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Why do sites that host papers not have a comments section for each paper?
Why do sites that host papers such as IEEE's not have a comments section for each paper? Sometimes there is something that needs to be added, corrected or clarified by the community but as far as I know there is no such a thing... or is there?

What could go wrong? First, what do you mean by community - anybody could add a comment? I'm sure nobody on the internet would get kicks out of defacing/trolling/harassing yet another website...

@JonCuster On this site everybody can comment and it's not that bad.

It's easy to imagine many things that can go wrong (starting with the huge overhead work related to building the forum infrastructure, because existing PHP-based or Wordpress-based solutions are inadequate for long-term archival), but it would be the most interesting to hear about what has actually been tried and did go wrong.

@FedericoPoloni Actually you need at least some amount of reputation (like 20 or 50) to comment. I don't recall if the association bonus counts towards this, but it does mean that someone completely unfamiliar with the SE network cannot comment.

@FedericoPoloni... On this site, if we did not have myriads of users flagging spam and abusive posts, it would soon be as useless as most other sites.

@TobiasKildetoft 50 points to comment, association bonus counts. But you can post questions and answers from a fresh new account, which is almost the same thing spam-wise.

@GEdgar So what? The publishers can do the same thing, and even pay some moderators. I think most authors would flag spam comments to their own papers anyway.

@JonCuster Not anybody, registered users usually have paid actual money to get access which cuts a big portion of random people logging in and writing trash. Also, researchers have critical thought and better judgment to decide what is important and what not.

And my time and critical thought will focus on a few papers and their relation to my work.

@FedericoPoloni but vaccines.stackexchange.com would be a cesspool in about 10 minutes flat.

Reason 1: Many publishers (still) see themselves simply as content providers. A reader goes to the publisher website, downloads a pdf and leaves. A publication is understood as a static (dead?) document, so post-publication activities are not encouraged technically.
Reason 2: The publisher website landscape is very fragmented. Even smaller scientific communities have to go to multiple publisher websites to get their content. So, a researcher would need multiple logins to add comments on the different websites. A high barrier even today.
Reason 3: A simple forum-like comment covers only a few of the post-publication discussion use cases. It is good for general opinions and corrections. Annotations, however, are much more targeted and also cover use cases like corrections of specific mistakes in formulas, paragraph-level questions and statements, discussions around data and images, proofreading, and referencing of specific parts of a document (example of direct linking at PaperHive: https://paperhive.org/documents/jKRG3MqMuj66/revisions/QOdeW6lxZMHk?a=s:Vjw91UM7br1A).
These are some of the reasons why we at PaperHive [Disclaimer: I'm one of PaperHive's founders] chose to build a system that is connected to publishers' websites but enables the communication on a separate cross-publisher platform entirely dedicated to reading and discussing. We have a small widget that informs readers on a publisher website of existing discussions (see example on a partner's website: https://www.growkudos.com/publications/10.1016%252Fj.neurobiolaging.2014.04.026) but the actual reading & annotation happens on PaperHive.
All public discussions are under the CC BY license and we follow the W3C open annotation standard (which is the foundation for interoperability and portability). We have an API for the export of annotations (documentation in progress) and have on our roadmap to archive the discussions at one of the two most-widely used systems in publishing (Portico or Clockss).

Thanks for chiming in! Seeing that there is a W3C annotation standard and that someone uses it makes me happy, and CC BY looks very good. Though I'm wondering why I often get an infinite loading screen when I click on the "referenced text" in a discussion. If you are pulling these documents from the publisher page in real time, you should probably build safeguards for the case the publisher page is down or changes its structure or the document gets re-scanned and the references lose their target.

On a deeper level, though, let me describe what to me is the most uncanny part of your site: It all relies heavily on an internet connection. Unless I have missed it, I cannot find an "download the whole discussion for a given paper as a PDF" (e.g., concatenate the paper with the discussion threads, and replace the yellow highlighter by some sort of endnote markers) option. But that becomes useful, once discussions become long and meaningful and begin containing their own research. Perhaps StackPrinter could be a good model here.

Either way, what you've built there looks like a great step forward! I'm looking forward to eventually referee papers on such a platform...

Minor thing: Is there a way to search for a given subject and sort by "how much discussion has been recently made about the paper"? That could significantly improve adoption, as it would automatically provide people with examples of usage relevant to their discipline (once such examples exist).

Seconding @darijgrinberg 's last comment.

Thank you for the comments, @darijgrinberg!

You have a point with the dependance on publisher's tech. However, changes in publishing are extremely slow. Html and text-matching will be one way to secure portability of comments.

"Download annotations" is on our roadmap. Thanks for the StackPrinter hint!

There are already researchers conducting peer review on arXiv papers within PaperHive. They review the papers privately and send the annotated documents to the editors of some journals. The open access publisher LangSci Press also has their proofreading and peer review on PaperHive

is this like Diigo?

There are a few third-party sites where you can do this. For instance, https://paperhive.org/ and https://scirate.com/. None of them has a large user base, at the moment. There used to be more (http://www.arxaliv.org/, https://selectedpapers.net/) but they seem to be down.
(Disclaimer: I am a friend and a former colleague of one of the founders of Paperhive.)

Does PaperHive support LaTeX/MathJax? How easy is it to export all discussions related to a given paper from PaperHive? (Or even view them all together, without having to click around a PDF.) What are the plans for long-term archival and availability? What is the copyright policy on comments?

@darijgrinberg I can answer only some of these questions: Paperhive supports Mathjax in comments; the comments are CC-BY licensed. For the other ones, I will point out this thread to the Paperhive people and hopefully they'll answer themselves.

Thanks for this! Such a site would be very useful, but I am wary of something that will fold in 5 years and leave behind a lot of non-migrable (for reasons of format or of licensing) resources. So far, many of the pioneering plants have withered and little has been left behind; if I hadn't archived my arXaliv comments, I'd have no idea where to find them now...

@darijgrinberg Answers by a Paperhive founder are in this other answer.

There are a couple issues with this that I've both seen and experienced:

It's probably not worth it, as few papers actually draw comments. Pubmed Commons, for example, means you can leave comments about a paper on it's Pubmed entry. I looked up some of my papers...there isn't a single comment. Not one. And while I'm not the most prominent researcher in the world, we are talking about a body of papers with 500+ citations. So...why bother with implementing this?
If you do get comments, you're vulnerable to things. For example, the anti-vaccination community launching a spam campaign. While you can restrict the comments to subscribers, what about open access journals? Crackpots with library memberships? Many of the same arguments that you should be able to comment apply to the public being able to comment. And that means moderation. Whose going to do that?
What are the obligations to commenters? Am I free to ignore them? Or, if J. Random asserts there's an error in my paper, do I have to address it. How much do I have to address it?

TL;DR: There's significant costs and not a lot of clear benefit, especially when there are ways to contact an author directly.

But that's the first reason I wanted to stress this issue: some papers might have errors, the rest of the world shouldn't suffer from those errors... or even worse... propagate the erroneous information onto another paper or use them to his/her advantage. If people notice something it should be pointed out and not hidden just because the author will have xyz problems.

@AnnaK. One of the problems though is that "Commenter Thinks There's an Error" and "There Is an Error" are not the same thing. What does the journal do if the author refuses to comment? Or the commenter goes on a string of nebulously goal-posting objections (see: every anti-vaccination argument ever). Or the author and the commenter disagree that the error is in fact an error? How long am I obligated to respond if indeed I need to respond at all? If there's an important error, that's what letters - either to the editor or the journal, are for.

Most of these problems are trivial (in my opinion). 1: Since these are comments, the author should not feel obligated to answer them. This is why conferences are: the real obligation to answer questions is there. The comment section should be something that people can comment and users to be able to see for years later. 2: Just a report button will do for people that disrespect the comment section, papers are meant to be read by grown ups not 5 yrs olds.  3: I'm sure journal and conference editors will be happy to receive tens of emails everyday for things posted decades ago (possibly).

@AnnaK. If I'm free to ignore it then whether or not there's an error is never really resolved. You've just added noise. As for the "report button", a report button needs someone on the other end to make the judgement over whether or not that's actionable. And again, if you just want to muse about a paper, there's already a mechanism for that in many journals.

Better do noise than let things slip silently.

@AnnaK. I'm not sure you'd say that if you were the person who had to deal with the noise. Also, again, if there's no authorial obligation to address the comments, odds are they're just these silent, useless things hanging out in the void. Blogs, journal letters, etc. are established mechanisms that have been used to address problems in papers before. What do you think is lacking in the existing methods? Just that they're not tagged to every single paper?


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Conference presenting: stick to initial paper submission or include recent improvements?
I submitted a paper for a conference. While the paper got submitted for publication in the proceedings, the feedback seemed quite negative. The main criticism was that the model I have designed uses too many simplifications.
I am giving a presentation at the conference in about a week and a half. Since I submitted the original paper I have achieved a significant amount, and have been able to improve my model and deal with a number of the simplifications.
My question is: for the presentation content, do I have to stick with the work that is going to be published, or can I also present some of the more interesting, newer work?
For reference, my field is engineering (renewable energy)

do I have to stick with the work that is going to be published, or can I also present some of the more interesting, newer work?

Absolutely present the improved model.
Conference submissions photograph the state of the work at the time of the submission. But from the submission deadline to the conference, many months can pass and usually people continue to work on their projects. Frequently, by the time of the conference, new results have been obtained, and these surely deserve to be presented.

In fact, some conferences explicitly state that they encourage speakers to present new developments and results that were obtained after their abstract/paper was submitted.

and if you didn't it's possible a lot of feedback would be about doing... what you've already done and thus would not be helpful or constructive.  Comments on the improved model will be more valuable and might otherwise be missed if the focus is the (resolved) issues.

Nonetheless, the OP should mention that what he is presenting is an improved version compared to the proceedings, otherwise people actually reading the proceedings version (the most interested people) might get lost.

It depends on the conference and how strict the rules are. My approach would be to use a quarter of the poster space to describe how you have made progress on the model, and how you are planning to further improve it. The rest would describe the model you have submitted.

I find it very odd to assume that the OP is presenting a poster since no mention was made of this.

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What questions to expect from Skype chat with potential supervisor for a Masters in Neuroscience?
I am applying to a Canadian University for a Master in Neuroscience. I have contacted a professor and asked for a place at his laboratory even though he only accepts PhD and post-doctorate students. However, he said that he accepted me as his student but wanted to have a skype meeting for us to get to know each other.
I am a medical doctor and his area of expertise is more philosophy-oriented. I am not an expert in this area. My questions are:

Will I be expected to have a well established research proposal even though I am a master student?
Are master students expected to have solid knowledge in the supervisor area even though they have a very different background?
What are some questions a master student can expect from a skype meeting with his/her possible advisor?

Related: How to approach potential PhD advisors and How do you prepare for a meeting with a Masters thesis advisor

Ok, my interview has already taken place. In case anyone has the same question, it was a very relaxed interview ( even though I was obviously very stressed).
The researcher asked me why I chose to contact him, what I wanted to focus on ( based on his previous projects), when I would start, how I was going to finance my studies and how long would I be willing to stay at his laboratory, etc.
I wasn't asked about neurobiology, physiology or any other scientific knowledge.

Very nice (upvoted both Q and A). It certainly will be useful for others. Good luck with your studies. I don't think medical doctors very often decide to switch from medical practice to medical research. Would you care to share your motivation, if possible? I'm just curious about transitions within and to/from academia and their motivational and other factors.

My motivation is mainly that I had so many unanswered questions on what the cognitive processes that underlie our everyday are. Also, during my medical practice I realized I was following guidelines in a sort of recipe-like way and I wanted a different kind of challenge. Hope it is helpful!

It is indeed helpful. Thank you for the clarification.

What you will be asked obviously depends a lot on the person(s) involved, whatever data they already have on you, how many applicants they have, and a lot of other details.

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How to present preprints that are not publicly accessible on a CV for math academic job search?
In the context of preparing a CV for a math academic job search
Is it advisable to list preprints which are not yet accessible to the wide public in the CV?
If so, should it be in a rubric of its own (i.e. separate from "research publications"), or can I put it in the same rubric but write something like "(draft, available upon request)" or "(in preparation)", depending on its actual status, to its side?

Your two questions are somewhat addressed in How “submitted”, “to appear”, “accepted” papers are evaluated in a CV?, and How to present projects that will soon be published on CV?.

If you have finished preprints, is there something stopping you from putting them on ArXiv so they are accessible to the wide public?

@SeanEnglish Well, to abstractize from my specific situation, there can be some variants, like: 1) the preprint is mathematically finished, but not stylistically, or some small but certainly attainable details are missing 2) the preprint is mathematically finished up to some point, but there might be possible additions which will make it much better, and which are not yet clear, so the author would like to wait with the uploading.

Oh okay. Personally I would call those "works in progress" rather than "preprints". Preprint to me suggests a finished document just waiting to be printed (or torn apart by a referee...). I listed one paper in progress when I did a (successful) job hunt, but I had a few more in progress that I didn't list because I don't think they count for much, and I didn't want people wondering why I have so many unfinished projects.

If the paper has been submitted, then of course you can list it as "submitted", whether it's public or not.
Otherwise, I think that about all you can do is to say "in preparation", but this won't really have much impact.  My impression is that "in preparation" means about as much to a search committee as "I had this idea for a paper", i.e. practically nothing.  They aren't really likely to believe a candidate's estimate that the paper is "99% done", since it's obviously self-serving.  And anyway, the last 1% is often where you discover a critical gap that takes months to fix, or can't be fixed at all.
If the paper really is done or nearly done, your best bet is to work hard and try to get it submitted or posted publicly (preferably both) before you send in your job applications.
If you can't get to that point, then the next best thing is to make sure that at least one of your recommendation writers is familiar with the project.  (If you have co-authors, ask one of them to write you a letter.)  They can write about how awesome it is and assure the committee that it really is practically done.  In this case you still say "in preparation" on the CV, but you have some third-party backup.

I hate that last 1% so much.

I second Nate Eldridge’s excellent answer, and in particular the opinion that “in preparation” means nothing and will be ignored.
“Submitted” is okay to write if true, but also doesn’t mean much if the paper can’t be viewed by the person reading your CV.
“Available upon request” is marginally better than “in preparation”, as it suggests you are willing to at least consider sharing the draft on the off-chance that someone will ask for it, but given that you’re putting the burden on people to contact you to ask for the paper when they may not feel comfortable doing that (or don’t have the time to start running after job candidates to ask them for materials that most other job candidates have already provided), is also not particularly helpful.
The best and most credible way, and one might say the only credible way, to claim a private preprint would be to include in the CV a private link (google docs, Dropbox, personal web site etc) to download the paper. Personally I would heavily discount any mention of a draft that doesn’t allow me some easy mechanism to view it. It’s nothing personal against you - just cumulative life experience that taught me that such claims often amount to nothing more than hot air.
Good luck with the job search!

You are a mathematician. Maybe I am overstating this a bit, but you should have no preprints that are not publicly available.

If it's accepted, it's on the CV and available, at least for those having subscription, see also below.
Before it's sent to the peer review, you upload it to arXiv, hence it's available (but not yet peer-reviewed). It probably deserves an own section in the CV, but it's there.
If the paper is in works yet, you do not upload it to arXiv yet, but also don't mention in as a paper on your CV.

The side benefit of this approach is that accepted papers are also available on the arXiv for anyone. And you can reference your submitted but not-yet-accepted papers in your next work immediately.
In most cases, you are allowed to update the arXiv version to the post-review revision state. You are not allowed to publish the final journal PDF on the arXiv, but who cares. For this, you need to check with the journal.
Even if not revised, the initial state of the paper is available to everyone, which increases visibility.

Just to play devil's advocate: Is "you should have no preprints that are not publicly available" necessarily true in all subfields of mathematics, including more applied ones where one might even publish in engineering journals?

So, I personally, had issues in other fields where this is not true. But from what I gather, more or less all of the mathematics and half of computer science is like this. But beware, "all generalisations are wrong".

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What to do when a thesis adviser refuses to recommend me?
After I completed my PhD program, during which I published one refereed paper, I applied for several academic positions.
For a while, my two main thesis advisers agreed to write letters of recommendation, but after a few couple of years, one of them told me he would no longer recommend me because I had not published enough. He even admitted that it was not his job to judge my publication record -- potential employers could do that -- but until I published again, he wouldn't recommend me.
I do admit that I should have published more during my PhD program, but I was always under the impression that my publishing would begin after I had got a relevant job. During the period between graduation and being refused a recommendation, I'd been a consultant, a college teacher and unemployed. I could have published on my own but, after the delay, I felt hindered by being unemployed and rather "burned out" after the thesis writing process. Catch-22? Even more ironic is the fact that I had asked my thesis advisers if I could submit my thesis in the form of a series of published papers (this was allowed under the rules), instead of as an unpublished monograph, and both said no!
Don't thesis advisers have a duty to both encourage candidates to publish and to recommend them for academic positions? At the same time, is it right that universities expect job applicants to already have publications before they arrive? What could I have done, other than publish as an independent after the fact? It is hard not to feel very bitter about the whole PhD process.
Addendum
Since it was not yet listed, I add How to handle not having my PhD advisor as a reference? is a related question.

Even more ironic is the fact that I had asked my thesis advisers if I could submit my thesis in the form of a series of published papers (this was allowed under the rules), instead of as an unpublished monograph, and both said no — did they motivate the negative answer at all?

@gerrit What do you mean by "motivate"? Don't you mean "justify"? I don't remember what/if any justification was given.

@BenCrowell The jobs were at institutions that required publications, i thought that was clear. I was successful getting a (1 yr) contract teaching at community college, i thought that was clear. No, i cannot force someone to recommend me -- but said person changed from writing letters to not writing them.

@user9957 I probably just mean justify.  I apologise, English is not my native language.

This is a tricky situation, and it's hard to interpret it without more information.  Thesis advisors certainly have an obligation to help their former students within reason and to recommend them for appropriate positions.  An advisor who gives up too quickly on a student is an unsupportive jerk at best (and it's easy to think of much worse descriptions).  On the other hand, nobody has an obligation to recommend a candidate they cannot honestly support.  Telling someone that is really awkward, especially when it's their own student, but the alternatives are writing a dishonest letter or writing a letter that undermines the candidate's chances, neither of which is any better.
Based on what you've written, there's no way of telling whether your advisor is a jerk or the two of you are just caught in an awkward situation.  I'd recommend asking your advisor some key questions:

Are there other positions you could apply for that might be a better fit for your background and accomplishments so far?
Based on your unpublished work, how could you prepare a good paper as quickly and efficiently as possible?

Hopefully you'll get encouraging and useful answers.  If you and your advisor can work out a plan that satisfies both of you, then that's great.  If not, you may have to give up on your advisor and apply with letters from other people.  That's far from ideal (the first thing everyone will ask is why your advisor didn't write a letter), but it can work if you get strong enough letters.
Of course publishing would help with getting strong letters.  Ultimately, I'd bet that publishing another paper or two is in your best interests, regardless of the situation with your advisor.  I can understand that it's upsetting to feel forced into publishing on your own, with no job in your field and no guarantee of getting one in the future.  However, it's probably a worthwhile investment of your time, and it's a valuable contribution to the academic community in any case (so regardless of what happens, it's something you can be proud of).

Regarding (2), the advisor ought to support this since they get co-authorship. It sounds like a good way to bring them back onto your side...

@mankoff Advisors can get co-authorship but that's up to the individuals involved. But let's not argue over that -- it is surely debated at length elsewhere :-)

Most who knew the person would approve of the epitaph "an unsupportive jerk, at best" and usually do think of worse ;-)

@user9957: That would be a truly mean epitaph. (You probably meant to write "epithet", but this is actually quite funny. Sorry about the necromancy.)

Don't thesis advisers have a duty to both encourage candidates to publish...

Many Universities prefer, or require, that a thesis be in the form of an expository monograph, which is absolutely different to several papers stapled together. If that is the case at your University, don't interpret your supervisor's adherence to this as discouraging you to publish.

...and to recommend them for academic positions?

A thesis adviser does not have an obligation to recommend a student for a position. Arguably they have an obligation to write a reference letter, but that letter should contain the adviser's honest and confidential opinion of your suitability for the job.
I would encourage you to still try to publish, as good references from your thesis supervisors are a huge help if that will win them over. If you publish your thesis results years later, this well help show that you are serious about getting back in the game.
You will need to prove that you are an excellent researcher to get an academic job. If you cannot get strong letters from your supervisory faculty, good publications become even more necessary.

When I said "this was allowed under the rules" I meant it.

@user9957 Hence why I also said "prefer". In some fields, a compilation thesis is viewed as a significantly weaker piece of work than a coherent monograph. "Allowed, but frowned upon" could be applicable to your case, perhaps. Adhering to your supervisor's wishes will likely have had positive consequences with regards to the overall quality of the documentation of your research.

In some fields, a compilation thesis is viewed as a significantly weaker piece of work than a coherent monograph. — why?

It can be much more difficult to compile a collection of publications into a publication thesis that is as expository or coherent as a monograph. For a compilation thesis, you should be able to regularly publish your results throughout the research period. If your results are expected to "all come together at the end", a monograph is the logical choice.

Do the rules say that this unplublished monograph needs to stay as just an unpublished monograph? My experience was that my thesis had to ba one coherent whole, but the material within it is published as several distinct papers. It takes some work to change between the two different styles, but leaving your thesis unpublished (if it's good enough to be and you want to stay in research) seems odd.

@JessicaB Is this a comment for the OP? I'm not sure the comment is relevant to my answer. You should leave it as a comment to the original question. Be aware that the question was asked last year by an inactive user, so you're not likely to get a response to any further comments.

I felt my comment fitted better with the discussion on this answer. I noticed the age just after posting. If the question is ever of use to someone again, maybe my comment will be too.

Recommendations are a method for discrimination
The only reason why recommendations exist is to discriminate potential candidates - to have some information that is correlated with the candidate being better or worse. If everyone gets a good recommendation, or even a recommendation as such, then the whole process would be useless, so everyone getting recommended is definitely not a reasonable goal. If an advisor sincerely believes that a candidate is weak, then the only ethical action is to give a clearly weak recommendation or no recommendation at all.
What to do if you don't get good recommendations

Become better - identify your weak spots and fix them. It depends on the field, but 1 paper during PhD and 0 papers in a few years after that sounds like a strong indicator that the candidate isn't doing solid independent research and thus can't be recommended. This can be fixed in the obvious way by doing such research.
Communicate your good things - if you have done solid work, then it needs to be communicated and shown in order to be appreciated. If you've done anything useful and worthwile, then you should get that published. This, coincidentally, seems to be exactly what the advisor suggested.

Demanding publication record in order to write a recommendation letter has no point at all to me.
Let us give an extreme example: someone publishes in Cell by his/her third year in graduate school and publishes again in Nature when he/she finishes the graduate program. This guy will not need a recommendation letter at all.
On the other hand, imagine a hard-working fellow who is acknowledgeable, knows the field in depth and is good at designing experiments, but got unlucky because the biology of his/her hypothesis was not what he/she, neither the supervisor, were expecting and, because of that, did not publish in a high grade journal or did not publish in a fast pace. This fellow is the guy who needs someone to state his/her qualities and to be vouched for. The recommendation letter is redundant for people with high grade publications, whereas it is usually essential for people without them.

No papers => No research. If you cannot publish on your own, you did not deserve a PhD in the first place. Postdocs are for helping others (graduate students) to publish. How can you help others, if you cannot do it yourself?

That a thesis advisor refuses to recommend a former student exposes the underlying tensions inherent during the supervisory process, or differences in what constitutes the core research question. The tensions are not exposed until after the student graduates. In my case, my supervisor used me as an "unpaid research assistant for three years" and sent my twenty texts to translate from a Southeast Asian language to English without even acknowledging my contribution to the research. He even stymied my PhD thesis submission by saying that my progress was marginal, even though I had finished 84% of the thesis six months before submission. I later realised that my supervisor was stymying my attempts to establish my credentials as a TA, soon after I would submit my thesis. He kept egging me to go back to India (he is incidentally Australian) and my thesis was undertaken in Australia.
Three weeks before I graduated my supervisor told me not to keep my hopes too high in the job market. I smelt that something was fishy and requested him to write a general letter of recommendation. My hair stood still on both ends when he commented adversely ion my social skills. I then decided not to solicit letters of recommendation from my primary supervisor. I instead, request letters from academics who are well-disposed to me. Of course, my supervisor's adversarial stance has affected my fortunes so far but I will never give up.

This does not answer the question, it simply tells a related story. Can you edit this to provide some more specific details relevant to the question?


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How to work efficiently under loose supervision during graduate studies?
I work in a very cross-disciplinary field, which has caused me some headache* over the past couple of years, partly due to the fact that my supervisor isn't very knowledgeable regarding the day to day (technical) details of my projects. He typically leaves any mathematical, or CS, aspect of the projects to me to figure out, and provides guidance when I have questions regarding the biology or biochemistry, as those are his fields of expertise.
From what I hear, he's similarly loose in supervision even with the other grad students who are less cross-disciplinary and more aligned with his expertise. While I see the point in the supervisor providing the freedom to the grad student to develop as he/she likes, in my experience it can be troubling at times, allow me to explain:
I often have extensive periods where I don't have concrete goals to work with, but only vague ideas. Similarly, since I don't get a lot of technical guidance there are often weeks-long periods where I don't "produce" anything but instead trying to dig information out on publications, CS blogs or StackOverflow, in order to solve a problem I encounter.
It's at times like these my daily concerns (stuff usually unrelated to work) take precedence over what I am actually trying to figure out. I find myself browsing for gadgets, or looking over my savings or reading the news etc. I have no illusions that this amounts to procrastination no matter how you look at it. Since I don't really need to report anything to my supervisor on a regular basis, these periods can be extensive which often leads to frustration. And having realised this, I would like to be more productive even when I am stuck at my project, hopefully minimise the time it takes until I come up with a solution to whatever it is that's hindering progress.
So my question boils down to: how can I make sure I work efficiently, i.e. I don't get distracted or succumb to procrastination, when I am stuck and only get very loose supervision?

* See relevant questions:

Is it possible to measure/evaluate one's progress or development in quantitative terms?
Ways of developing non-core skills during PhD studies?

Hehe, same here. Sometimes it's nice to have a lot of rope (at least for me), but it is also easy to hang your self;)

in this very battle, i lost ... ;)

http://zenhabits.net/procrastination/

This is a pithy refrain, but you always need to report something to your supervisor regularly! Even if it's 'I haven't anything to report'. See what he says to that :) Keep communicating. These folk have lots of experience.

I think the more general form of the question is: (a) what do I need from my supervisor and (b) if my supervisor cannot/will not provide this, then what can I do?
Here's a few things I think supervisors are most important for early on in graduate studies:
Discipline and Motivation
So you need to put in long hours to succeed in graduate studies and oftentimes you need to work "blind": you need to work on things you don't know will succeed or not, or where you have no fixed goal in mind. Discipline can thus be a major issue for any relatively normal human being. Supervisors are supposed to track your progress on a regular basis and ensure you are putting in the required levels of effort, to encourage with a carrot and to use the stick if necessary.
If your supervisor is not tracking your progress and setting goals for you, then you need to take your own discipline into your own hands. The simplest method is to set your own goals with deadlines, focusing on achieving one thing at a time. Make TODO lists that follow a rough plan you have in mind. If a task is too broad, it will never get done: each task should be small enough and phrased in such a way that you know how it can be achieved (even if the task is just "problem solve X for one hour").
Assign yourself regular hours to work. If procrastination is a problem, just start. Starting is the hardest part so unplug yourself from whatever you were doing, minimise the potential for distraction as much as possible, take a deep breath and start. It's that simple.
Experience
It is not enough to work hard, but you need to work smart. Inexperienced students often tend to invest more effort into unimportant minor details that they feel they can control, rather than important details where the outcome or process is uncertain. The job of the supervisor should be to provide context on the relative importance of various tasks, to stop students from getting bogged down in minor details and to keep the bigger picture in mind.
Experience comes into play in other areas. For example, if you're starting out in publishing, or trying to publish to a venue you haven't before, experience is crucial so as to know what form the paper should take, what sort of narrative is accepted, what sort of "boxes" have to be ticked.
There is no replacement for experience. However, you can find experience elsewhere than your supervisor. Are there more senior students or PostDocs you can collaborate with? Maybe there's a group outside of your institute you can collaborate with remotely? Working with other people (i.e., not having a monogamous relationship with your supervisor) is an excellent way to quickly level up your own experience and gain new perspectives!
Technical Expertise
Your supervisor is also supposed to apply his/her technical expertise to your supervision, particularly in the early days. But if they do not provide you sufficient time and effort in this regard, or if their own technical expertise does not cover your interests, or as you progress into more detail on your PhD, you will need to find sources of expertise elsewhere.
Again, talk with other people. Try to seek out people with the skills that you require and try to develop a mutually beneficial working relationship with them (i.e., don't expect them to help you out of the goodness of their hearts). Perhaps you could even find a co-supervisor or a "mentor" who can be credited on a thesis?
The Web is also your friend. When I was a graduate student, I learned far more from playing around and trying things and from reading (on the Web) than from anything my supervisors (or lecturers) taught me. One of the most important lessons from graduate studies is "independent study" ... learning how to learn. When you do a PhD you are supposed to be the world's leading expert on your chosen topic. The only way this can happen is if you develop your own technical expertise in your area beyond that of your supervisor and your other colleagues.
Funding
Presumably if you already have a supervisor then you have a fixed source of funding. However, you may need additional funding if you go over length or funding for conference travel, etc. This can be very difficult for graduate students to get involved in.
However, there are often calls that are aimed at students and require minimal input from a supervisor. These include student travel grants for conferences, governmental scholarships, prizes for submitted work, etc. Furthermore, other senior researchers will often have funds they can provide for part-time contributions; talk to people if you are stuck.
Summary
I think some of the most important lessons that have to be learned during graduate studies are:

How to discipline and motivate yourself and organise your own work
Understand the nature of research itself, the broader research community and how your work will be viewed by them
How to find, initiate and follow through on fruitful collaborations with other researchers and research groups
How to find your own sources of funding

The main goal of graduate studies is to gradually reduce your dependence on your supervisor until, by the end of your PhD, you don't need them any more. A good supervisor should understand and support you in this, particularly early on, but if this isn't working out, then you need to learn how to rely on yourself more (or find another (co-)supervisor).

I can't provide a definitive solution, but I can offer an example that works for me in periods when I'm feeling distracted but need to get things done. During such periods, I take advantage of what's known as the Pomodoro technique. The basic idea of this technique is that you should work in blocks of 20- to 25-minutes that are devoted to a single task: reading a paper, or writing a piece of code, or whatever else the task is to be. At the end of one such block (called a "Pomodoro"), you take a short 5-minute break, then begin a new unit. After four units, you take a longer break.
Other ways to help do this are to "block out" other distractions: use full-screen modes that avoid distractions, warning messages, and so on. Turn off the beeps and signals on your mobile phone (except for appointment alerts!). Suppress the "new mail" sounds and other warnings on your computer.
The other challenge is of course figuring out what to do in the blocks. That of course is a little trickier, but requires planning on your part. You should be thinking about this on a fairly regular basis (the frequency can vary, but at least every few weeks). Figure out what you've done recently, and what you need to work on next. Then, get it done!

For the specific case of being stuck on a particular bit, it depends a lot on the nature of the problem. If the block is a structural problem (equipment not working, etc.), then you have to wait for it to be resolved and work on other parts of your project in the meanwhile. However, if the issue is that you need to figure something out, then that really depends on how you solve problems best. Some people do so by working on completely different topics for a while, letting the problem "work itself out" in the subconscious. Other people attack it head on. Sometimes it's helpful to think about the problem in a different way: what happens if you start at the "solution" you want to reach, and work your way backwards? What are the consequences of continuing your current method of solution? Does it get you somewhere you can work from? Are there related problems in other parts of your discipline, or in other disciplines? How did other people try to resolve them? Will that work in your circumstances?

Thanks for a nice answer, I will try out the Pomodoro concept. I do think, however, that this answer focuses on general distractions, do you have any additions specifically considering a situation where one is stuck with a conceptual bit of the project and does not get helpful guidance?

I signed up just so I could answer this question ;-)
I recently found myself in a similar position at a new job. Not research, but still goal oriented with lots of investigation needing to be done.
It sounds like you're running into a problem that I still have to deal with: mistaking goals for "that other thing I need to do." For me, it was easy to forget that investigating how a particular thing worked, including research on StackExchange etc. WAS progress. That WAS a thing that needed to be done, and as such it should be on your to-do list. It's easy to (as an over simplification) have a to-do list that reads "finish research project." And then be overwhelmed by all the "other" things that have to be done in order to accomplish that goal. For me, my to-do list at one point consisted of "automate all 37 regression tests," and then I got frustrated with how much time I was wasting just figuring out how the automation process worked.
The reality was, I needed a line item for "figure out how to RUN automatic regression tests," followed by a line item for "figure out what components are needed to fully define a regression test," etc. Each of those things ended up needing to be broken down further, as well.
It's easy to think that you're not making progress, but that's probably just because it's not on your to-do list, when it should be.
EDIT: Then, if your to-do list is sufficiently granular, it will tell you "you're goofing off, not getting stuff done" ...and then you have to listen to it ;-)

+1 for the concrete example on how to subdivide tasks :)

And I signed up to start upvoting (including this one).

Congratulations, you have just been promoted to supervisor, you have to supervise a PhD student, set him some goals, check he doesn't procrastinate, push him to do his best, find venues to publish, topics to research, write papers to publish, etc.
This PhD student is you, and since you are not very experienced on research I can guess you both will have a somewhat hard time and probably the results will not be very astounding (having a good background helps to choose topics better). But if you both work hard I'm sure you both will learn a lot, and that's what students are for, aren't they?
On the good side of things, your new supervisor is 100% devoted to you, he watches you procrastinate, eat, sleep (kind of) and in every situation, even while in the shower. Very few people get that kind of attention.
Good luck.

Your sarcasm is duly noted, and even if I do deserve that, how exactly does this answer the question?

Who says this is sarcasm? This is what I did, my experience, worded in a fancy way. You procrastinate because you feel you need help and you wait for that help when, however (IMHO) it would be much better for you to simply keep moving even if it is at random. If you do something right then good for you, if it is wrong then you got a bunch of lessons there. Doing anything is always better than doing nothing.

There is no sarcasm in this answer.

as it stands I read this text as it's implying that I should stop whining about supervision and that it is somehow my own problem. If this answer does not have any sarcasm in it (as @JeffE suggests), then I suppose a clarification is in order, cus I am not sure what the point is. Following a clarification I am more than happy to change my vote on this answer.

Trylks: the guy who asked the question said this is sarcasm. I dunno; I'd say that's cause enough for concern about your wording. If nothing else, the first word of your answer doesn't come across especially sincere...Yet @JeffE wouldn't call that sarcasm I guess? Maybe we're all taking some of the explicit content too literally and some implicit "content" too seriously, but clarification always helps in that regard...

Clarification tends to infinite, so we all must choose a point to stop. I guess I can summarize it like this: If you see opportunities to grow and evolve where other people see difficulties and challenges, if you embrace these opportunities and don't run away from them, then the chances are you will grow and evolve. Procrastinating on the other hand only leads to failure, being crushed by these challenges, wasting your time, which is the most valuable resource you have in this world. I continue in the next comment.

It's not about whether it is your problem or someone else's problem. That kind of thinking is not constructive nor helpful. You can see a car that is running too fast coming towards you, the driver may not be paying attention to the road. You can decide to cross the road anyway, and you may die. Obviously it is the problem of the driver, he is who was driving in a wrong way, he may go to prison, but you may go to the graveyard. I would avoid that kind of thoughts, I would not label the situation as "someone's problem", it's a situation that you don't like, what can you do about it?

Understanding this requires a change of perspective. You can choose to change your perspective or you can keep reading my words from your current perspective. In either case this is irrelevant when compared with the "car". BTW: you can't change your vote. We could also discuss whether my answer is clear now and who's problem it is ;P

@Trylks if you added your last three comments to the answer (by editing your answer) then I can actually change my vote, and it would also clarify what you meant with your reply. At any rate, thanks for your two cents on the subject.

@posdef and Trylks, check out: Last clear chance

Here is what I did to get through my research.

First you need to set a complete project time line, even if you feel it is not accurate, from the first day you start to the last day you finish. You list all the major parts of your research, when you plan to begin working on each section, and when you plan to complete them.
Find people (other faculty) that can help you on the predominant topics of your research. Seems like you may have two: Tech, and Biology. I had three on my research: Math, Distributed Computing, and Literature/General CS. I told each professor what area of my research I wanted focus from them on. They did not touch any parts of my research I did not ask them to focus on... it worked out rather well I am happy to say.
Meet with each of them. When you meet with them to discuss your research, ask them either (1) what needs improvement, or (2) how to solve your current issue.
Don't leave their office until you set a time up to meet with them again about what you just discussed, to present your results or status. No more than two weeks ahead! And follow up with them in one week via e-mail to tell them your status... this also keeps them on the ball in helping you if they have some things to look at (like reading your research).
Put the data from #3 and #4 into a diary, and include how it meets your time line from #1. Modify your time line as necessary. Send out a regular update report to your committee and other contributing professors with all this information, plus a copy of your current research as Draft (version your drafts). Meet with your committee 2 to 3 times per semester (Beginning, middle, ending).
Meet with your Supervisor after every report you send out and ask him how you are doing. May only take 10-15 minutes during his office hours. Schedule follow-ups if your supervisor finds red flags. He has all the data now to make a determination on how you are doing.

Doing this kept me on the ball every day. I kept setting obligations with professors, and met them. I sent out reports regularly for their review to keep me accountable.

This sounds nice in theory, but surely the professors you are talking to are only useful if they are paying attention, and my experience is that it is hard to make academics pay attention unless they think they will get a paper or money out of it, and sometimes not even then. How did you manage it?

Well, actually.. the 600 character version is the expert Professor who was to be my supervisor left. All of the other professors said my research was too complicated for them to have time to dedicate to me. The one that accepted asked I work with a team of other professors I was to line up. Soon after, my supervisor became the Graduate Studies advisor and had extremely limited time to give me. I was expected to follow through on my written plan without supervision. The other professors, especially the Math professor, were already over-busy with obligations. They all worked with me after hours.

Sounds like the people concerned were quite helpful. Glad it worked out. Did they provide useful feedback, or were they just a mechanism to make you stick to a work schedule? In my experience, it is rare for people outside the speciality to really have a good idea what is going on, and they usually don't have time to devote to understanding the issues. So as a result, one is generally on ones own with the details of the problem.

I also want to add that the Math professor spent the most time (3x more than the others) on my CS research. He was not on my committee, and declined to be named on my research. He received only some kind of academic merit points. He stayed late with me, and we had extended e-mail conversations, many times. He was extremely nice. Another professor who was on my committee continues to help me with the continuation of my research post-graduate. My degree is from Western Illinois University. @Faheem, maybe you're right in regards to major research universities - I don't know.

@Faheem, you are right about being on one's own. I believe the committee is only there to help you stay on the road before you, not to drive. You are in the driver's seat, and also have to decide the travel path you will take on your own. The professors I worked with were all very helpful. They gave me a lot of good ideas. They asked lots of questions, and gave lots of feedback. They also made quite a few corrections to keep me from going off the road, especially the math professor. But I had to be proactive. They did not come after me, I went after them for course corrections.

Glad to know that your professors helped you out. They sound like they were good to you. I agree with your statement that you are "in the driver's seat, and also have to decide the travel path you will take on your own". That's a good summary of the process of doing research. :-) It is also worth noting that you don't necessarily find the best mentors at major research universities. The people there may just be too busy and/or important to pay attention. In any case, it sounds like you did Ok.

This began as a comment, switched to an answer, and just kept getting longer, so I'm gonna have to split it into sections...
Reframing the problem
I disagree that it's "procrastination no matter how you look at it," and I wonder how many ways you've actually tried looking at it. I say this somewhat confrontationally, but very sympathetically, as I've struggled with the sense that I'm just procrastinating throughout my free time in higher education, and ultimately rejected it. There's a lot more to life than work; this is easy to forget in grad school, and there's a lot of pressure to do so. Ask yourself whether you care about the things you spend your time on for other reasons you haven't fully acknowledged, or whether you're judging those pursuits as wasteful by someone else's value system, not your own. I see from your other questions that you have struggled (as I have) with the sense that other people judge success by the wrong criteria, and ignore opportunities for lateral growth if it doesn't follow their narrowly defined path to [_insert_short-term_work_goal_here_].
If you sincerely think those other concerns of yours aren't valuable, ask yourself if you could stand to work instead every time you notice yourself switching your focus over to one of those concerns. If you can't, you may find that there is some necessity to the (non-work) concern at hand, and may want to reevaluate it again at that point while you're in the moment. If you still feel there's no value to it, ask yourself whether you are just looking for something else (anything, really) to do instead of working. Ask yourself if you don't want to work on some level, and if so, why that might be so.
Given your situation (which was also my situation at times, in ways), you may be finding yourself more free from extrinsic motivation (pressure, expectations, "or-else" negative consequences, and so on) than you have been for much of your academic career. The transition from inflexible, specific, structured deadlines (which probably begin in middle school and carry all the way through the first year or two of a Master's program) to a more diffuse sense of partly internalized pressure and guilt for not being a more diligent workaholic is a subtle transition that occurs most dramatically in grad school (or so I'd say, based on our shared experience with hands-off supervisors). As you slowly realize you're falling behind in some sense because you're taking time off from work to handle your own life, you realize you can't count on those old, structured sources of extrinsic motivation that almost feels like a fight-or-flight response to an encroaching predator (e.g., the "cram-or-fail" decision on the night before a final exam). Those of us who make it this far have probably mostly chosen to run into the jaws of the beast and do battle with it in our flight from abject failure, but some of us have only done this when we feel ourselves running out of time to make a choice of which it's going to be.
Avoidance-avoidance conflicts like those resolve themselves (or force you to resolve them) because when the deadline comes, you have to choose. Without the climactic anxiety of the confrontation that motivates a resolution (however hard-won it may be even in these cases), conflicts can linger much longer in the post-deadlines careerscape. The emotional experience is different: the anxiety is more insidious than in-your-face, and can be tolerated much longer. You can start to feel the internalized sources of anxiety more as you worry less about others' judgment; you can become your own worst critic, and feel more guilty, depressed, or apathetic than truly anxious in the old familiar sense. This is still extrinsic motivation, but it's introjected in that it's internalized: you are now the source of your own negative self-evaluations. (This need not be exclusively true to apply.)
Reframing the solution
This kind of problem takes a different approach to resolve. You can probably find a million self-help blogs about how to be your own supervisor and boss yourself around so you can go back to the old model of operating under artificial, externalized pressure. E.g., "I must spend one hour working everyday before breakfast," or, "Whenever I read the newspaper, I must count the time I spend and put the same amount of time into [staring blankly at] my project." You can find a lot of similar answers to "How to avoid procrastination during the research phase of my PhD?" the second most popular question here at the moment. One of the problems with approaches like (some of) these is that they'll give you a whole new way to go to war against yourself; you'll have to take your infractions very seriously if you're going to take the system seriously at all, and you're probably not going to want to. You'll have to tell/force yourself not to do what you want to do, even when you have good reasons or special opportunities (unless you complicate your system and give yourself vacation time, indulgences, or mulligans, which might not be a bad idea). Another problem is that when you've put in your time or satisfied whatever other requirement you've assigned yourself, you'll feel just like you always did (if you were like me in this regard too) after finishing your self-assigned "homework": ready to go blow off the steam however you can, which probably leads you back to those "procrastinatory" habits you're fighting. If it does, that's a sign that those habits might be the ones that replenish your energy, fulfill you emotionally, and help you feel more like a whole person, more like yourself, and less like a dusty, malfunctioning computer that's been cooped up in a cramped cubicle for too long.
I think the better approach than stealing happy hours while you're off-the-clock (or stealing them from yourself while you're on) is to work more introspectively on your motives and values. I would think this—I'm a personality psychologist—but it's done me a lot of good. I still don't necessarily focus when I should (I'd probably have more publications by now if I did), but I don't feel like I'm wasting my time when I'm not focusing on work. I focus on what I'm doing instead, I enjoy and value it (or through patient introspection and experience, I gradually come to the conclusion that I don't, and I quit), and I don't beat myself up for it during or afterward. I trust that when I want to do something, there's probably a good reason, and I strive to understand it. If I can't find a good reason, I often find that I don't want to do it anymore; problem solved (usually). This has led to some extended "vacations" from work, during which I focus on other things I care about (e.g., a video game, or Stack Exchange!), but when I get to the bottom of what I'm after in these pursuits, and I get it, I'm enthusiastic to return to my work, and I bring new ideas to it. I integrate these diverse experiences, and I enrich my work in the process.
What I'm describing is a shift away from judgmental devaluation of extracurricular "distractions" to a recognition of and reconciliation with my broader set of values, which include my career, achievement, and financial success, but don't end there. I'm my own boss now (read: unemployed :P maybe you shouldn't listen to me!), so I get to enjoy that freedom (and pay the price for it)...and I do enjoy it. I enjoy my work too! Not feeling constantly indebted to it is very important for that feeling, that autonomous, intrinsic motivation (see the same links as before) to arise. Finding joy, fascination, excitement, and the energizing yet relaxing release-through-work of the flow state is all about letting yourself love what you do when the time is right, and knowing it's right because you've defined what you need to do on your own terms: terms of what you want to do (intrinsically), or at least what you really care about (identified motivation, which is often good enough; same links as before). Once you really understand what you're after, your sense of purpose, you can start organizing your projects around it and deriving natural, enduring motivation for your work. You won't want to quit and do something else so often, you'll start waking up eager to work, and if anything, you'll suffer for finding it harder to pull yourself away from your work to eat, sleep, make sweet love down by the fiyah, or whatever else there is to do with life that starts to seem strangely less important.
Acknowledgements, credentials, disclaimers...
I know this sounds like a new-age meditation mantra or performance-enhancing nutritional supplement commercial, but I assure you, these are at least the implications of honest-to-goodness psychological theories of motivation (which are my area of expertise), passed a few times through a thick filter of personal experience. I'm not a typical success story myself (if a success story at all so far), but I have succeeded in rediscovering my love for my work and motivation for focusing on it in a big way by introspecting on these matters of my motivation and values, and indulging my urges to do other things than work at certain points throughout my graduate career. I think I'm a much better psychologist for having "walked the walk," even if I haven't talked enough talk yet to convince others with my publication record, and I know that when I publish the manuscript version of that dissertation I linked above, it's going to be a hell of a lot better for all the time I've spent delving into statistics (and Cross Validated!) over the past few months when I "should've been" writing instead for fear of not publishing rapidly enough. Because I allowed myself to redefine my work in terms of what I value rather than in terms of what was going to get me the most immediate recognition and paycheck (again, extrinsic motives), and because I'm lucky enough to afford the opportunity costs, I put in two months of probably the hardest and most consistent work I've ever put into refining my research, put to rest all my old insecurities about my rate of progress, and apparently can't stop raving about everything I'm learning and how much better I feel about it all now. I don't yet know how long I'm going to be able to keep this up before I start "procrastinating" again (one might argue I'm doing that now), but the plan is to stay this way as long as I can: self-directed, secure, deeply enthusiastic, and well-aligned with my values and overall sense of purpose. The productivity has already started flowing out of this life transition, but it would take a lot more talking to prove it, so I'll leave it at that for now.
I should also note that there's some risk in this approach. It's a long road, you may not have the time and freedom to follow it as far as you need to for the results you might want, and it may not ultimately lead where you think you want it to right now. This is the stuff career transitions and midlife crises (not that I would really know about those first-hand just yet) are made of: confrontation with what you really want and care about, and its juxtaposition with what you're actually doing. Better to get it out of the way while you're young, I say, but maybe not when you're less than a year away from finishing your PhD, if there's some risk you won't as a result. If you can't afford to take your time, this isn't for you. It's a long-term approach that ought to pay off in the end, but there are certainly no guarantees, and it might take a very long time indeed. If you've had the patience to read this far, you just might be ready for it.
I mainly offer this because you remind me of myself, and both of us remind me of what I study, and I'm currently my own guinea pig undergoing very informal road-testing of these theories, for which I could provide plenty more references, but which take some contextualized interpretation to apply here. It's definitely too soon to claim conclusive support for the theory from my own life, but I feel like I'm closing in on that result very rapidly now. In whatever you choose to do, I wish you the best results, and hope you'll come back to tell us what you choose and how it goes. If this self-indulgent autobiography of mine doesn't get downvoted through the pavement, I'll consider doing the same. Cheers!
P.S. In response to your comment on @aeismail's answer, I want to emphasize that part of the benefit of my approach for me has been taking my former advisor's voice out of my brain and rediscovering my own voice. Those two months of hard work (seriously almost all-day everyday studying!) were in pursuit of my own solutions to my own research problems. Because I started listening to myself better and allowing myself to direct my own research according to my priorities, I've learned probably a year's worth of statistics that helps me handle the conceptual bits of my own project in ways my graduate advisor was never going to even while I was still there. If you can give it the time, and accept that you're your own best supervisor, and avoid being or becoming your own worst critic, you can solve those problems as well as anyone can. Ask your supervisor and everyone else you can for input and guidance, but know that you're ultimately the one who has to steer the ship, and don't take your hands off the wheel for a second! But do pull over once in a while to stretch your legs and smell the roses; it's just another way of putting gas in your tank.

Your answer is exceptional advice, but you have also left out just how hard your advice is to follow.

I'm amazed I was able to write so much and still leave anything out! Good point!

@NickStauner i wanted to wait until I can read and re-read your answer before I respond. It's really a gold mine, this answer of yours. THank you for taking your time to write it all down. Whether or not it'll help in practical terms is uncertain, but I am certain that it provides important insights. I can assure you that I will be coming back to this answer from time to time.

The Pomodoro Technique is great for when you find yourself in a cycle of procrastination. Combine with self binding. I've also had a lot of luck with creating minimum output requirements and tracking; Beeminder might help, at least until you've internalized the habits you want to build.
The important thing is to set yourself up for success.
I would suggest trying to attack the problem from many directions:

Spend some time each week renewing your coverage of the literature. As you get further along a project, you'll find you have a better grasp of where to look, and what it is you want. You may find incredibly important work for you after months of search, just because it took that long to find the right words.
Simultaneously, spend some time each week collating the information you have; create a wiki on your topic, and keep it up to date. Build a mind-map. These exercises will help you identify links and gaps in your conception of the problem.
Narrate your work: Keep a blog, a journal, that you dump every wisp of thought or spark of information into. Doing this will help you avoid loosing a spark of inspiration, while also freeing your mind to work on whatever task is actually at hand.

You've touched on a number of related problems, some of which are common to all grad students (anyone can procrastinate, even if they have a supervisor that requires more regular feedback), and some problems that are specific to your situation (a supervisor that is not very knowledgeable about your project).
There's no reason that your supervisor has to be the only person who helps you with your project. There are many other professors and academics around who might be more familiar with your specific goals, so make use of them. This can include professors who you've taken courses with (choosing course projects that relate to your research is a great way to kill two birds with one stone, so to speak). But there's no reason you can't just approach a professor out of the blue, and ask them if they could meet with you for an hour to help you with a specific problem. Most professors would be very glad, and the worst that can happen is they say "no" and you're back to where you started. You can also contact academics around the world, for example if you've read a paper by her or him and need help figuring out the details. Most academics love to talk about their research and get their ideas out there, so they'll probably be happy to help.
In regards to your more general problem of procrastination, that's something that I'm still struggling with. One tip that I have is to treat it like a job: Put in a solid 8 hours every day, from 9 to 5 ish, just like you would have to at a job. Then go home and relax in the evenings. When I started grad school, I was wasting a lot of time during the day, and then I'd get home and feel like I should do some work because I did nothing all day, so I'd work in the evening. That meant I didn't relax in the evening, and so I'd procrastinate more the next day. Procrastination is not really relaxing, because you always feel like you should be doing something else, so you can't switch off. If you can separate your work and the rest of your life into nice blocks, and make sure you do some really relaxing leisure activities in your off time (reading, sports, music, etc.), you'll feel a lot better (at least I did).

About finding other professors to help. My Committee asked me to speak to another CS professor for a referral to find a Math professor. That math professor referred me to the final math professor who actually was the one to help with my research. Ask around for some contacts from professors you know. They may be able to refer you to another professor that can help. Maybe even a potential mentor at another university - you never know.

The word you are searching for is self-discipline!
When I get distracted it is mostly because I lose the motivation for some topic. The next time when you get distracted from your work, take a break and/or try to work on another part of it.
Because your supervisor doesn't set goals for you means not that you can't set them for yourself. Important is, that you don't exaggerate it and thereby set yourself too much under pressure. Always setup goals that you can achieve in the given time!
In short:

Take regular breaks to get your head free. This is often underestimated!
If you get distracted, work on another part of your topic
Set goals for yourself that you can achieve in the given timespan

Daily goal: write at least x page(s)
Weekly goal: finish section y
Monthly goal: finish chapter z

If you made progress or finished an important part reward yourself to keep up your motivation

PS:

Don't spend too much time on stackexchange
If you are on facebook, limit yourself to one visit per day!

The problem with S.M.A.R.T. goals is that they are useful when you know what needs to be done. If I am stuck with a particular spec/feature that I have no idea how to solve then I can not set specific, measurable, realistic, attainable and time-bound goals.

@posdef: I disagree with 4/5 of your conclusion. Maybe you can't be specific with your goal, but what's stopping you from setting a MART goal? :P Maybe something like: see how much progress I can make toward understanding my spec/feature problem, on a scale from "none" to "solved it!" (solving can include the conclusion, "It's not possible."), as judged by myself, my supervisor(s; optionally), and colleagues I trust, over the next day, week, month, and quarter (separate goals). Worth a shot maybe? Good way to track yourself and see how much your concern is justified vs. needless, at least.

@NickStauner i see your point... it's worth trying out, at the very least.

you need feedback or you will die, you are perfectly entitled to request to meet with your supervisor for an hour a week. If they are unwilling to give even that then there is usually a clause in most grad studies contracts that will allow you to nominate a "second supervisor" (replacement) if you are unhappy. Chemistry (of the personal type) plays a large role in the success of teams so it is important to work with someone you like.
Following on .. if you have spare cycles and are happy with your progress see if there are others in the dept you can collaborate with - perhaps you will be credited on their publications too.
Publications are the currency of academia, like it or not, and time needs to be spent specifically targeting publishable work. So try and figure out how what you are doing today will lead to publications. Your supervisor didn't get there by accident they know very well how to play the game by now.
Which brings me to my final point, it sounds like perhaps there is a communication gap twixt you and your supervisor, ask yourself if you have been prickly or defensive with them at any point - if you have then throw your ego out the window, listen carefully to their suggestions and get it done. You will need their good word above all else in order to succeed.

That's a dismal outlook...not that I haven't heard of circumstances it suits unfortunately well...

yes, whenever I have seen the above situation it has never concluded well, so am warning strongly against it.