Day of the Dead

We got together for some mexican food and heaps of beer last weekend with the coolest workmates. What wasn't cool was the keg, temperature wise of coarse. How long does a keg stay warm in the australian sun? With a little backup, all day...

BEEEEEEEEEEEEEEEEEEEEEEERRRRR!

Quesadillas, tamales, guacamole, piñata, yuuuuuuuummy!

Hilarity ensues after 7 hours of drinking canadian-style beer in australian-style sun, as you can immagine.

FIRE IN THE HOLE!

dusting the blog

So I am searching for a restriction map for a particular vector, and I can't find the bloody figure my collaborator sent online (I'd like the colored figure). I gave up when I ran a google image search and this is what I got:

I chuckled after registering the last image and reckoned it was time to pour myself a glass of vintage Crown Royal and call it a night.

Great Barrier Reef

Just got back from a 4-day live aboard trip on the Kangaroo Explorer,

2 hours by boat off the coast or Cairns. Amazing time.

The oceans are another world. Seeing such spectacular biodiversity really makes you

appreciate how lucky we are to live on this planet and be a living part of this universe.

More info (and delicous photos) to come.

Diving @ Cook Island

Heading off to the Gold Coast tomorrow morning, bright and early (well the sun won't be up yet, so just early).

Going diving to Cook Island, off the Gold Coast. I'm hoping the water hasn't cooled down too much yet.

Also, hope to see my first leopard sharks. Fell short last trip, but the grey nurses and manta ray made up for it.

Heron Island II

I spent 5 days on the island, 3 of which were for work. In the other 2, I was lucky enough to get some scuba diving time in. We managed to get on the resort's dive boat standby (there is a small resort hotel on the island) for 65$ a dive. Quite funny, the dive sites are just a 5 to 10 minute boat ride to the outer reef. The reef drops from 1-2 to 20-30 meters + about 1 Km off the island, and that is where the most diversity resides.

The great barrier reef is amazing! Fish everywhere, but it's the size, diversity, and sheer beauty that impresses the most. Those 35 minutes passed like a blink of an eye. Here's what I logged for my first ever non-training dive:

Coral cascades, water temp 26 degrees, 13m visibility, saw nudibranch, white tip reef shark snoozing on a sandy patch (they are one of the few sharks that can lie still without suffocating).

That's not much information for a first dive in the GBR, eh? Well I was quite busy taking pictures and videos with an underwater camera. Not such a good idea.... Didn't take much of the dive in and the pictures aren't quite extraordinary. Nonetheless, there are a few you can enjoy.

Next post will be a video mash-up.

Some nerdy RNA structure stuff

Just thought I should let you know there is a recent decimal release of RFAM (10.0), most novelties are a consequence of the Infernal 1.0 release although there are also nomenclature changes that are quite convenient. It now contains 1446 ncRNA families, including the self-proclaimed "deepest alignment of all time" containing over 1 million tRNA sequences. Read more here.

Also, I know that some of you are interested in generating secondary structures for your favorite RNAs. I just discovered this amazing website that allows users to display 2D RNA structures comprehensively. There was a recurring problem with most 2D RNA display programs as they weren't flexible with the representation, e.g. overlapping stems would mess up your nature paper figure. This program, VARNA, even accommodates pseudo-knots and uses animations to switch between sub-optimal structures :) Check it out here.

Heron Island, Part 1.

Last week marked the first Mattick lab group retreat in over 3 years. I was fortunate enough to have most of the planning go smoothly and things turned out good. It was quite spectacular to isolate ourselves on a small mound of "sand" for 3 to 5 days. I use sand loosely because essentially the island is composed of parrot fish poo, bird droppings, and the odd other organic material. Nonetheless, just standing on this Capricornian island 70 Kms off the coast of central Queensland is a unique experience. (Un)fortunately there is a resort hotel (more like cottages) on the island in addition to the research station and the ranger station. Heron island is in the Great Barrier Reef national park and bears UNESCO world heritage status for obvious reasons. You get that feeling that surviving on the island primitively would be a phenomenal feat.

The main vertebrates on the island are egrets (not Herons), black noddies, seagulls, sea eagles, rails, and at night, the wedge-tailed shearwaters. The latter, also referred to as mutton-birds, make the freakiest sound at night, a sort of erie cooing that grants the island a haunted aura. Also, they are quite easy to step on. Rare are those of us who did not receive the partings of the very talented dive-bombing noddies.

PhD Confirmed !

Sorry for the lack of recent posts, I have been completing my PhD confirmation report and my confirmation presentation to the departmental seminar for the past 6 weeks. Here is a video summary of the presentation, but without my comments unfortunately. Things went great and my interview with the thesis advisory committee was most constructive. So I am an official candidate for the doctorate :D

The title of my presentation highlights the main focus of my research, which revolves around characterizing the prevalence of RNA structure in mamalian evolution.

Snakes, Surf, and Sharks

January was a cool month! Well, not temperature wise at least. Saw a lot of native fauna to start off 2010. To start, I went out spotlighting with some friends. Essentially, we go around with heavy flashlights spotting animals at night. I got to see a greater glider, ringtail possum, swamp wallabies, tawny frog-mouths, rock geckos, plenty of cane toads, and massive orb spiders. Here is a picture from Jeremy of the glider, taken with his pretty high-tech camera gear:

A few weeks later, I got to follow Jeremy and some mates through the forest near Mount Glorious, just 45-60 mins North of Brisbane. I saw some massive tree frogs, a plethora of small pond-dwelling frogs, ugly cane toads again, small golden crowned snake (slightly venemous), three carpet pythons including a 3.3+ meter one (massive!!), a Subtropical Antechinus which is a carnivorous marsupial mouse-like animal (read the link for some funny facts about them), and a melomys (indigenous arboreal rodent). We also got to see a lessor sooty owl, even snapping a fairly decent picture of it which, apparently, is quite rare. Our friend Stewart got bitten by this 2m python while helping it across the road:

Last weekend, we went to Stradbroke Island with some friends where we rented a beach house for 4 days. What a great time we had! the weather was typical, hot and sunny, not a cloud in sight, and the beach was amazing. Crystal clear 24˚ blue water, clean surf that wasn't too big but enough to short-board with. We had an adult grey kangaroo graze on the front lawn one night. Went snorkeling in the North gorge twice, where I saw some cornetfish and really large sea hare for the first time.

On the walk back one night, we saw a group of eagle rays swimming and jumping near the rocky shores. Then a large leopard shark cruised by slowly (my first shark sighting!). I then saw a large shadow swimming pretty fast, which turned out to be a 3+ meter shark, probably a lemon, tiger, or great white shark. It spooked the kids that were fishing nearby as it surfaced about 20 meters away from them.

The next day, during an awesome surfing session, the surf rescue blokes showed up on a jet ski, yelling at the surfers to watch out for a shark and get out of the water. Seconds latter, I saw a fast-moving shadow in a wave, it swam around frantically as many surfers panicked out of the water. One of which was Esteban, our friend from Mexico on his longboard. The shark swam about 20 meters towards him in a few seconds, then decided to turn away about 4-5 meters from him and buggered off! Esteban didn't see anything, but I sure did. The bronze whaler shark was at least 2 meters long.

The previous day, Tim had spotted a leopard shark going about his business near him during a surfing session. On weekends and busy days, the surf rescue patrols beaches with helicopters, looking for sharks and strayed surfers. If they spot any near popular beaches, they circle around the area to signal the crew of life-savers on the beach. Then, a jet ski patrol goes out and tries to scare the sharks away. They also have large baited hooks that hang off floating plastic drums offshore, which attempt to snag the larger sharks. This seems a little bizarre as the sharks are there anyhow and the meat probably just attracts more. Just watch this story of a 3 meter great white getting bitten in half by a monster shark last october, right off the spot where we were surfing:

Group retreat

I am organizing our group's scientific retreat, which hasn't occurred once in the last 3 years! We've decided to have it at the University of Queensland's Heron Island Research Station, on the Great Barrier Reef.

Alright, I won't go into the details too much... but here is a nice video to give you an idea ;)

For more information (and if you have 8 minutes) you can also check out this link.

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Landing a plane on the equator

Singapore at dawn.

Bonne Année!

Bonjour a tous. J'aimerais m'excuser aupres des 2 ou 3 lecteurs qui visitent souvent mon blogue pour cette petite pose des fetes ou je n'ai pas trop ecrit de nouvelles. Laissez-moi vous dire comment c'est bizarre de feter Noel dans un climat sub-tropical dans l'hemisphere Sud. D'abord, il y a tres peu de decorations de Noel ici, les gens ne se laissent pas autant influencer par l'esprit des fetes. D'ailleurs, il n'y a que tres peu de musique de Noel a la radio et dans les magasins. Ici, les gens se reunissent en famille a Noel pendant le jour et celebrent en mangeant des salades fraiches, des fruits de mer, et du BBQ. Puis, une petite saucette dans la mer en apres-midi pour se rafraichir du soleil plombant. Bizarre...

Je suis parti le 27 Decembre pour Sydney en voiture avec 3 autres personnes (tous francophones!). Nous avons longé la cote Sud-Est pendant 3 jours tranquilement en s'arretant a droite et a gauche. Que de belles vues! Il y a aussi surprennament beaucoup de forets et parcs. On a vu des crabes, un bebe serpent de mer, des énormes araignées, mantes religieuses, phasmes, un perroquet qui ne vole pas (ou peu) et une tonne de poissons, raies, poulpes, et éponges (en apnée bien sur). Nous avons aussi fait 3 vignobles et une microbrasserie dans la Hunter Valley, au Nord de Newcastle. Je n'ai pu m'empecher d'acheter 2 delicieux vins "Iron Gate": un chardonnay sans chene et un "wooded" semillon. Au diable le budget (malgré moi).

On a passé le jour de l'An et le debut de 2010 a Sydney, une ville dont les charmes commencent a me seduire. Si ce n'etait de sa grandeure et de la concentration de gens, ca me plairait d'y habiter. Nous sommes aller faire du snorkeling a Cronulla ou nous avons vu des "cuttle-fish" en periode de reproduction et une panoplie de petits poissons et invertébrés.

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Nous avons aussi fait du snorkeling a Gordon Bay, 5 minutes au Nord de Coogee Beach. Il y avait beucoup de raies (une cinquantaine), des poissons de toutes sortes, des oursins geants, des pieuvres, et on a meme vu une peau de serpent de mer.

View Larger Map Apres avoir manqué mon avion pour revenir a Brisbane, j'ai du acheter un autre billet (au diable les dépenses...). Maintenant je dois manger du kraft dinner toute la semaine. Zut... ils en ont pas ici!

Sinon, retour au boulot bien anticipé depuis quelques semaines. Les prochaines semaines s'anoncent tres occuppées.

Jeudi soir je suis allé faire du "spotlighting" dans une petite zone de conservation écologique en banlieue de Brisbane. Le "spotlighting" consiste de se promener la nuit avec des torches afin de repérer des animaux nocturnes. Il s'avere que la majorité de la faune australienne est nocture: ce n'est pas surprenant car le jour quand il fait soleil on creve de chaleur!

En deux heures, sur un sentier de 2.1 Km, on a vu plusieurs animaux tout de meme. J'ai ouvert le bal en appercevant un "greater glider" qui nous regardait curieusement perché sur une branche d'eukalyptus. Mon ami Jeremy a pris plusieurs photos avec son appareil haut de gamme avec flashs sans-fils et un objectif immense de 400mm. Ensuite, on a tenté de repérer des petites grenouilles bien camoufflées sans succes. On a aussi vu 2 "tawny frog-mouth", 3 "eastern stone geckos", un "ring-tail possum", quatre "swamp wallabies", des chauves souris macro et micro, et puis une tonne d'araignées!

J'y retourne la semaine prochaine mais dans une zone plus peuplée en reptiles. Je vais tenté de trouver des pythons et autres serpents! Je prendrai alors mes propres photos!