Inexpert, or how to identify Ontario Dragonflies (sometimes)

I’ve been chasing dragonflies again, up at the cottage, and have  been obsessively trying to identify all of the species. Blame my scientific training, I say. And, as you might imagine, this is not going terribly well, because I’m a molecular biologist, not an entomologist, and I didn’t take any DNA samples.

Readers who are familiar with Grrlscientist’s blog and her regular “Mystery Bird” feature, know that identifying different species, even ones we think we’re familiar with, can be very tricky indeed. In this part of North America, birdwatchers mutter darkly about the five nearly-indistinguishable species of Empidonax Flycatchers – Acadian, Yellow-Bellied, Least, Willow, and Alder – or the various and assorted “Peep” sandpipers, which I won’t bother to list for you. If you’re interested, this guide from the American Birding Association will give you some idea of the problem. Even the lowly Mourning Dove has a habit of looking like other birds, as Joey Slinger points out in his excellent Down and Dirty Birding. And it doesn’t end there – my edition of the classic Peterson Field Guide to Eastern Birds contains four dense pages, amusingly labeled “Confusing Fall Warblers, etc.”, which will drive you completely mad if you look at them for too long.

dove stretching
A Mourning Dove, pretending to be an umbrella.

But all this pales compared with insects.

Really hard bird identifications are, for the most part, not the norm, although I’ll readily concede that the difficult ones can be every bit as impossible as any fly, wasp or bug. Insects, however… well, that can be a different story. And dragonflies, compared with all manner of other creepy-crawlies, are actually comparatively easy, for the most part, with “only” 172 species recorded in the Province of Ontario. A much easier number to deal with than, say, beetles, or flies. Nevertheless, for the non-expert (and I most assuredly am not one), identifying these creatures can sometimes be very, very challenging indeed.

Dragonfly - Canada Darner?
This one is probably a Canada Darner – but maybe not.

Once in a while, I’m even accompanied by a friend who is a real, live, card-carrying entomologist from the Royal Ontario Museum, who, although originally an expert in parasitic wasps, spends a lot of her time identifying insects from in and around the Greater Toronto Area and other parts of southeastern Ontario. Despite having access to her expertise, a copy of the excellent Dragonflies Through Binoculars, and the entire internet at my disposal, the ID of this one eluded me for quite a while:

Lunch
Mmmm, tasty.

Turns out it’s a female Eastern Pondhawk, demonstrating one of the confusing issues – sexual dimorphism, with females this gorgeous bright green, whereas males are blue. Believe it or not, few of the sources I consulted had photographs of both genders. I’m not even going to attempt to identify the unfortunate Damselfly it’s eating. Half a dozen photos later, it was completely gone.

Here’s another – the female Common Whitetail. Note the complete and utter absence of a white tail, which is blindingly obvious in the adult male:

Female Common Whitetail Dragonfly
No white tail, and twelve wing spots. Males have a white tail and eight spots.

Now, I don’t consider myself to be particularly bad at this. The trouble is that dragonflies are really variable, much more than you might expect. I’ve come up with four major issues that make this tricky:

1) They can vary regionally, so that the same species in one familiar location might be a lot darker, or a lot lighter, somewhere else. This will drive you nuts if you don’t know about it, and maybe even if you do. The devilishly complicated Sympetrum Meadowhawks provide a fine example (see Meadowhawks will make you crazy for an amusing introduction). For added fun, sometimes the names vary, too – that Common Whitetail is also known as the Long-Tailed Skimmer, for example.

Meadowhawk
A Meadowhawk. Do you know the species? Yeah, neither do I.

2) As we saw above, females and males can look really, really different, making it very hard to identify one, if all that you have is a picture of the opposite gender. On the other hand, sometimes they look identical, which helps with the species, but makes telling the males and females apart impossible except by behaviour, or a much closer anatomical examination than is possible with a camera.

3) Immature individuals can look quite different from adults – sometimes just enough to trick you into thinking that they’re something else. Immature male Common Whitetails have the same non-white tail as females, but the wing spots of a male.

4) Sometimes, they can vary in colour, even in the same location. Those Canada Darners can sometimes look like Green-Striped Darners. This will also drive you nuts.

What’s perhaps even more surprising is that, even though there are comparatively few species, and Dragonflies and their kin are large and showy, nevertheless there are few really comprehensive, online field guides. Although our Ministry of Natural Resources does a valiant job, there are still just not enough online images collected in an expertly-reviewed collection to safely navigate me through issues 1 through 4, above.

Dragonfly in flight
It’s even worse when they’re not sitting still.

So what’s a casual nature observer to do? We can’t all be experts at everything, and it seems that sometimes even the experts are overwhelmed to the point at which regular folks are doomed. But that, in a perverse way, is part of the fun – because finally nailing an ID can be very satisfying, at least until someone comes along and tells me that I’m wrong.

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The curious confluence of science and surfing

If you’re in Toronto this weekend, I’ve got an event for you:

Aloha Toronto.

Now, I’m sure you’re not thinking to yourself, “ah yes, Toronto Canada, a prime surfing destination!”. But this weekend, you should be, because starting tonight, the good folks at the Paskowitz Surf Camp are bringing their show to town, all in support of autism research and care, Surfers Healing, and The Hospital for Sick Children. There’s a kickoff party tonight, a luau on Saturday the 25th, and loads of free activities Saturday and Sunday.

Izzy Paskowitz and Josh Tracy, Toronto
The guy who started it all – former pro Izzy Paskowitz, with fellow surfer Josh Tracy.

Surfers Healing was started by Izzy Paskowitz, one of the sons of the legendary Doc Paskowitz, patriarch of what’s been called the “first family of surfing”. Starting from Izzy and Danielle Paskowitz’s experiences with their autistic son Isaiah, Surfers Healing has grown to an organization that has brought thousands of autistic children to the ocean, and now to the sometimes-chilly and broad reaches of Lake Ontario, for some therapeutic fun. Having spent an hour or so in a downtown hotel conference room this morning with Izzy and some of his colleagues, I can tell you that these guys are the real deal – serious surfers who are also passionate about working with autistic kids, and raising money as they do it.

J Riddle and Jeff Ekberg, Aloha Toronto Press Conference
Another surfing legend, J Riddle, with Surfers Healing’s Jeff Ekberg.

And if that’s not enough to get you out on what promises to be a beautifully sunny Toronto weekend, how about this? Garrett McNamara, famous for surfing a record-breaking 30-metre wave last November, will also be on hand. If you like extreme sports, surfing, or both, and feel like being star-struck – this is definitely the guy.

We do a lot of autism research here at SickKids, which, in the way of all science, sometimes leads us down unusual paths. Talking with professional surfers who know more about working with autistic kids than I ever will was certainly a different way to spend a Friday morning – but a fun and welcome one.

Get on out there, Toronto – the waves are waiting.

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August 4 – Mountsberg Raptor Centre

Look what I see – the brand-new, shiny Occam’s Corner, with an inaugural post by Stephen. Well done Occam’s Crew and colleagues at the Guardian for making this happen.

Right, that’s that out of the way. Now, on to a photograph of an owl.

Male Snowy Owl
Either Harry, or Ron – I don’t know which, and he wasn’t saying.

Once in a while, and probably not frequently enough, I have the opportunity to give myself a good, hard, metaphorical kick for not getting around to something sooner. This past weekend offered up a good example, when I finally took the kids to visit the Mountsberg Raptor Centre. Not even an hour away from home, it’s in a picturesque bit of Halton Region near the Niagara Escarpment, itself famous for being the geographical feature that puts the falls in Niagara Falls. Mountsberg is so close to home that I’m embarrassed I’ve never been there, despite first learning about it a couple of years ago from my Flickr acquaintance Brian.

One wet owl.
Octavius, a human-imprinted female Great Horned Owl. She’s a bit wet after a nice spray bath on a hot day.

The Raptor Centre is located on the grounds of a sprawling conservation area, full of woods, wetlands and a few family-friendly sites including a hobby farm and a barn converted to a play area. But the main attraction is the birds – twenty-eight of them, spanning fifteen species. Many have been rehabilitated from injury, some placed after being seized from illegal keepers, and others orphaned. None can be released into the wild with a reasonable hope of survival, so in Mountsberg they live, occasionally engaging in education and outreach activities, or falling prey to passing scientist-come-photographers.

Juvenile Bald Eagle
A juvenile Bald Eagle, whose name I don’t know, putting on its best “I’m going to slash your face” face.

Although you could argue that perhaps we should just leave well enough alone, rather than expending time and effort rehabilitating and caring for injured birds, I for one am very glad that Mounstberg and places like it exist. I certainly learned plenty about these birds that I didn’t know:  that the Barn Owl is likely extirpated in Ontario, although plentiful elsewhere in the world; that the Gyrfalcon is the largest falcon species, and comes in several different colour varieties; and that the American Kestrel usually only lives a few years in the wild, but is happy to go on ticking for at least sixteen in captivity. I also discovered that almost any bird of prey looks fierce if you point a camera at it, even if it’s happily enjoying a spray bath, or just about to gobble up a delicious snack of raw chicken. And it’s clear that the staff are highly trained, dedicated, and really love the birds they care for and work with.

Peregrine Falcon
One of the Peregrine Falcons. Much easier to photograph when sitting still, than when dive-bombing a pigeon at 300 kilometres per hour.

So I’m marking this day trip down as a success, and hoping I can haul my lazy self to some other local attractions before the summer’s over.

More photographs in the Mountsberg Raptor Centre set, over on Flickr.

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Non-science hobbies (again) – the Honda Indy Toronto

Race Winner - Ryan Hunter-Reay
One race winner, two cars, and three sponsor banners. Check, check, and check.

Those who’ve been following me for longer than I’ve been a resident at Occam’s Typewriter will know that I have a passion – some might call it an obsession – for photographing fast-moving vehicles. Most of the time, it’s just for me – a hobby coupled to an enjoyment of motorsports. But one weekend of the year, it becomes more – a job, albeit an unpaid one, as a fully credentialed media photographer for the IndyCar dust-up on the Streets of Toronto circuit. This is where the teams, drivers and cars that run the Indianapolis 500 show up in downtown Toronto, on the Exhibition Place grounds, for a weekend of fairly loud, and very fast, competition. And what a weekend it is – full of challenging assignments, a shot list as long as my arm, and three full days of hard slogging around the track. Like my science day job, it’s about working with a team, meeting milestones, and going the extra little bit to deliver results. By the end of Sunday, the twice-a-day hand-in deadlines meant I’d reviewed over 1,500 photographs, and delivered just a hair fewer than 200 as my part of the equation – on time, each day. Compared with some open-ended projects I’m occasionally obliged to stickhandle at work, the sense of satisfaction and completion is a welcome change.

This was my third year on the team. You can read all about last year starting on race day here, and work all the way back to my inaugural year in 2010 from there, if you want to. As for 2012: here are some highlights.

Thursday:

In the morning, I watched the resident clown at the children’s hospital where I work film an interview with IndyCar driver Oriol Servia, and came up with a great joke: “Who’s the clown with the camera?”. Neither he, nor anyone else, thought it was funny.

Oriol Servia - Racing for Kids, Toronto
Mr. Servia, a champ with the kids. The clown’s out of shot to the left, not laughing.

Next I toddled off to the track to shoot a few press conferences, including one with Formula 1 legend Rubens Barrichello, a true gentleman of the sport, in the best senses of the word.

Rubens Barrichello, Honda Indy Toronto 2012

Then I completely missed the opportunity to be driven around the track at race speed in a Ferrari, because I’d left early to go home and rest up for the coming weekend. Argh.

Friday:

I wandered around pit lane and a few other places, including a favourite haunt on the inside of turn one, adjacent to the Princes’ Gate, a Toronto landmark. The day involved photographing practice sessions, drivers autographing things, and fans having fun.

Simona de Silvestro, turn 1, Toronto 2012
Swiss driver Simona de Silvestro, getting her speed on.

I also finally met a friend of my brother’s, who drives the IndyCar medical vehicle, after the third year of saying I’d try to find her at the track.

Saturday:

For the second year in a row, I was dispatched as part of the “you idiots didn’t take any photos in front of the turn 9 Pizza Pizza billboards yesterday!” detail. Just for fun, I snapped a photo of exactly the same driver, in exactly the same car, in front of exactly the same billboard. Felt pleased with myself for being so cheeky. But not that pleased, because last year’s photo was better.

Then I chased a few drivers around, including eventual second place finisher Charlie Kimball and local boy James Hinchcliffe engaged in some off-track shenanigans.

Kimball and Hinch
Hinch seems to have sprouted a spare head, and a couple of extra legs.

Along the way, I nailed a couple of “keeper” shots – an IndyCar jumping a curb, and an Indy Lights car blowing some flames. Jealous noises from the rest of the team.

Afterburners

Sunday – RACE DAY!

First, I ran around a bit cleaning up some sponsor billboard shots, and then set off at the request of a supporting series (the Star Mazda Championship, in case you were wondering) to get some photos of a couple of specific drivers and their cars. Sorted.

And then, the main event… I stationed myself in pit lane for the starting grid and pre-race activities, elbow to elbow with crews, drivers, guests, other photographers, race officials, and goodness knows who else. Once the grid started to clear for the race, I was able to snap a few shots of teams awaiting the coming storm.

Pit Crew, J.R. Hildebrand / Panther Racing, Toronto 2012
The team of the car that was in front of that billboard on Saturday. The driver is J.R. Hildebrand, but I have no idea where he is.

It’s not trivial wedging yourself into the driver’s seat, as last year’s series champ Dario Franchitti demonstrated.

Dario wedges himself in.

And then – the race, which was all kinds of amazing from my vantage point, out on the “island” between pit lane and the front straight. The shot of the day, for sure, was this one – the iconic Princes’ Gate in the background, a pack of cars late in the race, heat haze and smoke and tire rubber flying.

Honda Indy Toronto 2012

There was also plenty of pit stop action, with huge grandstand crowds in the background – the other reason I needed to be out on the island, the only vantage point from which it’s possible to get this shot.

James Hinchcliffe pit stop, Toronto 2012
Canadian James Hinchcliffe again… before his engine let go.

And so on to the finish, and a win by Andretti Autosport’s Ryan Hunter-Reay, who you can see in the yellow car at the top of this post. I wasn’t in the right position to catch the chequered flags flying like I did last year, but instead was able to capture a nice reaction shot from the team, including team owner Michael Andretti, himself a seven-time winner of the Toronto race.

RHR's crew celebrates
Mr. Andretti’s the one in black standing in front of the journalist in the ESPN vest.

And then back to the media centre for one final round of hand-ins, and for one more year, that was that. Exhausting, great fun, camaraderie and sunscreen and water and a lost lens hood all into the bargain.

More photographs, as usual, in the Autosport collection.

Posted in Hobbies, Photography, Racing | Tagged , , , , , , | 4 Comments

Light Fighting

One advantage of working more-or-less right downtown in Toronto is that it’s possible, on occasion, to make time during the day to catch some interesting things going on.

I’ve spent some time recently wearing my official photographer’s hat for the Honda Indy Toronto, the annual race around the streets of Exhibition Place, which is coming up in early July. I’ve worked this event with media credentials the past two years, which you can read about here and here. From photographing famous Canadian driver James Hinchcliffe with the Mayor of Toronto, to covering a kickoff for a fundraiser to support kids’ activities, to being on site for the unveiling of this year’s trophies, there’s been a lot going on these past weeks. Photos of all of that are right here.

Even so, I found a little slice of time to sneak down into Toronto’s financial district for a lunchtime concert by blues-rock guitarist Colin James, celebrating the release of his latest album. This is a guy whose music I’ve known since his 1988 debut, but have never seen live. Along with his rock-pop efforts, he’s also recorded three albums of big-band swing in the same vein as the Brian Setzer Orchestra and is a mean blues guitarist, and an impressive vocalist, to boot.

Colin James tears it up in Toronto
Colin James lays down Dylan’s “Watching The River Flow“.
1/30th of a second at f/5.6 and ISO 2,000.

I’ve done very little live music photography, with the exception of a large convention I’ve written about previously, but I do know that lighting for such events is usually best described as “awful”. Concert photography discussion groups, like this one on Flickr, are full of complaints about lighting, endless discussions of lens and flash choice, and one-upmanship about the worst conditions possible (shooting punk bands in unlit basement clubs being a popular example). What I’ve learned is that even stages that look brightly-lit are actually really dark by comparison with daylight, and that the mix of spotlit and shaded areas can be a real bear. The trick is to get as much light into the camera as possible, which you can accomplish in three ways:

1) Open up the aperture. The wider the opening into the lens, the more light gets in. Aperture is measure in f-numbers, also called “f-stops” or just “stops”. The f-number is a ratio of the focal length (that number in millimetres written on the side of the lens; longer for telephoto, shorter for wide-angle) and the diameter of the hole in it letting light in. The larger the hole, the smaller the f-number. A lens that can manage a small f-number lets a lot of light in, and is referred to as a “fast” lens. f/1.8 is very fast; the lens I used for the photo above manages f/5.6, which isn’t. Fast lenses, generally speaking, require much bigger pieces of glass, making them larger, heavier, and a lot more expensive. Because of how it’s calculated, double the light getting in to the camera (one “stop”) means a change in the f-number of the square root of 2 (which is about 1.4). For example, f/5.6 is one stop slower (narrower aperture, less light, bigger f-number) than f/4.

2) Slowing down the shutter speed. The longer the camera’s shutter stays open, the more light gets in. I shot that photo at 1/30th of a second, which is pretty slow, and you can see that Mr. James’ hands are blurred as a result. That doesn’t bother me, because his face is still sharp. Any slower and the photo would have been a a blurry mess – trust me, I tried. Doubling the shutter speed results in twice the light getting into the camera, so 1/30th is one stop faster than 1/60th (are you following this? It’s a slower shutter speed, but lets more light in to the camera, so in terms of exposure it’s considered “faster”).

3) Raising the ISO sensitivity. ISO is a funny term, left over from the days when film was rated depending on how sensitive it was to light. Higher numbers meant “faster” film that was better for low light. In digital cameras, we use a similar scale. Raising the sensitivity two-fold is equivalent to letting twice as much light in, so ISO 400 is one stop faster than ISO 200. The trade-off is that increasing ISO always results in decreased signal-to-noise, and increased graininess. That’s why photos taken in the dark with a camera phone look grainy, and more or less why fast film was notorious for being grainy too.

On this shoot, the light was sufficiently bad that I needed to drop the shutter speed as slow as I dared (and 1/30th is pretty darn slow for anything that’s moving), and crank the ISO up high enough to get the exposure bright. ISO 2,000 is likely to be pretty nasty looking on anything but a professional full-frame camera, but I think it’s ok here, if you accept that grittiness can be good, and that I’m not going to be printing poster-sized copies.

Colin James Band, First Canadian Place, Toronto
It gets worse – 1/40th of a second at f/5.6 and ISO 2,500.
Covering Van Morrison’s “Into The Mystic“.

You might wonder why I simply didn’t use a faster lens – one with a wider maximum aperture. With more light coming in, I would have been able to either speed up the shutter to avoid blur, reduce the ISO to avoid grain, or a bit of both.

The answer, no surprise, comes down to money. By spending roughly five times what I did on my lens, I could have been using the classic 70-200 mm f/2.8, which allows for a maximum aperture of f/2.8. This is a perennial favourite of sports shooters, photojournalists, and even fashion photographers everywhere, and is referred to by one motorsports friend of mine as “the moneymaker”. Canon users are familiar with this formula as well, for the same reasons. I do own a very fast lens, but it has only a 35mm focal length, far too short for isolation shots of performers on stage. It got a workout for wide shots at that convention, though.

If you’ve been following along, f/2.8 is two stops faster than the f/5.6 I was able to use (remember, f-stops go in powers of the square root of two, and 2.8 is half of 5.6). That means I could have stayed at ISO 2,000 and bumped the shutter speed to 1/120th of a second, which would have frozen the motion of his hands, but not really have improved the sharpness of his face much. Or, I could have reduced the ISO by four-fold (remember, ISO goes in powers of two) to 500, which would have been much less grainy. That lens also has other advantages, including reportedly very quick autofocus, but at over a thousand dollars per extra stop of light, it’s just not in my budget. However, since photography is all about making the most of what the situation hands you, and working within the limitations of your gear, I’m not disappointed with the results. And if Mr. James should ever come knocking for a paid photoshoot, I’ll rent one for the day, open it up to f/2.8, and shoot like crazy.

Colin James at FCP, Toronto
1/60th of a second at f/5.6 and ISO 2,500.

More photographs, almost all of which are at stupidly high ISO and miserably slow shutter speeds, are in this Flickr set.

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June 6

I started off this morning by thinking about, of all things, the Canadian Senate, what its uses are, and whether the country needs it or not.

But then, thanks to a couple of tip-offs via Twitter, I remembered that today, there are other things to think about, and remember, for many different reasons.

Canadian nickels - V for Victory
The years may be wrong, but the messages were clear.

June 6, 1944.

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This was the weekend that was.

As Cath noted, last weekend was a holiday here in Canada. Victoria Day, the traditional time for opening up the cottage after a long winter, or launching fireworks into the air, or just generally sitting around on a patio or deck having a good time. We did remarkably little of any of the above, although the neighbours were certainly in the mood, with fusillades of fireworks going off on Saturday, Sunday and Monday nights (what happened to Friday?).

This weekend is also (Oh no! Look out! Here it comes!) the beginning of motorsports season at the big track nearby, meaning I was out in the trees and rolling hills of Canadian Tire Motorsport Park, until recently known as Mosport International Raceway. No matter, the infusion of sponsorship dollars has made big and welcome improvements to the track and its facilities, even if purists railed at the name change. I’ve written about this historic track many times, even here at Adventures in Wonderland, where things are “supposed” to be a bit more science-y. I’ve made the motorsports-science link once before, but this time I’m not even going to try.

Formula 1000 racing, Canadian Tire Motorsport Park
Some small, but very fast, Formula 1000 cars.

Friday and Sunday were all-day-at-the-track days, in the company of a few good friends: my IndyCar shooting pal John and his wife Kathleen, and occasional motorsport.com shooter Mike Tan. Not too many mosquitoes, lots of sun, and some serious hiking up and down the hills – good for the heart, and maybe even the soul.

Trans Am, Canadian Tire Motorsport Park, 2012
Shot of the day – a Mustang, kicking up rubber on the Mario Andretti Straight.

As I often do, I spent time lurking in the trees, trying for the slow-shutter-speed “foliage panning” shot. When it works, this kind of thing can be spectacular. When it doesn’t, it’s just a mess. This one turned out all right, but it could be sharper and a bit more dramatic. Something to work towards, next time.

Your Race Winner - J.R. Fitzpatrick, Vortex Brake Pads 200
NASCAR Canadian Tire Series winner J.R. Fitzpatrick, and some trees.

Of course, being a holiday weekend, I didn’t spend all of my time at the track – just two of the four days (yes, I took Friday off too, feeling I needed it after all of those grants some of us have been working on). Hardly any time at all, really. The other two days were a pleasant, but still tiring, mix of Junior Wintle #2’s riding lessons, a jog down to a local park on Sunday night to watch the fireworks blasting off from the nearby amusement park, and a trip with my brother to the zoo.

Going solo.
The young lady and Lola the horse, earlier this year.

And that was the weekend that was. A typically exhausting holiday weekend that involved absolutely nothing that I could reasonably refer to as either “work”, or “science”. Now, all I have to do is recover.

Sometimes you wake the bear...
This Polar Bear has the right idea.

Posted in Hobbies, Photography, Racing | Tagged , , , , , | 2 Comments

Hither and Yon

Things have been a bit quiet around this blog lately, largely due to a major infrastructure grant application (now nearly, but not totally, finished), as well as a number of side trips, and Easter weekend. Not that I’ve really been too busy to post anything – I just haven’t been using my available time for writing blogposts, instead of for other things.

On the home front, weekends have begun to be punctuated by my daughter’s riding lessons at a nearby stable. That’s been a nice change, not ever having been a horsey sort myself, although my wife was an avid rider before I met her and is enjoying being back around horses. I find them rather endearing, if a bit large and prone to whacking me when I’m not looking. As long as I take appropriate care around the carnivorous, pepperoni-pizza-eating creature preferred by the young lady, I should be safe enough, I guess.

Brushed
The horse in question, being brushed by a certain young rider.

Earlier in March, I made a trip up to Peterborough, to give a lecture to the Biotechnology Forensics Technologist program at Fleming College. The students come each year to tour the lab, but this year we couldn’t secure a room for my usual lecture. No matter – it was a brilliantly sunny day, and the two-hour drive through rural Ontario made a nice change from the office. I took the opportunity to stop off and see the famous Lift Lock on the Trent-Severn waterway system – closed until navigation season starts again, but still impressively massive, it being the highest hydraulic lift lock in the world. It boggles me that this kind of thing works at all, even more so considering that it’s over a hundred years old.

Peterborough Lift Lock
They don’t make ’em like this any more.

The trip home allowed some dawdling along side roads, looking for interesting pieces of Ontario’s small-town history. In Columbus, a pretty little place now almost completely engulfed by suburban Oshawa, I found a handsome church, set far enough back from the road that I could shoot it under the inevitable overhead power lines.

Columbus United Church, Ontario
Another chance to try out the venerable Voigtländer.

The next road trip was a one-day nip over to the Tannery District in Kitchener-Waterloo, for a facilitated discussion as part of a review and strategic planning session for the University of Waterloo’s world-leading co-operative education program. We take Waterloo co-op students pretty much continuously, so it was nice to be involved. Naturally, I made a few detours, stopping off at Woodside National Historic Site, the boyhood home of Canada’s longest-serving Prime Minister, William Lyon Mackenzie King. Unfortunately, the house itself is indefinitely closed due to toxic contaminants found in the basement, possibly from waste dumped by a nearby, and now long-gone, coal gas plant. Nevertheless, the house was handsome, and the first crocuses of spring were peeking through the dead leaves of autumn under a chilly March sun.

Woodside National Historic Site, Kitchener, Ontario
Woodside National Historic Site, Kitchener, Ontario.

Where next? Why, Winnipeg, of course – a city I’ve been to exactly once before, something like thirty-five years ago. This time, the trip was for a symposium around planning for a Genome Canada grant to study Fetal Alcohol Spectrum Disorder, a condition regrettably common among disadvantaged communities in northern Canada. Once again donning my “new sequencing technologies” hat, I gave a short presentation, and spent the rest of the day learning more about the challenges, clinical and societal, that it poses. Some of the stories told, of children in and out of foster care and the justice system, were both astonishing, and heartbreaking.

Manitoba, from the air
Manitoba, east of Winnipeg – where the Great Plains begin.

And so, back home again to get stuck into that grant proposal, interrupted by an Easter weekend jaunt to the other end of Lake Ontario, visiting family in my hometown of Kingston. My intention of photographing the city’s many old stones was sabotaged by exceeding laziness, and the temptations of staying in and gorging on too much Easter chocolate. Now, I’m simply planning the usual summer car racing and cottage excursions, and beginning to think seriously about a conference in Bangkok in October. So not exactly a world traveler, but at least I’m getting out and learning a bit about local history, a subject in which I’m woefully under-versed.

Sunset - Kingston, Ontario, April 2012
An Easter weekend sunset, recently.

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Thank you 40 million times (video)

I’m not usually one to use a blogpost to point to “cool stuff on the internet”, but in this case I’ll make an exception.

It’s no great secret that I work at Canada’s largest paediatric hospital, a place with something more than 8,000 employees, some 2,000 of whom are in or affiliated with its Research Institute. Lots of exciting things go on in the SickKids R.I., but the most exciting in recent memory is the ongoing construction of a new Centre for Research and Learning. This new building will bring together researchers currently distributed across half a dozen sites, and cost about $400 million in total; a further $100 million investment will create an endowment to support operating expenses. Significant buy-in from the Canada Foundation for Innovation and the Government of Ontario has underwritten two very large pieces. Nevertheless, there was still around $200 million that needed to be raised. A plethora of small initiatives (including a highly successful cookie-baking competition among our group, which I didn’t enter, and an art exhibition, which I did) have gathered an impressive amount of funds so far, but what’s really been missing is an A-list, enterprise-level, naming donor – one with a lot of money and a large heart.

SickKids
The hospital in question.

Enter Peter Gilgan, the founder and CEO of Mattamy Homes, with a stunning donation of forty million dollars. As you can read in last week’s announcement, it’s not the first time he’s been involved in raising money for the hospital, but this kicks it up to a whole new level. This represents the single largest philanthropic donation to a children’s hospital in Canada, ever, and believe me, a it’s a very welcome one.

So where’s this cool internet stuff, then? Well, as part of the run-up to the announcement, the SickKids Foundation (the good folks who work with donors to raise all of these funds) put together a rather nice video. The reason I mention it here is that it prominently features The Centre for Applied Genomics, where I work – most, but not all, of the lab equipment and people pipetting are from our group, including the two you see on the splash screen in the YouTube link below. I can claim a tiny role in helping to facilitate the filming, as a kind of lab “fixer”, although the project was organized and overseen by very experienced Foundation personnel and a crack video crew. I stayed conveniently out of shot, in favour of more photogenic colleagues – some of whom have appeared in other videos, such as this rather excellent one.

So, without further ado, here it is: Thank You 40 Million Times, featuring a bunch of molecular biologists, among others. We’re slated to start moving in just over a year from now, in April/May of 2013 – exciting times, indeed.

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Ottawa, Listeria, Genome Sequencing, and some pretty pictures. What more could you want?

Recently, I found myself in Ottawa, a city best known as Canada’s capital, and notorious for being picturesque, quiet, and freezing cold half of the year. It’s also a city I’ve spent surprisingly little time in, given that my salary is currently funded by an agency headquartered there, and that I grew up only a couple of hours’ drive away. Ottawa is also full of attractive buildings, including some in an endearing Gothic style of architecture that appears to particularly nice effect in the post-dawn light of a winter morning.

East Block and War Memorial, Ottawa
Parliament’s East Block and the National War Memorial.

However, I was really there for a workshop about the food-borne pathogen, Listeria monocytogenes, jointly hosted by Genome Canada and the Canadian Food Inspection Agency. The session brought together scientists from a truly astonishing diversity of government agencies, the private sector, NGO’s, and academia, for a day of facilitated discussion. And with good reason – Listeria “mono”, as the experts frequently call it, can make you very sick – with a reported mortality (yes, I did say “mortality”, as in “kills you”) of 20-30% in some cases. It was also the cause of death of twenty-two people during a 2008 outbreak traced to cold cuts produced in Toronto by Maple Leaf Foods, which you can read about here. One of the speakers outlined in a very nice talk the extensive testing and monitoring now undertaken by the company, as a direct result of that tragic event.

Suburbia - Ottawa - from the air
Suburban Ottawa, from the air. It looks cold, because it is cold.

Listeriosis is still a potential problem for the food industry, and recent outbreaks of other pathogenic bacteria in Germany and the United States have focused attention in this country back on this unpleasant bug. The meeting was framed around the application of new genomic technologies (primarily “next-generation”, or high-throughput, genome sequencing) to the detection and typing of the various Listeria species and sub-strains, which explains my presence. Currently, detection is by well established microbiological methods (homogenize, culture, plate, select and/or screen), a point that was reinforced in talks by a number of speakers from both government and industry.

But the real eye-opener for a somewhat up-to-date molecule hacker like myself was the description of current methods for species and strain identification. The state of the art is chopping up the bacterial chromosome with a restriction enzyme, followed by fragment separation on a pulsed-field gel to form a diagnostic pattern of large DNA fragments. And while this has been effective, resulting in the establishment of very useful reference databases, I couldn’t help but feel a little déja vu. The last time I ran a pulsed-field gel was in 1996. When ten years later I suggested to some colleagues at my current place of work that they could use this approach to sort out some thorny mapping issues in ugly regions of the human genome, I was almost laughed out of the room. This is old, old technology.

Another speaker from a nearby university outlined a more modern method using multiplexed simple sequence repeat markers (also referred to as “short tandem repeats”, or STR’s, or by older folks such as myself as “microsatellites”). These are tiny bits of repeating DNA sequences that in humans vary between individuals, and in Listeria vary between strains. It’s a symptom of the state of the testing industry that some in the audience seemed skeptical of this “new technology”, while others muttered darkly about how they were doing this in the mid-1990’s. Not naming any names, of course.

But that’s par for the course in a highly-regulated industry, and even modern hospital laboratory diagnostics are not fully caught up to the advances in “research world” – as well they shouldn’t be. It takes time to translate cutting-edge approaches into robust and validated clinical tests, and even longer to have them broadly adopted by agencies with limited budgets, differing regulatory requirements, potentially complicated funding and reimbursement schemes, and varying mandates. But there were encouraging talks too, emphasizing that some of our government agencies, in particular the National Microbiology Laboratory of the Public Health Agency of Canada, have been using high-throughput sequencing for research projects, and were in fact a very early adopter of the technology. Notably, NLM sequenced the H1N1 viral genome in response to the 2009 influenza outbreak, and continues to apply it to various other projects within their mandate. One point of this workshop was to bring other centres with considerable capacity and expertise, such as the Genome Canada Science and Technology Innovation Centres, to the table, and to identify research gaps, industry needs, and potential synergies between the various stakeholders. As a side benefit, I learned a lot about an organism I was only passingly familiar with. And in all of this, I’d say the meeting, as a start, was a success.

Rideau Falls, Ottawa - February 2012
This photograph of the Rideau Falls was a success, too. It’s the first time I’ve done a long-exposure shot of moving water. Taken long after dark in freezing cold weather, using a tripod borrowed from my good friend Markus.

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