Archives: Blog stuff

Quick and dirty: importing from Bibdesk to Mendeley


My bib files are starting to get a little hairy and I’d like to use some my devices to read papers and sync directly on the go, so I’ve been considering giving a service like Mendeley another shot (though I’m still deeply skeptical of Elsevier’s role in the project1.

When I went to go import my bib file to Mendeley, though, my local files were all left behind.  I use Bibdesk to manage my bib files, and though the resulting import of references went well, all of my linked pdfs were missing.  This is apparently a known issue with Mendeley’s import from Bibdesk, and it doesn’t seem to have been fixed.  Meanwhile, people have come up with workarounds and some have been posted (e.g. here), but I couldn’t find one that worked out of the box (especially since Bibdesk changed to base64 encoded urls a while ago).

  1. For another view, we interviewed William Gunn from Mendeley a while ago on Breaking Bio.
Dolphin-assisted birth is stupid, and yes, dolphins rape.

Dolphin-assisted birth is stupid, and yes, dolphins rape.

Despite the title, the stupidity of dolphin-assisted birth isn’t actually what this post is about. The reason for the title will become clear in a moment, but before I get there, let’s recap. As was reported in the Charlotte Observer some days ago, Heather Berringer and her husband Adam plan on travelling to Pohoa, Hawaii, in an attempt to let Heather have her child in the company of a dolphin pod there. To be honest, I’m a little fuzzy on the supposed mechanics of this birth method, other than the fact that it occurs in the presence of dolphins in the water. How the pregnant mother is supposed to be assisted in the event of an emergency is beyond me, but I’m sure the “Sirius Institute” has it covered1.

  1. The astute reader will notice that this comment is dripping with sarcasm.

A Bit of Behavioral Ecology in 2012

Well, 2012 has come and gone, and WordPress sent me a link to one of those fancy year stats reports a few days ago.  So, if you’re voyeuristic enough (and bored enough) to poke through the stats on this blog, have a glance at the 2012 stats!  This blog had about 10,000 views last year, which makes it a baby blog in social media terms.  That’s all right for me, because my goals for the blog have always been modest, but I’m aiming to increase that a little for 2013.  Stick around, we’re only going to go up from here!

The blog lights are on…?

A light bulb

Image by nikonfilm35, used under a CC license

Okay, so I decided to take the plunge and move the blog over to a self-hosted install at my own website (  I’ve also purchased a redirect from WordPress, meaning that old links / search engine results should go to the new space.  Now, though I think that I’m up and running, there’s bound to be errors or wrinkles about the place.  So if you see anything amiss, please let me know in the comments, on Twitter, or by smoke signal!

(Why did I move, you ask?  Partly because I’m a geek who likes to tinker with stuff, and – though a fabulous platform that does the community a great service – was starting to feel a bit limiting.  The other part is because I have vague plans for new content on the blog that may include things like video, and I’d like to make sure that I have room to grow.)

Happy blog-birthday to me!

Photo by Will Clayton @ Flickr

Well, okay, I’m a little late;  my first post went up a little over a year ago, on November 3, 2010, but the spirit is the same.  One whole year!  If what I’ve read is any indication, that probably puts me somewhere in the top 10-20% of blog survival statistics.  The achievement pales in the face of people like Razib Khan, who have been blogging for nearly a decade, but I have to start somewhere.  And if this blog does even a tiny bit of what I had intended it to do in the first place, it’s worth every moment of my time.  So how well have I achieved my goals over the last year?

Here’s a bit of what I wrote in my ‘hello world’ post:

[…]I haven’t found many resources for quality writing on behavioural ecology outside of journals. So I’m going to try and contribute something useful by using this forum to write about things that I think are cool in the world of behavioural ecology and science in general, and hopefully raise the profile of our field a little bit.   What kinds of things will this blog cover?  Well, I have pretty diverse interests but I do skew towards the modeling side of things, so I hope that potential readers can forgive me for that.  In general, though, you can expect to see material on recent papers in the field, “basic concepts” posts in areas that I’m familiar with, and whatever other random noise floats through my head on the topics of biology and science. And of course, I welcome contributions, comments, and ideas from you, the loyal reader.  (Of course, right now, I’m shouting into the void … but hopefully that will change!)

Looking back over what I’ve written and where the blog is now it’s clear that I have an imperfect track record, but it’s one that I can live with.  I’ve managed to share my thoughts on cool papers, gotten into a couple of debates, done some book reviews, posted some filler, and generally had a grand time of it.  I haven’t done as much evangelizing for the field of behavioural ecology as I thought that I might, but now that I’m reminded of this goal I hope to do more of that in upcoming weeks. And as for readership, I’m actually quite happy with how things have progressed.  Since I started being a little more active on Twitter, I’ve managed to get a bit more attention for the blog, and I’m happy to report that my daily views are … wait for it  … greater than zero every day!

(Insert wild crowd roars here)

Of course, the numbers don’t matter  – I’m unlikely to ever be a powerhouse blogger like, say, John Hawks, but who cares?  (He’s way smarter than I am, anyways. :-) ).  What matters is that I reach out to and connect with cool, smart people like those that hang around on this series of tubez that we call the Internet;  in that regard the blog has been a great success, and I’m going to keep pushing to make it better.  As always, if anyone has comments, requests, or suggestions, please leave a comment below, send me an email, or drop me a line on Twitter!

Why I’ve been silent…

Note:  This post explains what’s been going on around here for the past while, and provides reasons for the radio silence.  It contains personal details that may be of little interest to some readers, so be warned.

I haven’t been able to post here in a while, but there’s been a reason for the silence.  Partly it’s because I’ve been involved in the process of moving across the world to Sydney, Australia, where I’ve begun a postdoctoral position at the University of New South Wales.  Moving from Canada to Australia has been a great experience, and I love my new home, but it’s also a massive process which requires pretty much all of a person’s time.

I also recently defended my Ph.D., another process which took a lot of time and energy.  It was complicated by the fact that we had to leave Edmonton, fly to Toronto for a family event, I drove to Montréal to defend during said family event, and then we flew to Sydney from there.  Frankly, it was a hell of a week.

However, as important as all that has been, it’s not the only reason I’ve been quiet.

The biggest reason that I’ve been quiet is that the day I drove to Montréal to defend, I received word that a friend and fellow Ph.D. student, Matthew Ian Helgesen, died suddenly and without warning.  Since hearing of that, I wanted to write about it here to express my feelings;  I’ve also been blocked on writing anything else until I did that.  But it’s taken me a while to come to grips with it and be prepared to say anything.

I met Ian when I came back to Edmonton during my Ph.D. (to help my wife deal with her mother’s terminal illness).  He was a student in the lab where I did my M.Sc., and as the Psych department at the University of Alberta was kind enough to give me an office to work at while I was in Edmonton, I thought that I would spend time with my old lab and perhaps do some work with them.

Ian was there from the moment I wandered back into the old digs, and I felt an immediate kinship with him. He was a geek’s geek, the sort of person that I could turn to and make a joke about British sci-fi or statistics or computers and get a laugh.  He was doing research in areas similar to the work that I had been doing before I left that lab, and we ended up collaborating on a couple of projects that were just beginning to bear fruit when he died.  Looking back, I had been worried because he was having health problems that were interfering with the pace of work (they seemed non-threatening at the time, though it’s impossible to know;  I still don’t know what eventually led to his death), and a part of me worries that I didn’t pay enough attention or that I missed something I should seen.  I know that that’s not true, logically, but it’s an impossible thought to shake.

Ian’s death shocked a lot of people, friends and family both, coming at as young an age as it did.  I can’t help feeling that he never had the chance to reach his potential, scientifically;  I’m hoping to help his (and my old) supervisor publish the work that we were doing at the time, but I’m certain that there was more and greater things to come from him.

I never got the chance to know Ian as well as I would have liked.  In part it was a lack of time, in part it was because Ian was a deeply private sort of person.   Even despite that, though, he was a good friend and colleague, and he’ll be sorely missed.

With that said, my future plans include writing more on this blog, especially related to behavioural ecology;  for my postdoc I’ve joined a group which isn’t in this area, but it’s still a field of great interest to me that I hope to continue publishing in and this blog will be a good place to express those ideas and interests.  So I’ll see you all around the blogosphere!

From my upcoming PhD seminar..

I haven’t had a lot of time to post in the past few days as I prepare for my Ph.D. seminar at UQAM on the 15th, and I get on a bus Monday to go to Montréal (from Edmonton!), so it’s unlikely I’ll be doing anything inspiring from there either.  So, just to prove that I’m still alive, here’s a slide from my slide deck for the presentation I’ll be giving…

Note:  this is the required seminar that I have to give, not my thesis defense.  (That’s still to come, hopefully in a couple of months!)

Exam time!

Blogging has been light, but that’s because I’m currently in the last week of what amounts to my candidacy exam. I’ve got a number of topics I want to write about in the hopper, though, and I’ll be back soon.

Interesting new site -> “Phylointelligence: Evolution for everyone”

At this point, my site stats tell me that this blog has somewhere around 1 reader, and that might actually just be me (wait, am I violating some sort of blogospheric fourth wall here?). So, I feel a little ridiculous posting links that no-one will read,  but this site is such an interesting idea that I’m willing to shout into the void:

Phylointelligence: Evolution for everyone.

The site is well-designed and though the content is still a little rough, I like the idea of cataloging the evidence for evolution in a way that is accessible to general readers.  I also like the focus on the overlapping lines of evidence which support evolution.  It’s a site that I’ll be keeping an eye on, and if I can find the time, maybe I’ll even contribute something to it…

[h/t: Pharyngula].