Sunday, April 28, 2013

An Analytical Chemist Does #RealTimeChem Week

**Disclaimer** The pictures included below are from Friday, April 25th. All things being equal -- putting words into a blog is harder to do in RealTime then any chemistry.

What is #RealTimeChem?
The official explanation can be found here, but from my own perspective as a Twitter user, the purpose of RealTimeChem is to empower chemists across the internet to share a snippet of their daily-routines and habits with the rest of the online community. Got out of bed too fast and need some caffeine to get your through the day? #RealTimeChem. Close to finishing a graduate degree and glued to a computer screen writing a thesis? #RealTimeChem. Stuck in your fume hood running a column to isolate that amazing compound which will get you published in JACS? #RealTimeChem. Or perhaps you're just smashing glassware as part of your regular spring-cleaning (ahem,@ChemistHulk); it's still #RealTimeChem. The message here is that being a chemist isn't the same across the board - we each have our own unique research area or career paths (for those of you lucky enough to be employed) - so sharing these experiences with the community provides reassurance that we aren't alone in our endeavors, while at the same time showing chemists as real people- the latter shocks me too.

Why did I need to contribute a blog post?
The contributions to #RealTimeChem have been rapidly increasing since it was first conceived. This week, however, is extra special; it's been advertised extensively as the week of #RealTimeChem. Chemists of the internet have been dragged out of their lab dungeons and collectively united into joining the festivities. The simplest and most common means of involvement is through Twitter - I saw some rough statistics a few days ago of how the week has been going: upwards of 4,000 Tweets from ~700 unique users (as reported by @rapodaca), numbers which have surely increased by the time of this writing. And because this is the inaugural week of #RealTimeChem, the ante was upp'ed and blog posts documenting your RealTimeChem were encouraged. There certainly haven't been 4,000 of those, but for the extra-savvy in the crowd who found time to contribute, @JessTheChemist has been hard at work doing daily post round-ups on her blog The Organic Solution

Somewhere mixed in all of this is my motivation for attempting to join the blog-savvy crowd (of which I am not). I've followed the hash tag for the better part of the week and, after eliminating messages pertaining to coffee breaks and never-ending grading sessions, the majority of actal chemistry that's been reported has been from those of you who best associate with, well ... making stuff. Yes, you know who you are - you spend most of your time in a fume hood, doing reactions and running columns to isolate products that give you 25% yield which you'll later publish as 75%. And yes, your work will change the world as your clever reaction schemes make new materials and drugs that will redefine how we live. Though my tone may not sound convincing, I am quite truthfully in awe of your talent - your resourcefulness and patience are skills you will successfully transfer to other areas of your life. However. There are other breeds of chemists, and their lives do not involve reactions, columns, or reagents that could evacuate an entire floor. I've been inspired to tell my tale on their behalf. 

My background is mass spectrometry, though during my last three years as a graduate student at the University of British Columbia, I've redefined myself as a bioanalytical spectroscopist. I know that's a mouthful, but it really just means I use spectroscopic techniques (i.e., lasers!) to analyze different types of cells (cancer cells, embryonic stem cells, blood cells, etc.). The main benefit of this approach is that you can determine the chemical composition of a sample -- what it's made of -- without needing to break it down or do any type of separation. As you can imagine, it's a bit of a niche field and makes up only a small piece of the financial pie in the analytical world, but selection the right analytical tool for a given job is dependent on the application. Groups around the world involved with bioanalytical spectroscopy make groundbreaking advances in the biomedical sciences and contribute to new technologies that ultimately will initiate a new age in health care. 

My intention in this post is to describe a "real time" day in the life of a chemist on the other side of the tracks: no reactions, no columns, no yields - just shiny floors and dark rooms. 

#RealTimeChem - Analytical Edition
The University of British Columbia is a beautiful campus (yup) on the west coast of Canada, and my daily struggle to get my hind-parts there at a reasonable hour involves hopping on public transportation. Vancouver is known for being very environmentally-friendly and offers numerous bike-lanes throughout the city, but I haven't reached that level of ambition... yet. 

Time: 9am

When I first decided I wanted to pursue a graduate degree, one of my requirements was that I become involved with research that would be interdisciplinary -- my experience in the fundamental physical chemistry world was tedious to explain to friends and family. A driving force for attending UBC was the prevalence of such multi-faceted research opportunities within the chemistry department. 

I ended up joining a group that's based in the Michael Smith Laboratories, a building named after Michael Smith (Nobel Prize winner in 1993) and home to many diverse labs working on some type of biotechnology. The building itself doesn't feel like one you'd find in a typical academic setting but instead has a feel that reminds me of an institution. 

I guess what I'm saying is that working on the interface of multiple-disciplines means that the typical working environment is not quite the same as what lifestyle synthesis folks --at least of the graduate school variety -- deal with on their day to day. Have you ever seen a hallway this quiet, or well lit, that's devoid of boxes and empty solvent bottles?

After a quick jaunt down the tunnel -- did I mention the floors are buffed on a daily basis? --I arrive at the glorious entrance of my lab. You'll notice that all of the standard WHMIS designations are plastered in plain view, as well as our status as a biosafety level 2 lab. 
Time: 9:30am

You've also picked up by now that there aren't an ordered array of fume hoods beyond this door, each overflowing with flasks and hot plates and stir bars. Nay. Beyond this door is the means to do spectroscopy - to shine light on an object and study how that light interacts. One thing we take pretty serious in the laser-world is safety; there's no way your eyes are getting exposed to any stray beams when you're decked out in one of our stylish pairs of eye-protection (sorry, I don't think there are Ray-Ban models).  Furthermore, you can't inadvertently open door #1 and interrupt an experiment in progress behind door #2 because, there isn't a way in! The doors are connected to an interlock system that quite literally puts them on lock-down when an experiment is in progress.

Once behind door #2, however, you'll notice that there aren't many features in the lab that you might associate with "chemistry" -- at least, chemistry of the synthetic variety. There are some features worth pointing out though, the most obvious being that - gasp - there aren't any windows. Not that big of a shock, I hope, as any contribution from that big round yellow thing in the sky would probably make it difficult to distinguish water from oil.  You'll also notice that there are isolation curtains to separate various pieces of equipment from the lab environment/minimize renegade light.  

The one necessity when working in the spectroscopy world is lots of POWER.

Everything is fairly obvious to operate though, as you can hopefully interpret the functionality of the big-red button,  the key, and the one-armed bandit. 

Although there are multiple laser systems housed in the lab -- each with their own application that's generally dependent on the particular wavelength of excitation light -- the commercial instrument below is the workhorse which currently bears the burden of my research (yes, it's in a different part of the lab).

The system provides a unique setup that couples a spectrometer with a microscope, which creates the potential to selectively choose an area of the sample that might be interesting in some way. When you think about a cell, this can obviously be advantageous to identify where certain components - such as DNA/RNA - are distributed.

At this point in the day, it's time to start the system and warm this bad boy up. The buttons (left to right) are responsible for the microscope lamp/camera, the microscope translational stage, the excitation laser, and the detector. 

Calibration is an important part of any chemical instrumentation,  and we take no shortcuts here either. The purpose of the calibration is to ensure that the data we record in our spectra is in fact relative to a known quantity that's been previously well-characterized - for us, that calibration tool is a silicon wafer. The translational stage is controlled by the ball-adapter (strikingly similar to something I'd expect to find with a video game console) and the the appropriate objective lens of the microscope is used to focus the laser onto a clean spot on the wafer. 

Time: 10am

Taking care of instrumentation set-up is step 1 of any day, but once things are calibrated and ready to go, I hike to another building on campus to retrieve samples from a collaborator. One thing about being a chemist involved with interdisciplinary research is that you're going to be immersing yourself in a topic where you have a critical lack of background experience. Over the last three years at UBC I've picked up the basics of cell biology --  both from an academic and experimental standpoint -- as proper use of a biological safety cabinet wasn't exactly an item on the curriculum of my core-chemistry classes; neither was cell culturing, for that matter. Putting those feathers into my cap was challenging but made me appreciate all the cool science I wasn't exposed to when locked away in a library learning partial differential equations. 

I hope I don't sound disappointed, because with collaboration being a big part of my life, seeing a connection between different sciences has made me appreciate my chemical pedigree more than ever (should I use that chemistry-is-the-central-science cliche now, or later?). What I've also become acutely aware of, unfortunately, is how much more baller the biology people treat their buildings and lab environments.  You've had a taste of MSL, but this is another building at UBC called the  Life Sciences Center, and behind each of those glass panes is an individual lab. Neat, right?

Something else I've become very conscious of is the tricks of the trade for these biological folk. Things aren't blindly sealed and capped in unmarked flasks and taken from one lab to another - samples are meticulously labelled and transported on carts in plastic bags for secondary containment and the waste isn't just solvent but every used wipe and glove and pipette tip has a different home. 

When I obtain my samples and get them from point A to point B, depending on what I'm intending to quantify that day, there are a variety of preparatory steps I need to take. These steps sometimes involve lonely elevator rides going between floors and more empty hallways where the shine of the floor is continually taunting me, yearning for a spill or a stain of some kind ... the kind that only a chemist can provide. 
Time: 10:30am

Perhaps the most exciting part of this day is when I get to do actual chemistry. One of the cellular components I sometimes quantify is ATP - the validated protocol involves an extraction step with perchloric acid (HClO4 - yes! I can sometimes do chemical formulas, too). I don't know how many of you work with this chemical on a regular basis, but in all my years of undergrad and prior to being trained at UBC, I had never seen a fume hood tasked with washing condensed vapors into a basin; I'd be curious if they're more commonly used than I'm aware. 

Time: 11am

Once all the dirty work is done on the biology side of things, I high-tail it back to the  MSL to get a start on the spectroscopy. Gold mirrors are frequently used as the substrate for the cells as they provide signal enhancement and, unlike glass microscope slides, cause no interfering background contribution. A 70% ethanol solution is used for cleaning purposes and kim wipes only function to blow my nose or soak up excess solvent - optical wipes are the higher quality alternative for actual-cleaning purposes.  

Time: 11:30am

 When the samples are ready and the instrument parameters are set, the experiment for the day is all-systems-go. I normally do a blank background first while grabbing lunch, and then return to the nice, peaceful, relaxing dark room that has become my second home. 

Time: 1pm-close

Thanks for reading, internet friends. 

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