Filed under Personal opinions …

Apr 16 2013
2 Comments
Personal opinions, Scientific life

Academentia and the iPad: an update from 2010.

iPaddr

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? ↩
Apr 02 2013
1 Comment
Personal opinions, SciComm, Science

On the good and evil of scientific stories.

tl;dr: telling a good story is a vital tool in science communication, but it’s easy to go too far for a simple narrative.

If you’ve read this blog, attended a talk that I’ve given, or sat in on one of our lab meetings, you would know that one of my pet issues in science is communication. Scicomm, as it often goes by now, means more than explaining science to the public, though that is of course a large part of it. It’s also about how we communicate our science to other scientists, either in our field or ourside of it. Journal publications, conference talks, seminars, monographs, all of these things – and more – fall under science communication to me. And if you had found yourself as a fly on the wall when I was editing one of the Ph.D. students’ papers or critiquing conference slides, you would almost certainly hear me talk about story.

More precisely, you’d probably hear me say something like “what’s the story?” when I got through a rough draft of a manuscript, or after I watched a practice talk for an upcoming conference. When I say “story”, what I mean is the narrative and plot that ties together the work that you’ve done into a cohesive whole that the audience can follow and emphathise with. In the first chapter of his book Storycraft, Jack Hart cites this definition of story from Jon Franklin:

A story consists of a sequence of actions that occur when a sympathetic character encounters a complicating situation that he confronts and solves.

Story, as Hart says, consists of a recounting of a chronology of events (narrative), and the selection of arrangement of material so that a larger meaning can emerge (plot). Hart says:

For Eudora Welty “Plot is the ‘Why?’” Or, as the novelist E. M. Forster famously put it, the narrative is that “the king died and then the queen died.” The plot is that “the king died and the queen died of grief.”

I raise these issues because this is a problem that I’ve thought about at length when it comes to scientific communication. You might object that communicating science isn’t about a story, a narrative, or a plot, but I would strongly disagree. When you give a talk at a conference, you do exactly as Hart recounts: you construct a narrative and select material to form a plot (‘we identified some limit to our knowledge, we formulated some hypotheses, we did a test, we got some results, OMG science”), even if this looks nothing like what actually happened. You might be more familiar with this process in its rage form. Don’t fool yourself, this is story crafting. In its simplest form the scientist is the protagonist, the complicating situation is the unknown s/he is trying to banish as described in the introduction / methods, and the climax is wrapped up neatly in the results before the gentle falling action and dénouement in the discussion.

Story in formal scientific writing is often limited to the imposition of this narrative and plot structure, though stating it this way belies its importance; if you’ve ever reached the end of a journal paper and thought ‘what the hell was that paper about?’ (and we all have), chances are reasonably good that you’ve just experienced a failure of story. But when science is communicated to a wider audience, story begins to feature even more strongly. Whether written by scientists, science communicators, or journalists, it is easier to see this in action when the masters of the craft are in action. David Quammen, in his book Spillover structures his description of the hunt for Ebola and its reservoir around the story of the medical researchers who have tracked it through the jungles of Africa, winding in and out of their struggle to identify the source of the disease and the effects that it has on the people of Africa and elsewhere. It’s a detective story, which Quammen uses as a hook to lubricate the discussion of everything from molecular biology to mathematical epidemiology. But it’s the story that drives us through what would have otherwise been a textbook on epidemiology.

If I haven’t made it clear by now, I think that story’s important. Yet I also think that story has a dark side, one that we must be ever vigilant about as scientists, and it’s this: the push for a good story can obscure the truth. Science is messy, and full of complications and stumbles. There’s not always an answer, or a happy ending, and sometimes what we thought was right for a long time turned out to be incomplete, or even wrong. This fact is what makes writers like Quammen and science communicators like Carl Zimmer so valuable; they capture that messiness without letting it overwhelm the story, and in so doing make our science interesting to people. But if the push for a story goes too far, it can result in over-simplification and even simple and dangerous untruth.

I was reminded of this when I came across a post by one of my favourite writers on visual design, Garr Reynolds; Garr wrote the book Presentation Zen, and a series of other books like it, and I still recommend them to other scientists as a good way to get a handle on how to make your presentations suck less, visually. Recently, however, Garr wrote a post praising a video containing the work and narration of Paul Zak. The post, entitled “Neurochemistry, empathy & the power of story”, is itself curiously meta, as it disucsses work by Zak on neurochemical responses to the ‘dramatic arc’; in short, Zak claims that oxytocin and cortisol are part of the neurochemical suite that responds directly to the structure of a story, and can even be used in a predictive fashion (here, to predict the amount of donations that will be given when viewing a tearjearker story of father dealing with a young child dying of cancer versus the same father walking in the park with his son).

The irony of this, of course, is that Zak himself is an adept storyteller who has constructed a narrative around oxytocin as the ‘moral molecule’, reducing good and evil to the action of a single neurotransmitter. Here’s an excerpt from a Guardian article1 on Zak from last July:

What drives Zak’s hunger for human blood is his interest in the hormone oxytocin, about which he has become one of the world’s most prominent experts. Long known as a female reproductive hormone – it plays a central role in childbirth and breastfeeding – oxytocin emerges from Zak’s research as something much more all-embracing: the “moral molecule” behind all human virtue, trust, affection and love, “a social glue”, as he puts it, “that keeps society together”. The subtitle of his book, “the new science of what makes us good or evil”, gives a sense of the scale of his ambition, which involves nothing less than explaining whole swaths of philosophical and religious questions by reference to a single chemical in the bloodstream.

Here, we see the danger of story. In constructing a simple story with a compelling and digestible arc, Zak has swept the truth of this research under the rug, and the truth is that research on oxytocin is messy, contradictory, and provides few clear answers. As Ed Yong describes it, oxytocin can have distinctly contrasting effects depending on who receives it; some people may exhibit more social behaviour, while others in the same situation may exhibit more antisocial behaviour under the same dose of oxytocin. It can promote trust, or increase xenophobia. It may be that oxytocin is part of some motivator system: for example, people like James Goodson have worked to show that in birds like the zebra finch it2 is implicated in the ‘social behaviour network’ and may be instrumental in zebra finch flocking, though as in many other animals, this effect can be strongly sex-specific (usually to females).

All of this complication and mess is ignored in Zak’s story, which does a disservice to the reader who comes away with a simple view of the world that just doesn’t hold water. A friend of mine, a lawyer, asked me awhile ago if what he’d heard about this ‘cuddle chemical’ was true, and was visibly disappointed to learn that it was much more complicated than that. The problem here is that we are disposed to like a good, simple story; it has more emotional impact, which in turn makes it easier to remember and explain to others. Certainly, nobody wants to spend as much time reading journal articles and learning about nonapeptide hormones like oxytocin as I did for my PhD exam in order to tell a story at a party. This is why we have people like Ed, and Carl Zimmer, and Maryn McKenna, and all of the other great science communicators, writers, and science / scientist bloggers: they do the hard work of curating the facts and telling the story without losing the truth. Contrast Zak’s writing with Ed’s takedown of the oxytocin mess. It’s just as good a story, but it treats the truth with respect, and the truth is that we’re just not there yet. We have tantalizing ideas and scraps of evidence on how oxytocin affects us, but we can’t draw definitive conclusions. As Ed discusses, the hype around oxytocin has even led to people using it in an attempt to treat autism, with unknown and possibly harmful effects.

This isn’t an isolated problem. The TED talks have become a serious problem in this regard, and though I’ve seen some great TED talks over the years, they’ve grown to the point where the push for good stories has overwhelmed the ability of science to provide them. I saw the most recent example on Boing Boing when Maggie Koerth-Baker pointed to a problem in the widely-circulating story spun by 19-year old Boyan Slat on a plan to remove plastic from the oceans, namely, that it won’t work. Here again, we see the elements of story at work, this time surrounding Slat himself. A 19-year old phenom who rises to glory on the back of an award-winning school research paper, a hands-on problem-solver producing solutions and starting a foundation to implement them. It’s a feel-good story with a likeable protagonist who is tackling a problem that scares us all; it’s a shame that the scheme probably won’t work, and may even do more harm than good if ever implemented. The issue at hand, though, is that the story told by and about Slat is compelling but oversimplistic and potentially dangerous, just as the one told by Zak is3. As Maggie points out in her post:

Here’s a mantra to remember: TED Talks — interesting if true.

And the same is true with anything you read in the popular press about science. It’s interesting, if it’s true.

Now, I began this post by pointing out that I’m a big proponent of story in science, and I stand by that statement. Story is an important, and I would argue, necessary tool when we come to communicate the results of out work, for the same reasons that it can go badly wrong. A carefully crafted story draws the audience through the science, ties it together in a way that they can understand and remember, and adds punch to the work so that the audience cares enough to pay attention. Yet this process, while vital, needs to be kept in check by the demands of the search for the truth and the admission of messy detail and incomplete knowledge. The tension between story, which yearns to be complete, and science, where more research is always needed, must be respected and maintained lest you end up with bone-dry science or a compelling – but misleading – tale.

  1. or as Ed Yong puts it, ‘ad’ ↩
  2. under the name of mesotocin ↩
  3. as an aside, I’d like to say that despite the problems inherent in Slat’s plan and how it ended up going viral, I hope that he keeps trying. He sounds like a smart guy, and failure is a great first step on the road to success. ↩
Sep 17 2012
1 Comment
Personal opinions

I guess I’m just not a real man.

If you’re a man, and you really like [insert chosen thing here - I'll use Star Trek for this post], and you’re a fan and you talk to other people about it, and you spend time watching the TV shows whenever you can and you go to conventions and put effort into dressing up to have fun;  well, then, you’re a freak who should die alone.

Photo by Falashad, used under a CC license.

On the other hand, if you’re a man and you really like sports, and you’re a fan and you talk to other people about it, and you spend time watching matches on TV multiple times a week and you go to games wearing the team jersey and you get drunk and act like a jackass and maybe start some stuff on fire when you lose;  well, then, you’re a real man.

Photo by Matt Gibson (www.matt-gibson.org), used under a CC license.

Explaining the stupidity of this is left as an exercise to the reader1.

  1. Despite what it may look like, this isn’t about me.  I just heard about someone who’s a fan of Star Trek get rejected by a woman at the ‘should I contact him?’ stage for solely that reason, and it struck me as stupidly unfair ↩
Tagged , , ,
Aug 11 2012
6 Comments
Biology, Personal opinions, SciComm, Scientific life

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 ↩
Tagged , ,
Jul 23 2012
Leave a comment
Personal opinions, Scientific life

Darwin on confirmation bias.

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

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.

  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. ↩
Tagged
May 12 2012
6 Comments
Personal opinions, Scientific life

Goodbye, Australia. Well, not yet, but I’m working on it.

tl;dr:  I get mad at the Australian government.  

Update: Well, it passed.  And, joy of joys, it comes into effect October 1 (which, given that today is September 24, shows the government’s rush to get ahold of my pay).  So, what I wrote below is now certain:  I’m leaving Australia as soon as I can.  That won’t be any time soon, as my contract here is for another two years and I need time to find another position, but being jerked around like this just makes it clear that Australia won’t be my home.  I know, too, that I’m not alone in this.

The Australian government has made a series of interesting decisions lately, beginning with the decision that I first heard about in February to abolish LAFHA for temporary residents.  If you’re not Australian, you probably don’t know what LAFHA is (you may not know what it is even if you are!), but in short it’s a tax concession for people living away from their primary residence (Canada, for me).  Under LAFHA, the portion of your salary allocated to food and rental accommodation is tax free.  This means that I pay tax only on the remainder of my salary after food and rental accommodation has been deducted, which of course means that I pay less tax and receive more take home pay.

It’s hard to explain how much of an impact this has on my financial situation as a temporary resident in Australia.  Without LAFHA, I would never have come to Sydney in the first place;  the cost of living here is simply too high.  And the truth of the matter is that even with the extra padding we put into our budget, we still managed to underestimate how expensive it is to live and work at UNSW.  I make  80% more than I would have as a postdoc in Canada, but I now have half the standard of living that I did as a Ph.D. student in Canada.  In Canada, with my wife’s salary as a teacher we made about equal to what I do here in Australia; she’s unable to secure full-time employment because the NSW government doesn’t allow temporary residents to hold permanent contracts and so she’s reduced to uncertain casual (substitute) teaching.  Yet despite being nearly on par in terms of raw money, our lifestyle is severely curtailed here.  In Canada we could rent a nice two-bedroom condo for the same amount that we pay to share a dilapidated house with two other people in Sydney.  In Canada, we could afford a car (a modest used Echo, but still);  in Sydney, I can’t afford anything more than the bus.  We were able to save significant amounts of our paycheck in Canada, while here savings is a serious struggle; saving the money to take a trip for our 5 year wedding anniversary was a much greater challenge.

Now, yes, first world problems.  But if I can take as read for a moment that we’re terribly privileged, the fact is that – financially – coming to Australia was a mistake.  I don’t regret it for the experience;  the lab I’ve joined is great,  and I’m learning enough here that I can consider it an investment in my future productivity as a scientist.  I’ll certainly make the most of my time here.  But yesterday, my wife and I made the decision that we are going to leave Australia as soon as we can, perhaps even early than we had originally planned.

Why?  Well, after waffling for months on whether the abolishment of LAFHA was going to go through the Australian government handed down a decision a few nights ago as part of the Federal budget clarifying their intention to abolish LAFHA.  On the bright side, it appeared that the government had listened to the concerns of people like me – who had based their decision to move here in part on the fact that LAFHA was in place – and instituted transitional rules so that existing arrangements would be honored until 2014.  While I still feel that the decision is a stupid one in terms of Australia’s future (the subject of another post), at least that didn’t screw us over too badly.  But then, I received this e-mail from the senior UNSW HR people yesterday:

UNSW has recently been advised of a correction/clarification made by Treasury in relation to the LAFHA information in the Federal Budget announcement on Tuesday evening. Treasury have now indicated that the transitional arrangements (i.e. 2 year grace period until 1 July 2014) were not intended to apply to temporary residents (which includes employees on a 457 visa). Please see the attached update bulletin from PWC for more information.

Hence, I regret to advise that it appears that LAFHA will be removed for temporary residents from 1 July 2012, as previously anticipated.

So, it turns out that government is deliberately targeting temporary residents like me and that the transitional arrangements were a lie. Now, in a month and a half I face a reduction in my take-home pay of somewhere between 15-20%.  Just try to imagine losing a fifth of your take home pay and tell me that this is something that you would feel is ‘fair’.

The fact is that there are two Australias.  The first is the everyday Australia that I see when I walk around Sydney, full of good people who I enjoy living among. The second is a xenophobic Australian government that feels free to jerk temporary residents like me around.  This second Australia is going to drive skilled workers like me out of the country and this situation is going to be even worse in academia because unlike in business, we can’t simply renegotiate our contracts to make up the difference.  There’s simply no more money to go around and by removing LAFHA the Australian government has placed its universities in an untenable position.  Universities rely on the free flow of scientific talent to construct world-class research programs, and in a single stroke they have managed to completely disincentivize me and others like me from coming to this country.

On the other hand, perhaps I should thank the Treasury.  My wife and I had debated over whether to remain in this country when my postdoc was done, but the lack of respect with which we have been treated by the Australian government has made that decision remarkably simple.  I’m going to work hard here, and learn what I can, and at the first opportunity I will leave.  So goodbye, Australia, sometime soon.

Tagged , ,
Apr 24 2012
1 Comment
Personal opinions

Congratulations, Alberta! Uh, I think….

Well, the CBC has called it:  Alberta has elected a Progressive Conservative government.

I never thought that I would be vaguely happy to hear that my home province has elected a Tory government;  they’ve been in power for over 40 years now and I would have been happy to see a change, but I am glad that the homophobic, racist, anti-science Wildrose party hasn’t taken power.   And the fact that Alberta has now elected its first female premier is something that shouldn’t be ignored or minimised.

What I’m still upset about, though, is that Alberta has decided to put the Wildrose party in second place, crushing the Liberals and NDP by comparison.  Danielle Smith wouldn’t be out of place running along side Sarah Palin, and now she’s forming the official opposition in Alberta?

For shame.

Tagged , ,
Apr 20 2012
Leave a comment
Personal opinions, Science

Hurrying to go to better things.

Over at Why Evolution is True, Jerry Coyne addresses an article by Andrew Riggio, in which Riggio questions the thought processes of a man named Paul Lord who thanked God for saving him from a tornado that struck in Oklahoma, killing several (including 3 young girls) but sparing him.  Noticing that (unsurprisingly) the comments have exploded into a sprawling mess, Coyne pulls out a few for special attention including this one:

Kleb  •  22 hrs ago
Wooooooow. Bitter much? The author’s argument presupposes that from God’s point of view death is bad. People of “true faith”, as his last sentence mentions, are equally grateful to God for His providence in death as in life. Look at the great heroes in Christianity. When they died they weren’t bawling and begging God to spare them, they were profoundly relieved to be joining Him and, at the same time, deeply grateful for the ride they had been on in this world. From a Christian perspective, then, there is no inconsistency here. The survivor is grateful for the life God has given him here, as he should be, but that doesn’t mean he isn’t also looking forward to meeting the Lord.

Whoa!  Should we be grateful to God for asking 6 million Jews to join Him during the Holocaust?

Seeing this reminded me of something I read a while ago in John Aberth’s great book Plagues in World History.  Faced with the crushing mortality and morbidity of the First Plague (the Justinian plague that ran from roughly 541 to 750 CE), Christian preachers responded the only way that they could, from the pulpit.  In reply to the bubonic scourge, Aberth notes this particular line of thinking:

By the seventh century, sermon cycles were being compiled to be recited on a regular basis whenever plague struck a region as part of the Church’s now standard response to urge its flock to repent in the face of God’s wrathful chastisement;  this at least is the overarching theme of four homilies composed at this time in Toledo, Spain, which, as expected, are replete with quotations from the Old Testament.  Yet, one sermon, the third in the series, adopts a strikingly different tone by employing the carrot rather than the stick [...].  In a remarkable passage, one that seems to be inspired by the New Testament, in particular the letters of St. Paul, the preacher now dangles the promise of immortality during the Christian afterlife or resurrection in order to help his listeners conquer their fear of imminent death from the “groin disease”:

But what should we say?  You who take fright at this blow (not because you fear the uncertainty of slavery, but because you fear death, that is, you show yourselves to be terrified), oh that you would be able to change life into something better, and not only that you could not be frightened by approaching death, but rather that you would desire to come to death.  When we die, we are carried by death to immortality.  Eternal life cannot approach unless one passes away from here.  Death is not an end, but a transition from this temporary life to eternal life.  Who would not hurry to go to better things?  Who would not long to be changed more quickly and reformed into the likeness of Christ and the dignity of celestial grace?  Who would not long to cross over to rest, and see the face of his king, whom he had honored in life, in glory?  And if Christ our king now summons us to see him, why do we not embrace death, through which we are carried to the eternal shrine? For unless we have made the passage through death, we cannot see the face of Christ our king.

(emphasis mine)

Kleb the commenter has one thing right:  a belief that death is acceptable and even preferable to this life, whether from God’s point of view or from the worshipper’s, is certainly not a new phenomenon.  I wonder at the power this line of thinking must have held when those who contemplated it were faced with a disease that can kill 60-90% of those it infects and may have wiped out as many as 25 million during the Justinian plague alone.  In the mean time, though, I’ll be thankful for the efforts of modern medicine and science which have brought the plague to its knees. (Even if we are on the verge of squandering that advantage and resurrecting the plague’s power through antibiotic abuse, but that’s an entirely different post).

Apr 11 2012
1 Comment
Personal opinions, Rejection Watch, Science

Rejection Watch Vol. 1, Supplementary Online Material

Photo by Troy C. Boucher Photography, used under a CC license.

Submissions for Rejection Watch have dropped off, which doesn’t really surprise me;  the traffic on this blog isn’t quite strong enough to sustain a feature like that (yet!), though I don’t regret the attempt.  The submissions I did get were fantastic and if anyone out there still wants to send me material, I’ll be happy to resurrect it whenever they do.  In the mean time, though, a couple of relevant posts from around the web have cropped up in the last day or so, and I feel like they make great supplementary reading for those of you reeling from academic rejection.

Rosie Redfield (she of debunking-#arseniclife-fame) over at RRResearch posts her rage over a crappy review of her postdoc’s paper:

We finally (after two months) got the reviews back for the postdoc’s manuscript about DNA uptake bias.    It’s a rejection -  the reviews were quite negative.  The first reviewer was very unfair; they didn’t find any fault with the methods or data or analysis, but they attacked our brief discussion of the functional evolutionary context of uptake bias.  This is all too common for my papers.  The reviewer is so hostile to the idea that bacteria might take up DNA for food that they don’t focus on the science.  Because the paper was rejected we don’t get to do an official response to the reviews, so I’m relieving my frustration by responding to them here.

She goes on to do a detailed, blow-by-blow response to the objections of the two reviewers.  The whole thing is a great read, even if you’re not in this field;  the feeling of ‘oh, that happened to you too?’ is too good to pass up.

Meanwhile, over at The Bug Geek Crystal has found a new pit of despair:

So you know that I handed my draft manuscript in to my advisor last week.  He sent back a document covered in red ink. Then my labmates pointed out all the dumb things I did, and showed me all the cool things I COULD have done but didn’t.

My advisor, a real funny guy, said, “You should make a new graph about the revision process,” and I was all, “Ha ha ha that’s so funny.”

The graph she makes is pretty awesome, but one of the things that struck me was that even the most well-meaning revisions from people close to you (advisors, labmates, colleagues you respect) can cut deeper than the blunt hammerings of an anonymous reviewer with a grudge.  I think that this is because it inspires different emotions, rage for reviewers and despair for labmates.  When we have a personal relationship with those who have dripped red ink on our work, it’s hard to avoid  the attack on your sense of self:  this person knows me, and didn’t think my work was perfect, so there must be something wrong with me.  I should have done better, I screwed up.  These are people that you (usually) like, that you want to look smart in front of.  Contrast Crystal’s feelings of despair with Rosie’s feelings of rage;  when anonymous reviewers trash our material, unless we think that they’re right we can work up a really good mad and use it as fuel to revise. In the academic setting, it feels to me like rage is a more productive emotion, a provocation to defiant action (‘I’ll show you Mr. Anonymous Reviewer who will never read this paper again!’) while despair has a soporific effect that leaves us drained and dragging ourselves through the revisions.

Of course, this is just a sweeping generalisation based on my own experience that is almost certainly wrong in some fashion.  But hey, maybe you can leave an anonymous review?  Then I’ll show you.

Tagged
Mar 30 2012
11 Comments
Biology, Evolution, Personal opinions, Scientific life

Science journalism blows it, dolphin rape edition.

A few weeks ago I got into a discussion on Twitter with Ananyo Bhattacharya, online editor of Nature News and writer for The Guardian’s science section, after he put out a call asking for ways to improve science journalism. During that conversation, I argued that one way to do this is to create a culture of journalism that values scientific knowledge and expertise as a core value[1]. Ananyo seemed unimpressed with my viewpoint, and suggested that the main point of science journalism was to pry into the dark corners and root out biases, fraud, and the like in science. He views scientific communication and scientific journalism as two distinct things (and thinks that journalists doing ‘PR for science’ is ‘drippy’). Indeed, when asked directly during a Royal Institute forum on science journalism whether journalists should read the original papers behind the stories that they write, he dismissed the idea:

“If the question is ‘must a good science journalist read the paper in order to be able to write a great article about the work’ then the answer is as I said on Tuesday ‘No’. There are too many good science journalists who started off in the humanities (Mark Henderson) – and some who don’t have any degrees at all (Tim Radford). So reading an academic research paper cannot be a prerequisite to writing a good, accurate story … So I stick to the answer I gave to that question on the night – no, it’s not necessary to read the paper to write a great story on it (and I’ll also keep the caveat I added – it’s desirable to have read it if possible).”

He further suggests, in the same comment (original source), that if journalists had to read original papers than no one could report on particle physics[2].

I’m not going to try and hide my bias here: I don’t like Ananyo’s viewpoint on this. I don’t think that it will lead to good writing, either of the communication or journalistic variety, but more importantly I think that forcing journalists to read the papers before they write an article might have stopped stupid @#$@ like what happened today from happening at all.

The story: I received an e-mail this morning from Dr. Bill Sherwin, a member of the Evolution and Ecology Research Centre (E&ERC) here at my current institution, the University of New South Wales. Bill is one of the authors on a new paper coming out in the Proceedings of The Royal Society (B), entitled ‘A novel mammalian social structure in Indo-Pacific bottlenose dolphins (Tursiops sp.): complex male-male alliances in an open social network’. The paper is a nice little exploration of the characteristics of social networks in dolphins found in Western Australia; in essence, they were testing whether two hypotheses about the nature of these social networks were tenable given the data they’ve observed. In particular, they tested whether dolphins show signs of engaging in ‘community defence’, where higher order alliances of dolphins form to patrol and defend a larger community range, similar to chimpanzees, or if it follows a ‘mating season defence’ model where male groups shift their defence to smaller ranges or sets of females when it’s mating season. The comparison to terrestrial species with complex social cognition (such as primates and elephants) is an interesting one, because it provides yet more insight into the relationship between the development of complex cognitive faculties and social relationships.

So far, so good. Bill gave a simple explanation of the paper in an email that he was sent out to the E&ERC this afternoon:

We put out a paper that said “dolphin male alliances are not as simple as other species”, but it has stirred up quite a lot of interest, because somewhere in it, the paper mentioned “bisexual philopatry”, which when translated out of jargon means  “males stay near where they were born, AND females stay near where they were born” – nothing more or less than that.

‘Quite a lot of interest’ is one way to put it. ‘Idiots crawling out of the woodwork’ is another. Here’s the headlines of four stories that were written about this paper:

Dolphins ‘resort to rape’: Dolphins appear to have a darker side, according to scientists who suggest they can resort to ‘rape’ to assert authority. [The Telegraph]

Male dolphins are bisexual, US scientists claim. [news.com.au]. (Note that this is an Australian website, and Bill is Australian).

Male bottlenose dolphins engage in extensive bisexuality. [zeenews.com]

And by far the best of the lot (guess who it’s from?):

The dark side of Flipper: He’s sexual predator of the seas who resorts to rape to get his way. [That's right, The Daily Mail].

……..

Are you kidding me? If the ‘writers’ of these articles had read the paper, they would have noticed that it contains nothing about the sexual behaviour of the dolphins they studied, bisexual or otherwise, aside from brief mentions of the possible consequences of social networks on reproductive success. It certainly didn’t mention anything about bisexual behaviour, homosexual behaviour, or rape. Now, it’s well known that dolphins engage in homosexual behaviours, and I’ve seen papers arguing that they use sexual coercion as well (Rob Brooks confirms this). But these topics have nothing to do with this paper at all. Even a cursory glance through the original source would have killed these headlines – and the first few paragraphs of the Mail story – which aren’t just a miscommunication but border on outright fabrication. The articles themselves are weird mixes of sensationalist headline with a regurgitated paraphrasing of the much better Discovery News piece that they are treating as the primary source. Here’s the problem, though: it’s Discovery News that makes the original mistake about ‘bisexual philopatry’, interpreting it as bisexual behaviour (hot male dolphin-on-dolphin action, as it were). A reporter who had read the original source could have corrected that mistake fairly easily, or could even have been driven to ask further questions. Without that, however, the press cycle grinds mercilessly forward to Flipper the bisexual rapist.

For my part, I was happy to see that James Randerson’s informal survey of science and health writers showed that many of them do read the original papers. And the kind of people who write things about science that I trust, whether they’re professionally trained in science or not, are not the sort of people who do boneheaded things like this. Ananyo might retort that ‘asking questions’ is enough (he suggested as much in his comment above). Matt Shipman said much the same thing in the piece that Ananyo was commenting on. Yet of all people, Ananyo should be wary of this answer, with his focus on investigative science journalism. A scientist writing an email or doing a phone interview can tell you just about anything that you want to hear; a press officer can write a terrible press release; a wire service will probably distort what comes down the line. But a scientific paper is the One, True Source. It is a public record of what was done, and it is the first and best place to start for answers about a study or a scientific topic[3].

Don’t mistake my criticism of Ananyo’s position of reading scientific papers as a general attack on scientific journalism. I think that there’s a lot of great science journalism out there, and that there are even more great science journalists and communicators. Despite the perennial swirl of internet discussion on the topic, I don’t actually think that the whole field is hopelessly broken like some seem to. I just happen to believe that scientific papers, the products of our time and energy as researchers, form an integral part of the process of talking about science (and it’s part of the reason for my support for Open Access publishing). And I think that disgraceful trainwrecks like the reporting on Bill’s paper are a perfect illustration of the need for these papers to be a part of that process.

[Update: Rob Brooks has also discussed this issue over at TheConversation].

——-

[1] Because of Twitter’s space constraints, this was misconstrued to mean that I was agitating for all science journalists to have a Ph.D. in a scientific discipline. Though I wouldn’t be upset if this happened, that’s not what I meant: it is more than possible to have a deep love and knowledge of science without having a degree in a scientific field. Hell, Carl Zimmer probably knows more about viruses and evolutionary biology than I do, and his only training is an undergraduate degree in English. My argument is only that having scientific training increases the probability of a writer or journalist having a good grasp on how science works, not that it’s the only way for that to happen. I will continue to argue, though, that those having a love of science (professional or amateur) will, on average, produce better science writing and science journalism than those who don’t.

[2] He also claimed that most of the people asking journalists to read papers are biologists and medical people, who write easier-to-understand papers. I would have to turn this back on him: if biology and medical papers are so easy to understand, why shouldn’t journalists read them every time?

[3] Yes, there’s no guarantee that what is written in the paper is true. But the chances of detecting fraud are essentially zero if you don’t read the paper to begin with, and if you’re a journalist looking to catch the next Stapel, chances are that you’ll have to wait for the scientific community to find him and tell you about it anyways.

Tagged ,
← Older posts