some of the code produced by inferior WYSIWYG front ends for editing web pages?)

Just to add - LaTeX has been getting easier to learn and use with the rise of a number of online LaTeX editors that do the compiling for you and offer a real time preview of the output, such as writeLaTeX.com. We're hoping this will lower some of the barriers to entry (I'm one of the developers of writeLaTeX, and so any feedback is much appreciated, thanks)

I strongly disagree with your claim that Word is better at collaborative editing. Track changes is okay but it simply doesn't compare with the power and robustness of version control software. Consider what would happen if you both make changes to the same revision of a word document.

@Jack: VCS is not part of LaTeX. Whereas Word has change tracking built-in. In fact, I said as much in my answer above.

@WillieWong: No, it's not part of LaTeX but one of the principle benefits of LaTeX is that it plays nicely with VCS. To ignore it is missing a major part of what makes LaTeX better. Like many such tools, LaTeX is sensibly viewed as part of a suite than a standalone option otherwise you may as well complain that LaTeX has no editor when in fact everyone who uses LaTeX uses a well featured text editor to work with it. The point remains that proper VCS blows Word's "Track Changes" out of the water.

@Jack: I do not disagree with you that a good VCS is, well, good. But you cannot 'sell' LaTeX to the masses by saying that "oh yeah, for this other thing? LaTeX totally wins if you install this other power-user software". Like it or not, the Unix philosophy is not very ingrained for most "users" of computers. LaTeX has enough of a learning curve as it is, you don't want to scare users away in the beginning by saying "oh, and you also need git, and asymptote, and while you are at it learn lua..."

@WillieWong: On this, I think, we shall have to agree to disagree.

you should try ShareLaTeX https://www.sharelatex.com?referal=ed73b7dd
you can collaboratively edit on that, and without any prior configurations

"Most journals provide templates for both Word and LaTeX, so there's no real winner there." - Citation needed. Almost no journals in my field provide LaTeX templates.

@Fomite: The three big-name publishers, Reed-Elsevier, Springer, and Wiley account for 40% of the academic publications. Elsevier has a standard article class, as does Springer (see also the CTAN listing). Wiley has one for books, but it seems they are slightly less keen on LaTeX for their journals.

@Fomite: and for some of the other publishers. Nature does not have their own class, but gives simple and clear guidlines, PLoS and PNAS both provide templates, as does Science. Granted, the popularity of LaTeX is field-dependent, and it is quite possible that in your particular subfield it is not as popular to prepare manuscripts in LaTeX.

... but on the flip side, in my field manuscripts not prepared in LaTeX are often looked upon with suspicion. So the cut goes both ways.

Re: separation of content and formatting. Take a look at Knuth's TeX book, there are hand-tweaked formatting modifications all over the place. Many of them are necessary because TeX is so dumb regarding character shapes -- it knows nothing about a character except its enclosing box, so it can't possibly do a decent job.

@bubba: if that's the sort of details you care about, you might find microtype useful.

@WillieWong: I do not disagree with your statements about how Word integrates certain parts of version control tools that would come in separate packages for LaTeX (and how that is easier for some users). I think, though, it should also be noted, that the document exchange part of VCS is not integrated in Word, but that a separate system, such as a SharePoint Server, is required, to actually work collaboratively on a document. In that case, conflicts are handled in some way (because changes are visible to all users in real-time), but it is not contained out of the box; with a plain ...

... Word installation, for example, you have the comments and track changes features - as well as options that can be manually invoked to reintegrate several versions of a document -, but you still have to exchange the latest documents by e-mail or by having everyone work on a mutual exchange directory on a network drive - and heaven forbid if two people work on that file on such a network drive simultaneously and one of them simply overwrites the file that the other one has just saved their day's work to.

@O.R.Mapper: good points, in all. I should mention that also a VCS is not a magic bullet. For example, for large documents if one does not take advantage of \include and \input statements and works with a monolithic .tex file, conflict resolution will take more time than those saved by not using e-mail to pass the file back and forth.

@bubba The TeXbook is about TeX itself and the "plain TeX" format, not LaTeX.  One of the big contributions of LaTeX was its strong encouragement of separating content from formatting.

@AndreasBlass -- the same comment holds for the LaTeX Companion.

@bubba, Knuth writes in TeX, the low-level language on which LaTeX is built. Yes, you can can screw around with such micromanagement in LaTeX too, but that mostly negates it's usefulness.

@O.R.Mapper, with Word you are forced to use the dumb GUI, the (crappy) VCS included, and so on. With LaTeX you choose the tools you most like (and can use them also to edit and save code, random text snippets, experimental data, ...).

@vonbrand: Unfortunately, "choos[ing] the tools you most like" is not a selling point towards users who want an everything-out-of-the-box solution. Accordingly, in my experience, these users tend to perceive it as a negative to have n + 1 tools (n editing tools + 1 VCS), compared to n tools (n editing tools, each with its integrated VCS features).

Word
Advantages:

Minimal learning curve
WYSIWYG
Ridiculously high install base; almost guaranteed that anyone can read/edit your file without modifying anything
Easy-to-use reviewing tools (view changes, add comments, etc)

Disadvantages:

Layout can be a real bear to get correct
Math is difficult, slow, and often ugly
Included bibliography editor is virtually unusable for most scientific writing; you'll need to buy a third-party solution to manage your bibliography

LaTeX
Advantages:

It's just text; anyone can edit your file
You don't have to worry about layout, it's all automatic. Just put the words down there and you're golden
Produces aesthetically beautiful documents
Easy to use math, symbols, etc
Once learned, much faster and more intuitive (e.g., \label and \ref for referencing, as opposed to Word's fairly kludgy "Cross-referencing" window which requires way too many clicks to insert a single reference)

Disadvantages:

Fairly steep learning curve
Collaborators unfamiliar with LaTeX will have difficulty reviewing your manuscripts
Many features require libraries, which you have to find/be made aware of (view changes, etc)
Layout changes are difficult (i.e., will require time for you to hunt down solution and implement it)

+1 cross-referencing in LaTeX is a breath of fresh air in comparison to Word.

"Layout changes are difficult" is an advantage of LaTeX, not a disadvantage.

Could you elaborate a bit more on why this is an advantage?

Some layout changes are extremely easy in LaTeX, and I find it an advantage (switching between double spaced, figures and tables at end review format to nicely typeset two-column)

Also, hearing my colleages comment under their breath at Office2010, I beg to differ on the minimal learning curve...

Maybe what is meant here by minimal learning curve is that just about everyone can open word and start typing. Using e.g. Word effectively has a much steeper learning curve.

@JeffE - Spending time figuring out how to change the default margins, or how to allow plots to take up more than 80% of the page, or other details like that can be a royal pain in the keister.

@eykanal But...you're using the class the journal provided (i.e. revtex in my business) so you don't want to change the margins or column count. And if you're writing a book or other independent publication you'll be using memoir or a similar class where those things are clearly and copiously documented, right?

@eykanal: Having done my fair share of LaTeX hacking, I agree with you completely.  Which is why even I don't get distracted by it very often.  Also: \usepackage[margin=1in]{geometry} \def\topfraction{0.9}

Figure placement is a bear in LaTeX. Not so much in WYSIWIG editors.

Additional disadvantage of LaTeX: some of its core has not evolved in years. For example, web page citation formats are still not supported properly in BibTeX

@Suresh Figure placement is easy in LaTeX: the compiler does it for you. Forcing the figure placement is harder and can be a real bear, but I find that I generally don't need to mess with it.

I agree that "layout changes are diffucult" is an advantage. In order to set up some layout, you should have some experience. For example: Many people want to have the same margin on left and right pages and then print their document on double sided. Or they want the first pages in a chapter to look like the rest.
Normally, if some students are telling me that they want to change all those things, I give them some professional text book and let them find out what is done there.

@dmckee figure placement may be automatic, but it's often crappy, especially with two-column format.

"Collaborators unfamiliar with LaTeX will have difficulty reviewing your manuscripts" - disagree, everybody can open and annotate a PDF! I agree that collaborators may dislike this compared to Word, though, and complain that it makes things difficult, and this may cause friction. And it isn't quite as nice as Track Changes.

The zeal of (La)TeX afficionados never ceases to amaze me. The answers given here are quite balanced and rational, IMO, which is pretty unusual in this on-going debate.

Yes, most everybody can read a Word document. On the other hand, the people I know who even are aware that Word can be used to format larger documents, has ways of tweaking formats, manages crossreferences, and all what is required for "real work" can be counted with the fingers of one hand.

I am currently studying for a PhD (engineering, almost done) and I supervised some student projects (diploma thesis and so on). Therefore I experienced both,the typical Word and LaTeX workflow.
Most of the points are already mentioned in the very good other answers. I just want to add some general comments. Since I am not a geek I think that I can give roughly an average opinion.
The Typical Word User

Almost every student was complaining about mysterious behaviour like disappearing pictures or lost formatting.
In addition, it happened quite often that large documents get somehow corrupted and it wasn't possible to edit/open it again. Then the students had to fall back on one of their backups.
The larger the document the harder it is to keep the typography consistent. Because it is so easy to edit the text manually (this one bold, that one italic and so on) the students usually pay little attention to the systematic use of style sheets (don't know if that's the correct English term).
Dealing with complex mathematical expressions is painful.
Many of the settings are done using some menu entry and so it is very hard to document the settings or to make comments on how or why someone did something.
Only one out of 100 students knows that you can work with vector graphics (in this case EPS) in Word. So most of the figures are ugly.
In the last days of the thesis it is an advantage in Word that you can -- in the case of an emergency -- just draw anything everywhere in order to meet specific goals.
It is hard to reuse content in Word -- I mean reuse it that way, that a change at one instance affects all instances.
...

It is not important whether all this happened because of a unprofessional use of Word -- the point is, that it happens.
The Typical LaTeX User

You need a friend!: It is almost suicide to start using LaTeX on your own when you start writing your last and most important thesis at university. This can only work if you have a friend or colleague (like me) who can give you a template and a crash course.
Almost all students who decided to use LaTeX reported that they had fun using it! I think the main reason is that the documents look very professional without doing much.
In addition, students find it "cool" that the output is directly a PDF with hyperlinks and so on. Most of the normal WORD users don't create cool PDFs.
Students like the fact that they can easily input PDF files like datasheets to the appendix. This way they even appear in the table of content (TOC). I have never seen a Word document with a detailed TOC for the appendix. This is especially important in the field of engineering.
Using/creating bibliographies is not fun. But after they figure it out it works fine.
The concept of using a distribution like MiKTeX or TeXLive is new to most of the students and confusing at the beginning. In addition they sometimes can't distinguish between LaTeX itself and the LaTeX text editor (e. g. Texmaker). Therefore I made a video tutorial for that ;): http://www.youtube.com/watch?v=RL15I-6NQFQ

Very good answer. It is true that the WYSIWYG editors are getting better in separeting content and layout as Willie Wong pointed out. But I don't know many people using it.
Up to my experience, this is the normal workflow. But maybe the people had fun with LaTeX since only the brave ones tried. I know some people giving it up after a very short try.

Despite this post being "already" 1.5 years ago, it still holds so true. It kind of made me smile...

We built up a central BibTeX database (including all texts referenced, another file for papers written by us, another for theses, and so). Everybody used it and added to it, occasionally one of us went over new entries (version control!) and fixed/completed them.

As primary author I usually use LaTeX, most colleagues use word, so I (have to) use that when contributing to papers.
Advantage of LateX:

Mathematical equations were mentioned already.
More important for me is that pure-text formats work better with literate programming tools like Sweave/knitr (I do data analysis in R)
These tools also produce graphics and automatically put them into the paper
pure text formats work well with version control

I use latexdiff to produce versions with highlighted changes automatically
git diff --color-words is good for seeing changes and is not confused by changes in the line.

Lightweight in terms of computational resources for typing
Publishers have document classes that will format the text. Allows to produce nicely readable author's versions.
By loading few packages (or even only setting some option) you can switch back and forth to the ridiculously unreadable format the publisher demands.
Bibliography styles: changing the style allows to switch back and forth between e.g. references with title and linked doi and the journal's requested format without.

Disadvantages:

many coworkers don't use/know it
believe it or not, but even pdf files can be problematic wrt. printing/display.

Side Note:

Lyx provides WSIWYM on top of Latex.

Advantages of Word

Almost everyone has it

Disadvantages

Resource demanding
No/difficult literate programming (Openoffice works, though not as nicely as LaTeX)
Problems between versions
(Problems with merging versions which is supposed to work)

Literate programming and paper.
Here's an example. I didn't go the full length of literate programming for the whole article: the simulation in section 3 took some week on our server blade, so that was done separately and I just pulled in the result graphics. But I wrote section 4 in Sweave, so the calculated numers end up automatically in the text. A slightly modified .Rnw file of the calculations in section 4 (knitr version) is supplementary-code.Rnw in the sources.

(I just saw that I forgot to upload the .Rnw for the whole paper to arXiv, and it wouldn't let me do it when I just tried - I'll correct this, probably when I have the final volume/pages for the journal)
Why Sweave and knitr: I prepared the document in Sweave (and without any caching as two of the coauthors use R as well. So they automatically have Sweave. I wanted to keep the dependecies low. However it turned out that they did not wish to run it. Next paper will use only knitr, and cache longer calcluations.
It is a trade-off: typing in the numbers is faster than the lengthy Sweave/knitr code. But then you need to re-read the paper so carefully to make sure you have no typo somewhere in there, which takes a lot of time, too.

Could you expand more on the literate programming?

I second Paul's request. I would love to see an example of literate programming being useful in writing a scientific paper.

@WillieWong combining R and LaTeX seems to be the pinnacle of reproducible research. Creating the paper, including the statistical analyses, requires you to just rerun the scripts, i.e. a one step procedure. In practice I find it hard to implement, especially because some of my analyses take quite long. Take a look at knitr for a good integration of R and LaTeX.

A list of examples of reproducible analysis: http://stats.stackexchange.com/questions/1980/complete-substantive-examples-of-reproducible-research-using-r

@JeromyAnglim: thanks for the link. I wasn't aware of that list.

Re: pdf produced by LaTeX - I have found also that some documents aren't "searchable" or "copyable", but they tend to be older docs (ps2pdf?). In some very strange cases, you can copy and search, but the text doesn't correspond to what appears on the screen (strange character encodings).

@PaulHiemstra: I suggest saving the results of your analyses to a database. Then you won't have to run the analyses every time you compile your LaTeX document.

@Fuhrmanator: I suspect the PDF viewer has its part in that.

@O.R.Mapper Here's an example of a broken PDF. Try it with whatever viewer you can find: http://carbon.utsi.edu/downloads/JRobertson_MSER.pdf Read more at http://www.reddit.com/r/techsupport/comments/1ewdwz/

@Fuhrmanator: I cannot reproduce the issues described in the forum posting - when using full-text search on the PDF while displayed in the PDF viewer plugin of Firefox 31 on Windows (in general, a viewer that I dislike, due to some other issues such as lazy loading), the search for the does not fail as described in the forum, but correctly highlights occurrences of the word the (at least the first few of them, as far as I tried). Likewise, searching for ac like that correctly highlights that substring, e.g. in Abstract, then in characterisation, then in fraction etc.

@O.R.Mapper Interesting. I will check out that PDF Viewer.

The following is based on LaTeX and Friends.
Cons

Difficult to learn and use.  True, but it will save you time in the long run, even if you're writing a minor thesis.
Not WYSIWYG. True, but there are many IDEs. For example, TeXWorks, TeXMaker, MacTeX, LyX, ....
Little support for physical markup.  True, but this is a good thing.  It ensures your document style is consistent.  Also it saves time because fiddling with style will cost you time.
Using non-standard fonts is difficult.  This used to be true but nowadays installing new fonts is relatively easy.
No spell checking.  True, but some IDEs support it. Also you can spell-check at the command line level.
Too many packages.  Yes, it may be difficult to find the right package.  However, asking a question in TeX Stack Exchange or comp.text.tex  will quickly give you an answer.  Also you usually only need a few core packages, which you can package as a user-defined library.
LaTeX is for techies only. False, LaTeX is used in mathematics, computer science, physics, life sciences, humanities, ....
Encourages structured writing.  Some people don't like this. Others do.

Pros

Separation of style and content. LaTeX is a procedural markup language sitting on top of a typesetting engine. You make the purpose of your writing explicit by annotating (marking up) your writing. LaTeX uses the markup to typeset your writing in the right style.
Trust. In a recent TUGboat (Volume 33, Number 3, 2012) Boris Veytsman writes an interesting paper that shows that using Computer Modern (the default LaTeX font) increases the level of trust people have in written statements: it came second, closely following Baskerville, which came first. At the lower end of the scale of trustworthyness is Comic Sans. (Results based on results from Morris.)
Generation of plots and tables. LaTeX has packages that automate the generation of plots and tables. You provide the data and the packages do the typesetting. If done properly, this ensures that all plots and tables are typeset in the same consistent style.
Technical diagrams. LaTeX has packages that can generate technical diagrams such as trees, state transition machines, petri nets, and so on. Using these packages guarantees a consistent presentation.
High-quality typesetting and good automatic hyphenation. This inludes kerning, real small caps, common and non-common ligatures, glyph variants, .... LateX's hyphenation is second to none.
Many conferences and publishers accept LaTeX. This is useful because it guarantees your paper will comply with the conference's formatting guidelines.
Turing-complete programming language! This lets you compute things that you can then typeset (similar to a spreadsheet with input and output columns).
Write notes/book/presentation in same source file.  This is related to the previous item.  LaTeX can make decisions and this lets you write several output documents in one input document. For example you may have a presentation version and a notes version. You can share text for both versions and use some text for just one version.
LaTeX is highly configurable. For example, you can define your own book/paper style and package the settings as a library so you can use them over and over again.
You can translate LaTeX to html, ps, pdf, DocBook, ...
Automatic numbering of sectional units, figures, ... This guarantees consistency of the output document. In addition LaTeX provides a consistent and easy cross-referencing mechanism.
Excellent Bibliography support. LaTeX automates the typesetting of the citations and the generation of the bibliography/references.  It lets you control the style of both citations and references. The result is a perfect bibliography and consistent citations.
Very stable, free, and available on many platforms. Who doesn't want that?
Large and active, friendly, and helpful user-base. Ask a question in  TeX Stack Exchange or comp.text.tex and you usually get a detailed answer in minutes.
LaTeX has comments. So you can remember why/how something worked.
Can produce coffee stains on your papers.  So you have consistent coffee stains on your papers!
Most importantly: LaTeX is fun!

Coffee stains are definitely a must.

I would echo the pro about LaTeX having comments as a very useful tool. As a novice writer I find it helpful to organize my writing (even within paragraphs) by adding comments to say what the goal of that chunk is (e.g. Summarize main findings) or to include some raw results in comments next to the text summarizing them.
Of course you can get comments with WYSIWYG editors but I find the purpose is different (mainly collaboration and revisions) rather than notes to self.

@av1 It's a very useful feature indeed. If you like annotating your writing with comments, you may want to check out folds, which are supported by some editors.

I am a freelance writer, writing mostly articles and fiction, and I prefer LaTeX over Word for a few reasons:

I work much faster in Vim, which is perfect for editing LaTeX markup
I write in a modular fashion, so LaTeX's \input{} (command/markup/whatever) is indespensible.
I can convert LaTeX markup to any format I need, most of the time directly: pdfs, docs, html, epub, etc.
Word's graphical nature is too much overhead when I can simply open vim, type what I need, add a preamble, some markup and a style file, run the document through aspell and be done.

This site is mostly for Graduate Students and Academia, I do not  think this is a proper forum for these kind of answers, fiction writing is too different from scientific writing

@Leonpalafox yet in this case I think the answer is relevant.

@Leonpalafox Graduate students in English, or MFA students, will surely be surprised to know that they don't belong in Academia.

An additional advantage of LaTex that I haven't seen listed among the many answers here is that:
LaTex source files can be (fairly) easily generated by a script or other program.  In some research areas, you might be generating lots of data that needs to be put into tables or figures in your text.  In my case, I had a computer simulation that generated the data.  I programmed the simulation output to add a little bit of LaTex instructions here and there in the data and the output file then became part of my LaTex source document.  No cut-n-paste.  No danger of re-typing a value incorrectly.  If I found a bug in my simulation (hypothetically speaking, of course), then I can easily regenerate the data and associated markup very easily.

LaTeX

Open source free software. Even the FSF thinks so.
Stable: The current version of LaTeX is from 1994, the underlying program (TeX) is from 1982. You can easily process a document made with LaTeX 2.09 in 1987 with a modern TeX distribution on modern hardware
Runs on any modern operating system on any hardware

Word

Closed source expensive proprietary software (MS Word)
Unstable: The document format of Word is constantly changing. You will be hard pressed to open a document from say Word 2003 with a recent version; getting all your formatting from a Word 5.5 document (1991) will probably be impossible. ODF created by Open/Libre Office helps here.
Runs only on Windows and OSX (Word) or Linux (Open/Libre Office). Porting Open/Libre Office to a different operating system is a major undertaking.

I'm afraid these (well-know) facts don't address the academic side of the question. Noöne here wants to launch a (∞+1)th flamewar on this topic…

Open/Libre Office runs on Windows, Mac, Linux, FreeBSD, OpenBSD. What else do you need it for, a Commodore 64?

@F'x: Stability isn't an issue in academia?

@FedericoPoloni: I remember the effort of porting it to OpenBSD: It was massive and a major undertaking. Oh and for the other os - what about an iOS port?

@MartinSchröder good point - I don't own a tablet, so I didn't consider tablet OS's at all.

@MartinSchröder what I meant is no point in your answer is specific to academia…

@F'x: Stability is specific to academia, since works there can take years (e.g. thesis) and books can be updated for decades (e.g. tacop).

@MartinSchröder there are plenty non-academic writers who take years to write a book, and plenty technical books that are non-academic and yet updated for decades (dictionaries and standards, to give only two examples)…

I'll post my take on this, as a Word user who has oft pondered switching to LaTeX but has decided not to (but has collaborators who do):
Word:
Advantages

Universality. While Microsoft Office isn't 100% ubiquitous, I'm willing to say that very nearly everyone has the ability to modify Word or Word-like documents in some form. A Word file can by and large be sent under the assumption that the recipient will know what to do with it. I'd be similarly willing to bet that the installed base of any sort of TeX distribution is far lower.
Non-technical. There isn't much of a learning curve to Word, and there is a pretty steep one for LaTeX. I collaborate with a lot of non-technical colleagues, who will be writing or commenting on policy or clinical questions. Getting them to use Doodle to schedule a call is hard enough, I cannot imagine what LaTeX would be like. On the other hand, virtually everyone who can use LaTeX can also use word.
"Track Changes" is a decent reviewing tool, and may be considerably more intuitive than looking at diffs in a version tracker or something like that.
In some fields, Word will be the assumed-upon format for journal submissions. This is, of course, not universally true, but it's worth noting in the sometimes computation-heavy world of Stack Exchange that academia as a whole doesn't necessarily use LaTeX.

Disadvantages

Word. Is. Not. Layout. Software. Attempting to use it as such is an exercise in frustration.
Word definitely emphasizes text over mathematical notation. While it has been getting significantly better, and isn't actually an impediment in my work, for very equation-heavy documents, it will become tiresome.
Citation management requires a third party package of some sort - the one that is built-in is criminally poor.

LaTeX
Advantages

LaTeX is just better for math typesetting. Whether this is important or not is a question, but that LaTeX is better at it is something about which reasonable people can't so much disagree.
As text-based documents, LaTeX files play really nicely with version control software.
The overall layout tools available for LaTeX are vastly superior to Words, and much more amenable to templates, standard code, etc. You could write a script to automatically put in all the preambulatory info (affiliation, headings, etc.) for a LaTeX document. Doing that in Word would be...hard.

Disadvantages
As a disclaimer, some of these are fairly subjective.

Anything listed as one of Word's advantages. The biggest for me is the high probability that a collaborator will go "What am I supposed to do with this?" and we'll end up in Word anyway.
In my experience, compilation errors and the like definitely crop up when trying to pass LaTeX files between multiple authors.
Laying out an adequate LaTeX document is easy. Laying out a nice LaTeX file is hard. I often encounter a sense that "Once it's in LaTeX it's done", and while that's more true than it is for a Word document, it's a far cry from something that's professionally typeset.

I've seen my share of Word documents that misbehaved horribly. One particular case was a template to apply for internal monies here. The secretary who created it went to the trouble to add tables that calculated some of the data automatically (some percentages, summary of costs, and so). Infuriatingly, it worked only on her copy of Word; on other, exactly the same computer model, operating system, and so on, the tables just calculated gibberish. Take some old document, it will get repaginated (fun when you carefully tweaked the text so no page starts with an equation).

@vonbrand In my experience, it happens more with LaTeX documents than Word, but of course it can still happen.

LaTeX works the same everywhere, Errors crop up when packages aren't installed, or a part of the text is transplanted elsewhere. Laying out nice LaTeX is trivial (stick to the standard classes), laying out a complex, non-standard LaTeX document requires a professional (small wonder, typesetting is not trivial), but there are classes (memoir) and bundles (KOMA) that allow a non-specialist to tweak a lot.

@vonbrand I've had teams working together for years still end up sending early in the morning emails right before a deadline with errors. It may work that way in theory, but again, in my experience, it crops up a fair amount.

I've recently switched to LaTex whilst at university and the response has been great. I have written an number of reports regarding projects and tutors were happy to see somebody using the proper software.
I have found that with larger projects that it can be split up into sections and I'm currently writing a document that is split up into a number of chapters which is very easy to manage the document.
With regard to technical documentation such as tables, diagrams and equations it does require some learning but it is very useful indeed.
Another thing to note is that the document structure is kept consistent throughout, sections and chapters are correctly numbered as well as the references, footnotes and figures all being correctly numbered.
Also, use BibDesk as it helps out tremendously when using a number of citations.

+1, although what is proper of not is a point of debate.