I am really grateful for the echoes in the scientific blogosphere on my live onblogging doctoral thesis trial. (I especially liked PZ Pharyngula Myers’ thesis story which inspired me to put some pictures and texts into Comic Life.)
What is crucial here: this way I can perfectly match my professional daily job with my blogging activities and amplify it.
I am ignorant about the details yet but I would really like to use the WordPress content management environment as a true working surface for preparing the thesis.
Also I would like to share the background story of editing a thesis with a lot of how-toos.
All the progress here will be done through little steps and the thesis project by no means will turn Pimm a one-channel, thesis-only adventure.
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Let us assume you met all the local and global requirements in order to start to write your thesis: enough experimental work, published articles and ongoing manuscripts.
Moreover, you want a little more than just compiling your published articles and existing material together. You aim for quality.
What are the initial steps that come into your mind?
Well, for me the first steps are: figuring out a unifying concept behind all my experimental work and finding a proper thesis title.
Deep, healthy lifespan extension 
Wonderful. I’ve been looking for a new way to procrastinate, and here it is! I imagine that with all the tinkering with my blog and messing around with scripts that I could do if I were to follow in your footsteps, I could successfully procrastinate “just writing the damn thing” for quite a while.
Thanks, man!
Seriously, though, the way I’m doing it is to write it like a grant proposal. I have three main questions that my work has all more or less gone to address, so I have the past, present, and future directions for each of those.
As far as the title goes, Darwin likes to use a brainstorming approach, writing out bunches of slight variant and mutations of the first title you come up with, and picking among those.
Grady, thanks, really good answers. Those 2 were my advanced questions that will be explicated in future posts. With titles, that was exactly my method too and I will introduce the variants to demonstrate it.
Have you read Highsmith’s Agile Project Management, or any books on Extreme Programming (XP)? While they focus on software development projects, I’ve found (as you’ll hear more about soon) that the methodology used for planning a software project maps very well onto a science or engineering research project, of scope ranging from a single experiment to a thesis or grant-driven research program.
One of the best practices for scientific writing (and I can vouch for this both from academic and professional experience) is the Planning Game from XP. It helps you break the project down into small pieces, clarifies your vision of what can and can’t (and should and shouldn’t) be done, forces you to estimate how much effort every little piece might take, and in the end makes you focus not just on small pieces but on the small pieces that provide the most value fastest.
Most important in research, it lets you adapt to changing conditions as you make progress. You end up closer to where you should be, and don’t have to revise burdensome outlines, or explain why you’re “off track” when you re-plan the remaining work every week or two. Instead, you can argue (to yourself, or watchers) that what you’ve done might change what you should do next.
It’s sometimes considered all hokey and management-consulty to anybody who has only been exposed to the slapdash talking-and-scribbling design-up-front model used in the Academy. But it’s one of the most rigorous, demanding, and rewarding approaches to planning around.
Unsolicited advice: Read a little about it, and see if it strikes a useful chord.