Archive for October, 2010

The platypus is is a much-maligned animal as far as mammals go. This monotreme, endemic to Eastern Australia/Tasmania, has since been mislabeled as a marsupial, inaugurated as a college football trophy, and commandeered as the mascot of a Mac OS X developer tool.

Anatomically, the platypus is a mess. Platypus lay eggs like a bird or reptile but also has hair and lactates like a mammal. But it has no nipples… ?! It is semi-aquatic, with a beaver-like tail to aid in propulsion. And like fish, it can detect electrical currents, which is how it hunts for prey.

And don’t even think of pulling any smart ass jokes (How do you pluralize platypus? Platypi? Platypusses?) – as one of the few venomous mammals, this bad boy can poison you 80 different ways!

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This week’s Vancouver Sun featured a series of stories on the precarious situation of sharks. All over the world, the numbers of sharks of all species are declining at an alarming rate. Sharks have been around a long time – they are descendant from an ancient lineage of fish with cartilaginous skeletons. These bad boys of the seas have been around in some form or another since before the time of dinosaurs! But over the last century and a bit, they’ve been mislabeled as killers, ignored by biologists, and now hunted voraciously to make soup.

I made the mistake of reading the comments in the Vancouver Sun article and was soon incensed by the level of ignorance. Many comments suggested that the oceans would be better off without the presence of these “vicious” predators. Yes, sharks are predators. But removing the predator from the food chain is disastrous. Look at the UVic bunny situation – it’s a classic example of what happens when prey animals are allowed to run rampant without a natural predator to keep populations under control.

And while it is true that sharks have always been hunted for food, like many other fisheries, it has progressed to a level that is unsustainable. Humans have become better hunters and the demand for shark products has never been greater. But now, we cannot even make the claim that they are hunted for food. It is the demand for shark fins that fuels a majority of the shark hunt. The fins are so valuable and command so much money in Asian markets that many fisherman will simply cut of the fins and throw the shark back.

Luckily, sharks are starting to get more attention from both the public and academia. More and more people are rejecting the necessity of shark fin soup at Asian weddings and questioning the need to eat something that is endangered.

For more information, please consider “Sharkwater” – a documentary about one filmmaker’s experience with the plight of sharks.

[Photo from reefnews.com via Google Images]

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David Dobbs is an AWESOME writer with a real talent for developing engaging stories that really make you think.  I wrote a brief blog on his article “The Science of Success” which was published in the Atlantic earlier this year.

The Open Notebook recently did an interview with him and it can be found here.  Enjoy!

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There’s been a lot of numbers floated about lately as UBC’s animal use has been discussed in the media – Here’s the figures from the CCAC website which documents research animal use throughout all of Canada.

This is taken directly from the CCAC 2009-2010 annual report.  They have some figures up on the website if you’re curious.  Animal use has basically held steady in Canada for the last 5 years or so at around 2 million assorted creatures.

And I’ll emphasize again, these are the numbers for all of Canada.

EDIT: I realized after publishing that the figure is far too small to be legible.  😛  However, if you follow the link to the annual report, it is found near the end of that document.

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So I got some more posts upcoming but had a bit of a busy weekend – I picked up an extra weekend shift and also visited the parents.

  1. I made an edit to my Metacam post after discussing it with a much respected colleague.
  2. Lots of stuff in the local news about the peril faced by sharks.  I wrote about this issue earlier in the year for a different newsletter and I’m trying to find my original article to post here… stay tuned and stay away from shark fin soup.
  3. Check out “Brain Cuttings”, a new eBook by Carl Zimmer – awesome.  Here is a review and interview by Steve Silberman.
  4. I’m writing an article about public opinion of stem cells – would love to hear everyone’s thoughts.  What do you think of stem cells?  Leave a comment or message me privately.

Thanks all.

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This may be the first plane crash due to crocodile.  Check it out here and please, leave your exotic pets at home.

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Earlier this month, the Atlantic published an excellent article by David H. Freedman on the abundance of subtle bias present in biomedical research. It’s probably not a surprising revelation. After all, humans are at least to some degree, self-interested beings. But how does this unconscious bias affect research?

When people read scientific papers or see presentations from researchers, the information is laid out in a very chronological manner. One experiment leads to another and usually, some sort of pattern emerges. By the end of the paper or seminar, some point or new discovery is made. But research doesn’t actually happen that way.

Usually, a researcher or student starts with some sort of idea.  And then, you try to support that idea through evidence gathered from tissue culture, from bioinformatics, and from animal studies.  It could happen in any order and usually does.

At each step, you are trying to prove a certain idea. Of course you want to succeed. So in tumour studies you pick mice which are receptive to a certain cell line, or for vascularization studies you might do tissue culture with cells that are good at sprouting… But  are these choices the best scientific choice, or do they represent the best choice for a “successful” experiment?

Dr. John Ioannidis is a meta-researcher – he studies other studies for patterns. Lots of other studies. His research team has shown that when applied to human health, much of what is published in biomedical research studies is exaggerated, misleading or sometimes, just plain wrong. And worse – many studies which have proven to be wrong are still cited and used by current researchers and doctors.

Ioannidis even developed a mathematical proof which shows that most of the time, researchers will come up with the wrong findings! From the article:

Simply put, if you’re attracted to ideas that have a good chance of being wrong, and if you’re motivated to prove them right, and if you have a little wiggle room in how you assemble the evidence, you’ll probably succeed in proving wrong theories right.

His study looked at 49 of the most-cited, most prestigious medical findings of the last 13 years.  45 of these papers claimed the discovery of some sort of effective treatment.  Since publication, 34 of these claims were retested – 14 were found to be plain wrong or grossly exaggerated.  14/45 is 31% – Almost a third of the most cited medical research is wrong?  This is scary business.

An observant lay person would notice the same patterns: Alcohol is bad. Oh but wine is good. But too much is still bad. But people who drink anything at all live longer than people who abstain.  Substitute alcohol/wine/drink for “hormone replacement therapy” or “carbohydrates” or “vitamin C” and you will have reconstituted most of the major health headlines from the last 2 decades.

What’s a health conscious, scientifically literate person to do?  Ioannidis advocates the publication of negative results in addition to positive results.  He believes that if scientists were not punished (through grants, funding, publication etc.) for lack of positive results, then the tendency to spin out dynamic stories and dramatic “discoveries” would taper off.  I tend to agree.  If  research is being done conscientiously and carefully, the results you get are the results you get.  Most of it is probably dreadfully dull.  But to try to spin it into a story, to make it “fit” into a bigger picture… that’s not science any more, that’s fiction.

And I should note that Ioannidis focuses on health-related research.  I would venture that aside from conflicting egos and personalities, lesser funded areas of study such as plants, evolution or biogeography (to name a few of my interests, haha) suffer less from the need to constantly publish “breakthroughs”.

From Ioannidis:

“Science is a noble endeavor, but it’s also a low-yield endeavor,” he says. “I’m not sure that more than a very small percentage of medical research is ever likely to lead to major improvements in clinical outcomes and quality of life. We should be very comfortable with that fact.”

Science is important and should certainly continue but the public and the publishers need to foster an environment for science to operate honestly.  People need to realize that science is constantly evolving and each publication is a drop in the water.  Each To continually expect “breakthroughs” or “potential cures” will only lead to disappointment.

And yes – Ioannidis admits that he may be similarly biased in his own research.  🙂

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Today CALAS-Pacific had a webinar on a system called MouseOx by STARR Life Sciences which measures oxygen content in mice using infrared light. I’m not in the best of moods today – I seem to have come down with some sort of flu – and this seminar did a great job with getting me riled up. Grrr…

The apparatus itself is a good idea. It’s a non-intrusive way of measuring oxygen content and can be used in a variety of settings from research science to veterinary offices. But you know what would have been better? PowerPoints that showed up on screen. Narration that is clear and understandable. And more than 15-20 people showing up.

After the webinar wrapped up, a gentleman who had been sitting off to the side stood up an announced that there was some reading material available by the door for anyone who would be interested, and then he left.

Meanwhile, I stopped to ask some of the CALAS members what they thought of the talk. The general response was that they were “happy to be allowed to come” but that they “didn’t understand it”. This is what I have been saying, no, shouting, into internet cyberspace for the past year! Members are eager to learn and to improve their skills and knowledge, but CALAS-Pacific is not providing the appropriate training opportunities! What good is telling them about pulse oximetry when they don’t understand what arterial blood pressure is, or how hemoglobin works?

Duly informed, I made my way to leave and was planning my blog when I was accosted by the former Program Co-Chair for CALAS-Pacific who shoved a stack of papers in my face and demanded, “Are these yours?” These were the papers that the quiet gentleman had left behind. Huh? Um… you and everyone else saw that some unknown man left after announcing he was leaving papers for CALAS members to read. Clearly they belong to him. Why accuse me? And what am I being accused of!? :/ There is little more I hate than passive aggressiveness.

I ignored a glare and left our illustrious CALAS execs and former execs to themselves, grumbling over pieces of paper.  I am still not entirely sure what that was about, aside from using it as an excuse to make snide remarks to me.

Now, I am returning to the safety of my couch to nurse my flu.

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Hi all,
Just a reminder that CALAS-Pacific has finally gotten around to gracing us with another seminar Wednesday Oct 20 and guess what? It’s a webinar! :p Your member dollars at work…

I think this one is at least somewhat interactive, but I’m not sure. The speakers will be discussing a new technique for measuring oxygen content in mice.

It will be held at the BC Cancer Research Centre at 675 West 10th Ave, Vancouver BC tomorrow from 2:30 – 3:30. Enter from the main doors and head to your right to get to the auditorium.

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It’s finally here!

The UBC Beaty Biodiversity Museum opened it’s doors today, Oct 16, to the public after a series of tantalizing summer previews.

I was there mid-afternoon and wow, there was a lot to see! Volunteers in red shirts were swarming the area, ready and eager to answer questions from the public. I was gratified to see so many people volunteering for the museum but a part of me was bitter – why did it take UBC so long to bring this museum into the public eye?

The entrance to the museum is the same as during the previews: an awe-inspiring, 360 degree walk around the blue whale skeleton to the lower levels. Once there, rows upon rows of carefully sealed cabinets held the vertebrate, avian, fish, fungi, plant, bug and fossil collections. Each cabinet was labeled with beautiful photographs of the contents, a far cry from the sticker-and-marker approach taken when the specimens were housed in the old Biology building!

And most importantly – the displays!

Many of the specimens that UBC owns were donated from private collections amassed in the 1800s and early 1900s, when it was more popular to have mounted stuffed animals on display. Included in this group are numerous antlered species and a beautiful penguin specimen! More recent specimens are thanks to the diligence of volunteers (like myself in days gone by!) who painstakingly turn dead animals (often road kill or birds who have crashed into glass buildings) into carefully dried and preserved specimens which can be used for teaching, display and research.

Now, interspersed between the cabinets, these specimens are proudly on display. Mounted birds, jars of fish, carefully pressed plants and even fossils, embedded into the floor – all this, and more!

Many activities were running during opening day, including cake cutting, a presentation from Dr. Wayne Maddison, and a scavenger hunt that earned participants a pin to take home.

For myself, my favourite activity was the craft station, where participants were asked to write a message on a maple leaf shaped piece of construction paper. The messages would adorn a wall in the far end of the museum. I dedicated my leaf to the late Dr. Rex Kenner, who worked tirelessly in the museum, maintaining the collections year after year, with UBC cutting the budget, limiting work hours, and generally being the pain in the ass bureaucracy that it is. My leaf read: “For Rex Kenner – It’s finally open!”.

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