The Biochemistry of Light

Many of us have experienced the beauty of marine bioluminescence. After my experience in the Broken Islands and reading a post by The Little Biologist I started thinking…

Bioluminescent waves in the ocean, which I was able to see and swim in last night at Pachena beach near Bamfield (1)

When we see bioluminescence in the ocean what we’re really looking at is millions of tiny plankton, called dinoflagellates, emitting light. But what makes these organisms glow? The answer, of course, is chemistry!

An example of a bioluminescent dinoflagellate (2)

A process called chemiluminescence is used to refer to all light producing reactions. In this specific chemiluminescent reaction, luciferin is reacting with oxygen and luciferase to create oxyluciferin.

Luciferin is a chemical found in the dinoflagellates derived from chlorophyll, the pigment that makes plants and algae green and photosynthetic. The luciferin needs luciferase, a catalyst, to react with oxygen.This reaction creates high energy oxyluciferin which creates light. The oxluciferin can then be converted back to luciferin, but this is a very slow reaction.

The luceriferase catalyst has some amazing uses in biology. Every gene has a promotor region which can either turn the gene on or off. Luciferin can be placed next to this promotor region, and then whatever physical trait that gene acts in glows, that means the gene is on! This has been used in many studies, including some on prostate cancer.

Mice with luciferase under UV light(3)

For more on bioluminescence see Jim Morin’s work.



Kayaking the Broken Islands

The Broken Island Group is a beautiful group of islands between Bamfield and Ucluelet. The outer islands shelter a large area from the open ocean, so although you are in the middle of a large inlet of the open ocean it quite calm compared to the large channels around it.

A map of the broken island group, the smaller square is where we did our kayaking, see below.

An outline of our trip, the red line is our first day (which was a round trip) and the pink line is our second day. Notice the attempt to go between Benson and Clarke. It was a very windy day and the huge waves and strong winds from the open ocean made our original trip plan too dangerous.

My friend Mo invited a few friends from Vancouver to join us in Bamfield and the 6 of us rented kayaks from Broken Island Adventures. We took a water taxi out and set up camp on Gilbert island.

Home sweet home on Gilbert island

A sealion near our campsite on Gilbert. He was chasing a little school of fish and was so fun to watch.

Our first day we paddled to Wouwer to see the great tide pool. Our lack of map reading skills, combined with our inability to decide whether to go by compass directions or the shape of islands on the map made our journey there pretty hilarious, but we made it!

Getting ready to leave for Wouwer island

The hike in to the great tide pool, you have to beach on one side of the island and hike to the other side.

Mo in the great tide pool, she brought a whole wetsuit and I, in true unprepared Christina fashion, went in in my undies. The great tide pool is a huge tide pool that you can actually snorkel in! There are some amazing creatures in it, including moon snails.

A nice paddle back to our campsite with the wind to our backs and we soon had a nice little fire going and a lovely little camp dinner.

A gorgeous sunset on our way back from Wouwer

There was an amazing bioluminescence bloom this August. Bioluminescence is created by plankton which will give off a blue-white light when disturbed. Most of the other girls hadn’t seen bioluminescence before and wanted to swim in it. I’d already gone skinny-dipping in the great tide pool and wasn’t keen about getting back in the ocean, but remembered a canoeing trip I’d been on through the bioluminescence last year and came up with a better idea. After convincing Mo we hauled our kayaks down the beach and into the ocean. We paddled through the bioluminesence, leaving trails of light behind us and glowing balls where our paddles touched the water. The further from shore we got the more brilliantly the water glowed. Fish swam below us, creating streaks through the water. Occasionally an entire school would swim beneath us creating a wave of blue-white light. There was also a meteor shower the same night. There is no way to capture or describe how magical and amazing that night was. We paddled around the inlet watching the stars, the trails left by our kayaks and paddles, and searching for schools of fish for at least an hour.

A general idea of what bioluminescence looks like. It was completey dark except for the stars and the water was very still, so it would only light up when we moved through it. *

The next morning was foggy and damp, we made breakfast and I went out for a quick paddle around the island while the rest of the girls got ready. I stayed quite close to shore and paddled around Gilbert and a neighboring island. It was a beautiful peaceful way to start the day. When I got back everyone was ready to go and the fog was starting to burn off. We were planning to make our way over to Turret Island by going across Coaster Channel. The idea with crossing this channel is hugging the shore of the islands surrounding it, which makes for a long trip.

A foggy morning paddle

Coaster channel was quite choppy and when we were picked up we were informed that we probably shouldn’t have crossed it in those conditions. Luckily we made it, and even more luckily the other girls talked me and Mo out of attempting to go around the open ocean side of Clarke island as we’d planned.

The girls in Coaster Channel at the start of our day long paddle

This doesn’t do it justice, but this is what we were going through in Coaster Channel on the way to Benson. It was choppy with huge swells and we would occasionally have waves break on the fronts of our kayaks

The beach at Benson Island, an important First Nations archaeological site, where we stopped for lunch

A magical little mossy forest on Benson island

I was happy to be finished our day of paddling

We were picked up by the Broken Island Adventures water taxi and safely brought back to Bamfield where we enjoyed dinner and promptly passed out, still feeling the waves moving our bodies.

* Photo from

Biotic Impacts on Tide Pool Chemistry

I began a research project at Bamfield Marine Sciences Center a couple months ago, and I’ve finally finished collecting and analyzing my data!

A view of the ocean near BMSC

Just a quick recap of what I was looking at: There is quite a bit of information available about tide pool chemistry and how it fluctuates. For example: pH tends to be higher during the summer months and oxygen content increases during the day and decreases at night. I wanted to look at how biotic factors, such as animals and algae, affect their environment chemically. By affecting their environment, organisms affect other organisms within that environment. Some organisms co-exist quite nicely, while others can indirectly compete. An example of a nice co-existence is a seaweed called Cladophora columbiana which lives quite happily in specific areas just because of the chemical secretions of invertebratesinto the water.

Every organism in this tide pool is affecting the chemistry in the water and therefore the other organisms

I described my experimental design for my light and dark experiment in my last post:  basically I tested an algae, sea star and sea snail in light and dark conditions to see how they were affecting pH and oxygen levels.

I also did an outdoor predator prey interaction experiment where I looked at the effects of mussels and sea stars interacting on pH and oxygen content. I wanted to see how each individually affected the tide pool chemistry as well as how they affected it together. There have been studies that have shown that just the presence of a predator, it’s chemical cues and the sight of it, affect the behaviour of prey just as much as a physical interaction between the two. I wanted to test this, so I looked at the sea stars and mussels with a mesh barrier and without a mesh barrier between them.

My predator prey experiment

The beautiful view from my “office”

Four days of data analysis later, I actually got some interesting results! I found that algae act differently in light and dark. Algae photosynthesizes in the light, so it is increasing oxygen and pH, but at night pH and oxygen actually decrease. In sea stars and sea snails the pH and oxygen content decreased during the dark and the light. In my control treatment, which contained only sea water, oxygen and pH stayed the same during the day, but actually decreased at night. This could be due to microorganisms which are opposing each other chemically during the day, but at night the ones which were photosynthesizing and creating oxygen stop counteracting the ones using the oxygen and creating carbon dioxide. To summarize light and dark have significant effects on tide pool chemistry. This could contribute to very different environmental conditions and tide pool communities during the night and day, or summer and winter when daylight hours decrease.

Data management and analysis, aka the things my nightmares are made of

In my predator prey interaction treatment there was no difference between the tide pools containing both mussels and sea stars with a barrier or without a barrier, both decreased oxygen and pH by the same amount. This implies that the mussels are responding the same way to the physical and chemical presence of a predator. Fish and other animals have been shown to change their behaviour when they can sense a predator, so these results are not that surprising but are still pretty interesting to see!

A rainy day of predator prey tide pool sampling

I still have a lot of data and I’d like to play around with it a little more, and I’d like to clean up my paper a little, but over the last couple months I really improved my skills in the whole scientific process. I learned so much about experimental design, reading scientific papers, applying for permits, using various equipment and data management and analysis. Nothing in school can ever prepare you for working with thousands of data points, my organizational excel and R skills have improved so drastically over the last few weeks that I am finally understanding statistical analysis used in papers I am reading.

I learned so much this summer, and I’m excited to apply my new research knowledge to another project this fall!