Thesis in a blog post

The end is nigh. I have submitted my Ph.D. dissertation, “Stable Isotope and Geochemical Investigations into the Hydrogeology and Biogeochemistry of Oil Sands Reservoir Systems in Northeastern Alberta, Canada,” to my examination committee and will defend my thesis on September 11 at 9AM. If you happen to be in Calgary and would like to attend, everything should be open and some of my work I’m presenting publicly for the first time ever! This is unusual in the modern science-industrial complex, where Ph.D. theses are sometimes completely published in journals before ever being compiled into a thesis. Because of this, few people actually ever read your thesis, or use it as a reference: all the good stuff has been published elsewhere in a more accessible format! Part of the reason why my work is being presented for the first time at my defense is that parts of the work resulted from industry collaborations, that required certain data to remain confidential. We have finally extracted the good stuff, the research that can be presented openly, and put it together in a thesis that should be beneficial to industry, government, and water resources groups doing work in the Athabasca oil sands region. I’ve put together a short summary of my thesis work below:

      • I compiled public data and mapped the salinity of McMurray formation waters across the entire Athabasca region, and came up with a new geological explanation for why there is so much variability in the groundwater chemistry of one formation. The McMurray formation contains most of the oil sands deposits, so there are fairly widespread implications for our regional-scale observations. This work was partially presented at the CSPG/CSEG Geoconvention in May of this year, but we have refined the message and identified some key features to look for when evaluating water systems on a smaller scale, such as an oil sands lease area.
      • Evaluating the geochemical composition of water in the McMurray formation used to be difficult. The bitumen in the oil sands are very hydrophobic, so drilling groundwater wells into the bitumen-saturated reservoir to find out the chemical makeup of water isn’t easy, and most of the time it just doesn’t work at all. However, Gushor has been producing small volumes of water from drill core in addition to the oil that they extract for routine geochemical analysis of bitumen. As you might suspect, the water is wildly contaminated by drilling fluids (water-based muds are used to lubricate the drill bit), so analyzing its chemistry seemed like an expensive and somewhat absurd undertaking at first. However, using stable isotope geochemistry we were able to make a few calculations and can now determine the stable isotope composition and the Total Dissolved Solids (TDS) concentration of the original formation waters, completely eliminating the contribution of drilling fluid! This is an important development because of the very substantial variability in water chemistry in the McMurray formation that can change by thousands of mg/L over short lateral distances (kms or less). We can now map these changes in water composition using drill core samples that are being routinely analyzed for petroleum geochemistry, giving hydrogeologists a brand new tool to investigate water systems in oil sands lease areas. What’s even more awesome is that we can do this water mapping in three dimensions, identifying changes in water composition both vertically within a single reservoir, and laterally when multiple wells are sampled across a lease area (Mark Rabin and Jason Wilkins cleverly dubbed this technique 3DH2O over breakfast one day, feasibly we could make this 4DH2O if we sampled the area at different times, perhaps to find out where injected steam has moved around). We did a proof of concept study using this technique to map the heterogeneity within an active SAGD lease area, and found some really interesting results, but unfortunately you’ll have to wait for the paper to see them (sorry!). I’m also doing this work as a consultant for a couple companies if you’re reading this and are interested in exploring the water systems of your own oil sands lease area.
      • While we were thinking about differences in water chemistry in the McMurray groundwater across the Athabasca region, it also occurred to me that there is a very active biological community in the oil sands reservoirs. Microbes exploit the oil-water interface to consume petroleum hydrocarbons, usually by methanogenesis. However, microbes are influenced by the aqueous geochemistry of the reservoir system, and methanogens are particularly sensitive to increases in salinity. To see how bugs can be influenced by the variations in salinity that we see in the Athabasca region, I created some oil sands microcosms with salinity values that span what we observe in the Athabasca oil sands region in cooperation with the wonderful people of the Gieg Lab in Bioscience. Special thanks is owed to Dr. Sandra Wilson, who tolerated and encouraged my sometimes clumsy transition to becoming a part-time molecular biologist. We monitored the progress of the microcosms over a year-long period, and saw some very real differences in the isotopic composition of methane, and the inferred metabolic pathways of the microbes under the different salinity conditions. Unfortunately, biology in the lab doesn’t always look like biology in environmental systems, and while the bugs behaved very differently under different salinity conditions in the lab, the methane they produced didn’t look anything like what we see in the field. More work required on this one, but I think this study identified some further questions and research directions that we could take to work on the idea of salinity controlling biodegradation in parts of the oil sands regions.
      • Finally we tried to put some timing on methanogenesis in a coalbed methane system, which is analogous to oil sands systems in many ways. While not completely similar, both CBM and oil sands are shallow organic carbon-rich reservoirs with active hydrogeological systems and rapid carbon cycling due to microbial activity. Using compound-specific natural abundance radiocarbon analysis we found no detectable radiocarbon in dissolved inorganic carbon or methane, even at the shallowest reservoir depths (<100m), suggesting that microbial carbon cycling of coal is occurring much faster than inputs of dissolved inorganic carbon from shallow groundwater. This work was conducted in Montana, collaborating with the fantastic Drs. David Vinson and Jen McIntosh without whom this project would not have been possible.

These papers represent the main bulk of my thesis work that has been conducted over the past few years, and I’m pretty happy with how it all turned out. Like all Ph.D. projects, there are serious bumps in the road that happen, and you can either let them derail you completely or let the bad things slide and find other opportunities. I tend to choose the second option, having realized from many years of playing baseball that hitters that fail 7 out of 10 times at bat are called “hall of famers.” Sometimes you strike out, and when that happens you just have to get back up to bat and take another swing. There were periods during my degree when the data we were getting was junk, when corporate confidentiality took an entire project away from me (this will never be published, sadly), when we couldn’t get funding for any of our best ideas, and that time when I spent an entire summer in Europe developing a project that never came to fruition (ok, this one wasn’t so bad…). Looking back at the entire Ph.D. process as a whole, things tended to work out pretty well. I’m very grateful for the funding that supported this work, from NSERC and our sponsors at Suncor and ConocoPhillips who all continue to support excellent university research, plus the awards to collaborators in the Gieg Lab and McIntosh group that keep their research machines humming smoothly.

If you’re interested in the work we’ve done, please don’t hesitate to get in touch with me, I’m happy to share more details and data as it becomes available for us to publish. As for me, my next steps in my career and life are finally being ironed out, and I’ll be sure to write about them soon.


ps – the last few months I have spent my time writing in the amazing city of Toronto, Ontario. I decided that a change of scenery would accelerate my writing, and I think I was right about that. I highly recommend this tactic for other Ph.D.’s – sometimes it’s easy to get caught up in the day to day lab buzz, and you spend your time doing anything but writing. As for TO, Toronto is an incredible, vibrant city with so much going on at any time it’s easy to get wrapped up in all the amazing things that are happening here. The Jays have been terrible, but entertaining, the music scene has been fun, and lakeshore is beautiful as always whenever I needed a bike ride to clear my head and get some exercise. Thanks for being a great writing buddy, TO; you’ve been elevated to header-image status on this blog.

The Scientific Method

I haven’t posted here in a while, most likely due to thesis writing and abundance of industry-related confidential projects I’ve been working on. This is my first post-Calgary post, however, as I’ve recently moved to Toronto, and it will be a short one.

I just discovered this genius one-minute clip of a Richard Feynman lecture from the 60’s that deserves to be widely shared. As a scientist who does primarily the latter part of the equation right now (testing hypotheses with experimental data, rather than modeling) I couldn’t agree more. I love modelers, I love the questions the increasingly complex numerical models can generate, but I think it’s highly relevant to remember that it is data that ultimately drives science.

Without further ado, here’s the clip:


Ok, I admit, every academic ever has written a piece about procrastination. This isn’t new. If you are looking for universe-altering insight turn away now, and recognize that I am CURRENTLY PROCRASTINATING BY WRITING THIS BLOG. However, if you’re interested in how I procrastinate and my self-reflection on my ‘useless time wasting,’ here’s my rant today while I procrastinate from writing a chapter that I don’t have a good vision for yet…

There are some days when I think procrastination is a necessary part of science. Sometimes I think it’s productive for writing to procrastinate a bit before starting. I tend to write in big blocks, where I will focus for hours on the paper I’m writing, or not at all. The last few days have qualified as “not at all.” I think this is OK, perhaps collecting my thoughts, letting my brain fire some electrons around the paper that isn’t quite as structured as it could be. Perhaps this shuffling of electrons will give organization, new insights, or ways to communicate the things I’ve learned over the past few years into the document known as “the thesis.” Perhaps I should distinguish procrastination in general from productive procrastination, otherwise known as “thinking” I don’t think that enough thinking happens today. Few people would consider what I’ve done this morning productive. Stared off into space at my local coffee shop, not writing anything, just clearing my mind of the things that have complicated it in the past few weeks. There’s a strong probability that I won’t write a single paragraph this morning before lunch, but I think that’s OK. I find after a good procrastination/thinking session, my brain is more apt to flow freely and produce organized thoughts and paragraphs that actually make sense when put together. I’ve written entire papers in a single day that sound far better than the piecemeal potpourri of paragraphs I’ve put together over the past couple days. Sometimes procrastination, and thinking, is better than trying to mash keys better than a million monkeys. So if you’ve read my brief Friday rant, go spend some time procrastinating this week before trying to be creative. It just might help you achieve your goals faster.

– Ben

ps – naturally, after clicking “publish” the quote that was given to me advertising the WordPress Pro bundle was exactly relevant to my writing today:

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Summer’s almost over and so is my research.

A second guest-post from my undergraduate summer student Alison Banwell this month. Alison has wrapped up a good chunk of research from the summer and will continue taking courses through the fall and winter semesters. 

Because of this summer I can now follow, and maybe sometimes take part in, conversations on isotopes, oil sands, shale gas, and know how to make a poster to present research. The poster knowledge will definitely come in handy, since I’m planning on presenting a poster of my own at the undergraduate research symposium. I’m actually pretty excited since what I found turned out to be pretty interesting.

This summer I was measuring the isotope geochemistry of an oil sands core.   In my core there were organics, calcites, and pyrite. The isotope values of these compounds indicated microbial biodegradation. This is thought to be the dominant process that breaks down oil in the oil sands, but the important part is looking at where the biodegradation occurs when compared to the oil-water contact. The ground water and the oil don’t like to mix, so there’s a transition zone between the two, but the water is necessary to the microbes that break down the oil, and so biodegradation is different throughout the core depending on where it is compared to that contact.

Another exciting thing is that while I was searching for pyrite in my samples, I found coal. The bitumen and the coal do not have identical histories, since the coal was formed where we found it and the oil migrated from somewhere else closer to the Rocky mountains over a long period of time. This gives us a unique chance to look at how biodegraded the coal is to see if it matches up with where the oil is biodegraded. The measurements on the coal aren’t quite finished yet, so I might get to continue on in September for a little while, but for now I get a bit of vacation time.

Maybe I’m just nerdy, but I like to think about how at the beginning of the summer, I had no knowledge of any of this, and now I can look at petroleum systems  and understand what is happening. The other great thing about this summer was that I took my second geology course ever, from Ben again. Geology 203 was great for me, since as I was learning things in class I could see their real world applications and how they fit into the research I was doing. This was extremely helpful.

It was awesome to get the chance to learn so much and get an idea what it means to actually do research. I think I can compare it to what it would be like to be a grad student, except without any of the stress since my degree doesn’t hinge on whether I actually found anything or not, and everyone is willing to help and explain things. This summer has made me realize that being a grad student is definitely something to look forward to, and to keep on looking for opportunities like this one. If an undergrad student can handle something like this, more students should get a taste of research early in their academic journey, since it gives you a great perspective on learning that you just wouldn’t have without it. I know it changed my view of how I see university, and I think it was totally worth it just for that.


Adapted Geological Time Scale Mnemonic

I miss Persian Camels. Specifically these ones: Persian Camels Ordinarily Sit Down Carefully. Perhaps Their Joints Creak Together Quietly. With the (somewhat) recent removal of the Tertiary in the geologic time scale and potential addition of the Anthropocene, a new mnemonic must be born. Here is mine, adapted from several others I found online.

Camels – Cambrian

Often – Ordovician

Sit – Silurian

Down – Devonian

Carefully. – Carboniferous

Perhaps – Permian

Their – Triassic

Joints – Jurassic

Creak? – Cretaceous

Persistent – Paleogene

Natation – Neogene

Prevents – Pleistocene

Hip – Holocene

Aging. – Anthropocene

Please share if you find it useful.

My Summer Research Project: Why not?

I’m Alison, and I just finished the first year of my Environmental Science degree at U of C. When thinking about a summer job I figured I’d email my professors from first semester asking if they knew anyone who had a project that could use a newbie who likes to learn more cool stuff. Since, first years are generally regarded as the babies of academia, I didn’t really expect too much. Lucky for me, my Geology 201 prof Ben had something I could do. He met with me and briefly explained that I’d be doing work with oil core samples, by looking at isotopes from those samples. With nothing else to go on I figured, why not? I know that isotopes are atoms of the same element with a different number of neutrons, and that oil core samples probably come from the ground somewhere in Alberta… With all my previous expertise, they took me on.

Measuring samples for carbon-13 analysis on the microbalance.

My science knowledge is from high school and first year (which overlaps quite a bit). So my first week was just learning more about isotopes, like what a stable isotope actually is, and how we can use them to learn about environmental systems. My previous knowledge from physics, chemistry and geology helped give me the basics: isotopes have the same number of protons, a different number of neutrons, and different isotopes of the same element react slightly differently, because they don’t have the same mass. Makes sense right? They’re different, so they get used differently in chemical reactions. Now, a stable isotope is nonradioactive, so no radiation occurs and it exists forever through the geological record. Carbon and sulphur are two elements that have stable isotopes. By looking at what’s referred to as the isotope ratio, it’s possible to figure out how the carbon and sulphur got there in the first place! For example, having a lot less Carbon-13 (a carbon atom with 6 protons and 7 neutrons) than usual means that the carbon is most likely organic – the carbon was once alive.

So in the core samples, I’m going to take a look at the organic carbon (in the oil mucky stuff itself), some inorganic carbon (in carbonate rock that is actually pretty easy to find in the oil muck), and some sulphur (in the pyrite grains). Pyrite’s that shiny fools gold that’s so easy to recognize, but I still needed some help looking for it since the grains are so small. And the first time I thought I found something exciting, it turned out to just be some ink on the rocks from the drill cutting procedure. Things like that you just have to learn as you go. And by looking at those isotopes in those places, I’ll hopefully be able to help figure out how the rocks and oil got there in the first place. Or that’s the plan anyways.

So now that I know the plan, hanging around a lab all summer seems like a pretty good time. I have to ask about pretty much everything (like, if I wanted to weigh something, what would I weigh it in? I’d never used a weigh boat before today, but that’s how you do it). But I get to learn and see more everyday. I feel like even if I just hung around and watched I’d learn a lot more cool things about a lot more cool stuff. Which in my mind is really what science is, so why not?


*** editor’s note: Alison will be a contributing author on the blog this summer while she works on her project. Stay tuned for more details on her work!

When you strike out three times in one game …

To continue with Peter Newbury’s (@polarisdotca) baseball analogy week, when you’re playing baseball, and have struck out three times in one game – you go up to bat the next time even more determined to get on base. This mentality is one of the reasons I think baseball players make good scientists – when you’re working in the lab, sometimes your procedures don’t work – again, and again, and again. Determination to get a result is sometimes all that matters.

Sometimes in the lab it’s faulty equipment. Sometimes the reagents have expired. Sometimes you don’t know what happened and have to go back and troubleshoot. After doing my DNA extractions and PCR reactions last month, my positive controls have DNA, my negative controls are free of DNA (both good things) and my Agar Gels seem to look clean of any problems. Unfortunately, my real samples aren’t showing any bands of DNA anywhere. Possibly there isn’t much DNA in the samples to begin with (they’re methanogens after all, low-biomass communities), or the oil in the samples interferes with the extraction process. Either way, I’m starting from scratch this week to get results, and not giving up – the geochem and isotope data look great in this experiment, and having some proper DNA sequencing will be the Mariano Rivera (or Tom Henke, if you prefer) of this study – providing the last bit of evidence to close out a really great story.

Baseball is life. Life is baseball. Particularly true in science, these analogies never seem to end.



Tom Henke, closer for the Toronto Blue Jays first World Series win in 1992. Photo: