Always remember it is YOUR project and YOUR paper and YOUR thesis.
October 18, 2014 8:37 AM   Subscribe

"As the academic year begins again, new PhD students across the country (and further) are slowly settling into their fresh surroundings. I stayed at the same university when I made the switch to postgraduate research but I still remember feeling quite lost at the start, not knowing what to do or where to be. I’m now entering the final year of my studies and have (I hope) picked up some useful knowledge along the way.

"So I’ll cut right to the point: below is a list of handy tips, tricks, general advice and things I wish I knew when I started my PhD. The list was put together from chats with other PhD friends of mine, but is by no means exhaustive (nor is it in any particular order, though it did get quite long…). Hopefully it will help somebody. Please share your comments at the bottom if you have things to add – the more the merrier." Things I wish I knew when I started my PhD… from Between a rock and a hard place.
posted by joseph conrad is fully awesome (59 comments total) 64 users marked this as a favorite
 
I think there's at least some major-specificity here. At least in Biology, using Latex and Bibtex would just give you file formats that absolutely nobody else you work with could handle. With regard to Latex, when are you ever formatting your own documents? That's the journal's problem. And modern citation managers will do things like slurp the citations from the webpages you visit, and they'll output a formatted citation list too, so they might be a better choice than Bibtex.
posted by Mitrovarr at 9:05 AM on October 18, 2014 [10 favorites]


Good list, but I have one weird trick for PhD students. Read on to see why advisors love me.

Treat it like a job. Because it is a job. Many items on this list would be redundant if more people just acted as if getting a PhD was exactly the same as being a tenured professor, without the money and prestige (I suppose you can call it that) that comes with tenure.

Too many people think getting a PhD is like undergrad, or maybe like a master's program. It's nothing like undergrad. Work for eight hours a day every weekday and I promise you won't be overworked, particularly after you finish coursework. Don't socialize during business hours. Wake up early and go to work, wherever it is that you work (home office, on-campus office if you're lucky, the library), sit down and turn off the Internet and focus, make sure you break for lunch and then sit back down to work, and you will be wildly more successful than most of your peers.
posted by sockermom at 9:09 AM on October 18, 2014 [33 favorites]


and always remember, to thine own self be true.

Treat it like a job. Because it is a job.

A temp job, where the whole business depends on you but they pay you like an intern and then eventually replace you with someone younger and less experienced... it's that kind of job.
posted by ennui.bz at 9:13 AM on October 18, 2014 [12 favorites]


ennui.bz: A temp job, where the whole business depends on you but they pay you like an intern and then eventually replace you with someone younger and less experienced... it's that kind of job.

Well, it's also an education. You come in completely unqualified (unless you already have a Masters) and have to be trained up extensively to do your job. There are a lot of demands placed on your advisor and your graduate committee. Honestly, if you are paid enough to live on (not a guarantee everywhere!), I don't see anything wrong with the Ph.D. model. Except possibly that we're training too many of them for the limited job marker that exists.
posted by Mitrovarr at 9:22 AM on October 18, 2014 [2 favorites]


A temp job, where the whole business depends on you but they pay you like an intern and then eventually replace you with someone younger and less experienced

and yet the whole time they're forwarding you motivational self-help maxims and lifehacks and organizational tips and telling you that if you only get a little more exercise and stay positive and work just a little bit harder then a promotion and a permanent job will surely be just around the corner.

So yeah, pretty much "a job," in the contemporary American sense, which is to say it means both an actual job of work and also an attendant batch of bootstrap prosperity gospel and meritocratic mythology.
posted by RogerB at 9:25 AM on October 18, 2014 [5 favorites]


As someone who did grad school in the humanities (stopped with a masters in the early 90s), I laughed at the parts about funding.
posted by immlass at 9:43 AM on October 18, 2014 [1 favorite]


Actually, as a phd adviser of nearly 20 years, with a solid track record of placing students on the tenure track, my advice is to treat it like a calling, not just a job. There are way safer and easier jobs that can use your intelligence. You need a reason that goes beyond the job.
posted by spitbull at 9:43 AM on October 18, 2014 [15 favorites]


Also frankly if you need this list of tips to succeed as a phd student you need to rethink what you're doing. Most of them are blindingly obvious.
posted by spitbull at 9:45 AM on October 18, 2014 [10 favorites]


I would add "talk to your librarians and learn how to use the library." As an academic librarian, I see loads of students who come to me after having wasted days of their time looking for a particular source. I'm not say you have to become some sort of information literacy wiz, but this is a skill that you aren't going to learn from your professors and probably not from your fellows. Talking to the writing center about getting organized can be a help, too. Yes, it's aimed at undergraduates, but they can teach you a lot about maximizing your efforts.

Also, be nice to the staff in the department and college office. Don't brown nose, but be polite and friendly and, if you can remember, ask them how their kids are doing. This can often be the difference between things going smoothly or not for you.
posted by GenjiandProust at 9:46 AM on October 18, 2014 [6 favorites]


I shouldn't even read threads like this. I wish I could go back in time and tell myself that starting a Ph.D. is the worst decision I'll ever make.
posted by LastOfHisKind at 9:46 AM on October 18, 2014 [4 favorites]


Not finishing it was the best decision I ever made.
posted by We had a deal, Kyle at 9:48 AM on October 18, 2014 [1 favorite]


> "A temp job, where the whole business depends on you but they pay you like an intern and then eventually replace you with someone younger and less experienced ..."

It's an apprenticeship. In broad strokes, it works almost exactly the same way as apprenticing to be, say, an electrician.

There are plenty of problems with specific PhD programs. Some pay below a living wage, or demand hours far in excess of anything reasonable. Some even make you pay for the privilege. There are even arguably widespread systemic problems, like training too many people for an extremely limited number of jobs.

But calling it a temp job where you get replaced is misunderstanding the basic nature of what it is.

(Although, to be fair, both postdocs and adjunct positions could probably pretty easily fit the description you've given.)
posted by kyrademon at 9:53 AM on October 18, 2014 [1 favorite]


Is the only thing worse than a PhD student a former PhD student?

When did finding out a PhD program isn't for you turn into a badge of honor
posted by MisantropicPainforest at 9:53 AM on October 18, 2014


When did finding out a PhD program isn't for you turn into a badge of honor

Surviving a Ph.D. program, either by successfully ejecting or overcoming the department, is a badge of honor.
posted by LastOfHisKind at 10:06 AM on October 18, 2014 [7 favorites]


Sometimes people fail to get a PhD by actually failing.
posted by biffa at 10:13 AM on October 18, 2014


At least in Biology, using Latex and Bibtex would just give you file formats that absolutely nobody else you work with could handle.

Strictly speaking, LaTeX would give you files that everyone you work with can handle: text and PDF. They might claim not to know what to do with the text file, but, frankly, it's self-explanatory when it comes to something that's mostly text. For something that's not really equation-heavy like biology, you could learn enough LaTeX in far less time than you'd spend faffing about with Word in the course of writing an article or two, especially with a collaborator.

Anyway, the new hotness is biblatex, which has the advantage over bibtex of having penetrable style files, which came in handy when I needed to cite an appendix written by one person in a book by another.
posted by hoyland at 10:26 AM on October 18, 2014 [5 favorites]


An adjunct class hero is something to be
posted by thelonius at 10:28 AM on October 18, 2014 [5 favorites]


An adjunct class hero is something to be

for some, it is a calling...
posted by ennui.bz at 10:34 AM on October 18, 2014 [2 favorites]


Sockermom, I treated my undergrad education as a job, and have no regrets about it at all. Wish more undergrads would do the same. We need it.

That said, my undergrad degree was basically in computational math and statistics, but I'm sure other subject areas could benefit from a bit of focus and rigor.
posted by JoeXIII007 at 10:43 AM on October 18, 2014 [4 favorites]


With regard to Latex, when are you ever formatting your own documents?

Every time you take a paper to a conference, every time you submit a paper to a journal, every time you write a draft of a paper in progress that you want somebody's feedback on. Or maybe biologists just have one big string of plaintext that goes on and on and they need 80 pages next to each other to fit it all, I dunno. Formatting a document doesn't mean having it in the exact format (you hope) it will take when published, it only means... well... formatting. LaTeX happens to do a better job of it than word processors do, at least in the way that word processors are almost always used.

...but yes, "Learn LaTeX" is not universally applicable since there are strong network externalities in using the same text processing system as most potential collaborators. Pity about disciplines where it's rare though, as it has some real benefits compared to word processors. Same is true for, say, statistical software -- "Learn SPSS" might make sense in some disciplines but doesn't in political science, where Stata and R are way more common among active researchers.
posted by ROU_Xenophobe at 10:44 AM on October 18, 2014 [2 favorites]


Badger of honor is distinctly different than a badge of honor.

Thought the list was actually fairly good - agreed that it is targeted to PhD's in a specific area with the discussion of LaTex and BibTex, but the advice to learn how to use your major modes of written communication (powerpoint, ms word, or other), visual information (photoshop, illustrator, pymol, excel, R, and so on) and your bibliography software is good.

My +1 comments that other things you learn in your PhD: that at a certain point you are the expert. That at a certain point neither you nor your advisor will have a clue what is going on. And that's the point of research. Also, he'd like to point out that you should RTFM in pretty much all situations if possible.
posted by sciencegeek at 10:50 AM on October 18, 2014 [3 favorites]


hoyland: Strictly speaking, LaTeX would give you files that everyone you work with can handle: text and PDF.

Here, let me explain to you how any of these formats would be accepted by collaborators, at least the ones I've worked with:

Text: "Why are you sending me raw text? Did you write your whole paper into the email? Paste it into word, format it, and send it again."

PDF: "This is very nice, but I want to make revisions. Send the word doc."

Latex: "I think your word document got corrupted."
posted by Mitrovarr at 10:52 AM on October 18, 2014 [28 favorites]


A temp job, where the whole business depends on you but they pay you like an intern and then eventually replace you with someone younger and less experienced... it's that kind of job.

I'd actually argue that it's more like starting your own business. You've still got to show up, glue your butt to the chair, and make it happen. Far too many PhD students I've known (and I've known a lot of doctoral students) treat it like a fun hobby that they engage in when they feel like it. They go on vacation every month, get and train puppies, get super involved in things like the Occupy movement, teach themselves to cook everything in Bittman's How to Cook Everything, or - and this is a big one - spend 24/7 socializing and gossiping about other people in their department. Another big distraction I've seen happen over and over is getting bogged down in process by learning tips to be better PhD students. There's only one true trick: just do it. If doing it like a 9-5 doesn't work for you, then go for it - you've got the flexibility to do that in this type of job. But you have to sit down and work every single day, for many hours every day. Six days a week, seven if you can stomach it. The only way out is through.
posted by sockermom at 10:58 AM on October 18, 2014 [4 favorites]


Learning LaTeX is nothing but a distraction if you're not in a field that relies heavily on equations or special characters.

I know MeFi has its passionate LaTeX adherents, but the reality is as Mitrovarr (my new hero) describes--if you want to share evolving documents with lots of people, documents that include formatting and can be edited or reviewed electronically, you need something a little more universally accepted than LaTeX, especially if you're not in math or hard science.

When I started my PhD, I had a bunch of people squawking at me to learn LaTeX, and I am *so glad* I ignored them. Doing a doctorate already has enough distractions attached to it; nobody needs another one.
posted by yellowcandy at 11:19 AM on October 18, 2014 [6 favorites]


Strictly speaking, LaTeX would give you files that everyone you work with can handle: text and PDF.

What Mitrovarr said, plus many journals do not actually accept PDF files - only Word and RTF. They do sometimes accept plain text files as well, but if you're going to forsake all formatting (including italicizing gene names and species names, adding superscripts and subscripts in chemical names and author affiliations, etc., etc.) you might as well save yourself some more time and just write it in plain text to begin with. And as Mitrovarr mentioned, the first thing your collaborator is going to do with your precious, pristine .txt file is... send it back to you, or else import it into Word and turn on Track Changes and then send it back to you.

I actually know and use LaTeX. When I actually had to put all my work into a single document for graduation, I used LyX (plus some bits of LaTeX where necessary) and JabRef and that worked great, because I needed very little feedback on the individual sections and the document would have been too large to comfortably work with in Word. But if you're writing a paper as a graduate student, no matter what department you're in, you're not going to endear yourself to anyone by making weird demands about using non-standard writing tools. (I can just imagine how that would go -- "dear senior colleague, can you please indulge me in writing my first paper using some kind of markup language you've never used or even heard of? It'll only take a few hours of your time to get up to speed!" Good luck.) And I literally have a Windows virtual machine on both my home and work computers essentially only to use Word, even though I primarily run Linux in both places -- that's how industry-standard it is in biology.

It is painfully obvious that anyone arguing that biology grad students should learn and use LaTeX, at least as anything more than a personal project, has never spent any appreciable time in a biology department.
posted by en forme de poire at 11:56 AM on October 18, 2014 [3 favorites]


The suggestion to start using a reference and paper manager way before you ever start writing, though, is a very good one. There are plenty of options out there - I use Mendeley these days because the browser plug-in is pretty great. JabRef is not a bad option either, since it has the ability to crawl PubMed for you. But having some method of keeping track of what you've read and keeping it available for referencing is crucial.

The rest of the list seems totally reasonable to me, particularly keeping detailed notes (I am only starting to get "good" at this), practicing presentation, taking notes in meetings... The one thing I totally disagree about is whether keeping on top of e-mails is a crucial PhD skill. Sure, you want to get back to people in a reasonable time frame -- but I'd hazard that most people's problem is not checking e-mail enough, but checking e-mail too much. I would also be really careful about checking it first thing in the morning. It's too easy to get distracted by something that seems urgent and waste a couple of hours on that before you realize you haven't done any "real work" yet and then you feel like you've wasted the whole fucking day. Not that I'm speaking from personal experience or anything.

Also log the fuck out of Metafilter</hypocrisy>
posted by en forme de poire at 12:08 PM on October 18, 2014 [6 favorites]


And for the relevant sciences: keep a good, detailed lab notebook or you're going to be cursing yourself at some point because you didn't keep good enough notes and you're having to redo something or you can't find something or ....

And hope that the person before you followed this advice because you're going to be cursing him/her and wishing great evil to befall him/her.

And when you finish your PhD or just leave the lab, the better your lab notebook is the fewer the emails/calls/texts you'll get from students/postdocs/advisor/undergrads/techs and so on. Ditto organizing your samples, reagents and protocols.
posted by sciencegeek at 1:01 PM on October 18, 2014 [1 favorite]


I found that keeping a semi-public lab notebook online (maybe just visible to people in your group) is a good way to guilt yourself into keeping it up to date. Just wish I'd bitten that particular bullet while I was still in grad school.
posted by en forme de poire at 1:07 PM on October 18, 2014


Also frankly if you need this list of tips to succeed as a phd student you need to rethink what you're doing. Most of them are blindingly obvious.

Eh, that's pretty uncharitable. You might be surprised how often some blindingly obvious
thing gets missed. I have had projects where four sets of eyes missed critical typos, had friends point out courses of action that were, in retrospect, natural but were invisible to me, and patiently explained simple things to very smart people only to have them mischaracterize it a day later. I'd say that this list is harmless if it really is all old hat to you and maybe someone will read it and go "d'oh!" and have a better PhD program. That's not nothing.
posted by GenjiandProust at 1:39 PM on October 18, 2014 [6 favorites]


"You might be surprised how often some blindingly obvious thing gets missed."

Not only 'blindingly obvious', but sometimes the obvious things get ignored, or put off. Then its, Damit I wish I would have took that more seriously.

And it's the format of the piece to be a list of clear "tips" in turn justified as useful. Its not Insightful to Reception of and Undertaking for the Development of Original Knowledge. haha
posted by xtian at 2:20 PM on October 18, 2014 [3 favorites]


What I loved about LaTex was that I could concentrate on the writing and not worry about the formatting, spacing, figure and image placement, etc.. It was also great to be able to generate a conference paper styled PDF and then, with one single line change, crank out the same content as a "tiny book". I printed out my thesis (~150pages) in tiny book format because I wanted to keep a copy around but didn't really ever care about reading it again.

I agree it isn't for everyone but it does generate gorgeous documents, it's absolutely amazing at dealing with math equations, and I've spent far far more time wrestling with Word over the years than I ever did learning LaTex.
posted by mbatch at 3:19 PM on October 18, 2014 [2 favorites]


It must be different in different fields. I've never had to do (or been allowed to do) the typesetting of my research publications. My university's thesis and dissertation office gave me a template for my thesis that had to be followed, and the journals I've submitted to all had submission guidelines that required minimal formatting (with images uploaded separately). Maybe it's just a conference paper thing to do it yourself (I did posters and talks but never conference papers).
posted by Mitrovarr at 5:03 PM on October 18, 2014 [2 favorites]


LateX is good for some scientists, unnecessary, and possibly more difficult, for anyone else.

Other advice:

Listen to your supervisor. About your topic, about how academia works, about how to get your PhD, about whether a conference is worth going to or not.

It's a truism that by the later stage of your studentship you will know more about your topic than anyone. Do bear in mind this is only for a small part of your subject area, Don't go assuming you know more on the wider field. Also your supervisor has no interest in seeing you fail, so don't be a dick about that.

Don't sneer at the other PhD students. Not because your topic is more academic or special or whatever, at the very least you stand to look like an arsehole when they all have PhDs and you don't.

Your supervisor has other stuff to do besides your thesis. This will be a pain for you in terms of getting feedback. Don't make this worse by doing 40,000 word chapters when 5000 is what had been asked for.

Beat in mind that you're most likely source of a post doc is with your supervisor. Be reliable. Deliver quality work. Don't be needy. Or whiny. Or look to be spoonfed. Write papers. Listen and demonstrate you understand what is required of you, for example by writing papers. They're good for you and your supervisor. This goes back to the advice about treating your PhD like a job. This doesn't mean don't ask for help, it means develop good judgement about what you should and shouldn't be doing for yourself.

All conferences in Hawaii or Lake Garda or on the moon sound cool, some will be a waste of time and money, your supervisor will know this better than you, so ask.

If you still want to go then call and lay on the poverty and student status, lots of events will let you in for peanuts.

Work out when you work best and work then. 9-5 is a good skill but some other times suit some people better. Treat it like a job but not necessarily a cubicle job. If you live near a beach then slack off on the first day of summer and whenever there is surf.

If your supervisor wasn't your supervisor who would be the best person in the country to be your supervisor? Work this out then ask to meet. That's your mentor right there. Potentially your other next employer.

Is there a student society in your field? Join it. Could you be an officer?

You're not going to get through without a social life. Usual uni clubs if you are still 21, post grad soc if older, or anything else, basically don't be a shut in. It won't be intellectual (probably), PhDs learn petty quickly only they are interested/can understand their topic.
posted by biffa at 5:19 PM on October 18, 2014 [3 favorites]


Late to this thread, but on the LaTeX derail: if you want to put your paper on the arXiv preprint server and not have people laugh, you need to format it yourself...
posted by RedOrGreen at 5:51 PM on October 18, 2014 [1 favorite]


Almost nobody in biology uses arXiv and many biology journals actually prohibit or discourage it.
posted by en forme de poire at 6:09 PM on October 18, 2014


It must be different in different fields. I've never had to do (or been allowed to do) the typesetting of my research publications. My university's thesis and dissertation office gave me a template for my thesis that had to be followed, and the journals I've submitted to all had submission guidelines that required minimal formatting (with images uploaded separately).

Yes. Math is "Here's the document class, go to it." I'm willing to bet no one in math at your university writes their thesis in anything but LaTeX (and friends--someone out there is using ConTeXt*). Somewhere along the line, someone will have dug through the university policies and found the actual specifications (if they really just hand you a Word template with no accompanying explanation) and put together a LaTeX template if there isn't an official one. (Amazingly, we had an official one. It's in need of an overhaul--it was written in the late 1980s and amended piecemeal since then, so there's some funky stuff--but we also have a nice clear list of specifications on the same site as the template. If I had had more than two weeks between defending and moving, I would have rewritten the thing entirely because a lot of the clever hacks are no longer needed.)

Everyone should note that I never actually said biologists should randomly start using LaTeX; I pointed out that the claimed technical hurdles were exaggerated.

*People in some humanities departments probably should be using XeTeX for writing in multiple languages, if they're not already.
posted by hoyland at 6:26 PM on October 18, 2014 [1 favorite]


This biologist uses Word and LaTeX. They're all just tools.*


*You can parse this as you wish.
posted by cromagnon at 7:09 PM on October 18, 2014


"Always remember it is YOUR project and YOUR paper and YOUR thesis."

OK, so it's definitely your thesis, but it's a rare paper or project, at least in my field, that belongs to one person. Sometimes, it is right to take the lead on these things, but rarely so for a grad student just starting out. And even when it's right to take the lead, it's not really a good idea to completely own the things.....
posted by Tandem Affinity at 7:24 PM on October 18, 2014 [1 favorite]


I listened to the "learn latex" advice, as a student in a field where no one uses it. I wrote my MA thesis in latex, which was fine, as I never published it. I wrote my phd thesis and several journal articles in latex, and spent fucking months reformatting it all into Word as required by publishers. Publishers who require camera-ready copy, but as word documents in case they do have to edit them further. After the third journal article, I gave up and started doing it all in word to start with. In the last two or three years I've seen that some major journals in my field have started to accept latex submissions, so I'm thinking of changing back, but they haven't got style files, so there's not much advantage to using latex there either.

As For the phd advice, I agree that most of the stuff in this article seems fairly obvious. There's a few things I would add:

Decide early on what you are most likely to need or want to do at the end of the phd, and tailor your experience towards making yourself a good candidate for that. If you are at a top university and you might have a chance at a research career, and that's what you want, pretty much ignore teaching opportunities, and focus on pumping out publications and getting small grants and awards. That is what will count when you apply for fellowships or postdocs at the end. If you are at a lower-tier university and want to continue in academia, you will probably be looking for a teaching heavy job, so you want lots of teaching experience, maybe some teaching awards, some professional development courses in that area, and a few publications. If you are geographically limited, you're screwed. I mean, you'll need to try to build yourself a niche at your current institution, so you'll need to find sources of external funding, and meanwhile line yourself up as a possible new hire. Figure out who is likely to retire and be replaced (which might be no one, sadly) and move your research in their direction. Make sure you get a supervisor who has a record of bringing in funding and hiring postdocs. Find out who else in the department is planning on major projects that will hire people in the future, and get on their good side. Learn some admin and programming skills so you can at least maybe end up getting hired as support staff on a future project. And finally, if you think you might not stay in academia, then you should find out what sorts of jobs your fellow students have gone into, find out what you might be interested in, and use the opportunities you get during the phd to learn the skills that will make you more attractive in those fields.

My other piece of advice is that the phd is a mind fuck and everyone I know who did one, successfully or not, came out somewhat broken. So hook yourself up with therapy early and often. Find out what your school provides in terms of counselling, sick leave, extensions, etc, before you actually need it. When you are a,ready deeply depressed, you won't have the energy to find these things out. The minute you suspect you are not entirely psychologically healthy see someone to talk it through. It's easier to put strategies into place to support yourself before things get bad and before you've developed unhealthy ways of coping like procrastination, avoidance, workaholism, perfectionism, or substance abuse.
posted by lollusc at 8:56 PM on October 18, 2014 [7 favorites]


I pointed out that the claimed technical hurdles were exaggerated

The relevant technical hurdles to using *TeX in biology that I and others have brought up in this thread are something like the following:
1. No track changes
2. .pdf is not amenable to editing
3. Plain text has no formatting
4. Collaborators would need to learn enough LaTeX to make edits
5. Some biology journals do not accept LaTeX/pdf format
Referring to these hurdles as "exaggerated" without actually addressing them or bringing up any relevant first-hand knowledge comes off as strange and a little condescending to me. Even if you were talking strictly about Mitrovarr's comment about file formats that "absolutely nobody else you work with could handle", it is pretty clear that by "handle" s/he meant more than "open."

(FWIW, by my estimation, though, I have wasted at least as much time "faffing around" with LaTeX than I ever have with [recent versions of] Word, especially now that there are reasonable reference managers for Word like Mendeley. LaTeX is still great for very large documents, like a completed thesis.)
posted by en forme de poire at 10:57 PM on October 18, 2014


I'm not sure where the whole biology tangent comes into this, the author of the linked piece is not a biologist and in my experience people who write these things intend them for others in their field. In my field (linguistics), learning latex is very good but somewhat optional advice, and in my subfield it is more necessary (and at a minimum, _extremely_ helpful when dealing with various conference proceedings and journals). I also collaborate with people who do computational linguistics, and there it is absolutely obligatory to know latex. So yes, there are many fields where this is in fact good advice, and I assume it is for the intended audience for the linked thing (some kind of geological modeling?). I certainly tell my students that if I need to (I mostly don't because they either already know it or see everyone else doing it and pick it up).

As to the overall piece (which was mostly not about latex), I found it to be ok but mostly obvious advice that you see on a lot of these lists. However, I will say that what is "obvious" to me now is not necessarily obvious to a 22-year-old first year grad student who has effectively never had a job. The other problem of course is that knowing rationally that something might be a good idea (e.g. the "write as you go" tip, which is one of the most important imo) doesn't entail doing it practice.
posted by advil at 8:09 AM on October 19, 2014


And for the relevant sciences: keep a good, detailed lab notebook or you're going to be cursing yourself at some point because you didn't keep good enough notes and you're having to redo something or you can't find something or ....

Also a good habit for post-academic careers. I find my notebook records very useful, particularly in deep and involved debugging. ("Yeah, I tried that three days ago; didn't work but the output was interesting...")
posted by We had a deal, Kyle at 11:06 AM on October 19, 2014 [2 favorites]


I'm only just starting down this road (right now this Fall! I am the article's target audience), but for now I've chosen Markdown / Pandoc / equations in LaTeX as my needlessly obscure and complicated format of choice. The advantage I see is that mostly I'm just writing text, and I can muck around with the details of formatting in whatever way my coauthors insist on.
posted by gurple at 11:31 AM on October 19, 2014 [1 favorite]


advil, I think you're correct that people are of course going to draw from their own experiences, but the author here doesn't even mention his field apart from the site footer. And as others have confirmed in this thread, the rest of the advice is very generally applicable to PhDs in the sciences (people across various fields have even called it "obvious"). People are discussing LaTeX because it is the one piece of advice given here which actually turns out to be pretty field-specific. I happen to care about this because younger biologists, particularly those who interface with other sciences like physics or comp sci, are actually very often advised by people from those disciplines (especially other students!) to learn LaTeX. While I'm sure that advice is well-meaning, it turns out not to be particularly helpful in my field, in a way that only becomes obvious after wasting a lot of time. So if we're going to discuss advice to prospective graduate students, I think a far better piece of advice would be "find out what writing tools your labmates and advisor(s) expect you to use, and become familiar with them."
posted by en forme de poire at 11:51 AM on October 19, 2014 [1 favorite]


(gurple, that's actually what I'm using right now to keep an online lab notebook!)
posted by en forme de poire at 11:58 AM on October 19, 2014


Referring to these hurdles as "exaggerated" without actually addressing them or bringing up any relevant first-hand knowledge comes off as strange and a little condescending to me. Even if you were talking strictly about Mitrovarr's comment about file formats that "absolutely nobody else you work with could handle", it is pretty clear that by "handle" s/he meant more than "open."

My reading of the situation was that Mitrovarr is without first-hand knowledge of LaTeX (not least since they suggested no one writes thesis with it), so I'm a bit baffled that I'm out of order for commenting without being a biologist. Further, I also asserted (and am about to assert again), that the amount of TeX knowledge required to work on something that's overwhelmingly text is roughly zero.

Somehow your hurdles 1 and 2 don't pose problems for fields where LaTeX is the default. 3 is kind of the point of any markup language. Maybe the handful of biology papers I've looked at in my life are a totally unrepresentative sample, but I think "enough LaTeX to make edits" is about a three minute explanation for people writing mostly text. I never said you're going to persuade co-authors to go for it (or even that you should try), but having enough knowledge to edit something is a really low bar. Your number five would be a good reason for biologists not to take up LaTeX. But then I never said they should, just that colleagues could handle the damn files.
posted by hoyland at 11:59 AM on October 19, 2014 [1 favorite]


not least since they suggested no one writes thesis with it

I can't find where in this thread Mitrovarr said or suggested that. (In any case, I have LaTeX experience and I agree with Mitrovarr here.)

Somehow your hurdles 1 and 2 don't pose problems for fields where LaTeX is the default. 3 is kind of the point of any markup language.

Biology papers do tend to have more authors than papers in other disciplines on average, so perhaps that has something to do with why they are particularly invested in using tracking changes.

However, I don't know how people handle this in other fields and would be interested to find out. When I asked one physicist how he tracked changes with LaTeX he said "just use version control and whatever you use to resolve conflicts in code" (I use vimdiff so I thought that was particularly funny, but even then, am I going to ask my collaborators to all download and learn git + KDiff3?). LyX has a simple Track Changes function, but again, it's an additional piece of software your entire group would have to download and learn. Perhaps there's something more straightforward out there?

Point 3 does indeed apply to any markup language, which is why I also wouldn't recommend that biologists write their papers in HTML (unless that's what everyone else in the lab does), and would instead suggest Word, Google Docs, etc.

And sorry, even aside from tracking changes, I still have to disagree with the claim that three minutes of learning LaTeX gets you all the ability to edit that you would ever need. Just off the top of my head, a lot of people I've worked with want to be able to print out the paper and see their revisions in hard copy -- that requires compiling the document and that is not trivial to explain to someone, particularly if they're running Windows instead of a Unix-alike and don't already have *TeX installed.

I'm a bit baffled that I'm out of order for commenting without being a biologist

Well, to be more specific, you were commenting about the way that biologists organize and write scientific documents without being a biologist. When one of my math friends found out that figures in biology are commonly in color and don't make sense in black and white, he said this was initially so unthinkable to him that it would have been like saying you needed to print out a figure in 3D pop-up book form for it to be intelligible. And yet here we are, with different technical needs about scientific authoring and publishing for different scientific disciplines.
posted by en forme de poire at 1:05 PM on October 19, 2014


As someone who did biology - yes, most people in the biological sciences use figures that don't make sense in black and white - however there are some of us who are exceptions because we are old and crotchety and existed before color printing was affordable.
posted by sciencegeek at 2:29 PM on October 19, 2014 [1 favorite]


I think the color / no-color thing has to do with the different types of data that are represented in biology vs. math. When's the last time that in math you had to do a full-page diagram with 45 different, tiny pie charts with 8 categories each? I'd like to hear a good way to do that without color.
posted by Mitrovarr at 7:47 PM on October 19, 2014


sockermom: Work for eight hours a day every weekday and I promise you won't be overworked...

... unless you've got a full time job, in which case, by definition you will be overworked.

Which is to say: this 'weird trick' only works if you buy into the idea that the PhD is your ticket to a transformed life: Get the PhD, get the job that you're getting it for. Except most people who get PhDs end up getting not much more money, if not less money. (Remember, most PhDs aren't in STEM.)

So if you trade in your career on a PhD program, yes, you can work on that PhD 40 hours a week. But if you don't mortgage your future based on the shiny-happy story your advisor and department paint for you about your future in the field, it's going to be harder.
posted by lodurr at 7:10 AM on October 20, 2014


kyrademon: It's an apprenticeship.

For a job you'll most likely never get.

Which is why the whole 'treat it like a calling' thing both makes sense and is so maddening.

It's quite a bit like writing or acting: If you're willing to work hard for no glory, you can make a living at it. But the overwhelming likelihood is that it won't be a good living. (At least as an Actor you've got a good union.)
posted by lodurr at 7:12 AM on October 20, 2014


I think the whole LaTeX thing can be subsumed under a statement like:

There are significant aspects of the workflow from initial idea to publication that are specific to particular disciplines, so you should learn what those and, at least initially, maybe be wary of running counter to them since this probably isn't the time to reinvent the wheel even if your reinvented wheel totally kicks ass.

That said, "LaTeX doesn't have track-changes" is kind of a weird thing to say; sort of like "C can't track changes" or "perl doesn't have track-changes." Tracking changes is an editor job, not a typesetter job, so you can track changes if you use an editor that tracks changes. Hell, if you really want to you can write your latex source in Word and pass it around, only dumping to an actual tex file when it's time to compile it.

Also, the author didn't mention another great reason to use latex *if* that's not something weird and crazy for your discipline -- the files. You don't need to worry that the next upgrade to WordProcessor is going to break the formatting/figures/equations/sectioning of your paper or that the version ten years from now won't even be able to open this year's files. Even the odd case of bit rot is much more survivable with plaintext than with a binary file format. The Time That Word Unrecoverably Ate My Equations was actually the biggest reason I moved to latex (except where coauthors work in Word).
posted by ROU_Xenophobe at 8:10 AM on October 20, 2014 [1 favorite]


Its an apprenticeship in terms of becoming a professional researcher, there are jobs that have the same skillset that aren't pure academic research positions. Going back over my five PhD grads, they are academic x2, academic research support, national level research prioritisation, national regulator. They don't all necessarily require PhDs but their prospects were considerably enhanced by having one.
posted by biffa at 8:16 AM on October 20, 2014


Some PhD programs are 'an apprenticeship in terms of becoming a professional researcher' -- most are not.

But let's just stick to STEM: Most STEM PhDs are not going to be professional researchers, except in the sense of pursuing an applied R&D agenda in a corporate setting, usually as some kind of technician. They'll make good money. A few "lucky" ones will pursue post-docs at which they make less money but do research, and when they're burned out and used up will mostly go and get jobs similar to those their non-post-doc associates got straight out of the program. A few will get tenure-track appointments of some kind, and if they can show progress they'll get tenure and do alright.

But that's STEM, and as I've noted, that's not most PhDs.
posted by lodurr at 8:25 AM on October 20, 2014


Some PhD programs are 'an apprenticeship in terms of becoming a professional researcher' -- most are not.

Yes they are. This is a fun argument.

Most STEM PhDs are not going to be professional researchers, except in the sense of pursuing an applied R&D agenda in a corporate setting, usually as some kind of technician.

But this is professional research.

But let's just stick to STEM

I am semi-motivated to see what out stats are for PhD's first jobs but I'm not sure we keep them. My feeling would be most of our (primarily engineering) grads do get post doc positions in academia. There is definitely a shortfall of permanent positions at lecturer and up level, and these have got rarer recently, but it will be interesting to see where the huge EU funding stream leave post docs (STEM and soc-sci) and whether we see more people make careers out of 2-3 year contracts which let them develop from RF to SRF to PRF and whether this allows anther route to permanence. This is obviously far from ideal in terms of job security and for other reasons.
posted by biffa at 8:59 AM on October 20, 2014 [1 favorite]


Yes they are. This is a fun argument.

Yes "most PhD programs are apprenticeships in terms of becoming a professional researcher"?

That seems prima facie false to me, based on common-sense understanding of the terms "PhD program" and "professional researcher," and my assumption (which of course is potentially mistaken) that most PhD programs are not in sciences. But given that last stipulation and since you seem interested in making a point of it, I'll just leave it at that.
posted by lodurr at 9:29 AM on October 20, 2014


I mean simply that most are apprenticeships for this purpose, not all lead to jobs but most involve learning about how professional research is carried out.
posted by biffa at 9:52 AM on October 20, 2014


Get the PhD, get the job that you're getting it for.
Again, the PhD is actually a job itself. It's not merely a stepping stone. Treating it that way, I think, is one of the reasons that people get jaded and unhappy. You're betting your present life on a potential future existence. That's never good.

The PhD is a guaranteed job for at least four or five years. I've been funded - meagerly, sure, but funded - every year for the past six years. It's a great job, because fundamentally I am being paid to become smarter. How cool is that? I'm willing to take a big hit in my income in order to get the opportunity to become more intelligent on someone else's dime. If you're not, you shouldn't be getting a PhD.

Personally, I didn't come in to my PhD thinking, "And then when I'm done I'll be a professor!" I thought, "I'm going to do something really neat for the next four or five years!" I actually think that given the state of the academy this is a pretty common mindset.

A PhD is a lifestyle, too, though. Part of the reason you're paid less, I think, is because it's a rite of passage. You have to really, really want it in order to "earn" the degree. You have to be able to do research with no funding for the research, with very few resources (we don't get help purchasing software, we don't get funding to go to conferences, and we sure as heck don't get office space). It's about "proving" that you care enough about the pursuit of knowledge; that proof comes from doing it on a shoestring and still doing it well. The PhD is a rite of passage. It's supposed to break you down. It's supposed to be hard.

I'm not saying this stuff is ideal, or that it's right. I think the doctoral process is pretty broken. I think academic publishing is pretty darn broken, too. The system is not a good system, but it's the system. And it does allow people to get smarter and make just enough money to support themselves doing it. Doesn't hurt if you have what I've heard called an "academic wife" (a term I really take umbrage with, but that's another story) - someone at home that can help pay the rent in a pinch, a person that can make you meals and make sure your house is clean. But that's not required - I know a lot of single people getting doctorates, too.

This is all to say that it seems pretty strange to me to treat the PhD like a stepping stone to a "better" job. It is actually what you are doing when you are doing it (well, that, or commenting on Metafilter, I suppose). I've spent almost six years doing this. It's definitely a job. It's what I spend my working day on. It's not a promise for a better future, it's my present.
posted by sockermom at 10:13 AM on October 20, 2014 [1 favorite]


The PhD is a guaranteed job for at least four or five years.

If that worked for you, great, but it doesn't strike me as a good approach for most people.

I'll use my wife as an example. She's working on a PhD right now, in Social Welfare. Her advisor has been after her since day one to 'treat the PhD program like a career' by quitting her full time job (teaching composition at a different college) and taking grant money. I.e., giving up a job where she can make retirement contributions and has health care, which paid for most of her coursework as an career development expense, for the unbridled contingency that she might one day get a tenure-track job and then might possibly get tenure.

She didn't think it was a good bargain.

Since she'll have published 6 papers in decent journals before she finishes her comprehensives, her advisor hasn't complained, but other people in the program are under constant pressure to 'make the commitment.'

And that commitment just doesn't pan out for most of them. Most of them end up doing more or less what they were doing before they started, except they've lost vestment, and lost time in their career path. It's seen as being a lot like taking time off to have kids. You might be better-positioned to get a management position, you might now be better position to get adjunct teaching gigs. But tenure-track positions are still thin on the ground.
posted by lodurr at 11:42 AM on October 20, 2014 [1 favorite]


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