Getting crafty in research

One of the things I love about my field of research is the opportunity to build things. Like a child building a rocket ship out of toilet paper rolls, I often don’t have the perfect materials or tools for the job so I have to improvise. When you are in the field and have a strict deadline and no nearby shops, you discover that you can build almost anything with some cable ties and other peoples garbage. In my recent project I had access to a few more gadgets than usual and have come up with something a bit more sophisticated.

The goal was to set up an experiment where I would train fish to swim down a corridor and go through a series of sliding guillotine doors. I had to make sure some doors moved at the same time and I was worried that me opening and closing doors would disrupt the behaviour of the fish. What I needed were some automated sliding doors.

Finished product first…

The first step was to come up with the best way to move the doors up and down. Should I use a pulley system? A series of gears? My choices were limited by the actual placement of the motors which had to be above the experimental aquarium and by the distance I needed the doors to move. After a few hours of online research I decided on using a rack and pinion system attached to a servo motor.

Physically making the custom gears for a rack and pinion would be pretty time consuming but I have a 3D printer in the lab which allows me to design and print my own creations in a matter of hours. The gears took a few tries to get right as the size of the teeth and the wheel had to be just right. I ended up finding an online calculator for rack and pinion gears which was a lifesaver. I made 3D drawings using Autocad Inventor. If you are a student, you may be able to get your hands on a free educational license for this software. Servo motor

With the design for the gears sorted, I then needed a motor to turn the gears. I used the Parallax Servo motor (https://www.parallax.com/product/900-00008) as this type of motor allows you to move the motor forwards and backwards, resulting in the up and down movement of the doors. This motor is also fairly cheap and can be easily controlled with an Arduino.

The motor arms had to attach to the pinion. Luckily for me, there was a design on Github for attaching something to the arms of this particular motor which saved me a lot of time. A housing was also made to hold the servo in place.

The motors and gears were then mounted above the tanks to line up with each door.

2017-09-11 15.28.37

Motors and rack and pinion gears mounted above the sliding doors

The next step was to attach the gears to the sliding doors. A very large aquarium was used for this project and I designed walls with sliding guillotine doors to fit inside. All the interior doors and walls were made with PVC and glued together. While I often have to make these structures myself, I was lucky enough to have the Oxford University workshop make this particular setup. I used cut aluminum rods to connect the doors to the the 3D printed gears.

The next task was to get the doors moving at the push of a button. For this, I used an Arduino Uno to send the pulses required to rotate the servo motor. The power output on one of these boards is limited, which would be fine if you are only using it to run one servo motor, but five motors require their own power adapter. As I wanted the doors to move up and down, I bought an on-off-on switch from RS components. I also bought a box to hide all the messy wiring.

2017-09-11 15.28.37-4
Electronics box with control buttons

My control panel had 4 buttons and had to move the doors up and down. After some more digging online (thank you Google!), I found a way to program the Arduino to run multiple push buttons on one circuit. The circuit board was then made and wires were run from the box to the servos.

Finally the doors were ready to try…

Although a lot of mistakes were made along the way, this ended up being one of the few projects where everything worked on the first try!

How do fish make a decision when faced with conflicting signals?

My newest paper called ‘Fish use colour to learn compound visual stimuli‘ has been published in the journal Animal Behaviour.

The aim of this work was to understand how fish respond when two pieces of visual information that they previously learned is conflicting. For example, there is a psychology experiment called the Stroop Test in which observers are presented with the name of a colour printed in either the same colour or a different colour and subjects are asked to read the word aloud. You can try this yourself with the following words:

RED BLACK BLUE GREEN

When people are asked to read the words composed of incompatible colours (e.g. BLACKBLUE) there is little change in how quickly they can answer. However, when people are asked to say the colour when the word is incompatible, they take much longer to answer (Stroop 1953, Macloud 1991). This suggests that when two pieces of visual information are in conflict, we rely on some information more than others. In this case, people rely on the word information more than the colour information, at least in this particular experiment. Stroop suggested that this occurred because subjects have more practice with one task (i.e. reading words) than the other (i.e. identifying colours).

We wondered if fish also pay more attention to one type of information than another. To test this, we used Picasso triggerfish (Rhinecanthus aculeatus) and trained them to discriminate between two circles that had both pattern (stripes vs cross) and colour (blue vs yellow) information.

Newport et al 2017 figure

We then changed the circles so that the patterns and colours were switched and therefore in conflict…

Newport et al 2017 figure 2

What we found is that the fish trained to choose the blue stripes, chose the blue cross when we changed the circles. We saw a similar pattern when the fish were trained to yellow crosses as they chose yellow stripes when we tested them.

This showed that the fish made their decision based on the colour of the circle and not the pattern.

Experiments like this are important because they help us understand what fish can see and what they think about the things that they see. This tells us a lot about how fish brains work and how their brains are different from the human brain. In this case, we learned that, just like humans, the fish brain can process colour and pattern information separately. It was equally possible that the fish wouldn’t be able to make a decision between the new circles because they weren’t identical to what the fish had previously learned. So even though the fish brain is a lot smaller than the human one, and made up of different structures, in this case, the two brains solved a problem the same way.

This experiment also shows us how important colour is to this species of fish. Picasso triggerfish live on extremely colourful coral reefs  and our experiments show that the fish likely use this colour information to tell objects apart.

Archerfish can discriminate human faces!

In June 2016 I published a paper showing that archerfish are able to discriminate between two pictures of human faces. They were then able to discriminate the learned face from a series of faces they had not seen before. This video summarizes the experiment:

This is a very exciting finding as human facial recognition is a really complicated task even for computers. Facial recognition is difficult because all faces have the same general components (e.g. two eyes, a nose and a mouth) so you have to discriminate them based on subtle cues (e.g. the shape of the eye, the distance from the nose to the mouth). Considering how similar features can be amongst family members, these differences can be extremely subtle. The features themselves are also changing constantly when we make different expressions. In addition, the orientation of the face and lighting can make a huge difference in what sort of information is available to the observer.

In my experiment, the fish were only presented with a frontal image of a human face under standard lighting conditions. This is a long way from full human facial recognition, however, it shows that fish are able to discriminate very complicated visual images and I will be continuing to test the fish under more difficult conditions in future experiments.

This paper is open access, so you can read it here for free. There has also been a lot of media coverage including The Washington Post, BBC, Livescience, Motherboard, The Guardian, Wired, CBC, Vox, The Huffington Post, Business Insider UK, Phys.org, Big Think, Mental Floss, IFL Science, CNN, Smithsonian, Gizmodo, and many more all around the world (it was apparently picked up by 175 news outlets). It even made it into the BBC’s ‘100 things we didn’t know last year list‘ at #15.

You can also see interviews I gave to Reuters, Quirks and Quarks and Deep Look on KQED.

The 3 second memory

Now that the fish have settled in, it is time to start putting them to work. In order to understand more about how the brains of fish work, I study their behaviour. While some researchers studying animal behaviour observe animals acting naturally in the wild, I run experiments in the lab designed to determine if fish can perform specific tasks.Whether or not they can perform a specific tasks can tell me important information about how their brains work.

A really simple example would be if we asked the question: do fish see colour? To answer this, we can present the fish with two identical objects, except that one is blue and the other is red. We can train the fish to select one of the objects, either the red or blue. If they can learn to select a particular object then we know the fish are able to see two colours. Now there is a lot more to testing colour vision, but this is the general idea of how I use behavioural experiments to answer complex questions.

I mentioned that I train fish… When I say this, most people give me a blank look and then ask: ‘but don’t fish have a 3 second memory?’ So before I explain how this is done, I need to pause and just clear up a little myth about fish.

FISH DO NOT HAVE A 3 SECOND MEMORY!!!

Ok now that we have that out of the way… To train fish, I use operant conditioning. Operant conditioning means that I use a positive reward to reinforce a behaviour that the fish would naturally do. In this case, the fish will naturally bite at things that are put in their tank. When they bite at the item I want, I reward the fish with a piece of food. This form of training only works if the fish are interested in performing the task. Luckily for me, triggerfish are curious by nature and love to bite at whatever I put in their tanks. And of course they love food!

At the beginning of this video, a fish is behind a white wall with a sliding door. When I open the door, the fish swims through. There they can see another white board with four circles on it. These circles are printed pieces of paper that are laminated. I stick them to the board with velcro dots.

You can then see the fish take a bite at the darkest one. This is the correct response from the fish, and I therefore feed the fish using forceps (because they bite!). My favorite bit is how the fish then swims back through the door to wait to start the process all over again.

I love this door that I had made as it provides a clear indicator to the fish of when a trial begins, and it protects me from being bitten when I put the stimuli board in the tank. However sometimes the fish get impatient with me and start spitting water at me out of the tank. Such demanding little fishies!

The triggers have arrived!

2015-12-10 10.23.08.jpg

It has taken a couple of months to get my new aquarium system ready for experiments and I am so excited that I finally have the fish I will be using for actual experiments.

For my research, I am using Picasso triggerfish (Rhinecanthus aculeatus) as my study species. These beautiful fish have so much personality. They are curious and expressive and will pretty much bite at anything. When working with them, you have to be careful not to leave your hand in their tank or you will get a surprising nip taken out of you!

You can see in my video below that they will attack things that come too close to the glass of their tanks as well (in this case it is my finger).

This species is found on the Great Barrier Reef in Australia and on coral reefs around the world. They are omnivorous and territorial. They spend much of their day swimming around their home region taking exploratory bites out of pretty much everything

photo-01-10-2016-7-51-58-pm   photo-01-10-2016-7-52-04-pm

In their tanks at the lab, the fish seem to enjoy rearranging the gravel by picking it up with their mouths and dumping it elsewhere.

 

The set-up

One of my favorite parts of research is the many opportunities I get to build things. Given a handful of cable ties, some duct tape and a saw you would be surprised what you can pull together.

Upon starting my new position as a research fellow at the University of Oxford, the first thing I had to do was build myself an aquarium system. I have used several different systems throughout my research career and had a good idea of what I wanted and what would suit my research. It was pretty exciting to be able to build a whole system just for me!

I decided to build two flow-through aquarium systems. A flow-through system means that all the tanks are connected by pipes and therefore the same water flows through all the tanks. First, I had to design the system and source all the equipment (tanks, pumps, lights, pipes, glue, you name it) which took quite a long time. Then came time to build it…

2015-11-03 16.53.50.jpg   2015-10-28 19.40.32.jpg

The laboratory space I was given already had racks for tanks so I needed to add tanks and plumbing. Getting all the pipes cut and in place so that water can flow through the system took a lot of time and effort. As I was several months pregnant at the time, my husband came in to help me do some of the heavy lifting.

2015-11-11 14.38.46.jpg

Once the plumbing was all finished, water was added and we watched for leaks. Unfortunately we had a leak in the bottom sump system where the water gets filtered! Luckily it was nothing one or two tubes of silicon couldn’t fix.

2015-10-28 20.48.10.jpg

In this type of aquarium system, the filtration happens in the bottom sump compartment. My system has a biofilter, a protein skimmer, and some algae.

2015-11-14 18.16.40.jpg

After several weeks, we were all finished and could finally add some fish!

Let’s get started

As this is my first blog post, I have decided to use it to catch everyone up on how I got to where I currently am.

I began my career in marine biology in grade school. In grade 4 we had an interactive project that lasted several months, where we learned all about the oceans. I loved the idea that researchers were underwater explorers and I (wrongfully) believed that every single day for them was a big adventure. Despite the fact that I lived in a landlocked city and didn’t actually see the ocean until I was about 15, my interest was piqued. In high school I attended a week-long marine biology field trip in St Andrews, New Brunswick. For a week, we got up in the early morning to collect samples, spent the remainder of the day in a wet lab learning about what we had collected and wrote up reports in the evening. By the end of the week, I had learned a lot,  was tired, and had pneumonia. It was at this point  that I decided to study marine biology in university. I also decided to never study marine biology in such a cold location!

I completed my undergraduate degree at Dalhousie University on the east coast of Canada. In my final year, I conducted a research project on fluorescence in phytoplankton. I chose this project because I thought things that glowed were pretty. That perhaps sounds like a silly reason, but I am still fascinated by the beauty of nature and how these spectacular sights have evolved. This project was hard and I don’t think I even understood my research question until about 3/4 of the way through! I made a lot of mistakes and really only succeeded due to the help of two female researchers in the lab. But boy did I learn a lot!! These woman taught me how to do basic programming in Matlab, how to order equipment from a catalog, how to remove adjectives from scientific writing… Actually this would be quite a list if I enumerated it all. They taught me how to think like a scientist but also the practical administrative skills as well.

After university I took a gap year and moved to London, England, working in the finance industry. After a year, I decided to get back into marine biology, so I booked a flight for Australia! I didn’t have any specific plans or a job lined up but when I arrived in Brisbane, I approached Dr Alexandra Grutter at the University of Queensland, as I was interested in her work on coral reef ecology. I told her I was willing to do anything required and would even work for free while I learned and so she accepted me into her lab.

For the next couple of years I worked and volunteered with a number of different lab groups around the university. I studied marine parasites, the visual system of fish and larval reef fish. I conducted research in both the laboratory and the field. I was lucky enough to work at the Lizard Island Research Station and experience diving on the Great Barrier Reef. I also put my database experience (from my time working in finance) to work in a landscape ecology research group, inputting  a huge amount of data on birds and tree species.

In 2011 I received a PhD scholarship at the University of Queensland and began working with Dr Ulrike Siebeck and Dr Guy Wallis. Briefly, the aim of my project was to determine how archerfish see 3D objects so that we could learn about how their brain processes visual signals. I loved my PhD. I loved the new discoveries, coming up with new hypotheses to test, trying to apply new technology to my experiments, applying for and especially receiving grants, and collaborating, or at least discussing ideas, with researchers in very different fields. During my PhD I was also involved in science outreach. I wrote some magazine articles on my own, answered the questions of journalists and was a science ambassador with the Wonder of Science program.

In the final year of my PhD, I applied for a Marie Curie Research Fellowship with the University of Oxford. In 2015, I moved from Australia to Oxford and began a whole new stage of my career.