Thursday, October 25, 2012

Planning Ahead and Writing As You Go

So even though I'm probably 2-ish years from graduating (plus some very large error bars on that number), I've started writing bits and pieces of my thesis. Not just in the sense that I'm writing manuscripts, which I'm also working on, but in that I'm trying to plot out the larger story I'm trying to tell. I also want to right everything down while I still remember why I did it in a particular way.

My advisor seems confused whenever I mention this approach. He's very strongly in the camp of write the papers, and copy-paste to make a thesis. Given his reading habits, it does mean fewer things he has to read, which is good for getting anything out the door. However, at this point, many of my results are of the "and this approach didn't work" variety. Not necessarily paper material, but things I feel should be documented for future students in the group. A quick poll of Twitter seems to indicate that the thesis is a good place to include this sort of thing, and it can always be deleted when you go to do the manuscript. Of course, according to the comments at GenomicRepairman, it seems unlikely hypothetical future students are going to read it anyway.

I also like looking at the bigger picture, because it gives me a sense of things I've *done*, not just the giant list of things I still need to do. When I'm in the writing mood, I'm trying to write up methods sections and working on piecing together background sections as I read. It also helps me plan, and find the holes in my story I need to fill.

What approach did you take (or are you taking) to thesis writing?


  1. As an advisor, I'm definitely in the camp of staple-three-papers-together-for-your-dissertation. As scientists, it is where our primary writing efforts go, because published papers is our major currency.

    But also: as a writer, I like to write in a way that makes me happy. In addition, I recognize that my own writing is "inefficient" in the sense that I write a lot that doesn't end up getting published--I think this is the process of writing papers, at least for me.

    So I think you can very naturally accomplish both as you write your dissertation. Primary focus on the publishable papers, but also include in your dissertation some of that other useful information that often gets left on the cutting room floor.

  2. My PhD advisor is very strict in the sense that all his students have to write their literature overview within their first year. This makes you reading the literature and you get a better feeling for the field. On the other had most students can't use parts of their writing in the actual thesis, because the project evolved in a slightly different direction during the years.
    But when I wrote up my thesis it was very good that this very time consuming part of the thesis was pretty much done already and I could focus on my data. I haven't prepared my thesis along the way and I didn't have many papers to "staple together", so I had to structure it and write it in one go. Quite stressful!
    Now I'm trying to encourage my students to always write bits and pieces - the same way as you do. I'd be happy to read their stuff, but they are trying to avoid writing as much as possible. (=

  3. As for the dissertation, I am also in the camp of papers first, dissertation will easily follow. However, in addition to original research papers, I try to have each student write either one review paper or one book chapter during their PhD. I get tons of requests for those and I have the time, the need, or the desire to write them unless they are in a really visible venue. However, for a student writing a book chapter or a review paper is an excellent experience, as it forces them to do a thorough literature review and kind of step back and think of the big picture. These become an integral part of the dissertation -- the dreaded intro -- besides being a nice bullet on the CV.

    I wonder if what you are writing up could make a part of a longer methods paper on its own. I am a great proponent of publishing everything that is new and nontrivial, even if it's not breathtaking -- it needn't all be high profile pubs or even PRB, but I think it's important that nontrivial stuff not be buried in a thesis alone. Ask your prof if there's a book chapter you can contribute to or an invited paper for a lower tier journal.

  4. yes your right whoosh PhD advisory are very stricken to there student but Thesis Writing is beneficial for every one thanks

  5. It is very hard to do that but your blog will help me to make things easy recently i am trying to doing thesis proposal writing .