Sunday, 7 April 2013

Where you gonna go?

Photograph by Carsten Peter, National Geographic

"I don't know...
 I don't know...
 I don't know where I'm a gonna go, when the volcano blow"

Jimmy Buffett started talking about it long before the people from the red, green, blue, yellow sides of politics tossed it around. This isn’t an issue that should be tossed around, this is serious business people! The volcano is going to blow and where are you going to go?

I’m not getting in to a story about volcanoes or the end of the world (already escaped that December 2012-booyeah!), rather I feel like giving a friendly reminder that climate change is going to make things uncomfortable for us and painful for generations to come. 

Are you already rolling your eyes or are you getting a sinking feeling in the pit of your stomach? Either way, you are probably like most people, brushing off the inevitable, a life altering situation, because it is not directly affecting you and your cozy comfortable bubble. I am not removing myself from this avoidance, I too am selfish at times- worrying about how many times I exercised this week, whether my hockey team won and whether I am getting the best deal for my upcoming vacation to Hawaii- but I do try to support earth saving initiatives by recycling, composting, eating organic local foods and limiting fuel consumption. I strive to be earth friendly because once in a while, during my delightful morning coffee, I am slapped with a nice cold slab of reality. In the course of my morning news scavenging, I came across a very frightening headline “In Sign of Warming, 1,600 Years of Ice in Andes Melted in 25 Years”.

The New York Times article, very well written by Justin Gillis, summarizes the COLOSALLY REAL finding of a study published online Thursday in Science- the world’s largest tropical slab of ice is melting faster than it ever has since the Ice Age. 

An immediate image from The Day After Tomorrow flashed in my mind- a giant tsunami wave pummelling over the nice little cliff I sit on at the University of British Columbia, sweeping right over the city of Vancouver… lovely.

Farfetched blockbuster scenes aside, this recent discovery of immense climate change should not be dismissed. Plants from thousands of years ago are propping up from the melted grounds of the Quelccaya ice cap, helping scientists date and measure the speed of ice recession. As a pseudo-microbioimmunologist I am very curious, excited, yet a little nervous about the potential microbes also being uncovered and released from thousands of years of preservation. Scientists have dug out scary pathogens from ice before- the Spanish flu’s H1N1 influenza for example- and we are still mass pandemic-free (insert importance for pandemic preparedness and research here). 

Unfortunately for my curiosity no superbugs have been mentioned in the studies, still the massively receding ice cap has offered a demonstration of how scientists can legitimately measure effects from climate change. 

The ice cap study has also fostered a bittersweet scenario that should be anticipated with climate change- the temporary melting has provided water to local communities previously suffering from inadequate supplies, however, as the scientists have measured, the rate of ice marginalization is uncomfortably rapid and will eventually have irreparable consequences. What will happen to the local communities and our global community when the natural levee breaks?  

Image from

Where will you be when the ice melts?

Thursday, 17 January 2013

Hello 2013 Blogosphere,

It has been too long (by the standards set forth by fellow Internets) since our last catch up. I’m terribly sorry- I have been cheating on you with work (that dreadfully boring other past time that pays the bills)!

Happy and exciting news for you this beautifully passing throwback Thursday: many fascinating little tid bits about past and present Scientific discovery are coming your way! Topics ranging from Greek Gods in Immunology?! to Electronic Self-Healing Skin!! to Flesh Eating Parasites and beyond! Hold on to your 2013 pantaloons! It’s going to be a nerdy jolly good ‘ol science communication time!


Wednesday, 12 September 2012

A Little Creativity in Your Academic Cup!

Image from

After spending the most rewarding and possibly the best 2 weeks of my scientific career so far, in the mountains at The Banff Centre, practicing, exercising, indulging in creativity with like-minded sorts, I have been refreshed, revamped, and reBanffed in to the world of scientific communication.  Before the time of SciComm 2012, I was not sure if the art of storytelling existed in the academic publishing world, though now, in my post-“Advanced Science Communication Course” I am reluctant to accidentally glaze over pieces of creativity in academic papers without appropriate appreciation. I would like to share with you, two short paragraphs from two papers that I have recently stumbled upon in my daily PubMed/Google Scholar searches. These short pieces of storytelling were not the typical dry and monotonous factoid filled introductions that typically plague and suffocate academic papers. Perhaps I am embellishing their significance, though they are pleasantly surprising for the nature of the papers and journals for which they are published. I hope when you read them you receive a little smile or sense of content and promise for the world of literature and creativity that is gently sneaking in to the generally stuffy world of academic writing.  Enjoy and if you have time, read through the papers as they are also equally interesting!  :)

From D.L. Eizirik and F.A. Grieco “On the Immense Variety and Complexity of Circumstances Conditions Pancreatic β-cell Apoptosis in Type 1 Diabetes”
Commentary in DIABETES, vol 61, July 2012, pg 1661
“In his masterpiece War and Peace (1869), Leo Tolstoy wrote: “The human intellect with no inkling of the immense variety and complexity of circumstances conditioning a phenomenon, any one of which may be separately conceived as the cause of it, snatches at the first and the most easily understood approximation, and says: ‘Oh, here is the cause!’” The field of type 1 diabetes has been plagued by this trend for oversimplification. As a result, individual pathways are often suggested as “the cause” of this complex, multifactorial, and probably heterogeneous disease, thereby leading to therapeutic attempts that nearly always end in failure.”

From T. C. Pierson & J. W. Yewdell “Measles  immunometrics”
PNAS, September 11, 2012, vol 109 no 37 pg 14724

“Like baseball, immunity is a team effort. Various innate/adaptive humoral/cellular components work in unison to clear infections. Determining the importance of each baseball player/immune element to winning/clearing is more difficult than meets the eye. Just as mathematical modeling of individual contributions (“sabermetrics”) revolutionized baseball, “immunometrics” will change our concept of immunity. Measles virus (MV) is a highly transmissible negative-stranded RNA virus that remains a major cause of childhood morbidity and mortality (1).” 

Monday, 25 June 2012

Yum Yum Gimme Some...Molecules!

It is officially summer in Vancity! Today was not completely warm and sunny (by the latest North American East Coast standards), but for living in a rainforest- I'll take any bit of post 20 degree Celcius and mid-cloudy sunshine weather I can get! As inspiration from such a beauty of a day, I'd like to post a piece about food and the science behind tasting food. I am not a food scientist, though that would be a really great avenue to explore in my post-PhD life, but I would like to share a brief review of two books written by people who know more about food science and are more appropriate speakers of the matter. 

As light entertainment and if you prefer to learn via video from the expert first, please enjoy the following TEDx talk... For those who prefer to read and listen to me before referring to the expert, please enjoy my review of two must read books apres-film :)

Have you ever eaten in the dark and if you have, is your sense or ability to extract taste from food dramatically altered? What do you think happens when you put scientists and food together in a dark room? These may seem to be slightly odd questions, but could they have the potential to be enticing experiments? Well, for the Wall Street Journal writer Diane Fresquez and Montreal sommelier Francois Chartier, these types of questions drove inspiration for their impressively flavoursome work! Both authors published widely successful books depicting the science behind tasting food and drink- Fresquez recounting her year observing people curiously investigating the secrets behind the great big world of flavors in the book A Taste of Molecules: Revealing the Secrets of Flavor and Chartier, in collaboration with Chef Stéphane Modat and Molecular Biologist Dr. Martin Loignon, uncovering and explaining the art, science and specifically the molecules, that tease our vast array of taste buds in Taste Buds and Molecules. In the bio-manipulated, genetically-modified world we get our meals from, it’s refreshing to learn about another, more friendlier and intriguing side of food science.  I prefer not to give away the stories and secrets that Fresquez and Chartier depict about the behavioral influence that particular food and drink and combinations thereof can have on our taste buds- rather I hope to titillate your curiosity in the matter and perhaps the next time you savor that deliciously aromatic BBQ feast on a warm summer eve, you will be inspired to pick up one or both of these books and explore for yourself the science of tasting food and drink. Bon appétit!   

Wednesday, 23 May 2012

Stuck Between Two Worlds of Words

Sitting in the chair at a hair salon the other day (yes-scientific chicks are concerned with their hair style), I was enjoying my ‘free time’- flipping through fashion mags and reading articles about all those other non-sciency important matters happening out there in life, when I stumble upon a striking image of two worlds of words. 
From World War 3.0 by Michael Joseph Gross, Illustrated by Stephen Doyle
This beautiful and intriguing illustration of a rigid structure of phrases pressed against a liberated, chaotic nest of words was created by Stephen Doyle. The image is featured in an equally striking article written by Michael Joseph Gross in the current issue of Vanity Fair. The article describes the history and current controversy surrounding the wars for control over Internet freedom. Though I tried to steer my attention towards articles that were non-science related-freeing my mind of facts and processes, I found myself deeply immersed in an article concerning my Science world and inevitably, my life.  

After staring at the illustration for what was probably an uncomfortable amount of time for most people, I realized the profound reflection this division of two worlds of words provided for my field of work.  The rigidity and constriction of research ideas- how they are funded, perceived, and communicated were bound to one world, versus the other side of the scientific community that embraces and supports creativity and freedom in scientific thought. A couple examples came to mind: the whistleblower, outspoken scientists that freely express their thoughts and passions in a typically stuffy, conservative field; the scientists that actively pursue the development of open access publications amongst the subscription-driven businesses that dominate the field with their ‘top impact factors’; and the scientists and aspiring scientists who actively chase research goals in the keen interest of discovery despite regulatory and financial restrictions.  I’d like to expand each of these examples with solid, justifiable thoughts so today’s post will be the first of a three part series.

Let this tale of two worlds of words begin then with the whistleblowers- the power women who coincidentally are from my academic community: Rosie Redfield and Suzanne Simard. 
Rosie Redfield
Click for a large print-resolution photo of Suzanne W. Simard
Suzanne Simard

These ladies represent passionate freedom thinkers that push the comfort level of conservative types in the Science world. Both women are scientists, though in separate fields, have both stood their ground for what they believe- just loud enough for all closed minded sorts to hear. In fact, Rosie Redfield was recognized for her boldness in critiquing the validity of a research paper published in one of the most respected or ‘top impact factor’ journals. Expressing her distaste for the evidence driving the conclusions of the paper, Redfield pursued the experiments herself, in her lab, blogging about the process and ‘actual’ results that were observed from the work. 

As a cheeky stab at a competitor, another ‘top journal’ ranked Redfield amongst their year’s best newsmakers- praising her fearless pursuit to expose the truth about work that would otherwise be unquestionable due its publication status. Within the conformed and rigid trust that holds the highest ranked published work, exists critical minds like Redfield’s, that break free from the rigidly trusting framework and are courageous in exposing errors in the system- taking hold of the reigns to drive forward true scientific discovery. Suzanne Simard is another gutsy researcher who has pushed casual and conservative thinkers to re-evaluate the conformity of their thoughts in the community and freely adapt to the literally changing climate. 

Simard’s research in to the symbiotic network that connects plants, forests, fungi and soil microbes and the influence of climate and forest disturbances on this network is not limited to the scripts of grant proposals, experimental papers or departmental seminars- Simard passionately communicates her research findings for all audiences, including policy makers, to hear. For an April 8 2011 issue of the Vancouver Sun, Simard expresses the dire need to change policies regarding forest stewardship. Simard presses that we will lose the resiliency of BC forests if governmental policies for timber harvesting and multiple land-use tenures are not properly evaluated and are not designed to consider the devastating effects of climate change. Against a society with a conformist attitude concerned primarily with financial and health issues- Simard breaks through, expressing the detrimental burden a loss in forest stewardship will cost to society- a price that will be paid by our generation and for others to come. If you ever doubted the value or misunderstood the imperative contribution and intricate nature of plants and trees in a forest community, I highly recommend you tune in to Simard's YouTube clip discussing The Mother Tree and the March 22nd episode of CBC’s “The Nature of Things with David Suzuki” called Smarty Plants.

The CBC episode profiles Simard’s work (in the last segment) investigating the beautiful mutual exchange of nutrients between fungi and mighty Douglas fir trees. Set amidst a breathtaking backdrop of towering Douglas firs, Simard eloquently depicts the selfless exchange of essential materials that supports the life of the forest. You can hear the fascination for discovery and respect for the findings in Simard’s voice as she discusses the significance of her team’s work. Simard’s research reflects her respect and passion for sustaining life in the forest- a concept delectably emphasized in her article for the Vancouver Sun. 

In a field of work guided by facts, processes, rules and policies, it is easy to get caught in a frigid frame of mind, where your thoughts and acceptance of scientific discovery become frozen, conforming to a firmly accepted structure. But within the open book of life as depicted in Stephen Doyle’s image (yes I’m getting even more metaphorical, just bear with me) the rigid structure of a conformed scientific community stands now against another side where the other pages are not so rigid and hold a freestanding escape of thoughts- another world of words.  Avant-garde researchers like Rosie Redfield and Suzanne Simard help create this new world of words, where faux-pas discussions about false  scientific discovery and the true impacts of climate change are embraced and push the conservative, acquiescent boundary that holds scientific advancement at bay. The next step from here, in this new world of words, is to allow free, open-access to this new world. Thankfully, a couple great inspiring beings have taken the initiative to steer the scientific community away from a business, subscription-based enterprise and to embrace the concept of Creative Commons…a concept to be continued… in another post… 

Monday, 9 April 2012

Free Your Mind- Microrecognize Your Natural-Born Cyborg

Let me introduce you to Andy Clark, Professor of Philosophy and Chair in Logic and Metaphysics at the University of Edinburgh in Scotland From Andy’s work you can be immersed into terms and concepts such as ‘microcognition’ and ‘natural-born cyborgs’. I am particularly drawn to his descriptions of our minds/human systems as cognitive hybrids, our bodies as electronic virgins. The Terminator movies with John Connor come to mind with the idea of cyborgs, but so does an image of a brain and all its neurons and circuits. Andy’s work opened my awareness of our neural circuitry and the importance of understanding our biology as a system to recognize our mind’s cognition, network, and composition.

Grasping knowledge of the circuitry and biology of our minds is not only important to aid debilitating diseases like Alzheimer’s and Dementia, but allows for an appreciation of how the mind works and perhaps how we can begin to identify with human nature. We may be able to decipher mechanisms behind our judgements and decisions. Knowledge of patterns and trends that result from certain mechanistic interactions between neurons and chemicals flooding our minds should be critical not just for advancements in Science, but should be a critical interest of each human, each biological electronic virgin.
Andy Clark discusses further the significant contributions biology and technology render in the study of human reason in a short essay as a part of Science at the Edge: Conversations with the Leading Scientific Thinkers of Today edited by John Brockman. I have been reading and absorbing the variety of scientific thought presented in Brockman’s book- fascinated by the breadth of scientific discovery that collectively resonates the lack in knowledge of our own biological systems. Brockman’s book is an impressive collection of progressive scientific ideas from the best of the best of distinctive fields. If you’re interested in competing your thoughts and current knowledge and philosophies about human biological systems with the best scientific thinkers out there, I recommend reading Brockman’s book and checking out his web space Also to note, John Brockman is a renowned progressive thinker who has been described as an “intellectual enzyme”. Not sure how you feel about personal descriptors, but as a participant in the scientific and general human intellectual community, being described as an ‘intellectual enzyme’ is quite the proper pat on the back and tip of the hat.  Brockman’s web space is not only a space for Nobel laureates and fancy prestigious and very smart thinkers to communicate, distribute, and create knowledge, but is a remarkable intellectual experiment that I encourage you to discover.

As an aside- as I sit in a coffee shop throwing thoughts together into phrases- I am always reminded of the mind’s power as I attempt to read, listen to music, and write in an environment filled with background noise of coffee grinders, screaming gossiping girls, and mind dulling jazz or indie-type iTunes daily playlist tunes. I am able to meditate in my thoughts and concentrate solely on the analytical ones, tuning the circuits of my natural-born cyborg.

Monday, 6 February 2012

Take a Risk, Get Dirty- Your Army's Got Your Back!

WARNING! ATTENTION! This post contains BAD pottymouth language and may be offensive. But, in the theme of today’s post- take a risk, don’t be a “*ussy” and learn about the mini artillery you harbor in your body in the strongest, most offensive way possible. (For this to make sense- watch the YouTube clip first or later or whenever)

Did you know that a mini-army circulating in your blood stream and between your tissues/organs/vascular systems runs rampant against rascal virus/bacteria/parasite enemies in a very strategic, almost unimaginably organized manner?

Conveniently, a news post I read this morning from SmartPlanet, featured the development of “unmanned drones” that are completely armed and run by computers. Unable to contain my innate science inclinations, the idea of robots independently carrying out missions to areas of concerning threats immediately spurred my knowledge of immune cells that scavenge out areas of imposing threats and are on a mission to protect their host or in keeping with the theme of drones- their homeland. 

It’s bizarre that I’ve centred this post about the immune system and its components around the theme of artillery, armies, drones etc. when I have little to no expertise or understanding of the military and its perplexing hierarchy of militants, medals, and machinery. Please forgive me if you’re a more informed citizen in such things and if I’ve completely butchered the meaning or value of the various arms and levels of honor.
Back to your badass mini army of defense against pathogens... Your first line of defense against any pathogen: bacteria, fungi, virus, parasite etc. are your natural barriers. Your skin and mucous linings protect you all day long, much like cement barricades shielding borders and quarantined zones. Unfortunately, sometimes the enemy has bigger guns and bullies their way across protective barricades. Sometimes the tight seals or junctions that hold your skin or mucosal lining cells together to form a barrier get loose from tares or cuts and an open invitation for pathogens gets created. Sometimes those sneaky buggers carry a protein/receptor/antenna-like structure on their surface that perfectly fits with something similarly protruding from your cells, latches on and creates a type of nasty handshake, where unintentionally and naively, your nice little cell welcomes in the sneaky pathogen right across the barrier. Almost like a covert operation, most pathogens aim to enter enemy territory, get done what needs to be done, and without revealing themselves, escape back to where they came from or to another covert mission. Once across the first line, pathogens need to escape the innate immune system. This includes your first line of militants. Once a cell is infected with a pathogen, the infected cell is under stress and releases SOS signals to neighboring cells and out in to the environment it resides. These SOS signals are known as cytokines or chemokines. The SOS signals can activate cells called Natural Killer (NK) cells and as their name implies- they aim to kill, but naturally :) Actually, NK cells act most like remotely operated attack drones, once activated or signalled to attack, they launch an assault of mass proportion of missiles (granules) against the infected cell. NK cells are fancy, they kill virus-infected cells AND can target and kill cancer cells. Unfortunately, they have no specific attack skills and must be monitored and kept in check. Other members of your mini army include the dendritic cells, aka DCs. 

DCs have long extending arms, much like a badass octopus, scope out areas that may have been breached and under attack, sample potential evidence, looking for evidence to report back to (here is where I may butcher the hierarchal order of command) the operating captain who can then report to the major, then to the colonel, and up to the general. In sci terms, if the DCs and other cells like macrophages sense something fishy, they will activate and signal to the higher chain of defense command known as the adaptive immune system to elicit a specific retaliation against the invading pathogen. I mention specific retaliation because this is a key component to this part of the immune system. If the DC or other innate immunity cell samples evidence from an invading pathogen, this evidence is typically a signature of the pathogen and can be passed on to cells of the adaptive immune system for a direct attack against pathogens carrying the specific signature. Cells that are made from your bone marrow known as B cells, work together with cells that come from your thymus known as T cells, and with presentation of this specific signature from cells of the innate immune system, B cells will make antibodies that are specific against the pathogen’s signature. Pretty cool right? It’s like an army discovering the weak point (there must be some military term for this) in the enemy and designing specific artillery to target and destroy the weak point. What’s even more amazing is that your adaptive immune cells that are designed to specifically target a pathogen signature will retain memory of this signature and if you’re ever infected again from the same pathogen, it is likely that this specific artillery of cells and antibodies created the first time around will target the repeat offender. The concept of immune memory is the mechanism underlying vaccination. When you’re given a vaccination, you are given a formulation of one or many signatures from that particular pathogen (virus, bacteria, parasite etc.) that will instigate your immune system to produce antibodies against the signatures. Your immune system gets primed, exposed and ready to face the particular pathogen, should you ever come in to contact for real with the enemy. The importance of vaccination for the idea of “herd immunity” and the controversy surrounding potential side effects of vaccination are issues to be discussed in another upcoming post.  

For now, please enjoy the George Carlin clip below that fits right in with how we all should feel about our immune systems. I think we underestimate its power and undervalue its worth, but George Carlin most definitely has the right attitude. He’s abrasive yes, but is correct in reinforcing the idea of getting dirty and exposing yourself to germs. Natural immunity, getting both cellular and humoral immunity, where your body has attack cells and produces antibodies against pathogens, is the best immune artillery you can build. I’m not suggesting poor hygiene or touching your face more than often during flu season, but try to avoid the fear of germs.  Contagion may be upon us one day, but apparently so may be an Apocalypse or even worse- Global Warming…but until these disasters are upon us, let’s just try to wash our hands and play nice, k?