Archive for December, 2010

Merry Christmas all!

It’s Christmas Eve here in rainy Vancouver and I will be finishing up a day at work before heading out for dinner.  I would like to thank everyone who’s been reading and supporting my blog over the last year.  We’ve gone from having 3-5 reads a day to over 50 unique reads per day!  I’m so grateful for all the support and I hope to continue the momentum through the New Year.

Be safe, as Christmas and New Years are apparently scientifically validated risk factors for death (thanks to Discover | Discoblog).

Drink wine, but not too much, and be sure to do it socially.

And though you may not believe it, your family and friends can help you live longer , so leave behind the fakes, the liars, and the unfaithful.

Merry Christmas, and happy holidays to everyone!

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I’ve been a bad blogger and have not been writing nearly as much as I should. 😦

This week and a bit has probably been one of my most unproductive since the summer, and for that I’m sorry. I’m a bit burned out I think with much writing, both coding and blogging. Hopefully a few days off at Christmas will recharge my batteries!

News the past week and a bit:

  • Shameless self-promotion: My latest blog is up on the Stem Cell Network and recaps the recent annual meeting of the American Society of Hematology.  Please check it out!
  • Earlier this year, Metropolis records released “Electronic Saviors”, a 4 CD collection of industrial music to benefit cancer research and patients.  On December 4, they presented the Foundation for Cancer Research and Wellness with a check for over $22k.  Angry music does solve problems!
  • It received limited coverage, earning only a brief mention in Scientific American, but this past Tuesday, the US Senate finally passed the Shark Conservation Act which bans the practice of taking fins from live sharks.  Shark fins are prized in soups and other delicacies, and unfortunately, many countries which profit from the trade still permit shark finning to occur despite the fragile state of many shark populations.  This is a long overdue step in the right direction.

I’m really going to try to push some posts out in the next few days.  Can’t say much more than that, as I have a crap load of stuff on my to-do list!  Stay tuned…

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From Dec 4-7, hematologists, scientists and trainees from around the world gathered in sunny Orlando Florida to discuss the latest in blood diseases and research. Over these three days, the Orange County Convention Centre was host to two poster sessions, presentations from clinical and academic leaders, and an impressive array of exhibitors.

I arrived late December 2 nd and spent the 3 rd shopping and exploring. Orlando is an odd place, with very little “natural” about it. Manicured lawns and carefully arrayed palm trees are the norm. Hotels and restaurants tempt the tourist crowds with ponds of koi, the fish sweltering in the heat and cooled down with influxes of cold water. It is a car city, with stores, hotels, and amenities spread far apart and divided by 6+ lanes of traffic. But it was bright, sunny and warm, and for that, I tried to overlook the funny taste of the water and the supreme lack of fresh food.

Things got going on Saturday with some sessions and breakfast talks already well on their way from as early as 7am. Exhibits opened at 10am sharp. Big Pharma was high in attendance, with appearances from Pfizer, Roche, Johnson and Johnson, and Genentech, to name only a few. Each company tried to out-do each other with high end “hospitality bars” which served gourmet snacks and coffee. Current clinical trials in the areas of leukemia/ myeloma diseases were highly touted, as well as advances in stem cell transplant techniques.

Over the next two days, there were scientific sessions and special lectures around the clock –far too many to attend, much less write about. There was a clear focus on clinical treatments and outcomes, not surprising when ASH caters primarily to clinicians. There were also a surprising number of studies on the usages of cord blood -a growing area for business and medicine. One special lecture of note was the Ham Wasserman lecture on stem cell mobility and homing. I will be writing about this topic in an upcoming Stem Cell Network blog! A few other lectures were interesting, mostly relating to genetic aspects of blood diseases, and I may touch on these topics in later posts.

I was a little disappointed in the poster sessions. Many posters did not have people available to answer questions, which sort of defeated the purpose of having a dedicated poster session. The food was also set up terribly, forcing people to line up even if they just wanted a bit of cheese and bread to nibble with their drink. On Sunday, I had the privilege of attending the President’s Reception, held in the Peabody Hotel. The Peabody is probably best described as a whole hearted attempt at grandiose elegance. I nearly had a heart attack when I entered the reception and saw that most people were seated –I went to the event knowing a grand total of ONE person. It didn’t help when the bartender asked me for ID. But, I eventually got connected with people, had some amazing food (though I didn’t eat as much as I would have liked, definitely the best food I had in Orlando!), and the open bar didn’t hurt either.

Post reception, I had drinks at Rocks, the hotel bar, where I learned that the hotel maintains a cache of special ducks which it parades out front once per day. Huh. Monday, I’ll be honest –I did very little. I was too lazy to get lunch so I grabbed food at the convention centre which subsequently made me violently ill. I have never been so happy to pack up and get to the airport!

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My last post on rodent anesthesia looked at the use of chemical anesthesia, in particular, the use of ketamine-xylazine to attain surgical unconsciousness. I identified several issues with the use of this combination, most importantly the lack of dosage control and lack of predictability in response.

So what are the alternatives?

If ketamine-xylazine is not used, most often researchers will turn to an inhalent anesthetic. Inhalents use a vaporizer to deliver a gaseous form of a chemical directly to the rodent via a hose or face mask (or through intubation for larger animals) in combination with oxygen.  The most common inhalant used in rodents is isofluorane gas.

Isoflurane is a halogen-based gas which causes muscle relaxation and unconsciousness.  It used to be used in human medicine, but is now principally used in veterinary medicine and research.

Gaseous anesthetics require more equipment than injectible anesthetics.  In addition to the vaporizer and assorted tubes and hoses, a scavenging system must be used.  Scavengers gather up leftover gases to prevent worker exposure.  Charcoal canisters which absorb residual gases are a common form of passive scavenging, while various types of ventilated hoods can be used for active scavenging.  Never use anesthetics without a proper scavenging system!  Chronic isoflurane exposure has been linked to cognitive decline.

[Aside: I had some bad exposure to isoflurane in the past and it is like being in a fog – you just can’t think.  Little bit terrifying.  Thank God for new careers!  Computers can only ruin my posture and eye sight! … ]

But using all this complicated equipment has it’s advantages!  The vaporizer allows the technician to control precisely how much gas is being delivered to the animal.  If you need to increase or decrease it, you know exactly how much you are raising or decreasing the dosage.  It is much harder to accidentally cause an overdose.  As well, since the gas is being continually delivered, there is no risk that the animal might being to wake up in the middle of a procedure.

For the animals, recovery from isoflurane is much, much quicker than recovery from ketamine-zylazine.  Isoflurane is excreted entirely via the lungs – no residual chemical is left in the system.  So once an animal is removed from the gas flow, it beings to recover immediately.   Full recovery occurs in only a few minutes and aside from regular post-surgical care, rodents do not generally require additional monitoring.

Unfortunately, isoflurane does not provide any analgesic properties aside from unconsciousness during the procedure.  So, analgesic must still be given before and after surgical procedures.

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In my last post, I introduced biogeography as a field which studies how populations and species are distributed.  Distribution is influenced by many factors including biotic factors.  It is a catch-all term which refers to factors relating or due to the biology of the the species, and may include dispersal ability, interspecies interactions, and breeding systems.

Dispersal ability

Dispersal ability is a measure of how well a species can spread from its original home and includes aspects such as fecundity, migratory ability, adaptability and gamete dispersal.  Fecundity describes the reproductive ability of a species.  Migratory ability describes how mobile a species is, and how able it is to move from one habitat to another.  Adaptability measures how well species can adapt to new habitats, such as after a dispersal event.  Gamete dispersal looks at how far a species can disperse its gametes and how well those gametes do after dispersal.

Elephants are not very fecund, for example.  They take many years to mature and when they do mature, they do not produce many young.  Low fecundity combined with slow maturity limits their potential dispersal ability and is a reason why populations are so vulnerable to hunting.

On the other hand, many wind-dispersed plants have a strong dispersal ability – their gametes can go wherever the wind takes them.  Dandelions are an example of a plant which is widely dispersed and distributed.  Thus we can find dandelions in lawns across North America.  But plants do not generally migrate, unless they are able to reproduce from shoots or branches which fall off and are carried by other vectors.

Interspecies Interactions

How does the species interact with other species?  Predator-prey relationships can limit the spread of populations, either through the limitation of food sources for the predator or through prevention of unchecked growth by the prey.  A good example would be the sea otter-urchin-kelp relationship.

Sea otters in the North-East Pacific have historically kept sea urchin populations low through predation.  Urchins feed on kelp as a primary food source.  When sea urchins are few, herbivory levels on kelp are low, allowing kelp populations to expand and diversify over time.  But in the last century or so, local populations of sea otters have become extinct due to hunting pressures.  As a result, the sea urchin populations have expanded and the kelp populations are diminished and diversity is reduced to a few hardy species.

For plants, interspecies interaction can also include the interaction with animal pollinators.  Many plants, especially those endemic to islands such as Hawaii, have very specific pollinators.  Orchids are especially notorious for specifically catering  to certain species of bees or moths for pollination.  Sometimes the shape of the flower may only allow a certain insect inside, or perhaps the scent produced only attracts certain moths.  Dispersal is then limited to areas where these pollinators are present.

Breeding systems

Seed-bearing plants are possessed with a variety of different breeding systems.  The breeding system of a species will often determine how successfully a species will distribute.

Some species are unisexual, that is, male and female plants are separate.  Holly is an example of a unisexual plant.  For unisexual plants, colonizing a new area requires (at least) two “dispersal events” to deliver a male and female plant in order for a sexually reproducing population to establish.

Other plants are bisexual – male and female are present on the same individual.  Rosaceae, the family containing apples and roses, are an example of a bisexual plant.  Within these plants, some are able to fertilize themselves (“self-compatible”) while some are not (“self-incompatible”).  Self-compatible, bisexual plants are the best dispersers.  Only one seed is needed to successfully start a new sexually reproducing population


All these biotic factors, and more, can change the distribution of populations over time.  But it’s not enough to be biologically able or unable to spread to new environments – sometimes it is the environment itself that limits or encourages population growth.  My next post will look at some abiotic factors that affect the distribution of species.

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While in Canada, many universities and institutions remain mum on their animal research activities, researchers in Europe are taking a proactive approach.  There are a few possible reasons for this difference in attitude.  The European research atmosphere is slightly different than that of Canada’s: Certain groups of primates have a legislated right to “inherent value” for example, while no such rights exist in Canada.  Whatever the reason, scientists in Germany and Switzerland have launched an educational initiative called the Basel Declaration which pledges to be more open about research and to engage in public dialogue about research.

As Nature News reports:

“The public tends to have false perceptions about animal research, such as thinking they can always be replaced by alternative methods like cell culture,” says Stefan Treue, director of the German Primate Center in Göttingen. Treue co-chaired the Basel meeting, called ‘Research at a Crossroads’, with molecular biologist Michael Hengartner, dean of science at the University of Zurich, Switzerland. Outreach activities, such as inviting the public into universities to talk to scientists about animal research, “will be helpful to both sides”.

I think that this is a good point that Dr.Treue brings up – the importance of dialogue cannot be understated.  He also makes a good point, that alternatives like cell culture are not always viable or indeed, may not be the “alternative” that activists would hope for.  Growing cells requires a hodgepodge of media to keep the culture alive.  One important constituent of cell culture media is fetal bovine serum, or sometimes fetal calf serum, which as the name suggests, comes from cows.  [Note: FCS and FBS are by-products of the meat industry and would be otherwise wasted if not used by research].  But it is important to note that the absence of research on animals does not mean that animal products will not need to be used in research and is a prime example of how science does a poor job of communicating what it does.

[Note: it is possible to grow cells serum-free, but the cost remains prohibitive at the moment]

And, there is the simple fact that cells grown as tissue culture are just not quite the same as cells in a living body.  Just ask Mark Post, who’s trying to create lab-grown meat.  Using biopsies from donor animals and tissue culture techniques, he’s trying to grow enough meat to create a sausage that looks and tastes like the real thing.  Dr. Post’s long term goal is to create meat without needing to slaughter animals.  While he’s succeeded at growing a strip of pork muscle, the “meat” does not resemble anything from the grocery store.  The tissue is weak and prone to cell death due to lack of stimulation and without the support of a proper vascular system to deliver nutrients uniformly.

A similar case can be made for the use of computer modeling.  I think computer models are great – they drastically reduce the cost of research by allowing researchers to narrow the field of interest.  But at best, computer models only reduce the number of possibilities.  When it comes to testing drugs, for example, a computer model cannot predict all the effects on a substance on a whole body system.  We simply don’t have enough information about all the interactions that occur in the body.  Yet.

That is not to say we should not pursue new tissue culture or modeling techniques.  Quite the opposite – these techniques will improve with time and refinement.  In time, they may even be sophisticated enough that human clinical trials are less reliant on animal data for safety and efficacy testing.

But in the mean time, hopefully initiatives like the Basel  Declaration will foster more openness between the public and the animal research community.

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Wow, what a crazy weekend.  I had a lot of fun at ASH 2010 and I’ll put up a post on that soon.  If any readers are contemplating a trip to Orlando, I have to warn you – the water is absolutely disgusting.  At the convention centre, at the hotel… everywhere…  I do not advocate bottled water, but I kid you not, the tap water smelled and tasted like swamp.  I am eternally grateful to live in Vancouver where the water is decent and good food is the norm rather than the exception!!

  • The world this week has been fixated on the Wikileaks cable releases and the subsequent back lash from the United States government.  I think as writers, we should all be concerned when governments begin to pressure private companies to take action against a publisher of information, be it Wikileaks or your local newspaper.  Where is the backlash against the person who actually stole the information in the first place?
  • Speaking of media – scientists and bloggers  have rallied together to critique and question NASA’s press release and publication on arsenic-based life, and NASA’s subsequent dismissal of the “credibility” of bloggers.
  • The recent shark attacks in Egypt are now being attributed to multiple sharks.  While frightening for tourists and  residents, I can’t shake the dark feeling that some people will again use these attacks to justify hunting sharks, when in fact, illegal feeding and irresponsible “tourism” is most likely to blame.

Not a lot of good news, I’m afraid!  On my end, I will be finishing up part 2 of both the biogeography and rodent anesthesia series this week, stay tuned!  I should also have a new blog coming up on the Stem Cell Network in the next week or two.


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Whenever I go on a trip, one of my favourite things to, do is to observe the local pant and animal life.

I was a bit disappointed in the plant life around Orlando.  For being so far south, it doesn’t seem to have anywhere near the variety of weird and wonderful plants that I’ve seen in other urban cities, such as San Francisco.  Historically, this area is classified as wetlands, though of course, the majority of the area has been built up and paved.   However, you can still see many ponds and small lakes dotting the terrain. [Edit – Apparently many of these ponds are man-made! Huh… ]

Compared to the west coast, the most novel plants are of course, the numerous varieties of palm tree.  They come as giants, as multi-branched shrubs and as delicate miniatures dotting the landscape.  While other plants seemed relatively mundane, I did notice that ornamental grass grows larger in Orlando than I have ever seen in Vancouver.

Animal life was a bit more interesting.  Florida in general is home to alligators, moles, opossums, and a variety of frogs, snakes and lizards – to name a few.  I saw a white heron-like bird (to be identified upon my return) in the area of Universal Studios, as well as many geckos basking in the sun.  [Edit – This is a Great Egret, a type of heron] Sadly, I also saw a small alligator with his snout taped shut in the Orlando Premium Outlet.  Poor little guy was being used as a tourist trap photo-op, at $10 a photo.

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I managed to drag myself out of bed on time this morning to catch my flight.  I had to repack half my bags after coming to the brilliant realization that Orlando is actually warm! Funny that.  A short cab ride and one Tim Hortons breakfast later, it’s time to board.  On route to Houston as I write this.  Clear skies so far!

Starting descent into Houston! Damn it’s warm!

Lunch in the airport. Good food selection at this airport! Opted for “Texas brisket” – soooo much food!

In the air again, Houston to Orlando. Lots if doctors and researchers on this flight – overheard some CLL conversation. It’s a two hour flight and I got two pretzel packs plus a drink. Pretty generous by today’s standards 😛

Still in the air. I think local time is around 5pm or 6pm so it’s getting dark outside. Bit of a bumpy ride. Met a physician who’s going to ASH.

Landing! Hello Orlando!

Checked in and starving. Where is all the food in the city? Going to try a bar down the road.

Verdict: There is no good food. Instant noodles it is… 😦

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I’m leaving for ASH 2010 on Thursday!  Woooo!  As I mentioned before, this is the 52nd annual meeting of the American Society of Hematology.  I’m super excited for the opportunity to attend and blog from this event!  Daily updates will be posted here on AlbinoMouse, while blogs from a few key events will be posted to the Stem Cell Network blog.

Links to check out this week:

  1. Peter from Science of Blogging discusses why all scientists should blog.  I could not agree more!  Before this blog, I was deathly sick of the daily routine that is research.  Writing about science really helped me to rediscover those things about science that I love the most.  Plus, I’ve met a lot of cool people and gotten some pretty neat opportunities as well!
  2. Continuing the tale of cool biologists: Side-Line Magazine reports that electronic music artist Sara Noxx is teaming up with forensic biologist Mark Benecke for a cover of “Where the Wild Roses Go”.  Dr. Benecke is a high profile consultant who has previously worked on identification of Hitler’s skull.  He’s also a punk musician on the side….!
  3. And now on the topic of rockstar biologists, did you know that Bad Religion frontman Greg Graffin has taught classes in evolutionary biology at UCLA? Thanks to DiscoverMagazine!

All for now.  Next time you hear from me I’ll be in Florida!

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