Wednesday, December 21, 2011

Merry Christmas / Happy Holidays, and Count Some Birds!

I hope you have a great holiday.  Some of the things I love over the holidays are: family, egg nog (homemade, not that stuff stores call egg nog), Canada Juniors hockey, turkey, leftover turkey sandwiches (with cranberry sauce and stuffing), and this year seeing my son get excited about anything related to Christmas.

Looking for something fun and outdoors over the holidays?  Participate in the Christmas Bird Count.  People like you (even if you're not a bird expert) count the birds you see on a specific day and send the information to a local coordinator.  There are counts organized between Dec 14 and Jan 5 across Canada and the USA.  Bring your family and make an event of it.

Tuesday, November 22, 2011

Tardigrades: little beasts found inside vol 125 issue 1

I'm thinking of highlighting one or a couple of articles in each new issue of CFN.  Depending on how ambitious I get, I might even have a Q&A session with some of the authors to give the "story behind the story" on how they did their research and why.  These are just ideas right now - don't hold me to them.  But I will at least discuss one article in 125-1 that deals with a very cool subject: Tardigrades (also known as water bears because they kinda sorta look a little like bears under the microscope).

Grothman, Gary.(2011) Tardigrades of Fish Creek Provincial Park, Alberta, Canada: A Preliminary Survey. The Canadian Field-Naturalist 125(1): 22-26.

My friend Matt Boeckner (who published a 2005 article on tardigrades in CFN) first introduced me to tardigrades a few years ago in Newfoundland.  "THEY ARE AWESOME!" he told me, but I was skeptical.  I studied Daphnia zooplankton at the time, and everyone knows nothing can be more awesome than Daphnia [citation needed to support my unreasonable opinion].  But the more he told me about tardigrades, and the more I learned about them since then, the more I realized that they truly are amazing because of how tough they are.  They can withstand conditions too extreme for almost any other animal, including desiccation, extreme heat, extreme cold, radiation, and even outer space.  They make cockroaches look dainty by comparison.

Gary Grothman surveyed the tardigrades of Fish Creek Provincial Park, Alberta.  Considering most tardigrades are too small to see with the naked eye (almost always smaller than one mm long), this isn't exactly birdwatching, or even butterfly collecting.  This takes patience.  Basically, he took tardigrate-inhabited material (e.g., moss) and dried it, then soaked it in water and poured the water through very fine screens to collect tardigrades, then he examined the tardigrades under a microscope to identify them.  He found a number of species, including eight new to Alberta and two new to Canada.  People seldom have affection for little invertebrates, but biodiversity isn't just charismatic polar bears and falcons; it includes the full diversity of life.  It is nice to know people like Gary are investigating the diversity of charismatic but tiny nature in Canada.

Say hello to Diphascon granifer, one of two species reported new to Canada by Gary Grothman in The Canadian Field-Naturalist.  Image courtesy of Gary Grothman.

Saturday, November 12, 2011

Little tiny owl spotted on CFN website (and it's spotting you too)

You know those mini-icons that appear in your web browser's tabs and Favourites bookmarks?  For example, there should be an orange-background "B" (for Blogger) mini-logo on your tab for this website.  These are called favicons (because they appear in your Favourites list).  They are not really essential for anything, but they look kinda purdy and give an extra opportunity to brand your website.

I figured out how to make a favicon for the CFN site.  I did this after my Mozilla Firefox browser updated to the latest version this week, and now any website without a favicon has a blank dotted box where the favicon should be.  The blank box reminds me of when I circle a missing answer on students' tests; it draws attention to the absence of a contribution.  So I did some Googling to figure out what these logos are called, how I can make one, and how to add one to my site.  Favicons are only 16 pixels x 16 pixels in dimension.  That's pretty small!  You can't be very elaborate with 16x16 dots.

I started by making the letters "CFN" in 16x16 dimension.  It looked budget.  My son could've done a better job, and he eats crayons.  So I found a site where you can upload images and convert them into 16x16 favicons.  Obviously you can't expect Mona Lisas on such a small canvas, but I was pleasantly surprised at the detail it could achieve.  So I decided to make a favicon for the OFNC's owl logo.  Now when you go to the CFN site the owl head will be staring out at you from your web browser's tab.  Watching you like a haw... like an owl.  I don't think people would peg it as an owl if they looked at it in isolation, but considering the large version of the image appears at the top of all CFN web pages I hope people will make the link.  Or at least I hope they won't misconstrue the favicon as something crude and boycott our journal.

If you're interested favicons for your site, here are the resources I used. - favicon creator. - forum discussion with instructions on how to add a favicon to journal websites using Open Journal Systems software (which CFN uses). - has some nice nature-related favicons for free, as long as you give credit to their website.  I didn't use any, but I was tempted to.

Monday, September 26, 2011

the website ... IT'S (A)LIVE!!!!

omg, lol, rofl!  The new CFN site is live and it's anhc (amazing natural history content ... I just made that accronym up but I doubt it will catch on).

If you are one of the two people who follow this blog (hi Mom!) then you'll know I've spent a lot of time, frustration, and drinks setting up a new website for CFN.  Well, it's done*.  Go see the website for yourself.

We've also published a new issue (volume 125 issue 1) that represents the first issue published by our new Editor-in-Chief Dr. Carolyn Callaghan.  There is some excellent natural history research in this issue, but it deserves its own blog post so I'll let you read it yourself and then I'll write a post soon telling you how awesome some of the research is (e.g., killer loons ... I'm not even kidding!).

* The site is not fully done, and likely never will be.  Good websites are constantly improving, and ours is no exception.  I have a long list of things I intend to set up over the coming days/weeks/months that should improve the experience for readers, journal volunteers, reviewers, editors, and authors.  The items highest on my to-do list will affect authors, editors, and reviewers - online manuscript management.  What could go wrong?

Wednesday, August 3, 2011

The software works (or: Shoo Hackers - Don't Bother Me!)

Our journal's new website is almost fully-functional now.  The latest step has been upgrading the website software to the latest version.  The new version has a bunch of features that should improve functionality on the back-end for me (e.g., improved subscription management), and a few features for readers and authors too.  But the main reason the upgrade went from a "I'll do it later" to "I need to do it now" was a security fix.  Our website had been hacked, as had a bunch of other journal websites using this software.

A popular way to hack a site is to make some malicious code in an executable (.exe) file and submit it to the website to run.  Sometimes hackers do this to take over the site to divert visitors to some site for which they receive financial benefit from the number of visitors.  Sometimes hackers are just jerks who like to mess around with other people's websites - it's how they get their kicks.  Weirdos, I know.  Anyway, we got hacked so our website was diverting people to some pseudo-search engine.  Our Jedi server hosts fixed the problem quickly.

Apparently a hacker had figured out a way to upload malicious .exe files to journal websites running Open Journal Systems software.  The software guards against these types of files, but there was a loophole (.exe files could be submitted as cover photo files).  The developers quickly fixed the problem in a new version of the software and urged everyone to upgrade to the new version.  So over the past couple of weeks our server Jedis, the software developers (who always take the time to answer my tech-illiterate questions), and I have figured out the troubleshooting required for any upgrading and we upgraded our software.  It seems to work fine so far.  And it look perrty too.

The fourth and final issue of volume 124 is almost ready for printing.  This will mark the last of Dr. Francis Cook's tenure as CFN's Editor-in-Chief.  Dr. Carolyn Callaghan is rarin' to go with volume 125.  Volume 125 will also mark the official opening of our new website.  We can't really have a ribbon-cutting ceremony for a website so I don't know how we'll celebrate a website "opening", but it will likely involve fewer speeches (yay!) and maybe more drinks (yay!) than a ribbon-cutting ceremony.  If you feel like you want to participate in our celebration, I invite you to visit the journal website and have a drink.  While you might technically be drinking alone while looking at a journal website, it can be a celebration in your mind.

Monday, June 20, 2011

Canada Post and CFN

UPDATE: Canada Post is back to work and mail delivery will be back to normal starting today (June 28).

Canada Post is currently in a labour dispute, and as a result there is currently no mail delivery.  I've heard some people talk about how they don't need mail anymore since they get most bills, letters, etc. online.  While I agree that the Internet has reduced people's reliance on postal mail, postal mail is still important.  CFN is certainly impacted by the labour dispute.

CFN sends author invoices, subscription invoices, and of course printed issues by postal mail.  I am working on ways to shift our invoicing from postal to electronic mail (e-mail is faster, cheaper, and less of a pain in the butt to file than paper), but we will still rely on Canada Post for a lot of CFN affairs.  Mail delivery has been suspended for about a week so far.  We hope the dispute will be resolved before the next CFN issue is ready to be mailed.  We apologize to anyone who has tried to mail us correspondence in the past couple of weeks - your mail should get to us once the labour dispute is over.  If the dispute continues for a long time we will provide an update on how we will proceed with CFN operations without the benefit postal mail (I really hope the dispute won't be lengthy).

Monday, May 30, 2011

Oikos Blog, and an update on CFN website progress

Looks like we've got company (and that's a good thing).  Another ecological journal has a blog: Oikos Blog, which I've just added to our blogroll (on the right side of your screen).  It is run by University of Calgary evolutionary ecologist Dr. Jeremy Fox.  I've just spent the past hour reading its posts and I'm very impressed for two reasons:

1. High quality of content.  Oikos is an excellent journal famous for publishing bold papers.  Most journals' editors shy away from publishing radical ideas that might lead people to question their sanity, but Oikos' editors seem justifiably proud of their craziness.  Their editors all look like the gentleman below (Oikos is published by the Nordic Oikos Society, hence the obligatory viking headgear they are forced to wear, just like Canadian Field-Naturalist editors have a strict Canadian dress code).  The Oikos blog, like the journal, raises cutting-edge ideas intelligently and provocatively.

2. Informal style.  I hate when a blog is bland.  There are plenty of organizations' blogs that are self-congratulatory, formal, and about as interesting as a bunch of press releases stuck together.  The Oikos blog is an enjoyable read, and Dr. Fox's self-deprecating humour is refreshing.  Personally, I skim a few blogs daily while a eat my lunch, and Oikos' blog will be on that list now.

As you may have noticed, I haven't written much in this blog lately.  A big reason for that is the new Canadian Field-Naturalist journal website isn't finished yet, and I'm reluctant to link to it until it's ready to go live to the millions of natural history-maniacs across Canada and around the world.  You only have one chance to make a first impression, so I'm keeping the new journal address a semi-secret until I have it well-polished.  So I can't post about some of the cool articles coming out in recent issues because it would be mean of me to talk about research you can't read for yourself.  And nobody likes a meany.

How is the new journal website coming, you ask (yup - I can read your thoughts)?  All content is on the site, and the search function is working fantastically.  But two things are not yet ready: PayPal for subscriptions, and editorial management for authors submitting manuscripts.  PayPal won't be ready for another couple of months at least (it's a lower priority - worst case scenario is subscribers will have to pay by cheque for another year), but the manuscript management portal is coming along nicely.  I will upgrade the website to the newest version of Open Journal Systems software that's coming out, which promises to have new features that should improve front-end features for readers and back-end features for journal management.  Once that is installed (and re-installed after I inevitably screw up the first installation), the site should be ready to be announced.  I'll open a luxurious bottle of Baby Duck sparkling wine to celebrate at that time.  Between now and then I'll be transferring paper-based subscription records into computer format (where is a team of trained monkeys when you need them), uploading new issues as they are published (volume 124 issue #2 is being printed right now), and otherwise trying to keep on top of things ... and hopefully finishing my PhD too.  What could go wrong?  :)

PS: I've also added another new blog to our blogroll: Natural History in Suburbia.  My friend and fellow insect-loving grad student Chris Borkent is its author.  Chris says it will mostly be about natural history in the Montreal area where he lives.  I hope it will feature insects prominently, but the first few posts feature flowers (gross).

Saturday, March 5, 2011

Naturalists: the naked truth

I was googling things related to Canadian naturalists lately, seeing if there are any websites discussing our journal that I should be aware of.  I stumbled across a link for The Federation of Canadian Naturists (FCN).  I was surprised and excited: how could there be a federation of Canadian naturalists that I wasn’t aware of?  So I clicked the link.

And then I found out that there is a difference between "naturist" and "naturalist."  The FCN main website defines naturism as: “Naturism involves the practice of complete nudity in a communal setting. It promotes wholesomeness and stability of the human body, mind, and spirit, especially through contact of the body with the natural elements.  Yup – they’re nudists.  I must officially be a natural history nerd because when the FCN website came up with its images of nude people rather than insects or plants, I was disappointed.

I have no problem with nudism/naturism, I just don’t think naturism would mesh well with naturalism.  Just imagine: poison ivy ... everywhere!

Friday, February 4, 2011

ATTACK OF THE KILLER ROBOTS!!! (or at least spam-bots)

Spam - whether it's the e-mail kind or the (supposedly) edible kind, it ain't good.  I just opened my spam e-mail folder and found dozens of messages with lines like "I NEED YOUR URGENT ASSISTANCE IN TRANSFERRING THE SUM OF (USD$13.7) MILLION DOLLARS ..."

Quite a few users have registered on our journal's website.  This made me happy, until I read the detailed information on these users and found some trends.  Their first, middle, and last names tended to all be the same and jibberish (e.g., CAT41 CAT41 CAT41), their phone numbers were all 123456, and their countries were all Afghanistan (the first country on the scroll-down alphabetical list).  Yup, these were spam-bot registrations, which made me sad.  I don't know what the goal of these spammers was, but there were often links to a handbag company's website in their information, so I guess they make money from that website's sales or web traffic.  So how do we get rid of spammers?

I've spent the past couple of hours figuring out a solution, but I think I've found it.  There is a way to require users to enter a "Captcha" when registering.  Captcha's are letters and numbers at weird angles that most machines can't read but humans can.  Other journals' managers who use our journal software assure me that Captcha's really work at preventing spam registrations.  They are annoying to type (and sometimes difficult to read unfortunately), but that's because machines are getting better and better at reading text, so the "are you human?" tests need to be more and more difficult.

Our journal software designers have stated they will move from Captcha to reCaptcha in future versions of our software, which is great news.  reCaptcha ( is like Captcha, but functions not only as a security feature but also helps transcribe old books.  There are many programs that are scanning pages from old books into computers, and then using Optical Character Recognition software to transcribe the scanned text into typed words to make books available digitally.  But some words are difficult for computers to read (e.g., they are weathered); reCaptcha uses these words to test if users are human.  It's great for security since it uses words machines have tried and failed to read, and it's good for humanity since it helps digitize old texts one word at a time (von Ahn 2008).  We will gladly use reCaptcha once our software allows us to.  In the meantime, Captcha's like "r33MD8" will have to do (which, ironically, is similar to the names of our spam-bot registrations).

von Ahn L, Maurer B, McMillen C, Abraham D, and Blum M. 2008. reCAPTCHA: human-based character recognition via web security measures. Science 321: 1465-1468.

Tuesday, January 25, 2011

I love it when a plan comes together

The A-Team's Hannibal might have been talking about plans involving Mr. T, explosives, and battles against gangs of evil-doers, but that feeling of elation when things work like they're supposed to is pretty nice regardless of the setting.

Our journal website seems to be working!  In fact, it's working even better than I had anticipated (I managed to trouble-shoot the issue-ordering problem so now issues are listed chronologically as they should be).  I have uploaded almost all of the old content (just a few book reviews left to go).  The site seems ready for action.  There are still a couple of details missing (e.g., I have to list the journal's associate editors and their subjects of specialization) but these are just details.  The site works!

I will announce the website very soon, after I verify a few more things are working fine.  This is a very exciting time to be associated with our journal.  And I can't help but get excited about the future prospects of natural history study in general.  I'll write more some other time about the general down (and now up I think) trends of natural history study in North America - for now I have some website work to do!

Saturday, January 22, 2011

2 steps back, 2 steps back, 2 more steps back ... the terrible polka of website programming

If I had a dartboard, I just might put a picture of the Internet on it and vent some of my frustration.  Ok, I don't know what a picture of the Internet would look like, so I guess it's not a well thought-out plan, but the point is I am frustrated with servers, software, and anything else that communicates in binary.

In my previous post I was excited about the server hosts changing things to allow me to upload articles.  Unfortunately there were other errors associated with the article meta-data (e.g., I couldn't italicize anything in the abstract, which is a big deal considering how many species' names are in our abstracts).  This is not the fault of our server host - it's just a problem I never could solve.  So instead of being able to carry on with my work setting up the journal site, I spent more time trouble-shooting.  Friendly staff associated with our server host company, the Open Journal Systems software system, and users like me (but more knowledgeable) on the software discussion forum were all very helpful, but left me realizing we needed to undo our software upgrade and start again.

So that's what we've done.  Our server host Jedis degraded (I don't know if that's the correct term, but it is the opposite of upgraded) our software back to the old version that was working fine.  And it actually seems to be working fine!  There are a couple of bugs with this software version, but they are very minor.  For example, because I'm uploading 2004 issues now (after already uploading 2008 issues), 2004 issues appear at the top of the list of issues rather than issues appearing strictly chronologically.  This is messy, but only a minor inconvenience.  The main thing is, all of the articles I had uploaded are still there ... the articles and their meta-data are preserved and online.

So, after many steps back and back and back I should be able to actually make some progress now.  And quickly too - uploading the last of the old articles is my #1 priority this week.  We will be ready to go live very soon.  I know the suspense must be killing you.  I'm really excited about the site working.

Ok, back to the other tab of my browser in which I'm uploading issues!

Sunday, January 2, 2011

Slapshots, Jedis, and website problems, oh my!

Meatloaf said that two out of three ain't bad.  What about one out of four?  That's how many of the "complete before Christmas" CFN tasks I actually completed before Christmas.  I think Meatloaf would agree that one out of four is not very good.

I blame two factors for my failure:
1. That guy on the other team with the big slapshot.  I got hit with it on the inside of my ankle in mid-December and it fractured my tibia.  What's he doing playing beer-league hockey when he can actually shoot the puck well?  Ok, a fractured ankle did not inhibit my success much - I'm just bitter about it because I can't play hockey for a month or two.  The real factor causing me to not complete the other tasks was,
2. Website problems.  The one task that was completed, upgrading the journal website software, produced problems that prevented other tasks from being completed either because they required the website or they were lower priority items than fixing this new website problem.

Our friends at the server hosting service we employ upgraded our journal website software to the newest version.  They do this sort of thing very well.  I suspect they are Jedis.  I quickly logged in to see some of the new features available that improve behind-the-scenes journal management.  Cool stuff from the looks of it.  Then I tried to upload some articles (another of my tasks) only to find that I was no longer able to upload files.  No error message telling me why I couldn't upload, or any other information, just an inability to upload files.  Not good.

I tried uploading different file types - nothing worked.
I tried uploading as different users - nothing worked.
I tried drinking hot gin toddies - that worked, but the website still did not.
Time for the online help forums.

I'm no web slouch - I help colleagues create websites and do other stuff that makes me feel young and cutting-edge even if I'm neither.  But when I'm reading through forum topics on website upload problems trying to figure out how I can give a folder a permission (for example), I feel pretty dumb.  And old.  And definitely un-Jedi-like.

Our server hosting friends saved the day by changing certain folders' permissions and now the site works and I am busy uploading old articles again.  There are some issues I still need to address on the website, but at least it's functional now - catastrophe averted.  I'm looking forward to uploading articles and completing the other tasks to get this site ready to go live.  Two steps forward, one step back, all the way along.