Backyard Brains welcomes 2019 University of Santiago interns

Backyard Brains is now in its second year of interns from the University of Santiago de Chile (affectionately called Usach). Last year we had a project recording the ganglia of snails – and this we will continue our voyage in the world of invertebrates with an old favorite and a new favorite. Cockroaches and Clams.

The ElectrocardioCLAM

Hi, my name is Eduardo Isla, and I am in my final year as a student of biochemistry working at both USACH and UChile (Universidad de Chile). I am completing my undergraduate thesis right now as well as working for two months at the Backyard Brains Chile office. My thesis is in a quite different area (virology) working on epitranscriptomics of HIV-2. In my spare time I like to play MMORPG games as well as explore outdoor photography. 

A lot of high school students like Backyard Brains’ Neuropharmacology experiment, as you can indirectly study synaptic activity in crickets, but it is time for an upgrade. First, a little bit about neurotransmitters

Did you know that neurotransmitters were discovered working on frog hearts? Everything began in 1921, when an Austrian scientist named Otto Loewi discovered the first neurotransmitter. In his experiment, he used two frog hearts. Heart 1 was still connected to the vagus nerve, and Heart 1 was placed in a chamber that was filled with Ringers solution. This chamber was connected to a second chamber that contained Heart 2. So, fluid from chamber 1 could flow into chamber 2. Electrical stimulation of the vagus nerve (which was attached to Heart 1) caused Heart 1 to slow down its heart rate. Loewi observed that after a delay, Heart 2 also slowed down. From this experiment, Loewi hypothesized that electrical stimulation of the vagus nerve released a chemical into the fluid of chamber 1 that flowed into chamber 2. He called this chemical “Vagusstoff”. We now know this chemical as the neurotransmitter called acetylcholine. It is also interesting to know English scientist Henry Hallet Dale had previously isolated acetylcholine. So, they both shared the Nobel Prize in Physiology or Medicine in 1936.

For the Backyard Brains neuropharmacology upgrade I will use some Clams, yes Clams. We eat them, but they are animals too, and believe or not they have a heart. So, I’m trying to adapt Loewi’s experiments into much simpler animals, easier to access/buy and less traumatic to work on. These experiments consist of using the Backyard Brains Heart and Brain SpikerBox to make recordings of electrocardiograms on clam hearts and the effects of different compounds. For this, first of all I need to record an electrocardiogram of the heart of clams. Afterwards, I will then treat them with various compounds to attempt to alter the heart rate. I also need to ensure that the record that we actually obtain is EKG and not movement of the electrodes. In these first few days I am trying to optimize the preparation, opening the clam while keeping the cardiovascular system intact.

The Quantified RoboRoach

Hi, my name is Claudio Moreno, and I am also in my final year working at USach in the lab of Neuroscience. I am doing my thesis in ion channel physiology, studying TRPM8 channels. TRP channels are the body’s temperature transducers, and TRPM8 is responsible for the feeling of  coldness. In Chile we get cranky when the temperature gets below 40 degrees Fahrenheit (I know, nothing like Michigan), and we can thank our TRPM8 channels for that.

When not studying TRPM8 channels I enjoy going playing video games and guitar. I’ve being playing guitar for 13 years and it has been one of the best things I have done to get my mind distracted during moments of high stress. I also like to travel to different cities and countries. I have travelled to many cities here on Chile (my country), and it’s really beautiful, so if you have an opportunity to come here, trust me, you won’t regret it.

The RoboRoach is one of Backyard Brains’ original inventions where you can control cockroach locomotion by electrically stimulating the antenna, but, strangely, Backyard Brains has never systematically measured the adaptation rate. Until now. To do this experiment we are doing a bunch of RoboRoach surgeries, so we can have a high enough sample size to compare sensory adaptation rate.

Once a RoboRoach is recovered from the surgery, we can start to see if we can control our RoboRoach and measure turning responses with time! And for that we built a lego tower, which has a floating ball the cockroach walks on, along with an optical mouse to read the floating ball’s movements. When the antenna neurons are activated with electrical stimuli, they will send this electrical information (called spikes) to the cockroach brain, stimulating the neural-motor reactions. The cockroach will change direction, and we can measure this change.

This contraption allows us to measure precisely the turning of the cockroach in response to stimulation of the antenna, so we can see how it adapts over time. Now it is time to collect the data and finally say with some degree of certainty the adaptation rates across cockroaches. Like all kinds of animals with a central neural system, you can expect that neurons can adapt to a stimulus (which Backyard Brains has anecdotally observed many times in the RoboRoach). Now it is time to quantify! I am starting to get skilled at the surgery, and below you can see my first successful antenna nerve recording!

Getting Started with the Muscle SpikerShield Pro

Hey everyone! I’m Pablo, a junior from Nido de Aguilas High School in Santiago, Chile. In my free time, I like to doodle and run.

My project is a multi-channel version of the experiment that my colleague and friend Cristian developed: it consists of using the SpikerShield Pro’s ability to get data from multiple channels to create a musical instrument. In this instrument, flexing a muscle is analogous to playing a key in a keyboard. Obviously, the amount of channels limits this keyboard to six notes, but according to my limited musical knowledge, this is enough to create a coherent melody. In fact, the Arduino program currently has four settings which can be accessed using the red button: Mary Had a Little Lamb, Frere Jacques, major pentatonic scale and the minor blues scale. All the notes are in arrays with six elements, each corresponding to a channel. To add more possibilities, holding the white button in the board makes all the notes in the current setting one octave higher. You can download my code here.

The “loop” part of the code works by reading the red button, white button, and all six channels. First, it decides which set of notes to use for that iteration of the loop, which is controlled by the red button, then it checks if the white button has been clicked, which affects the pitch of the final note it plays. The last step is to decide which tone to actually play, which the code does by selecting the largest reading of all the muscles. Now, you might be thinking that playing music with two vastly different muscles, say your forehead and your forearm, will never work because a signal from the forearm will always be bigger than the signal of even the strongest forehead flex. However, the SpikerShield Pro can control the gain from each individual channel (the little white knobs) which can make a channel more or less sensitive to a signal, so every muscle has a fair chance of being played.

One challenge I faced when I developed this project is the lack of documentation of this particular product for novice programmers. Most of the times I’ve played around with an Arduino, I’ve relied extensively on the built-in tutorials and online resources, but this time I only had the board’s schematic, which at first glance bears a closer resemblance to black spaghetti than a discernible circuit and the default program which sends the signals from the board to Spike Recorder. Running the aforementioned program was not a challenge, but reading the code, not being fully aware of what it was, proved to be confusing. I only started making progress once Tim Marzullo showed me an outdated sketch meant for this shield. However, with this project in the open, I doubt this is a problem other users will face; the heart of the code — presenting the sensor’s readings as an array and mapping those raw values to a usable scale — can be used for most projects.

The second biggest challenge was and still is, my absolute ignorance about music theory. I never learned to play an instrument, and the most complicated song I managed to play is “Hot Crossed Buns”, though that is probably a skill I’ve lost. I’ve always enjoyed music, but much like hot dogs, I preferred to enjoy the finished product rather than learning how it is made. After adding the melody of Mary Had a Little Lamb and Frere Jacques, I did not know what other songs to add. After a fair amount of research, I came upon pentatonic scales, which are comprised of five notes.

Though the musical aspect is worth examining, what attracted me more is its role in many musical traditions, ranging from the ancient Greeks to the Andes. During the 19th century, composers like Debussy used the simplicity of the scale to create a folksy in their composition, resulting in music like La fille aux cheveux de lin. Later on, rock, blues, and jazz artists adopted the scale as a tool for their respective styles of improvisation. I think this is the area where my particular instrument shows the most potential because it is only capable of playing one note at a time, and also because flexing muscles to create sound is very intuitive. However, this is a hypothesis I will let the reader confirm.

Backyard Brains High School Student Personal Projects

Backyard Brains is live from inside the classroom of Colegio Alberto Blest Gana in Santiago to present you 5 group projects brought to life by creative and passionate students. and the methodology we used to choose the projects. This high school has been like a second lab for Backyard Brains, where the students beta test our hardware prototypes and invent new classroom exercises. This year was the first year where the classroom made independent group projects, with a class size of about 15 students, ranging from 7th grade to high school seniors.  

It can be a challenge to involve students in independent projects when it is their first time,  so it is important to let the students conceive their own project ideas from the beginning. The ideas need to come from inspiration, not mandated from above. That’s why, to help out in the creative process, we devised an interview that would work like a conversation, where the student can start to imagine what they would like to build, or what problem they would like to solve. You can use this pdf as a guide

To guide some shy students that weren’t sure what they wanted to build, we suggested projects that the students could modify so that they could begin to feel that the idea we gave them is also their own.  We then place the people that had similar ideas and interests into the same group. As a suggestion, if you are working with students with very different ages, it is important to mix it up a little in this area: always have a mix of older students with younger students.

The interview resulted in 5 projects:

1. The Electrocardiogram of the Clam. 

This project was chosen by students that had an interest in animal physiological systems. Most of the students didn’t know before this experiment that a clam has a heart, because when you open it, the clam’s organs just look like a blob. It isn’t easy to notice distinct anatomical parts that look so different from the organs of vertebrates. After finding the heart, a challenge for students (and even for us teachers), we needed to make sure the heart was still moving and contracting. Unlike a vertebrate heart, the beat is not like a regular clock, it can stop a long time and then restart again.

When we saw a heart beat, we placed one red signal electrode in the atrium and the other in the ventricle. The third electrode (ground-black) was placed farther away the clam. These three electrodes were connected to the Backyard Brains Heart and Brain SpikerBox to make the recordings.

And glory of glories, we had success!

However, we don’t know if what the students recorded is in fact an artifact arising from relative movement of the recording electrodes, giving rise to a baseline shift that mimics in some ways the P and QRS features of a typical ECG. Our next step is to manually deform the heart to see if similar features arise. If not, then perhaps we observed a real biologically-generated clam electrocardiogram. You can download our recording here. 

2. Muscle-Keyboard-Interface.

In this project, chosen by one gamer and talented student, he used the electricity generated by voluntary muscle contraction to take over the keyboard of a computer.

 The appeal of this project is that muscle interfaces work like a charm, a microcontroller is easy to program, and it’s all very low cost. To accomplish this, we decided to control a very easy and accessible video game with the electrical impulses of the muscles, using our Muscle SpikerShield combined with the Arduino Leonardo. The advantage of an Arduino Leonardo is a computer can recognize the Leonardo as a keyboard input. The video game he chose was Google Chrome’s offline dinosaur video game: you can play it fine with only one key on the keyboard (the space bar makes the dinosaur jump…though pressing the down arrow key also makes the dinosaur duck). It’s fun, and you don’t need internet or any specialized gamer hardware to run it. You can download the code here.

3. Cockroach Labyrinth.

The idea of this project was to build a labyrinth to learn about cockroach behavior and food preferences. Could they learn the route to reach a preferred food source faster over time, say, a banana slice instead of a potato slice?

Unfortunately, this project was done in the open air during winter, with a temperature of 40-50 degrees Fahrenheit, a temperature at which cockroaches are not that hungry and not highly active, so using food as an incentive didn’t work. Also, another problem  was that the cockroaches were able to climb the walls of the labyrinth. Nevertheless, the students got over these obstacles and had success with one experiment:  they placed a lid on half of the labyrinth to make that section dark, and left the other half uncovered, so light could get in. They released the cockroaches, and after one minute, all of the three cockroaches were in the dark side, just like Anakin Skywalker.  A small sample size, but convincing evidence of what was suspected all along: cockroaches prefer dark spaces.

4. The Polygraph Lie Detector.

This project was from a group of students interested in the physiology of lying. At Backyard Brains we love to extract and read physiological signals, and as the traditional polygraph measures skin conductance, respiration, blood pressure, and heart rate, building a DIY polygraph is right in our wheelhouse. To keep it simple in the beginning, together with the students we decided to focus on skin conductance alone, something we have been asked to study before many times.

        When someone lies, there is the hypothesis that the persons subtly increases sweating. Since sweat is salty water, and salty water is much more conductive than dry skin, we should be able to measure a decrease in skin resistance across the palms when a person is lying.

The first experiment this group did was very simple. They checked the skin resistance using a multimeter and patch electrodes across our inner palms before and after running on the treadmill The results were the following:

Before running 5 kilometers

97  Kiloohms 

After running 5 kilometers (24 minutes)

12 Kiloohms

The results are crystal clear, a body covered in sweat is much less resistant to electrical current than dry skin.

The next step was to find a way to graph skin resistance in real time, and test it using lies instead of jogging. The students made a simple circuit in Arduino where the grey cables go from 5 V input to analog 0 in arduino, buuuutttt, the cable is cut and the person must grab each end of the cut cable with each hand. They then used the sample code “graph” which graphs the voltage value of the analog input, which, of course, will change depending on the resistance of the skin across the student’s hands.

When they tested using lies, there was no significant change in the value of the skin resistance, as the effect is simply too subtle, if it even exists at all, to measure using our equipment. Although the final test wasn’t successful, at least the students tore down the myth that galvanic skin response can detect lies by itself. That’s why complete polygraph machines also measures respiration, blood pressure and heart rate, and the combination of all these elements supposedly makes the polygraph a more reliable tool for detecting lies. If we continue this project in the future, we will look into integrating these other physiological signals in addition to skin conductance.

5. Muscle Electrophysiology in soccer.

 This group of students was interested in how electromyography changes when making different strength kicks in soccer: kicks made for small distances, like close passes, and kicks made for big distances, like aiming for the goal or to a player that’s far away. To do this, the group placed two signal electrodes in the abductor muscle of the quadriceps, and the ground on the knee. The students then placed masking tape in the floor, marking the distance in meters, and the subject kicked the soccer ball to a friend waiting at the various meter marks.

The different distances they used were 5 meters (16.4 feet), 3 meters (32.8 feet), 15 meters (49.2 feet), 20 meters (65.5 feet), 25 meters (82 feet), 30 meters (98.5 feet), and 35 meters (114.8 feet). Below is a sample of the data they recollected:

As you can see quite nicely, the amplitude of the EMG of the quadriceps increases as the soccer ball kicks become more forceful. This was our hypothesis, that as you recruit more and more muscle fibers during a movement, the EMG signal amplitude will increase due to the higher number of action potentials generated and the superposition that results.

This experiment on the physiology of sports was very fun for the students. They also tried baseball pitches, but the rapid “snap-back” movement of the arm would always cause the cables attached to the triceps to come flying off. With basketball, they did not notice a dramatic difference between two point and three point shots. So, as the students were happy to report, for now, soccer is the best for studying the physiology of sports using our equipment! We will keep trying with baseball for all the Detroit Tigers fans out there.

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These final projects were worked on once a week, for 1.5 hours, for 2.5 months, and on October 30th, the students presented their results to the community to much success. The sports physiology and the clam EKG experiment will be the first to be transformed into formal Backyard Brains experiments on our webpage, so stay tuned! If you are interested to having the students in your school working on personal group projects, feel free to contact us, and we investigate the world together!