Tonight’s Inspiration for an Atlanta Do-It-Yourself (DIY) Neuroscience Program


“Intelligence arises as the brain reasons, plans, and solves problems. Cognitive processing requires integrating information from multiple parts of the brain. Ideas, actions, and feelings can be internally generated in the absence of external stimuli. Language and communication provide us with a way to examine ourselves, our behavior and our own brain function.”

Night Science inspiration for a new high school after school neuroscience curriculum that I will turn into a book! I just had an idea that at the moment seems brilliant. Alas, every science idea at 2:30 am seems brilliant.  Here it goes, my first real blog post in about a year on this seriously modified personal blog.  This year, my job is to develop a curriculum for science, technology, engineering, and mathematics (STEM) high school after school education. So far, I have been working on developing some simple experiments for protein folding in the computer which would answer “The electrical activity of the nervous system is generated by ionic gradients and movement of ions through tightly controlled membrane proteins called ion channels and receptors,” a water quality laboratory which would answer the same principle if you consider that molecules in the environment influence neural activity (e.g. consider the recent disaster in Syria with sarin nerve agents, the two paintings are from here and to me symbolize the suffering of Damascus, Syria in the current war.  Perhaps educating students in neuroscience will inspire peace there):


1185025_10151571736931401_826935498_n 1236319_10151571736976401_468745980_n

and an electronics laboratory with a computer-electronics microchip (Arduino) that can be used to illustrate “Information goes from one neuron to the next neuron at synapses where the electrical information coming down the axon changes to chemical information to cross the gap between them. Then dendrites of the next neuron taste the chemicals and turn the information back into electrical information.” and “The electrical information going from the dendrites to the cell body and then the axon is reliable. The chemical information crossing synapses can be variable. Synapses can change and get stronger with learning or weaker if not used. As we learn, we strengthen the chemical connections between neurons so they learn to work together to produce the behaviors we want. Continuously challenging the brain with physical and mental activity helps maintain its structure and function.”

I want to incorporate a laboratory that uses a miniature electrophysiology setup, one that includes a heart rate monitor, and one that uses a miniature brainwave scanner. The idea is to synthesize all of these laboratories into one giant year long after school curriculum for neuroscience. Each activity will symbolize one area of neuroscience. For example, the worm can be studied with the miniature electrophysiological setup to study a nerve impulse rate along an a nerve cell.  This experiment would illustrate, “Neurons connect to form pathways or circuits to bring information from one part of the body or brain to another part. Systems within the nervous system consist of lots of neurons connected in parallel conveying information necessary for executing a specific behavior, e.g. spatial localization, reading, motor activities, decision making, etc.”  Once we teach about the electric aspect of the human body in understanding the natural nervous system, we can teach about artificial intelligence and life with robotics.  The culmination of the curriculum would be assembling a robotics laboratory.  That way the students could grasp electronics and movement of bodies as well as the concept of sensory input.

I will write the book as I apply for high school teaching jobs in private schools and apply to get a master’s of education. I will build a big blog documenting the progress on the curriculum and update the world on my DIY neuroscience after school program! A great application of my Ph.D. for a good cause, enhancing high schoolers’ passion for science and math!  This is what I did for my Ph.D..  Imagine defining distances by hand in this molecule and you can see what I did for my Ph.D. at U.C. Berkeley.  That is protein NMR in a nutshell, in other words it is tedious but fun:


I am working for the International Rescue Committee (IRC) and AmeriCorps this year. Imagine if on Facebook there were a donation advertisement for a high school DIY neuroscience curriculum from IRC like this page from the IRC Facebook newsfeed. I wonder how much money could be raised for a high school program like the Youth Futures program that is working with high school youth at Clarkston High School.  I hope to work with the IRC Youth Futures team to develop a way to create a financially stable DIY neuroscience program for the IRC.  The idea is to fund the program with donations.  Let’s get Clarkston HIgh Schoolers manipulating proteins, recording neurons, and learning about environmental contributors to human brain health.  All in the name of understanding the human brain.

To this end, this morning I started to look for resources online that might be relevant.  I searched Google for “high school neuroscience.”  I found a perfect site that currently does not appear to be working.  Perhaps the site will come back up soon.   It has a perfect statement for learning about humanity and behavior.  “Altered brains produce altered behaviors. Mental illness occurs when brains do not function properly due to injury, stress, genetic abnormalities, aging or infection. Damage to the front of the head can impair decision making or alter personality. Addiction can be viewed as a disease of the decision making system just as Alzheimer’s disease is a disease of learning and memory. Some injuries harm nerve cells, but the brain often recovers from stress, damage, or disease.”  To this end, the heart rate monitor experiment is very interesting.  I would like to include the human muscle EMG and the brainwave detector to record phenomena like a bad dream.  Imagine being able to read the mind of Edvard Munch when he painted The Scream (Image from this Wikipedia page)!  With modern technology we can do something similar, read on into this blog learn how.  This will be a reoccurring theme in the entries into this blog, my experiences trying to record brain activity during interesting experiences in various ways.  Such experiments and experiences might illustrate the following principle, “Nerves in the internal organs provide the brain with information about the body states generating our conscious perception of emotions. These feelings give an emotional stamp to all activities, necessary for events and ideas to become memorable. Feelings provide value information that is necessary for decision making. Facial expressions provide social cues to understand other peoples feelings (or body states), information that is necessary for us to interact socially.”


Like Freud, we could study our bad dreams and gain insight into cures for various factors that lead to sadness and suffering.  Thus, perhaps we could reduce human suffering.  In this heart rate recording I recorded my heart rate as a function of a nightmare during what was ordinarily rest.  On October 10, 2012, at approximately 6:30 in the recording the climax of my nightmare occurred leading to a massive heart rate spike of 183 beats per minute (bpm).  These data illustrate the following principle of the brain interacting with the heart, “Most of the body’s major homeostatic responses involve a nervous system component. The nervous system controls or interacts with every other organ system and creates the feedback pathways necessary for homeostasis.”


After the nightmare I could not sleep for a while so I went for a walk.  On the walk, I went by a church and looked at the Christian Cross.  During the dream/nightmare I remember that I shared Aristotle’s teachings with a man from the West Bank, Wittgenstein’s teachings with a military chaplain, and I gave James Cone’s text to a kind women.  A strange combination that only seems only natural to dream about at where I was at the time, Princeton Theological Seminary.  Somehow, during the experience at seminary my brain combined the recent events in the news, the philosophical and theological learnings of seminary, and my own nature into a big nightmare.  It is actually quite fortunate that I was recording my heart rate that night because it gave me extremely deep insight into my own brain.  That is the power of Do-It-Yourself (DIY) neuroscience.  It enables us to gain insight into ourselves.  We can encounter our own experiences during waking and sleeping hours and gain scientific and mathematical understanding of them.  Such a DIY neuroscience approach would be interesting to use to do a systematic analysis of dreams, a careful analysis of peoples’ responses to spectacles like movies and shows (e.g. imagine wearing a heart rate monitor, a brainwave detector, and a muscle EMG recorder in a good haunted house on Halloween), and individual variation in responses to educational experiences like working in the high school classroom.

For example, it would be interesting to study the dream responses of people to commonly prescribed neuropsychological remedies like Zyprexa.  This medication is commonly prescribed for schizophrenia and extreme forms of bipolar disorder.  I am grateful to my friend for providing me one of her tablets for the image below.  It would be interesting to obtain an electrical recording of a cockroach neuron recording on and off Zyprexa.  With this miniature electrophysiology setup such an experiment is possible.  Do cockroaches and other arthropods respond to commonly prescribed neuropsychological pharmacophores?  Can I use worms to do the same experiment?  In all these experiments we would be studying neural synapses.  Classic experiments were done at the giant squid axon.  This experiment would illustrate the following principle, “Illegal and prescription drugs mimic, prevent or interfere with the activity of neurotransmitters at synapses.”


MS Word files for laboratory ideas so far along with their text:

1.  11202013_folditdemoidea.docx

Student biochemistry laboratory using Foldit! Software supplemented by in class demonstrations

Purpose:  To enrich students’ understanding of important chemistry for life, the basics of protein structure and function.

Target audience:  The activities mentioned in this laboratory proposal can be broken up into two distinct segments for specific target groups of students.  First, students who are in the Youth Futures afterschool program that do not have homework on a particular given day can be encouraged to play the game Foldit!  An advantage of the computer activity is that the game can be played at any times and does not require advanced preparation or the long time required for in class wet laboratories.  Second, all the students in a given classroom can be given a one day (~1-2 hour) wet laboratory activity series as described below.  In this context, the activity assumes a more traditional pedagogical STEM (Science, technology, engineering, and mathematics) demonstration outreach approach.

Overview of activity:  In this activity, each student will play an educational video game called Foldit! ( to learn the basics of how proteins fold into compact three dimensional shapes that carry out specific functions in the chemistry of life.  The activity is well suited to students of high school age because it does not assume advanced knowledge of science.  Rather, the program walks the students through visually appealing cartoon-like representations of important chemical principles of protein folding to introduce students to fundamental concepts as part of a game.  At the beginning of the game, the students are led through a series of tutorials of increasing difficulty.  The students are led to learn about the basics of protein structure and function by practice based activities in the computer game.  The program represents a significant advance in pedagogical approaches to teaching because it introduces concepts visually and naturally in the context of a fun computer based activity.  Intermediate to advanced players of the game can participate in fundamental research into protein structure and function by working individually or in teams to try to solve important research problems posed by the authors of Foldit! in a competitive manner.  High scoring players can be included into actual basic research publications.  Indeed, a recent advance in HIV biochemistry has been conducted using the Foldit! software with citizen scientist players of the game.[1]  I envision the program being used in conjunction with in classroom explanations of key concepts and principles.  Simple in class laboratories could be performed to supplement the principles learned in the protein folding game.  To illustrate the fundamental principles of protein folding, three dimensional wooden puzzles can be used to abstractly represent the concepts of protein folding.  Plastic atomic models can be used to illustrate the concepts of what proteins are made of, amino acids.  Using a DIY (Do it yourself) biology laboratory science book,[2] simple experiments with proteins can be performed to teach students about the actually workings of real proteins.  To this end, we can perform simple protein isolation from meat and egg whites to demonstrate protein activity from real biological tissue.  In terms of practical engagements with students over time, the set of proposed activities can span from a series of months to a yearlong set of activities both with computers and in the laboratory and demonstration spaces.

Protocol:  Foldit! activities

  1.  The Foldit! software has 32 introductory tutorials.  The students will walk through the tutorials individually and with a science tutor.  The tutorials are arranged in a way that the game provides in program explanations of the principles of how to play the game and what are the basic concepts being taught.  Since the program does not explain all of the basic science behind what is occurring visually in the game, the science tutor will provide explanations in parallel to the in program explanations.  The first in class demonstration component of the laboratory will be the use of different kinds of three dimensional models to illustrate protein structure and function concepts that are not intuitive from the game explanations.

Real world protein modeling activities

  1.  The protein molecules found in living systems are polymers of smaller component molecules known as amino acids.  We can use plastic molecular models to introduce the students to the 20 natural amino acids and explain the different chemical properties.  These different chemical properties govern how the proteins fold up into different three dimensional shapes.  To illustrate the way that proteins fold up into compact shapes, we can use simple wooden three dimensional interlocking puzzles to show how folded three dimensional shapes form into distinct molecules.

DIY biology protein activities

  1.  Using meat and albumin proteins can be isolated using a DIY biology book based protocol2 in order to provide an introduction to real world activities of proteins.  The DIY biology book pairs with a separately sold kit ($192) that contains useful reagents for a whole series of laboratory activities that can be conducted as part of a whole year long laboratory course on biology.  The reagents from this kit are useful for many other applications beyond the protein isolation and activity laboratory.  In the meat experiment the enzyme peroxidase will be isolated from meat blood and used to explore how the enzyme breaks down hydrogen peroxide.  The detailed protocol for the peroxidase isolation from meat blood can be found in the DIY biology book.2  In addition to work with peroxidase, the protein albumin can be isolate from eggs according to a protocol in the DIY biology book2 to explore how certain types of chemicals can be used to denature enzymes.  One of the principles that connect the computer based Foldit! activity and the peroxidase and denaturation experiments is that proteins are required to fold into distinct three dimensional shapes to accomplish their tasks in living organisms.   If the proteins misfold they denature and if they fold into their proper three dimensional shape they can performs useful functions in a living organism.

[1] Khatib, F. et al.  “Crystal structure of a monomeric retroviral protease solved by protein folding game players.”  Nature Structural and Molecular Biology, 2011, 18, 1175-1177.

[2] Thompson, Robert Bruce et al.  All Lab, No Lecture: Illustrated Guide to Home Biology Experiments.  (O’Reilly: Beijing, China), 2012.

2.  11212013_waterquality.docx

Watershed field trip and water quality laboratory experiments to introduce students to environmental sustainability concepts around water sources for urban areas

Purpose:  This activity has a twofold purpose that work together to introduce students to concepts in environmental sustainability and water quality preservation approaches.

Target audience:    Since this activity incorporates a field trip and subsequent laboratory investigations into collected water samples, the activity will be spread over two to three days.  The students that participate in the activity will be walked through the field portion of the activity and the laboratory portion of the activity in 2 hour afterschool periods.

Overview of activity:  Students will first be introduced to an urban watershed to showcase different types of water sources from urban areas.  Students will collect water from the watershed in different areas and analyze the water for biological and chemical quality.  A potential site to visit is the old Decatur Waterworks site in Mason Mill Park near Decatur, Georgia (

Screen Shot 2013-02-23 at 11.09.25 AM

Figure 1.  Photograph of the Decatur Waterworks from an old archive on the left and an image from GoogleEarth on the right (

Starting out as a water treatment site between ~1900-1945 A.D. for Decatur Georgia, this site fell into disrepair for many decades.  This site has recently been bioremediated into an urban park that showcases different types of water sources.  Fast flowing streams of large and small sizes, retaining ponds, and former reservoirs are present at the site and present sources of different amounts of water quality.  Students will sample the water from these different areas and investigate the water quality using a variety of biological and chemical methods in the laboratory.  The overall goal of the activity will be to identify which place in the watershed is best for using as an urban water source.  The students will analyze the pH of the water, analyze the water for basic contaminants thereby assaying the chemistry of the water, and observe the water samples under a light microscope to look for various biological organisms that may be considered as contaminants from the perspective of water purification.  The students will pool their data together into a class compendium and work together to make conclusions about the overall water quality of the area and decide which part of the watershed is the most idea source for water for an urban area.  What part of the watershed has the cleanest water from both a chemical and biological perspective?

Protocol:  Analysis of pH from water

  1.  A simple assay for the pH of the water will be conducted using pH paper.  The goal of this portion of the activity will be to place pH values on a photograph of the site to give students an idea about the overall profile of pH values on the watershed land.  The students will then be asked, “What pH is the best for treating the water from the watershed to make drinking water?”

Analyzing the water for basic contaminants and chemistry of the water

  1. The students will first collect approximately 1 gallon of water from different sites in the watershed, the same sites that pH values were collected from and allow the water to settle in a basin for a day to analyze the overall particulate matter composition of the water and to look for any films on the top of the water that suggest the presence of oil run off from roads or other urban pollution sources.  The overall water turbidity, particulate composition, and presence of any visual characteristics of the water like surface films will then be placed on the same photograph as the pH portion of the activity.  The students will then be asked the question, “What water site in the watershed has the water with the lowest turbidity, particulate composition, and surface film presence indicating the most suitable water from the watershed to make drinking water?”
  2. Using a protocol from a DIY (do it yourself) biology laboratory book,[1] students will test for the boron concentration of the water.  For this part of the experiment reagents and equipment from a separately provided kit can be used to provide students with the necessary components to perform this specialized assay.

Observing the water samples under a light microscope to look for various biological organisms that may be considered contaminants from the perspective of water purification

  1.  The students will take the water samples from the same sites in the watershed as the chemistry and pH analyses and look at the water under a light microscope (perhaps provided by the Clarkston High School biology department) to search for living organisms.  The students will use stains such as iodine to stain the water samples to look at the internal components of living organisms in the water and to aid in the discrimination of organisms that can appear almost transparent under a light microscope.  The protocol for staining with iodine and additional stains is provided by a DIY biology books2 and reagents from a separately provide kit.  Additional stains can be provided.  The students will be asked the question, “What water has the least amount of living contaminates thus making it most suitable for treatment?”

[1] Thompson, Robert Bruce et al.  All Lab, No Lecture: Illustrated Guide to Home Biology Experiments.  (O’Reilly: Beijing, China), 2012.

3.  11222013_Arduinoprogramming.docx

Electronics programming activity to teach students about how computers can be used to understand simple electronic circuits

Purpose:  This activity has the goal of utilizing an affordable microcontroller called Arduino, a simple electronic device that can be used to develop programmable electronic circuits, to teach students how computer programs can be written and utilized to control devices.

Target audience:  This activity targets students that are interested in learning about the science and mathematics of computers.  Any student can be incorporated into the activity using strategically organized groups.  Placing students with a strong aptitude in science and mathematics with students that need more help in this area can be used to spread the learning potential over an entire class of students with varied strengths.

Overview of activity:  Students in this activity will be introduced to a series of simple tutorials to teach students about the details of programming in the Arduino environment.  The basics of how to write simple programs will be taught to the students by introducing them to prewritten code obtained from the Arduino web community.  The advantage of using the Arduino platform for science outreach activities is that the platforms is open source and has a strong community of developers that provide sample code of all varying complexities.  The website contains a series of useful programs for pedagogical use.  This outreach activity will focus on helping the students grasp simple concepts in computer function.  The overall goal of the activity is to help students grasp the basics of programming logic and circuit design to help them grasp the idea that the modern world is built on a platform of electronic communication and interaction.  The curriculum seeks to give students insight into the idea that it is useful to understand the basics of computers and electronics to better understand how the electronic and digital world work.

Protocol:  The website contains information on various tutorials that can be used to guide the students in learning about the principles of electronics and simple computer programming.  Please look at each of these websites to obtain a more detailed understanding of the activity.  The core activity of the approach is the grasp the fundamental principles of how to apply a voltage to a circuit from a microcontroller, how to wire together a basic circuit, and how to implement simple programming logic into a program.  Each weblink offers a detailed protocol for the activity 1-5.  It also shows the teacher how to wire together the circuit of interest and provides code that can be used in a demonstration of the given approach.  The idea is to have the teacher do a demonstration to the students of the given practical activity.


This example shows the simplest thing you can do with an Arduino to see physical output: it blinks an LED.


Demonstrates the use of the analogWrite() function in fading an LED off and on. AnalogWrite uses pulse width modulation (PWM), turning a digital pin on and off very quickly, to create a fading effect.


This example shows how to send data from a personal computer to an Arduino board to control the brightness of an LED. The data is sent in individual bytes, each of which ranges in value from 0 to 255. Arduino reads these bytes and uses them to set the brightness of the LED.

You can send bytes to the Arduino from any software that can access the computer serial port. Examples for Processingand Max/MSP version 5 are shown below.


The bar graph – a series of LEDs in a line, such as you see on an audio display – is a common hardware display for analog sensors. It’s made up of a series of LEDs in a row, an analog input like a potentiometer, and a little code in between. You can buy multi-LED bar graph displays fairly cheaply, like this one. This tutorial demonstrates how to control a series ofLEDs in a row, but can be applied to any series of digital outputs.


Pushbuttons or switches connect two points in a circuit when you press them. This example turns on the built-in LED on pin 13 when you press the button.

Here’s a crazy idea, what about recording the brain of Jesus Christ during the delivery of a talk like the Sermon on the Mount (Image from Wikipedia page here).  Since “Some neurons continue to be generated throughout life and their production is regulated by hormones and experience,” I wonder if universal compassion can be evolved in humanity through such an experiment.  😉

The Sermon on the MountCarl Bloch, 1890

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About kayaerbil

I am a Berkeley educated chemistry Ph.D. who is moving into the area of working on developing appropriate technology for communities that are subjected to socio-economic oppression. The goal is to use simple and effective designs to empower people to live better lives. Currently, I am working with Native Americans on Pine Ridge, the Lakota reservation in South Dakota. I am working with a Native owned and run solar energy company. We are currently working on building a compressed earth block (CEB) house that showcases many of the technologies that the company has developed. The CEB house is made of locally derived resources, earth from the reservation. The blocks are naturally thermally insulating, keeping the house cool in the summer and warm in the winter. Eventually, a solar air heater and photovoltaic panels will be installed into the house to power the home and keep it warm, while preserving the house off the grid. A side project while in Pine Ridge is a solar computer. I hope to learn about blockchain encryption software for building microgrids. In addition, it is an immediate interest of mine to involve local youth in technology education.
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