Knowing and believing

I’ve been thinking a lot lately, a dangerous concept I know, about one particular, glaring weakness of mine. And it’s becoming increasingly obvious just how much of a detriment it is to my productivity levels to have this problem.

This week, I started an experiment I’ve been putting off for a while now. I’m the sort of person who likes to know things. I like being an expert, being able to do things on my own. I like understanding what it is I’m going to do before I do it. I have pages and pages of typed notes and laboratory protocols, outlining experiments I haven’t started yet. I prefer to read and re-read papers or text books before I even set foot in a laboratory.

An example of my OCD
An example of my OCD

I’m beginning to realise that this attention to detail, while a very good thing, could probably be easier if I, you know, talked to people.

I mentioned before that I’m a Chemist by training. I can take a screwdriver to a FTIR Spectrometer and do multivariate statistical analysis in my sleep now, but give me a coral and a PAM flourometer and I feel lost.

Now, most reasonable people, when faced with this situation, would probably go and ask for help right? Not me; no my damn pride is laid on too thick and it’s hard to break through it sometimes.

So I thought I’d give you a beginner’s guide to Science-ing for stubborn people:

  1. Suck it up and ask someone who knows more than you for help.
  2. Rinse and repeat.


I’m about halfway through this hugely important experiment (which I’ll tell you about in a separate post later I promise) and I have to say, I would absolutely not have been able to get everything sorted out by myself. It’s just not feasible at all. Even though right now I feel so far out of my comfort zone that I’m floundering, I know I’ve had the help of people who know exactly what they’re doing and who are much, much smarter than I am.

Science-ing. So much easier with help. Trust me.
Science-ing. So much easier with help. Trust me.

I think there’s a very big difference between knowing and believing something. I think I’ve known that asking for help is okay and no one’s going to think I’m an idiot (no matter how much I feel like one). But I’m really just starting to believe it.

It’s kind of nice.


So this is what I do…

I’ve been wondering over the last week what I should talk about next. I figured I should potentially tell you a bit about my research huh? I’m a Chemist by training, so a lot of this is still very new for me. I’ve spent two years attempting to get my head around the wonderful world of molecular biology and let me tell you, I have new-found respect for it.

So if you asked me at a party or if I was saying hi on the street, I would say something like “I look at the biochemistry of corals and their response to environmental stress”. Boring, but concise. Never fear; I have a long version.

In the last 3 decades, the Great Barrier Reef (GBR) has lost almost 30% of its coral coverage and reports show this trend is continuing. Losing the reefs is a more frightening possibility than you might think. In fact, many small Island nations throughout the tropics rely on the reefs for their food, protection and their cultural identities. In Australia, about two million tourists visit the GBR each year, accounting for a hefty chunk of Queensland’s revenue.

Google Earth image of the Great Barrier Reef
Google Earth image of the Great Barrier Reef

The loss of coral cover is linked to an increase in what we refer to as “mass bleaching events”. Environmental stress factors like increasing Sea Surface Temperatures (SSTs – have a look at the IPCC website) and light intensities have been known to cause these events. Environmentally, we understand what’s happening, but it’s a different story from a molecular point of view, and we need to know what’s going on at this level in order to get some idea of how to help them respond to their changing surroundings.

At their core, scleractinian, or reef-building, corals are a symbiotic relationship between the host coral and a micro-algae known as zooxanthellae. These algae are photosynthetic and so they can provide the coral host with essential nutrients like organic carbon. In return, the corals provide the zooxanthellae with protection and inorganic nutrients they can’t produce by themselves. It’s a mutually beneficial partnership which, unfortunately, is very delicately balanced and extremely susceptible to environmental change. When conditions become unfavourable or stressful, the coral will expel the zooxanthellae and they lose their main source of organic carbon. Sometimes the corals can recover and get their algae back, but sometimes they can’t. If the environmental stress lasts for a long time, they eventually starve and die. This is traditionally not awesome.


There’s currently a large amount of research into how the zooxanthellae’s photosynthetic systems work and my lab (C3) is responsible for a good portion of it. We know that under stress, they can experience a build-up of toxic oxygen radials that overwhelm the photosystem proteins. But we’re not sure why that happens in the first place. The underlying molecular triggers for the bleaching response are still eluding us but bit-by-bit, we’re filling the holes in our knowledge. Why do some types of zooxanthellae appear to be more tolerant to an increase in temperature? Why do some species, like massive corals, resist bleaching when others, like branching corals are pansies that seem to die when you breathe on them?

The answers to these questions could have something to do with their biochemical composition.

Proteins, carbohydrates and lipids play a critical role in ‘maintaining the status quo’ within any organism. By that I mean the amount of energy available drives biochemical processes that keep cells functioning properly; it’s why we need to eat. Within the coral symbiosis, the host and zooxanthellae exchange essential nutrients. In fact, the algae are sometimes responsible for up to 90% of the host’s organic carbon requirements. This exchange keeps them healthy and may affect their resilience to environmental change.

My research focuses on the symbiotic partnership from a biochemical point of view. To do that, I’m using a technique that has only recently started to be applied to biological and environmental questions things like this. It’s called Fourier Transform Infrared Spectroscopy. Essentially, every molecule in the universe is vibrating at characteristically different frequencies. FTIR spectroscopy picks up on these vibrations and plots them in a graph of a series of peaks called a spectrum. Each peak corresponds to a specific molecular bond within a sample. This means that I can map the protein, carbohydrate and lipid content in the corals in very little time and with very little sample preparation. We can use these spectra to model the shifting biochemistry within the organisms and how they respond to elevations in temperature or light intensity.

Tanks! Hooray!
Tanks! Hooray!

I have very limited experience within the world of science, but in my opinion, the scope of this technique and the things we can potentially do with it are very exciting. Modelling the biochemistry in response to environmental factors can not only add to our understanding of bleaching, but it could also result in a way of predicting mass bleaching events.

Cool huh?

First things first…

I’ve heard tell on the blogosphere that writing the first post is always the hardest. They’re not wrong at all. I’ve started and restarted this post so many times that I’ve lost count. I’ve held my finger over the ‘backspace’ key, my head hitting the desk with an exasperated ‘thunk’, my confidence in my writing ability disappearing…

But then I thought, “Seriously, how hard can it be?” To borrow a phrase, all I needed to do was shut up and write.

And so I am.

This is me… writing.

I remember ages ago, my housemate showed me a picture she’d found on the internet. It was a quote about Facebook and our perceptions of people:

“The reason we struggle with insecurity is because we compare our behind-the-scenes with everyone else’s highlight reel”.

Now I’ll be honest – I have no idea where that comes from, or even if that’s the right quote, but I think regardless of that, there’s a lot of truth to the statement. I’ve had a number of conversations recently along these lines with people who I thought were going fine; better than fine. People who I looked at and thought “Wow! Look at all of that super-awesome-science they’re doing!” I would look at them, look at my work and come to the conclusion that I wasn’t doing enough. In comparison to their Einstein-like aura of productivity, I was the monkey with a typewriter, hoping for Shakespeare.

I was sitting with a bunch of my friends from the Chemistry department a few days ago when one of the Academics at our university walked past. The conversation moved towards this direction and my friend Nicole asked, “Are you ever supposed to feel like you’re doing enough?” This is a woman who got first class honours,was offered her pick of projects at a number of different, high quality universities, and who has been lecturing as a 2nd year PhD student! The Academic just grinned and said, “Hah! No. You constantly feel like that until you hand it in. And even then…”

And so, I’ve called my blog “The Confusion Matrix”. I am becoming increasingly of the opinion that no one “has it all together” and anyone who tells you otherwise is selling something. (+10 points for the nerdy Princess Bride reference?) I hope this blog becomes an avenue for me to share my limited experience with life in general and with my PhD specifically. I’ll be writing about my research, conferences I go to, things I discover through talking with friends, opinions, embarrassing stories (of which there are many… trust me) and just anything that I’d like to think might be helpful or entertaining.

Perhaps one day I’ll be able to take the “Confusion” out of the title, but somehow I don’t think that’s going to happen anytime soon.