Gelatinization, or Science Makes Me Stay Up All Night

For the second time since I began my lab work, I have arrived at the dreaded gelatinization stage of sample processing.  I say dreaded because this is easily the most time consuming step and requires the samples be regularly checked at odd hours (e.g. 11:30 pm and 2 am last night).

Explaining gelatinization requires a little background about what exactly I do with all of the little
pieces of walrus bone I have gathered over the last semester.  The end goal of the entire process is to analyze the carbon and nitrogen stable isotopes of the collagen in the bones.  Collagen is a structural protein and is found in abundance in connective tissues and in bones.  Unfortunately, all that pesky calcium carbonate (the hard part of the bone) makes it difficult to get to the collagen.  So, after cleaning the bones in a sonic bath and removing any fats/oils using a chloroform-methanol solution, I get rid of the calcium carbonate.

This is a relatively easy process, if a little slow, and involves our old friend hydrochloric acid (or HCl).  Everyone probably knows about HCl as it is fairly ubiquitous, found everywhere from the high school chemistry class to the inside of your stomach.  The acid dissolves the calcium carbonate in the bone, creating calcium chloride, carbon dioxide, and water.  The reaction looks something like this:

This process can be a little slow, taking anywhere from a couple of weeks to a month or more.  As the calcium carbonate dissolves, little bubbles of C02 appear, indicating that the process is working.  I continue adding acid little by little, until all of the hard structure is gone and the bone is soft and rubbery.  Once the demineralized bones have been rinsed back to neutral pH, they are ready for gelatinization.

This step makes use of a machine called a vortex evaporator, which is designed for an entirely different purpose but is very useful for this process.  This machine continuously vibrates and heats the bone samples (colloquially known as the "shake and bake" step), causing the collagen to unravel from its complex and very stable structure, forming gelatin (hence the name "gelatinization").

During this process, the solid pieces of bone dissolve into the solution until they are entirely gone and only a few little tiny white pieces can be seen.  If they stay on the machine too long, however, the collagen will continue to degrade until it is useless and the consequences can be disastrous.  This is why the samples must be checked.... and checked... and checked... and... well you get the idea.  As a result, for the 2 or 3 days (or sadly, sometimes more) that this process is ongoing, I make the 20 minute drive to the lab many times at ungodly hours to ensure the process goes smoothly.

All complaints aside, the process really isn't all that bad.  Once a samples has gelatinized, I pour it into a syringe and squirt it through a very fine filter into a vial then place it in the freezer.  Once all samples have been filtered and frozen, they are put on the freeze drier for 24 hours.  Magically, the clearish liquid turns into a lacy, white, cotton candy-like substance, which is the final product of the process.  I then weigh out a tiny (~0.2 mg) piece, submit it for analysis on the mass spectrometer and VOILA! Science!

For those of you that made it this far and looked at all the boring black and white images, here is a disgruntled looking underwater walrus:

Photo credit: Pete Barrett, National Geographic

Couldn't resist...

And that's all for today, folks.

Casey and the Walruses

I recently realized that my blog's title is a little outdated, though I suppose my scope was a little narrow to begin with.  Casey and the Marine Mammals doesn't have the same ring to it.  Casey and the Marine Ecological Studies?  I don't think so.  The URL would have been much too long.

It bears mentioning at this point that my whale days are not quite over, as I am still working on publishing my manuscript from my MS thesis.  It has been a long and arduous process, which has definitely motivated me to write my PhD chapters in manuscript form.  I never would have guessed it would be so difficult to pare a thesis chapter down into a clear, succinct paper.  In light of these difficulties, I am happy to announce that a little side-project that developed in conjunction with my master's project was recently published in Marine Mammal Science:

Check it out here!

Thanks to Liz Vu and all our awesome collaborators for getting that one to press.  It's fun when science works the way it's supposed to.  In celebration, here's a picture of some humpbacks enjoying the crystal clear tropical waters of Hawaii.

I wish I could say I was doing the same, but I am definitely not.  Still dark and cold here in Fairbanks, but after today it will only be getting brighter!  Happy winter solstice everyone!

The Story of My PhD

So you may be wondering how a marine mammal biologist can be undertaking a PhD project in which there is all likelihood that he will never see his study species.  I must admit, I've asked myself that question once or twice over the past 6 months, but really the answer is quite simple.  My doctoral work is primarily concerned with animals that are already dead, be it for one year, 50 years, or 2000 years.  Here's the run down:

My dissertation is part of a larger project called, unsurprisingly, WALRUS, a large-scale collaborative project aimed at understanding the impacts of changing climates on Pacific walruses.  By investigating how historic (and prehistoric) changes in climate impacted walruses, we hope to gain a better understanding of the effects current and future climate change on today's Pacific walrus population.  To this end, we are using samples from modern (stranded dead or subsistence harvested by Native Alaskans), historic (housed in museum collections), and prehistoric (recovered during archaeological digs) walruses to study how their migratory movements, feeding behaviors, genetic diversity, demographics, and even stress levels have changed over the past 2,500 years.  The impetus behind this work comes from changes in walrus behavior observed in recent years, namely the hauling-out of thousands of walruses on land, which have garnered a lot of recent media attention through stunning photos like this one:

Source: Chukot-TINRO

These haul-out events are thought to be the result of a lack of available sea ice habitat, and can lead to overcrowding, trampling of smaller animals, over-exploitation of food resources in a localized area, and increased sensitivity to disturbance by humans and/or land predators.  As a result, scientists, wildlife managers, and conservation groups have become concerned about the health of Pacific walrus populations.  The WALRUS project is designed to provide these groups with a better understanding of just how adaptable Pacific walruses are to changing climates and will hopefully give us an indication of just how dire the current circumstances are for walruses today.

My specific niche within this larger-scale project is yet to be determined, but it safe to say at this point that there will be plenty of work for me to do over the next 3+ years.  Maybe this time I'll do a better job of keeping you, my loyal readers, updated on my progress.

Updating the Update

Hi again,

My last post was brief, to the point, and left much in the way off cliff-hangers, so I'm back to resolve some of those burning questions I'm sure you are asking.  Did he say walrus?

That would be a resounding yes.  The handsome fellow above is a member of my newest study species the Pacific walrus (Odobenus rosmarus divergens).  Translated into English that comes roughly to "the animal that split off from the tooth walking horse of the sea."  Makes perfect sense, right?  Well, when you break it down, it does.  "Odo" means "tooth" in Latin, while "benus" means "walk" or "walker."  Walruses (and that is the correct pluralization, sadly, not "walri") were given this name because of the tendency of the males to use their protruding tusks to help haul themselves out of the water and onto the sea ice.  "Rosmarus" has its roots in ancient Norse, meaning "horse of the sea."  Finally, the subspecies designator at the end of the name, "divergens," indicates that the Pacific walrus broke off, or diverged, from the Atlantic walrus (Odobenus rosmarus) some time in their evolutionary history.

Now the catch here is this: despite the fact that I am beginning a PhD focusing entirely on walruses, I may or may not get to see a living walrus during the course of the project.  How's that for another cliff-hanger?  That's how I keep my readers coming back for more.

More details next time!

Casey