{"id":312,"date":"2016-12-12T12:30:33","date_gmt":"2016-12-12T12:30:33","guid":{"rendered":"http:\/\/deberker.com\/archy\/?p=312"},"modified":"2021-11-06T15:57:08","modified_gmt":"2021-11-06T15:57:08","slug":"tips-from-the-other-side-writing-a-thesis","status":"publish","type":"post","link":"https:\/\/deberker.com\/archy\/tips-from-the-other-side-writing-a-thesis\/","title":{"rendered":"Tips from the other side: writing a thesis"},"content":{"rendered":"\n<p>After a relatively painless month or so of writing, I\u2019ve finished my thesis. I\u2019m yet to be examined, so whilst I can\u2019t comment on how to write a <i>good<\/i>&nbsp;thesis, I\u2019ve had a few thoughts on the process of getting from start to finish. Given the surprising lack of information on writing PhD\u2019s (which is&nbsp;baffling since everybody in science either has one or has to write one), I thought I\u2019d collect together a few things I wish I\u2019d known earlier.<\/p>\n\n\n\n<h1 class=\"wp-block-heading\">Before you start<\/h1>\n\n\n\n<h2 class=\"wp-block-heading\">Take notes throughout<\/h2>\n\n\n\n<p>Your thesis discussion&nbsp;provides you with a <em>tabula rasa<\/em> on which to scrawl your thoughts about your field. Time and time again, I\u2019ve found that the most valuable insights into the frailties of a particular approach come when you first learn about it. These little voices are sometimes subdued once you\u2019ve worked in the field for some time. Operating within a certain framework for too long, you come to accept its assumptions more easily (perhaps because <a href=\"http:\/\/scholar.google.co.uk\/scholar_url?url=http:\/\/www.nature.com\/nrn\/journal\/v11\/n2\/full\/nrn2787.html&amp;hl=en&amp;sa=X&amp;scisig=AAGBfm2TBuMjwEMXrgU6to0mta5HbqzMTA&amp;nossl=1&amp;oi=scholarr&amp;sqi=2&amp;ved=0ahUKEwjb38y8ye7QAhXMJcAKHcCJCywQgAMIGigAMAA\">desires and beliefs are entangled<\/a>?).<\/p>\n\n\n\n<p>I wish I\u2019d kept a single word document (or <a href=\"https:\/\/www.evernote.com\">Evernote<\/a> note) with my initial reactions to all of the ideas that would go on to form integral parts of my thesis. Once you\u2019ve become expert, you could then sift through these&nbsp;naive impressions to separate out the ignorant from the insightful. These might then form the useful material for&nbsp;your <b>discussion<\/b>.<\/p>\n\n\n\n<p>Similarly, in&nbsp;your <b>introduction<\/b> you will need to provide a reasonably approachable explanation of the key concepts in your thesis. Capturing the aspects that helped <i>you<\/i>&nbsp;understand the idea is one of the easiest ways to do this. Once more, capturing these key points&nbsp;as you go along would make your life much easier! Similarly, if you\u2019ve spent some time teaching during your PhD, try to keep track of what works and what doesn\u2019t &#8211; this might help separate the explanatory wheat from the chaff.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Read some theses<\/h2>\n\n\n\n<div>\n<\/div>\n\n\n\n<figure class=\"wp-block-image alignnone is-style-default\"><img data-recalc-dims=\"1\" decoding=\"async\" src=\"https:\/\/i0.wp.com\/c2.staticflickr.com\/4\/3480\/3762597413_d820da2d19_b.jpg?w=660&#038;ssl=1\" alt=\"\"\/><figcaption>Disclaimer: plagiarism in science is less acceptable than in art<\/figcaption><\/figure>\n\n\n\n<p>Most institutions have an online archive of theses; many authors also provide them on their personal websites. Reading the theses of people you admire and respect is a good idea, and even a pleasure (there\u2019s a certain pseudo-intimacy which comes with reading the product of 3-6 years of somebody\u2019s life). Reading around gives you an impression as to the diversity of lengths and structures that are acceptable, which is surprisingly large. You can even read quite far away from your own field: if the author has done a really good job, the introduction ought to be intelligible even if the material is unfamiliar (see e.g. <a href=\"http:\/\/www.inference.phy.cam.ac.uk\/mackay\/thesis.pdf\">David Mackay\u2019s 89 pager<\/a>).<\/p>\n\n\n\n<p>If you\u2019re in cognitive neuroscience and fancy reading a few, I\u2019d recommend taking a look at <a href=\"http:\/\/www.fil.ion.ucl.ac.uk\/~lhunt\/doc\/HuntLaurence_Thesis_final.pdf\">Laurence Hunt\u2019s <\/a>(beautifully written, very deep introduction, largely&nbsp;focused on two experiments) and <a href=\"http:\/\/static1.1.sqspcdn.com\/static\/f\/1096238\/22752296\/1369317078327\/DemisHassabisThesis.pdf\">Demis Hassabis\u2019s<\/a> (written with an impressively confident and visionary tone [foreshadowing his future ambitions], focused on putting forwards a particular idea with numerous experiments in support of it). I also dipped into <a href=\"https:\/\/www.google.co.uk\/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=2&amp;ved=0ahUKEwiYl87sy-7QAhXJA8AKHVl-DzIQFgglMAE&amp;url=http%3A%2F%2Fwww.petersmittenaar.com%2Ffiles%2Fsmittenaar2015thesis.pdf&amp;usg=AFQjCNHF8haQlW0NwIhVQe436UCH5DM1Jg&amp;sig2=-_z8E3jWWNn0eScIabwvJQ\">Peter Smittenaar\u2019s<\/a> and <a href=\"https:\/\/www.merton.ox.ac.uk\/people\/dr-helen-barron\">Helen Barron\u2019s<\/a>, both of which are excellent.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Sharpen your tools<\/h2>\n\n\n\n<figure class=\"wp-block-image is-style-default\"><img data-recalc-dims=\"1\" decoding=\"async\" src=\"https:\/\/i0.wp.com\/i.imgur.com\/KbV6JeX.jpg?w=660\" alt=\"\"\/><\/figure>\n\n\n\n<div><i><\/i><\/div>\n\n\n\n<div><\/div>\n\n\n\n<p>Broadly speaking, there are three tools you\u2019re going to need to use to write your thesis (assuming you\u2019ve finished analysing your data): a word processor, a reference manager, and some sort of graphics program for your figures.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Word processing<\/h3>\n\n\n\n<p>In some fields LaTeX is the norm. In ours, we use Word, so that\u2019s what I can offer advice about.<\/p>\n\n\n\n<p>Thing is, you think you know how to use Word, right? I too considered myself pretty competent, and then proceeded to&nbsp;learn a new thing about Word every 3 days whilst writing my thesis. Here are the things you should master, before you really get cracking:<\/p>\n\n\n\n<h4 class=\"wp-block-heading\">Styles<\/h4>\n\n\n\n<p>I always thought these were an irritation. They are actually super useful. You probably know the concept &#8211; tagging different pieces of text with a style that you can then alter in order to instantly change the formatting of all of the text associated with that style &#8211; but their function extends beyond that. In particular, they\u2019ve very useful for grouping together similar elements (e.g. all of your chapter titles), which makes numbering + table of contents generation a dream. At the very least, you should set up:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>A series of <strong>headings<\/strong> styles (h1,h2,h3 etc.) to provide chapter headings, subheadings, etc. If you start with word\u2019s built in ones, these will be usefully numbered.\n<ul>\n<li>TOP TIP: you\u2019ll find that you want your Chapter headings to be <em>effectively<\/em> numbered (because you want the subheadings to be 1.1,1.2 for chapter 1, 2.1,2.2 etc. for chapter 2), but you probably just want them to read \u2018Chapter 1: \u2026.\u2019 rather than \u20181. Chapter 1: \u2026\u2019. You can neatly hide the number associated with a heading by selecting the number, right-clicking, selecting \u2018Font\u2019 and then ticking the \u2018Hidden\u2019 button.<\/li>\n<\/ul>\n<\/li><li>A style for your references<\/li><li>A style for your captions<\/li><li>A style for tables<\/li><li>A style for your footnotes<\/li><\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">Captions<\/h4>\n\n\n\n<p>Similarly to the styles &#8211; the real utility of these is that they automatically number and you can swiftly generate a table of figures. You can set these up to number according to your chapters, so that they inherit the numbering from your Header-1 style (so chapter 1\u2019s first figure is 1.1, chapter 2\u2019s is 2.1). Slightly non-intuitively, on the Mac the caption insertion comes under the \u2018references\u2019 tab. You can label both your figures and your equations in this manner.<\/p>\n\n\n\n<h4 class=\"wp-block-heading\"><b>Cross-references<\/b><\/h4>\n\n\n\n<p>I had a few supplementary figures which I didn\u2019t want to label like the figures, but I still wanted to include references to in the Table of Contents (TOC). You can achieve this by inserting Bookmarks and then inserting Cross References in the TOC. These will automatically update if the page numbers shift (as they frequently do as you add and remove things).<\/p>\n\n\n\n<h4 class=\"wp-block-heading\"><b>TOC\u2019s<\/b><\/h4>\n\n\n\n<p>Somewhere near the end you\u2019re going to need to insert a TOC and perhaps a list of figures. This is a breeze if you\u2019ve set up your styes and captions appropriately. Again on the Mac, TOC\u2019s are listed under the References tab on the toolbar.<\/p>\n\n\n\n<h4 class=\"wp-block-heading\"><b>Track changes<\/b><\/h4>\n\n\n\n<p>Well no. <b>Don\u2019t track changes.<\/b>&nbsp;With a thesis of 200 or so pages and several swimming pools\u2019 worth of blood, sweat, and tears, tracking changes is a bad idea. Poor old Word can\u2019t cope with the complexity of a month or so tracked changes. It\u2019s a much better idea to just save lots of different versions as you go along. I had a terrifying experience where Word started refusing to save the twelfth draft of my thesis. Track changes was the culprit.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Reference manager<\/h3>\n\n\n\n<p>I had written a few papers during my PhD, so I was fairly familiar with my reference manager of choice (<a href=\"https:\/\/www.google.co.uk\/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=1&amp;cad=rja&amp;uact=8&amp;ved=0ahUKEwigweDFze7QAhUpCMAKHQijAREQFgggMAA&amp;url=http%3A%2F%2Fpapersapp.com%2F&amp;usg=AFQjCNGAYfmmlzSFm3tOmMYOlkTRjyCbjg&amp;sig2=ntXp_-KGZcI13tiaHDOGdw\">Papers by Mekentosj<\/a>). However, there were a few hiccups along the way that are worth reflecting upon:<\/p>\n\n\n\n<div>\n<h4><strong>Format late<\/strong><\/h4>\n<p>In <a href=\"http:\/\/www.papersapp.com\">Papers<\/a>*, and many other managers, you insert citations with wild abandon, and hit \u2018format\u2019 when you want these bookmarks to morph into references in the format from your favourite journal. I found that life was much easier if you delayed doing this until the <strong>VERY LAST moment<\/strong>. Repeatedly formatting and unformatting takes a very long time.<\/p>\n<p>*Additional note for Papers users: leave your computer alone whilst your references are formatting! If you scroll around in the document it will MIGHTILY screw&nbsp;everything up.<\/p>\n<h4><strong>Check your references as you go<\/strong><\/h4>\n<p>Many programs automatically fill in the bibliographic information when you import a paper. which is awesome. Problem is, this process is &lt;100% fidelity. Particularly with citations that you pull in from less well curated sources (like Google Scholar), you can end up with all sorts of garbage. It\u2019s very depressing when you think you\u2019ve finished your thesis and then you have to spend 10 hours checking all of your references. Try and quality-check these when you insert them and avoid this pain. In my experience in Papers, trying to find Pubmed BibTex\u2019s worked best for high-quality citations.<\/p>\n<\/div>\n\n\n\n<h3 class=\"wp-block-heading\">Graphics<\/h3>\n\n\n\n<p>For figures from data, my advice (inspired by <a href=\"http:\/\/redishlab.neuroscience.umn.edu\">Dave Redish\u2019<\/a>s dictum to new PhD students, as reported by <a href=\"http:\/\/www.zebk.com\">Zeb KN)<\/a> is that you try and rely upon Matlab or Python or R or whatever you\u2019re analysing in to do all of the grunt work. Fiddling in Illustrator seems like a good idea, but if you need to change anything, you have to do everything again (side-note: for a glimpse of what algorithmic graphics might look like, check out <a href=\"https:\/\/www.google.co.uk\/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=3&amp;cad=rja&amp;uact=8&amp;ved=0ahUKEwjnuancz-7QAhWpBcAKHWZuB38QtwIIKDAC&amp;url=https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DZfytHvgHybA&amp;usg=AFQjCNFqYaZdykynoZg1Sz6osyy0kKfFCQ&amp;sig2=O8gCGk-idjNVuD_jV7SqZQ\">Stop Drawing Dead Fish<\/a> by the <a href=\"http:\/\/worrydream.com\/#!\/LearnableProgramming\">incredible Brett Victor<\/a>).<\/p>\n\n\n\n<p>In Matlab, <a href=\"http:\/\/blogs.mathworks.com\/loren\/2007\/12\/11\/making-pretty-graphs\/\">check out this tutorial on making publication-ready figure<\/a>s. I&#8217;d advise <a href=\"https:\/\/uk.mathworks.com\/help\/matlab\/ref\/startup.html\">editing your startup file <\/a>to alter the default figure properties to make them better looking and easier to read (e.g. changing font sizes, get rid of horrible grey background). For complex multi-panel figures, I found <a href=\"https:\/\/uk.mathworks.com\/matlabcentral\/fileexchange\/20003-panel\">Panel<\/a>&nbsp;to be a useful toolbox.<\/p>\n\n\n\n<p>For other figures, you can use <a href=\"http:\/\/www.adobe.com\/uk\/products\/illustrator.html\">Illustrator<\/a> or <a href=\"https:\/\/www.gimp.org\">GIMP<\/a>&nbsp;etc.. I don\u2019t have anything particularly useful to say here, but some time savers:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Make all of your figures the same width. That way they won\u2019t shrink or grow when you put them into a word document and adjust them to fill the page, and so your font sizing will remain consistent.<\/li><li>Some useful illustrator shortcuts (on Mac):\n<ul>\n<li>Cmd K allows you to adjust the \u2018nudge\u2019 size i.e. the distance something moves when you press the arrow key. Very useful for shifting between gross and detailed work<\/li>\n<li>Cmd- and Cmd+ to zoom in and out<\/li>\n<li>Hit V to change the current tool to \u2018Move\u2019<\/li>\n<li>Cmd alt&nbsp;; locks\/unlocks&nbsp;your guides [NB you should use guides: <a href=\"https:\/\/helpx.adobe.com\/illustrator\/using\/rulers-grids-guides-crop-marks.html\">here&#8217;s a guide-guide]<\/a><\/li>\n<li>X toggles whether you\u2019re selecting the fill or stroke of an object<\/li>\n<li>Shift-X switches the stroke and fill (so if you have black stroke, white fill, you\u2019ll have the opposite after hitting shift-X)<\/li>\n<\/ul>\n<\/li><li>Illustrator also has text styles &#8211; like Word, this can be useful for swiftly altering lots of text (e.g. your axis labels or sub-figure numbering)<\/li><\/ul>\n\n\n\n<h1 class=\"wp-block-heading\"><b>Actually writing&nbsp;your thesis<\/b><\/h1>\n\n\n\n<p>Hopefully by this point in your PhD you\u2019ve got a reasonable idea about how best to sit down and work. I found that the same principles applied here. Some people like to use micro-scheduling methods e.g. the <a href=\"https:\/\/en.wikipedia.org\/wiki\/Pomodoro_Technique\">Pomodoro technique<\/a>, in which you complete a series of short work-rest bouts designed to ensure total focus whilst working. I generally don\u2019t find these useful unless I\u2019m doing something extremely boring. Most of the time, I found that chunks of about 2 hours worked better for me, and that the earlier I started in the day, the better.<\/p>\n\n\n\n<p>One of the things I thought about a bit were ideas about fatigue and disengagement (I read <a href=\"http:\/\/www.robkurzban.com\">Rob Kurzban\u2019s&nbsp;<\/a>superbly&nbsp;titled <a href=\"http:\/\/press.princeton.edu\/titles\/9271.html\">&#8216;Why everyone (else) is a hypocrite&#8217;&nbsp;<\/a>a while ago and it\u2019s great; here\u2019s a <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24304775\">related review paper he wrote with Joe Kable<\/a>). I figured that increasing the value of work, and decreasing the value of alternatives would make life easier. The concrete implementation of this was putting on the most interesting music I could afford to listen to whilst still working reasonably well. For deep work this meant <a href=\"https:\/\/www.google.co.uk\/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=1&amp;cad=rja&amp;uact=8&amp;ved=0ahUKEwiHrKfx0e7QAhWqI8AKHRRmBFUQtwIIHTAA&amp;url=https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DbXYHnYKuRy0&amp;usg=AFQjCNHP57UpHRI14gD4ILCEX-fYVFVi8Q&amp;sig2=iPkWKXiHEvqDWWyv2jN0bg\">Bach<\/a> or, if I was falling asleep, <a href=\"https:\/\/www.google.co.uk\/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=1&amp;cad=rja&amp;uact=8&amp;ved=0ahUKEwigrI_70e7QAhVHL8AKHe77BwsQ3ywIHDAA&amp;url=https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DtVqPx5mUj0g&amp;usg=AFQjCNFxp2VrQR41pvZZAoOImsVp7-Y_SA&amp;sig2=eEJ6d13J_Cf6KVGKr4bjzQ&amp;bvm=bv.141320020,d.ZGg\">Glitch Mob<\/a>; for lighter stuff (editing figures, checking references) I listened to stuff with lyrics that I knew well (e.g. <a href=\"https:\/\/www.google.co.uk\/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=9&amp;cad=rja&amp;uact=8&amp;ved=0ahUKEwj7uZCF0u7QAhUhD8AKHcHjBO0QuAIIUTAI&amp;url=https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DQ3VjaCy5gck&amp;usg=AFQjCNEPEZUJZNENgl4PIuvC_6kH7-fg7A&amp;sig2=jqPUQ1KV_S2ewSEqMJQxkw\">Bon Iver<\/a>). Cups of tea are also useful for increasing the momentary value of a state; if you\u2019re drinking a lot of tea, green tea is good to prevent becoming totally wired. If I was still working at 7pm, I often tried to shift to more discursive work and had a glass of wine or a beer (if you\u2019re in Bristol, <a href=\"http:\/\/wiperandtrue.com\">buy this<\/a>).<\/p>\n\n\n\n<p>If I was having difficulty focusing, I sometimes used <a href=\"http:\/\/noisli.com\">Noisl<\/a><a href=\"http:\/\/noisli.com\">i<\/a>&nbsp;for pleasant woodland sounds. It&#8217;s a good way to persuade yourself that you&#8217;re in the Alps when really you&#8217;re in Bloomsbury.<\/p>\n\n\n\n<p>The darker side of \u2018decreasing the value of alternatives\u2019 &#8211; I wrote my thesis at home with my parents, and didn\u2019t tell any of my friends that I was home. So I really had very little to do other than writing a thesis and other wholesome things (chop firewood, run, swim, and play the piano). I think this made it easier to focus.<\/p>\n\n\n\n<h1 class=\"wp-block-heading\">Finally&#8230;<\/h1>\n\n\n\n<p>One of the last things you need to do is write your acknowledgments. I found this to be a very enjoyable and fulfilling experience (I think I now appreciate&nbsp;why <a href=\"http:\/\/jamesclear.com\/gratitude-habit\">practising daily gratitude<\/a> is&nbsp;good for life satisfaction). It&#8217;s a chance to think about the people who helped you along the way, and the journey you&#8217;ve been on. Its the warmest, most personal part of the thesis &#8211; and probably the only bit that your friends will read :).<\/p>\n\n\n\n<p>Good luck, and <a href=\"mailto:archy.deberker@gmail.com\">let me know<\/a>&nbsp;about your own experiences + advice.<\/p>\n\n\n\n<figure class=\"wp-block-image is-style-default\"><img data-recalc-dims=\"1\" decoding=\"async\" src=\"https:\/\/i0.wp.com\/imgs.xkcd.com\/comics\/thesis_defense.png?w=660\" alt=\"\"\/><\/figure>\n","protected":false},"excerpt":{"rendered":"<p>After a relatively painless month or so of writing, I\u2019ve finished my thesis. I\u2019m yet to be examined, so whilst I can\u2019t comment on how to write a good\u00a0thesis, I\u2019ve had a few thoughts on the process of getting from start to finish.<\/p>\n","protected":false},"author":1,"featured_media":344,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"hide_page_title":"","_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[9],"tags":[],"class_list":["post-312","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-scholarship"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.9 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Tips from the other side: writing a thesis - Archy de Berker<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/deberker.com\/archy\/tips-from-the-other-side-writing-a-thesis\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Tips from the other side: writing a thesis - Archy de Berker\" \/>\n<meta property=\"og:description\" content=\"After a relatively painless month or so of writing, I\u2019ve finished my thesis. 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