Archives: Scientific life

Hug an advisor today.

Hug an advisor today.

It’s inevitable.  Put two or more grad students1 in a room, and sooner or later the talk will turn to advisors;  wait a little while longer and chances are good that someone will start complaining about their advisor.  This shouldn’t be surprising.  Bosses all over are fair targets for griping, and the power imbalance inherent to the student-advisor relationship certainly doesn’t help matters2.  After being stuck in a lab together for several years, it’s a wonder that the average science department doesn’t have hallways littered with bodies.

But there’s a flip side to this, which I think might be under-appreciated:  advisors can also be awesome.  No relationship like this is going to be perfect, but a good advisor will teach you, guide you, and give you a leg up the academic ladder.  They’ll help you when you trip and faceplant, they’ll give you the advice you need (even if you don’t want to hear it), they’ll introduce you to the right people, they’ll make you better scientists.

Grad student


I’ve gotten very lucky along the way3.  Michael advised me on the undergraduate independent study that first inspired to take the idea of a research career seriously;  he also humoured me when I bit off a project that was far too much for me to chew and helped me sort through the resulting mess.  Pete, my M.Sc. advisor, got me into studying biological questions and gave me a place to work when my Ph.D. went sideways.  Luc-Alain, my Ph.D. advisor, turned me into an independent scientist and put up with far more than I had any right to ask for.  Finally, my postdoc advisor Mark has to be one of the nicest (and smartest) people that I’ve ever met and has been supportive in all the ways that have made being a postdoc enjoyable.  I’ve been privileged to work with a succession of people who’ve taught me and made me better at this science thing, and today I’d like to take a moment to be thankful for them.

Many people have poor relationships with their advisors, and there are a lot of valid questions to be asked about the grad school experience.  I don’t want to diminish the problems of anyone who has had a poor relationship with their advisor (I’ve known my fair share of bad advisors, even if I’ve been fortunate enough to avoid having them myself).  But if you have a good boss, now might be the time to take a moment and reflect on the things that they’ve done for you.  Give them a hug, a handshake, a friendly email, or a fresh data set.  And one day, when you’re in their position:  remember what it felt like to be the student.

  1. Honours students, postdocs, RAs, …
  2.  And yes, people have done research on this.  Are you surprised?
  3. Seriously lucky.  I didn’t do any of the things you’re supposed to do when picking an advisor.

Some tips for an academic job talk over Skype…

I recently had the experience of applying for a postdoctoral position at A Very Important University and made the shortlist to be interviewed.  Now, let’s face it, that’s a pretty terrifying thing to start with;  it wasn’t made better by the fact that I was doing it over Skype to a location most of the way around the world.  Visions of technical glitches, bad sound quality, and an overall horrible experience both interviewers and interviewed haunted me.  So, I spent several days polishing my talk, thinking up ways to make the Skype process smoother, and even reached out to Twitter for advice.  And boy, did I get it!  There were some great suggestions out there, a few of which really saved my bacon.  Thus, to save you the trouble of figuring all of this out for yourself, I’m going to share what I learned with you.

Your voice here: social media for academics, objections edition.

“Twitter, huh?  That’s just a bunch of people talking about what they had for lunch, right?”  *headdesk*

Hands up if you’ve heard that one.  Or any of the other clichéd objections to the use of social media by academics:

  • “I could be writing papers instead of fooling around on Twitter!”
  • “I talk to too many people already.  Why would I go looking for more?”
  • “It’s all just noise.”
  • “I don’t want to have to deal with uninformed commenters.”
  • And many, many more.

Academics and social media: the talk that you helped me write!

When I asked about academics’ use of social media, I got a gratifying number of responses that helped inform the content of the talk I’ll be giving next week at the GSA 2013 conference here at UNSW.  I even used some direct quotes from people who responded, which was a great help in giving context to the benefits of social media for scientists.  Since I’ve finished the talk now, I thought that it would be appropriate to share what was essentially a crowd-sourced talk back to the community.  So, take a look, and if you have any thoughts or suggestions, please feel free to leave a comment.  One thing to note:  this is a longer version of the talk that I’ll actually giving;  my practice talks went over the 12 minute limit, so I was forced to cut some slides (which I anticipated).

View this on SlideShare, or page through below:


Academentia and the iPad: an update from 2010.


Daniel Bogan via Compfight


Prompted by a conversation on Twitter yesterday, I revisited my old ‘how I use my iPad in academia’ post and since it’s been about 2.5 years, it seemed time for an update.  So, some quick notes on how I’m using it now:

  • Reading.  I don’t use iAnnotate any more, since Goodreader added annotations and nice Dropbox syncing.  I keep a Dropbox folder with my current ‘to read’ pile of articles and books, which is slurped up to my iPad by Goodreader.  I read articles on the iPad, annotating and highlighting as I go, and then I sync it back to Dropbox.  Back on my Mac, I file the papers away in BibDesk (I haven’t seen a use case for ‘social’ reference managers like Mendeley yet – at least for me – and I’m not sure if I’m going to any time soon).  Other ebooks, including an increasing number of textbooks, are read via the Kindle app and iBooks.  I prefer the iBooks software, to be honest, but right now I read it where I can find it.  Truth be told, I’ve gotten so used to ebooks now that when I can’t find something in digital format it noticeably irritates me.
  • Calendaring:  I sync my Google calendar to my iPad and iPhone, and read my calendar on the iPad with Agenda.  I prefer Agenda for the clean interface, though it’s a minor preference for me.
  • Organisation:  I wrote back in 2010 that Things was moving too slowly for my taste and that I was going to search for alternatives, but I never found one I was comfortable with.  I tried a lot of them:  Today, Remember the Milk, Appigo’s Todo, Wunderlist, and more.  All of them had some sort of problem that turned me off, be it bad syncing or subscription plans for useful services (hell, no) or something else that bugged me enough to make me switch back to Things.  I honestly don’t think that Cultured Code really deserves as much of my money as they’ve gotten, but I keep coming back to them for some reason.  This is a highly individual thing, though, and your mileage is going to vary.  A lot.
  • Social media, of course:  I still prefer the stock Twitter app on the iPad over alternatives so far, though if I do switch it will probably be to Twitterific.  I’ve written blog posts using Blogsy and I use the WordPress app to administer the blog.  I’ve made a few Skype calls with the iPad, which turned out all right (though I prefer wired connections for video calling), and the iPad is really the only way that I check Facebook any more.
  • News:  now that Google Reader is going the way of the dodo, I’ve switched to Feedly and I couldn’t be happier.  For saving stories to read later, I rely on Pocket.
  • Navigation: I’ve found that Apple Maps has gotten much better recently, so I’m no longer unhappy that Google Maps isn’t on the iPad (still not sure why that is, though).  I use maps more on my phone anyways.
  • Note-taking:  This is a category with a lot of change since 2010.  Nowadays I’ve switched largely to Notability for note-taking.  I find its handwriting set up easy to use when I’m jotting down notes in a meeting or a seminar, and it’s intuitive for scribbling on manuscripts and sending them back to colleagues.  I use a stylus for these tasks;  I’ve enjoyed the Pogo Connect, but my wife enjoyed it so much for drawing that she actually stole it from me.   So while I wait for the Adonit Jot Touch to shop (grrr, delayed), I’m using a $10 Dausen stylus that actually works quite well. I’ve also used Noteshelf as a notetaker for its nice writing tools and early integration with the bluetooth styli like the Pogo Connect;  when the Touch comes, I’m not sure exactly what I’ll end up using full time.   And when I’m looking to do more free-form scribbling, or I’m noodling with equations or just sketching something, I like Paper; it’s simple but pretty and powerful enough to get the job done.  I’ve also become more and more reliant on Corkulous to make notes in.  Unfortunately, despite protestations to the contrary, Appigo shows no sign of giving a crap about further development of Corkulous, and I’m reaching the limits of what the app will handle in terms of notes.  Also unfortunately, there doesn’t seem to be a good replacement out there, so I’m considering making one myself.
  • Information collecting:  some people would put apps like Evernote into the notetaking category above, and the Evernote + Penultimate setup works quite well for some people;  I haven’t looked at it in a while, but I may revisit it.  Until I do, though, I’m using Springpad as a dumping ground for random bits of info that I need (travel plans, receipts from conferences, paper work I may need to reference, books I want to buy, etc).
  • Mathematics and programming:  when I feel like playing around with a bit of math or I need to plot a quick graph, I use apps like SpaceTime1, PocketCAS, and Quick Graph.  Programming on the iPad is still a bit of a non-starter, though that’s starting to change a bit.  I’ve had fun playing with Codea, which embeds a Lua interpreter, and if you feel like learning Haskell, there’s iHaskell (must have an internet connection, though).  I recently used Codea to whip up a quick simulation of genetic drift (Fisher-Wright model), and it worked great.  I’ve seen a few Python apps and the like, but I haven’t had any experience with them;  if you had, please leave a comment!
  • Drawing / diagramming / presentation :  Another category with big changes to it.  When I last wrote about academic iPad usage, there wasn’t much to speak of here.  In the intervening time, though, this space has exploded.  Now, I use apps like Procreate (others like Sketchbook Pro) to sketch and draw with the Pogo Connect,  iDraw to create vector diagrams for talks and posters, and Omnigraphsketcher to work up quick hypothetical graphs.  Most of this gets fed into desktop apps like Keynote or Pages (or other design programs);  the iPad versions of these apps are good as well, and I use Keynote regularly to present with, but I’m still hamstrung by the lack of font support in Keynote for iPad.  Another long-awaited and massively useful tool to arrive is LaTeX snippet tools;  on the desktop, I use LaTeXiT pretty regularly, and now apps like Mathbot are serving the same purpose for me on the iPad:  I can write a quick line of LaTeX and copy the typeset equation into another app like Corkulous.
  • Writing: big changes here, too, driven by changes in my desktop workflow.  With my recent shift to using Markdown as a major format for writing, I’m now free to use some of the great cloud-syncing editors for the iPad to start things off.  So, a lot of my papers, blog posts, etc. now start their lives in Byword, which is incidentally the first app to really turn me on to iCloud syncing.  When I have to interact with Microsoft formats – yuck – I use still use Quickoffice.  LaTeX on the iPad has come a ways, with apps like Texpad, but I still find them too clunky for common use.  I’ve also gotten into collaborative writing of LaTeX through web apps like Spandex (and a new one that I’ve been meaning to try, Authorea), so I’m not really fussed about dedicated apps for LaTeX any more.
  • Misc: A few other apps I can’t live without include Dropbox, OPlayer HD for entertainment on the go, Calcbot for quick arithmetic, Convertbot to … well, convert stuff, Photogene / PS Express for quick photo edits (especially to screenshots I take to paste into other apps), and probably a dozen others that I use regularly but can’t remember right at this moment.

Going back to my old post, it’s clear that my usage of the iPad has changed significantly since I last wrote about it.  Some of the frontline, day-to-day apps that I use have changed or clarified (e.g. I use only Goodreader now instead of GR+iAnnotate), and entire new uses for the device have popped up, like drawing and writing in Markdown.  Increasingly, the iPad has become an indispensable part of my daily workflow, and though I could live without it, I certainly don’t want to!

What are your favourite apps and workflows for mobile devices (iOS or otherwise)?  If you have any thoughts, please leave a comment or let me know on Twitter.

  1. which is apparently now called MathStudio?

Are grad students just lonely?

I was reading a paper today on computational modelling approaches to an interesting information situation known as the ‘standing ovation problem’, by Miller and Page (2004) (free pdf here), when I came across this nugget:

Methodological perspectives can be deeply ingrained. Prior to presenting the SOP to graduate students in economics, we tested it on Cal Tech undergraduates. Though Cal Tech undergraduates are hardly a random sample, we found that their modeling efforts differed in fundamental ways from those of graduate students in economics. The undergraduates assumed that individuals sat next to close friends (or, even went to the lecture with dates). In contrast, very few economic graduate students included the possibility of friends in their models. This difference might be a reflection of the social life of budding economists, but we remind you that the comparison group here is Cal Tech undergraduates. We suspect that the divergence in assumptions is much more due to the emphasis on individual choice that pervades most of modern economic theory, rather than social differences between the two groups of students. (p.9,emphasis mine).

I make no comment, but I invite comparison to the students of other disciplines or the reader’s own experiences.

Memoir of an academic talk.

tl;dr … well, honestly, go read something else if you don’t like long form.  This is 3600 words of navel-gazing detail, and I’m not about to apologize for it.

A companion piece to my earlier post on the process of designing a poster, this post deals with the talk on the same material for a different conference (vastly different audiences, so I don’t mind overlapping).  As I said for the post on designing the poster, this is a snapshot, or series of snapshots, of my process for doing science and preparing talks.  It’s not the whole picture, and I’m deliberately  exposing the warts and bumps that go with doing science;  I don’t get to control the image you form of me as well as I otherwise might, but I feel that the resulting material is more honest and informative.

In any case, I hope you enjoy it.  Please leave feel free to leave comments or questions, and I’ll do my best to answer them.


– Monday, July 23, 2012:  The ISBE 2012 conference is a couple of weeks away, so it’s time to start thinking about the talk.  The initial steps will be a little slow, but today I’ve created the presentation file as a symbolic step.  I haven’t yet conceived of the overall visual theme of the talk, so for now I’m adopting a simple black  on white approach. 

– Thursday, July 26 4:30 p.m. I’ve got about a half an hour before I need to leave the lab to go meet my long suffering wife for dinner.  Time to outline some content!  I’m working quickly, creating new slides and just typing main ideas of the story I’m telling into them.

– 4:51 p.m. 20 minutes later, I’m done a really quick outline.

A couple of things to note.  First, considering that this is a 12 minute talk, you may be wondering if 22 slides is too much. Yes, and no.  For most people, 22 slides is too many for this length of talk;  a good rule of thumb is – depending on the density of your slides – allow for at least a minute for any slide you’ll be saying more than ‘hello’ over.  This is a mistake that I see people make time and time again:  they make hugely dense slides with dozens of graphs, and then leave themselves about 15 seconds per slide.  This won’t work.  They either end up blasting through slide after slide of results, or they go way over time1 .  Aim for simplicity, and remember that simplicity is hard.  Simplicity doesn’t mean dumbing down your message, it means presenting your message in as straightforward and audience-appropriate2  a fashion as possible.  On the other hand, I deliberately present more slides with fewer ideas on each one;  this is a conscious strategy aimed at controlling what the audience is seeing and thinking about on a more fine-grained level.  However, this is a more difficult approach, and you should be careful about adopting it.  Long story short, if you have more than about 1 slide for every 30 seconds to a minute, you should have a good reason why. Also, the outline is hardly set in stone.  As when I did the poster, it’s an iterative process which will lead to me adding and subtracting material as I get into the content and the design.  I’ve already got some ideas that may add in a few slides, so I’ll probably need to subtract some elsewhere.

– Monday, July 30, 4:36 p.m.  Squeezing in a few minutes to work on the slides before I head for home.  I don’t have a cohesive plan for the design of the slides yet, so I’m going to iterate the content a little and see what suggests itself.

– Tuesday, July 31, 11:30 a.m.  Only got a few minutes in on the talk yesterday before I got distracted by an ‘emergency’ (read: time-suck).  I just realised this morning that I really need to create two versions of this talk, because I’m going to be giving it at a couple places I’m visiting in Europe after the conference.  This means that I need a 12-minute version for ISBE, and a 45-minute-ish version for the seminars I’ll be giving.  This isn’t as bad as it looks, because creating the 12-minute version requires cutting out a lot of material that I would otherwise put in;  while it makes for more work creating slides for the longer version, it’s more relaxing because I can afford to go into details that I would have to otherwise avoid in the shorter version.  This post, however, will focus on the 12-minute version which I will create first.

– 4:20 p.m. It’s been a bit of a slow day, but some of the pieces are starting to come together.  I’ve got a few of the visual ideas worked out, and though there is a massive amount of work left to do, at least I’ve got a direction.

You may notice a few things.  First, I’ve littered the slides with notes to myself explaining where I want to go with that slide, reminders about content to add or delete, and even notations on which notes might be suitable to cut from the final version.  Second, if you look closely, some of these images are decidedly low-res.  That’s because they’re “comps” of stock photos (from iStockPhoto), which are super-low-res versions that are watermarked so as to be unusable in a production document.  They are, however, useful for trying things out and deciding what image works best before you lay down money for the final image file.  This lets me play with the slide deck before committing (an example is the image of the dog and the bat;  I’ll only use one when I discuss rabies, but I’m trying them out to see which I like better), and it might even be possible to find free alternatives to the images I’ve used.  The final thing of note is that I haven’t addressed the typography of the presentation yet;  the font used in the slides so far is Keynote’s default Gill Sans, but my next step is to choose some appropriate fonts now that I have a bit of content in place.

– 2:36 a.m.  I’ve been working for the last three hours transcribing every common name and genus-level-or-above taxonomic name from the index of Odling-Smee et al’s monograph on niche construction in an attempt to set the stage for why I’m giving this talk;  namely, that viruses are under-represented here.  To make this point visual, I’m turning it in a word cloud (you can see the placeholder I whipped up in the slides above).  I’ve reached the T’s and I have to stop now because otherwise I’ll be doing this all damn night.

– Wednesday, 12:26 p.m  Back to it, and I’ve finally finished the index.  Now to throw it into R (using the “wordcloud” package), pretty it up, and insert it into the talk!  (And yes, I *will* go way too far for a detail no-one will care about).

– 1:06 p.m.  Here’s the new placeholder that I’ve created in R.  It’s still a placeholder because I’m going to try to match the fonts and colors to the rest of the slides;  making those decisions is the next step.


– 4:25 p.m.  I’m ‘auditioning’ some font and colour scheme choices.  To do this, I’ve duplicated my presentation and slides with in it, and I’m applying various styles to see how they work.  I’m looking for a bold, attention-grabbing combination, because I want this to stand out from a sea of similar-looking talks;  since I’m not adopting any sort of high-concept approach for this talk (mostly due to a lack of time!), I’m focusing on using typography and colour in a more aggressive way than is usual.  With that said, I could really use my wife’s designer eye on this, because I’m having anxiety attacks over what combinations might work.  I like the use of Bebas Neue and a script font for the headers, but I’m having trouble with a body font (because neither of those choices work well as body fonts).  I’m in a bit of a grey area because the presentation really only has a couple of blocks of text that need to be set, so I need to balance readability with mood.

Incidentally – and this is important – I’ve also been ducking into an unused conference room with a project to try this out on the bigger screens.  Always try your talk slides out on a setup that is as close to the final venue as possible.  You want to make sure that the colour combination that looks great on screen actually works when you project it!

– Thursday, 4:36 p.m.  I’ve been working on the slides throughout the day, in and amongst other things on my todo list.  Today I’ve been focusing on the results section, which has seen some progress.

I’ve made some subtle modifications, including breaking the green color of the palette into a brighter green for text on black slides (like the title slide), and a softer green for backgrounds.  If you compare this snapshot to the previous one, you should be able to see what I mean.  Also, I’ve started redoing my figures to use the fonts that I selected for the talk.  It’s a small thing, and perhaps no-one would consciously notice, but I believe in minimising friction for the viewer;  different fonts and designs between parts of the talk can be jarring even if the audience can’t figure out why, and I want to avoid that as much possible.  It may not be entirely doable (I still have to figure out a better way to present that tree, for instance, and I’m not sure if I’ll be able to find a way to change the font on that), but I’ll go as far as I can to homogenise the design.

– 4:52 p.m. I’ve ducked into the  conference room to check on how the slides are showing up on the screen.  I’m generally happy with it so far, but projecting it makes it clear which version of the word cloud I’m going to keep;  the script version is painful at large sizes.

– 11:04 p.m.  I’m continuing to work on the slides.  I’ve been going back and forth between the bat picture and the dog picture for rabies (another potential example of viral niche construction, methinks), but now it finally occurs to me that the dog picture just doesn’t read well to anyone but me.  So, it has to go.

– 11:55 p.m.  I’m working on a slide that suggests a speculative link between viral niche construction and sociality;  this is based off of work on a cat virus, so I’m using a picture of kittens to illustrate the point3.  My first version, though, illustrates a design issue:  if you use a picture that has eyeballs in them, the rest of the slide has to relate to the eyeline (somewhat similar to the concept of eyeline matching in film editing) or else the viewer gets uncomfortable.


As you can see, the kittens are looking down and I have text above them;  this creates a visual tension that has no reason for being there. Putting the text below the kittens, besides looking bad  because of the shading at the bottom of the photo, also fails because the kittens are all looking in different directions.  Once I’ve identified this problem, I have to find a new photo;  thankfully, the internet seems to be big on cats (who knew?).

– 12:09 p.m.  I’m wrapping up for the night.  I’ve made reasonable progress today:  aside from a set of slides in the middle that I’ve engaged my wife to do drawings for, the last thing that I need to do for this first, rough version is to redraw the phylogenetic tree and find a way to present it.

If you’re paying attention, you’ll notice that I’ve still got too many slides.  I’m going to be practicing this talk (including a lab practice talk next week), but it’s almost certain that I’m going to need to cut some material.  Like any other content editing, there’s going to come a point where I have to kill my darlings. This doesn’t bother me as much as it normally would, because most – if not all – of what I cut will end up going into the longer seminar version of this talk, where I’ll be making the same case in greater depth.  You can see that I’ve already started doing this, as I’ve moved some slides after the acknowledgements at the end;  these will be included in the longer version unless I cut them entirely.

- August 6, 2:26 p.m.  I’ve been fiddling with the slides over the last few days, just trying a few things out and moving things around.  I’ve decided on one of the cat photos, the middle one, as it’s the most engaging; my wife pointed out that this is because of the way they’re looking, including the one staring straight at you.  I’ve got her working on producing a diagram for me to explain the way baculovirus manipulates its hosts, which goes in the blank spot in the middle, and I’ve placed images in there to help get me over the hump.  Today, I need to fix the phylogenetic tree and place it in;  whether I use it in the short or long version, I’ll need it at some point.  And I want to get the short version done tonight if I can, because I plan on practicing it tomorrow before I present it to the lab on Thursday.  So here’s the current state of affairs:

– August 7, 2:15 a.m.  Small refinements now.  Unfortunately, even in consultation with my talented wife I couldn’t come up with a good illustration  for the slide I’ve been holding on the various genotypes;  thus, I’ve decided to break down and use (gasp) text.  I know, I know.  In the mean time, I’ve also managed to refine the tree diagram (which requires further refinement, but the pieces are there now).

– 1:02 p.m. I’m searching for images to illustrate the hypothetical genotypes (zombie, non-gooey;  non-zombie, but gooey).  I’m having trouble meeting the criterion of Creative Commons or stock that I can purchase as well as being the right image for the idea.

– 3:02 p.m. I’ve found images and replaced the phylogenetic trees. I’ve also replaced a slide that I apparently deleted at some point along the way without noticing;  you’ll notice that the second slide in the talk is missing if you compare the last two snapshots above.  Using OS X’s Versions, I was able to graphically browse to an old version from a couple of days ago, find the slide, and drag it and drop it directly into the current version of the talk.  It may not be git, but it’s still cool.  And it’s also a good lesson:  keep old versions!  Keep backups!

I think that the short version of the talk is in good enough shape now that I can practice it, so I’m going to go see if I can find a room with a projector to play in.  If you can, it’s best to practice talks under conditions that are as close to the real thing as possible;  that means standing up in front of a room, even if it’s empty, and playing your slides behind you as you address the room.  Muttering under your breath as you stare at the slides may seem like a good way to practice, but you’ll never find the timing problems and flow issues unless you force yourself to stand up and actually talk.

– 4:52 p.m.  I just finished practicing my talk for the first time.  As I expressed on Twitter:

Seriously, people.  Practice your talks before you give them.  Then, practice them again.  And then three more times.  What I’ve learned is that I need to do some rearranging, because the flow of ideas in the talk didn’t quite work;  I’m going to jettison a few slides and use them in the longer version, and I’m going to see if I can add a few elements to the text that I abruptly noticed were missing.

– August 8, 12:24 a.m.  I’ve spent some time rearranging slides and writing down what I want to say on each slide.  I like to have my material memorized to the point where I can present it without notes, but I sometimes find that writing down key points of each slide when I’m practicing helps me to achieve that goal.  Here’s the current state of the short version, with changes incorporated.

I’m still struggling with some aspects of the design.  In particular the genotype slide (slide 17) is bugging me;  I had to add the model diagram because it was too difficult to explain the genotypes by referring to the parameters alone.  Now that I think about it, though, I may try playing with text instead spelling out the assumptions.  But that can wait until tomorrow, because I need some bloody sleep.

– 11:49 a.m. Back to the conference room to practice again!

– 12:42 p.m. I tried it three times, but I’m still coming in too long.  The talk is supposed to be 12 minutes with 3 minutes for questions, and I’m clocking in at 18-19 minutes.  It looks like I’ll need to pare some things down to put into the longer version.  It breaks my heart, but I think that I’ll have to put the word cloud into the longer version;  it’s a great image, but under time constraints it’s not pulling its weight.  When that happens, you need to kill your darlings.

– 1:07 p.m.  I’m cutting it to the bone, but I’ve got things down to 20 slides (simplicity is hard).  The room I was using is booked right now, I’m going to have lunch and do some work until it’s open and I practice again.

– 4:35 p.m.  I’ve practiced this thing backwards and forwards, but I can’t get the time down!  From 19m 28s to 14m 12s, I’m still two minutes over.  I may have to remove the phylogenetic results, though it kills me to do so.  I know that they’ll be in the longer version where I’ll have plenty of time to go over them, but it still pains me.

– August 9, 12:49 a.m.  I’ve spent the last couple of hours finalising the design, including replacing all of the comp images with the full versions that I’ve purchased.  It’s pricy ($86 AUD for 50 credits on iStockPhoto), but worth it.  If you can’t afford to pay for good images, then find them under a Creative Commons license on Flickr, or take them yourself.  But always use high-resolution images!  And don’t steal them.

– 11:58 a.m.  Okay, further practicing yields no advances.  I’m going to have to cut the phylogenetic results in favor of asking people to talk to me if they’re interested.

12:45 p.m.  11 minutes, 58 seconds!  Finally, we’re ready.  Here’s the state of the talk before I give it to the lab this afternoon.  Don’t forget that I’ve got extra slides tacked on (after the slide with the big Thanks! on it).  I’ve also added a slide with photo credits;  again, acknowledge your sources and don’t steal other people’s work.

– 4:45 p.m.  Well, I gave it to the lab (and a distinguished visitor!), and things went pretty well.  It’s clear that the work I put into the design and practicing the talk has paid off, because I received multiple comments that it was a very polished talk.  There were some good questions, and a couple of good suggestions for minor improvements, but otherwise it’s done and dusted!

- August 11, 12:39 a.m.  I leave for the conference tomorrow afternoon, and I’ve just thrown my talk files onto my USB drive – and I’ve got them in my Dropbox, on my iPad, and in my email. You only have them in one place?  You’re begging for a disaster.  But, I digress.  At this point, it’s worth reviewing the lessons I learned while designing this talk.  First and foremost, as I wrote above, simplicity is hard, and you have to be prepared to kill your darlings.  I had more content than I could present, so I had to cut it down and make it as simple as possible.  Practice is king.  I practiced this talk no fewer than eight times to an empty room, and it paid off;  the people I finally gave it to were impressed at how fluent I was.  What they didn’t see was the hours I spent stumbling and swearing and fumbling my words.  If you suck in private, you’ll be great in public.  And finally, iterate, iterate, iterate!  To make good posters and good talks, you need to advance and revise, create and critique.  If you scan back through this post and look at nothing but the slide pictures I’ve included, I hope that you’ll get a feeling for this.

So, if you’re still reading after all of that, thanks for sticking with me!  I hope you learned a little something, and I welcome your thoughts.  But for now, I’m off to Sweden!

  1.  A minor rant:  if you go over on time on your talk at a scientific conference, you are being rude.  You’re holding up other presenters, you’re making it difficult for people to get between talks on time, and you’re generally making things worse for everyone.  I don’t really care about your excuses, because 95% of the time what they boil down to is ‘I didn’t care enough about my audience’s time to practice my talk and make sure that I could present it in the time allotted’.  I’ll cut students a little slack, but only because I’m going to whack their advisors over the head.
  2. What do I mean by ‘audience appropriate’?  I mean that you need to think hard about your audience and explain things they won’t be familiar with while avoiding long digressions on topics that are well-known to your audience.  Spending two minutes defining ‘genotype’ to an audience at a genetics conference will be a waste of your time, but it might not if you’re presenting to a science outreach high school event.
  3.  Yup, that’s right, kittens.  If that makes it into the final version for ISBE, I pity the poor fool who has to follow my picture of adorable kittens

If you've been paying attention to my Twitter feed or blog (and seriously, why aren't you?  /narcissismoff), you may have noticed that I've been reading a bit about Darwin lately.  I just finished Desmond and Moore's biography, Darwin, which I found really enjoyable, and when they mentioned his autobiographical musings on his rejection of Christianity, I sought out a copy of that to read.  In amongst his reflections, I saw this quote about the way he worked and the dangers of what we would now call confirmation bias:

I had also, during many years, followed a golden rule, namely, that whenever a published fact, a new observation or thought came across me, which was opposed to my general results, to make a memorandum of it without fail and at once;  for I had found by experience that such facts and thoughts were far more apt to escape from the memory than favourable ones.  Owing to this habit, very few objections were raised against my views which I had not at least noticed and attempted to answer.[1. Okay, so he loved commas.  Give the man a break, it was the 19th century.  Quote from p. 123 of The Autobiography of Charles Darwin, 1958, edited by Nora Barlow.  You can read it for free here.]
I don't know to what extent he managed to follow his own golden rule, but I think that the sentiment is quite important and useful to people in any field, scientific or not.  We should always strive to answer the strongest versions of the arguments against us, no matter how uncomfortable it makes us.  As scientists we tend to get this idea beaten into us by vengeful reviewers, after which we have to learn how to separate useful opposition and criticism from useless spite, but I think the reminder from Darwin's own hand is useful for us to remember.  Besides, it's just more fun that way;  being 'right' all the time (whether you actually are or not!) is boring.

Memoir of an Academic Poster

[Update: If you like this, you may also be interested in the post I did on turning the same material into an academic talk.]

What follows is the process, from beginning to end, of creating a poster for an academic conference (in this case, the Genetics Society of AustralAsia conference in Melbourne which begins this weekend). It should be made clear: this is happening right now. It’s science that I’m just starting to write up for publication, at the same time that i present it as a poster at the GSA and as a talk at ISBE next month. I’m posting this for several reasons: the hope that it helps someone in need, the entertainment value from my struggles, and a look inside how this part of science gets done.

Note: what you’re getting here is a peek inside a part of my process for doing science. There’s a few things it’s not. It’s not a finished product like the paper that we’re going to write will be. It’s not without warts, or hiccups, or half-baked ideas. And this post is not about the content as much as it is the design. It’s is a series of snapshots during my design of the poster, meant to show you a bit of how I do these things. I’m continuing to think about and refine the ideas in the poster, and I’ll be taking into account feedback from the conference and from people I show this to. So, if you show up and bleat out “lol thats stupid y u do tht?”, I’ll slap you. Having said that, questions about the process or the material are more than welcome.

(Update, August 7:  Thanks to a comment by Stuart below, I’ve realised that I never specified what tools I’m using here.  I created this poster on a Mac using Pages to do the layout, with ColorSchemer to help with palette selection, Pixelmator to deal with bitmapped images, LaTeXiT to insert equations, and Omnigraffle Pro to produce vector graphics like the model diagram and the niche construction explanation.  The graphs were created in R (using ggplot) and the model dynamics plot was done in Mathematica).

Thursday, 5:00 p.m. I’ve just had a meeting with Mark, my boss, discussing the results for the model we’ve been working on. This is the model that will form the basis for the paper. I’ve still got work to do, but it’s done enough that I can begin laying out the poster.

6:30 p.m. I finish up the first version of the layout.

Click the image to link to a .PDf version.

Note that I’m following, at least vaguely, the design philosophy of separating presentation from content. It proceeds iteratively, and I’m not showing you all of the steps, but even in this early version you can see that I’ve blocked out an outline of what the content should be and I’m creating the aesthetics in a parallel process. To see what I mean, imagine replacing all of my text in this image with your own content, and you’ll see that it’s not too difficult. You might need to add or subtract a box, for instance, but the general layout is flexible enough to contain your content no matter what it happens to be. This separation of content and presentation is behind a lot of the best publishing technologies; it’s why I use LaTeX and not Word, it’s why we have HTML (and friends) and CSS 1, and so on.

6:35 p.m. I begin to play around with the color scheme a bit. I’m mucking about with color palettes from COLOURLovers and importing them to Colour Scheme Studio, then exporting the palettes to a .clr file and importing them into OS X’s Color Picker (open the Colour Palettes tab on the picker, click the gear and select Open to import). For giggles, I’m playing around with a rather pseudo-Satanic palette called ‘Red Devil’.

Click for PDF

It’s not really working for me, but that’s okay. I’m planning on keying the poster to my graphs anyways, by using ColorSchemer’s awesome PhotoSchemer feature to construct a palette from an image of my graphs. Of course, that means that I need to produce the final graphs first and I haven’t done that yet, so it’s back to the grindstone.

6:57 p.m. I send the black and white layout to my wife, who’s in New Zealand at the moment. Her first degree is in fine arts and visual design, and she’s taught me almost everything I know about design, so I value her opinion greatly when I’m working on a project (you should have seen the face she pulled when I showed her my first-ever poster as an undergrad). She’s okay with the layout, but doesn’t like the header font. This confirms my niggling doubt that the font isn’t a great choice, so I’ll replace it in the second layout tomorrow.

Friday, all afternoon. I’ve been using Mathematica to analyse the model, but Mathematica’s graphics are terrible, so I’m reimplementing everything in R.

Sautrday 5:14 p.m. I’ve arrived back in the lab after spending the day running errands. I was up until 3:30 a.m. last night working on the R code to reimplement all of my plots from Mathematica so that I can make more flexible and aesthetically pleasing graphs. It took a significant amount of trial and error, but it was worth it. Now, I can start thinking about the design again. I’m starting with colours: the palette I used while creating the R code is here, and I also like this variation. My concern is that it might not be bright enough to catch attention in the poster session, but I’ll see how it looks when I try it in the layout.

5:48 p.m. I’m down the rabbit hole looking at colours.

Looking at the graphs, I’m worried that the gradient fill is more visually pleasuring and would be easier to design the rest of the poster around, but in terms of reading the graphs I’m thinking that more contrast in hue among the values will aid the viewer in picking out interesting values. I ask my wife via text in New Zealand and she replies with something awesome: “I prefer the first one, but if the second one reads more clearly, go for that. Form is important, but function is non-negotiable.” This is a great reminder of an important point. While it’s true that too many scientists ignore form completely, function still comes first.

8:15 p.m. I’m still tweaking the first set of model plots. And yes, it’s 8:15 p.m. on a Saturday with me still in the lab. Don’t you judge me.

8:16 p.m. To hell with it, I could be doing this for days. It’s time to iterate the poster layout. First, I need to find a new font for the header: to the internets! I wish that I was experienced enough to have a set of fonts as go-tos for this, or to be able to think of the right font at first go. But I’m not. So instead, I leverage Google and troll for suggestions.

8:30 p.m. I’m trolling fontsquirrel and Google for fonts, and I’ve picked a few to try out. Based on this random post, I hit on a couple of combinations of font families that don’t look too bad.

Museo Slab

PT Serif and Sans

9:33 p.m. The PT Serif and Sans have a nice clean feeling to them, and I’m leaning this way right now. I’ve emailed the samples to my wife for further advice, but she’s gone to bed so I’ll hear back in the morning. If you’re keeping track, I just spent over an hour playing with fonts. This either means that I have (a) great attention to detail, or (b) goddamn OCD. It’s getting late and I’m getting burnt out, so I’m going to work on this for about another half hour and then finally get out of here.

10:25 p.m. After spending a while fixing further problems with the plots (making backgrounds transparent, etc)., I’ve messed around with the design somewhat. It’s still early days, but a few of the elements are there.

Click for the .PDF

I’ve included one graph in each color scheme to see what works best, but I’ll make a final decision later. Also, one thing I notice immediately is that the author text in the top right now looks a little awkward. I’ve created a column line that the author text is crawling out of, which looks jarring, so I provisionally shift it left.

10:36 p.m. Am I seriously still in the lab? It’s time to go home.

10:44 p.m. Damn OCD. I realise that I’m still playing with the layout, seeing what gradient fills do. I’m not committing to these at this point, but restrained usage might be helpful. Also, I’ve added drop shadows to the colour boxes to separate them from the page a bit.

Click for .PDF.

Now I’m definitely going home.

10:53 p.m. Okay, for crying out loud, I’m walking out the door now.

Sunday, 4:49 p.m. Back in the lab. Just shut up.

5:36 p.m. I can’t find a good vector example of the niche construction diagram that – to me – encapsulates the idea so well. Even the ones in the published papers are, usually, low resolution or have bizarre stippling. Thus, I’m replicating it by hand in Omnigraffle. On the upside, I can then sync the diagram’s font to the font in my poster.

6:26 p.m. I’ve recreated the diagram and placed it on the poster. I’m now beginning to fill in the text, and I run into an immediate question: what do I do with references? In previous posters I’ve used the standard in-text citations and reference list at the end, but for this one I have the feeling that space is going to be at a premium. I can’t afford to throw reference list in anywhere here, so what to do? I consult an oracle, the Better Posters blog, and on the advice to get away with what you can, I decide to play with QR codes and/or a separate printed reference list to be handed out.

-7:27 p.m. Unsurprisingly, I have too much text in the first text box. I’ll probably spend the next hour trimming words to economize as much as possible. Every word I can get rid of now without diluting the message makes my life easier down the road.

Click for .PDF

8:39 p.m. I’ve just sent an email to the authors of the paper whose work started my interest in this topic, asking for permission to use one of their images in my poster and the talk I plan on giving at ISBE. Get permission for your images!

9:00 p.m. I’m struggling with the text. I’m beginning to think that I’m going to have to omit the phylogenetic work and leave that for the talk and paper.

10:48 p.m. I’m still struggling. I’ve put in the model details, but they simply take up too much space.

Click for .PDF

I ended up dumping one of the gradient boxes to try and fit more of it in (and because it was difficult to get the equations into white to show up on the box’s fill; not impossible, but annoying). Still, I’ve got too much. I think that I’ll have to cut the equations; they’re effectively redundant anyways, since the model diagram actually contains all of the same information. I wish that I could cut the parameter explanations, but I don’t think that I can afford to do that. They’re just incredibly awkward and space-consuming.

11:11 p.m. Okay, if I don’t leave the buses are going to stop running. But in the intervening time, I did rearrange the content somewhat. It’s still ugly as sin, but it’s starting to approach something useful.

Click for .PDF

Monday, 12:05 p.m. Had to pick my wife up from the airport this morning, but now I’m back in the lab.

3:25 p.m. Just got back a half hour ago from a talk by Paul Davies, which took up a good portion of my afternoon. On the upside, I’ve finally managed to squeeze everything in the left column, even if it’s still hideously cramped. I need more negative space, Captain!

5:30 p.m. I had such high hopes for this afternoon, but I have to swap out one of the plots and of course Mathematica is taking forever.

5:49 p.m. I promised my wife I wouldn’t work late in the lab when she got back, so I’m headed home. This is as far as I’ve gotten today:

Click for .PDF

10:13 p.m. My wife has gone to sleep; time to spend a few hours working on this thing!

12:37 p.m. The first semi-complete version is done! I need to finish off the conclusion sentences, fix a plot background to be transparent, and make about a thousand other tweaks, but I’m inching closer. I’m using colour in the headline now to call out key words (viral niche construction, and accenting our last names). You’ll also note that the QR code for references makes its first appearance.

Click for .PDF

Tuesday, 11:09 a.m. I’ve been working for about a half hour now, making small tweaks and fixing the text. (How tired was I that I equated virulence with R0)? I caught Mark – my boss – in the hall and worked out a quid pro quo; he’s agreed to look at my poster and help fix the text if I give him some new figures for his talk. So now I’m going to print it off in its current state, give it to him, and concentrate on fixing the rest of the design. We’re entering 10% territory here.

11:26 a.m. Of course the printer is borked. Of course.

12:35 p.m. Am I really still trying to get Mathematica to save this PDF properly?

1:21 p.m. I give up. Everything I try fails: Mathematica continues to clip my legend so that the last few characters are cut off. It looks fine on the screen, but the .PDF is clipped. I have to admit defeat and abbreviate the labels. It looks terrible, but there’s apparently nothing that I can do and I’ve already wasted an hour and a half of my life on this. As I put it on Twitter, very eloquently:

2:23 p.m. Mark gave me comments on the text and there’s only minor changes to make, so I can finish those tonight and actually get this thing done on time!

10:57 p.m. After a few final changes, a spell-check, a few mutters and curses and tiny tweaks, the final version is ready!

Click for .PDF


Conclusions and lessons learnt: I’m still somewhat disappointed with this layout, because I had wanted to do something more radically simple. But there are constraints when doing this sort of work, which I need to learn to be okay with; the fact is that some forms of content can only be simplified so far before the message begins to bleed away. That’s not to say that I think I succeeded here, but rather that I did the best I could and I’ll continue to search for ways to make it better. In the meantime, I think that the layout is functional if not fantastic, and I hope that it presents the deluge of information in as straightforward a way as possible. There’s a lot of quibbles you might make about my choices: my choice to abandon headings (‘intro’, ‘results’, ‘conclusions’) in favour of a straight read-through, colour choices and design elements, using a QR code for the reference list (I’ll have an envelope with paper copies of the same list as well, but still). If you have any questions or comments, please feel free to leave a comment or hit me up on Twitter.


Addendum: Should I be surprised that when I went to go print the poster the next day, the plot in the top left disappeared from the .PDF I submitted when viewed on a Windows machine? I had tested it on several Macs to make sure it worked properly, but we don’t have a Windows system around so I didn’t see the problem. I spent about two hours tracing it to a problem with – you guessed it – Mathematica. For some reason, the .PDF produced by Mathematica just disappeared when viewed on Windows. I couldn’t fix the problem directly, but if I exported from Mathematica to EPS and then had Pages import the EPS (forcing it to generate a .PDF of its own to place in the layout), it finally worked properly. As of now, the poster is sitting on my desk, ready to go when I get on the plane tomorrow. Wish me luck!

  1. Don’t know what I mean? Go to the CSS Zen Garden, click on the designs, and watch your mind being blown