Atom Board: Montessori Work

These atom boards worked very well for practicing how to interpret atomic symbols. The protons (blue) and electrons (red) are magnetic so they snap into place quite satisfyingly. Their poles are oriented so that the electrons will only attach properly to the slots in the electron shells and the protons only attach the right way up to the nucleus. The neutrons are wooden and non-magnetic.

Procedure for Building an Atom

Nucleus

Step 1: Number of protons (+ charge).

The number of protons is given by the element name. Carbon will always have six protons, Hydrogen will have one proton. I have students memorize the first twenty elements in the correct order, so they can quickly determine the atomic (proton) number.
¹⁴C: Protons = 6⁺

Step 2: Number of neutrons.

Neutrons = atomic mass – number of protons
The atomic mass is given at the top left corner of the atomic symbol: 14 in the example above for ¹⁴C.
¹⁴C: Neutrons = 14 – 6 = 8

Electron Shells

Step 3: Number of electrons (- charge).

Electrons = number of protons – charge
The charge is given to the top right of the atomic symbol. In this case, there is no charge
¹⁴C: Electrons = 6 + 0 = 6

Step 4: Electron Shells

Electrons go in shells around the nucleus.
Start with the smallest shell, fill it, and then add the next shell until you’ve placed all of the electrons.
The first shell can hold only 2 electrons, the second shell can hold 8, and the third 8. The electron configuration tells how many electrons are in each shell.
¹⁴C: Electron configuration: 2-4

They’ve also turned out to be useful when explaining ionic bonding. Since it’s easy to add or remove electron shells, you can clearly show how many electrons can be donated or received to figure out how many atoms are involved in the reactions.

Introduction to Pi’s (Raspberry Pi)

The family of Raspberry Pi’s are just really small computers. You can plug a monitor, keyboard, and mouse into one and it will not look too different from your desktop. They are small and cheap, but what makes them really useful is that they have little slots (called GPIO’s) that you can stick wires into that allow you to build circuits that can get information from sensors and control devices like LED lights or motors.

This is a quick introduction about how to set one up. You’ll find lots of great tutorials on the internet. This one is specific to my needs: it’s an introduction to the Pi’s for students who are new to them; I’m setting it up with a web server so we can control the devices through a webpage; and I’m setting it up so you can control the Pi “headlessly”, which means you don’t need the keyboard, mouse, etc..

Installing the Operating System

Downloading the OS

Download: The operating system files can be downloaded from the Raspberry Pi website. We’re going to use the Raspbian Desktop version with the recommended software.

Your typical computer has a built in hard drive that stores the data you save, the programs/apps you install, and the operating system (OS) that runs it all. When you start the computer the first thing it does is read the files that make up the operating system from the hard drive and set them up in the active, processing memory (RAM). Then when you interact with the computer (type on the keyboard, click the mouse etc.) you’re interacting with the operating system: you tell the operating system what to do, like start up a web browser (Firefox, Chrome, Safari, Explorer, Opera etc.), and it does it. And when your apps want to do something, like save a file, they have to ask the operating system to do it.

On the Raspberry Pi the data for the operating system is not stored on a built in hard drive, but on an SD card (or microSD), which means that you’re going to have to install the operating system yourself to get your Pi running. You can find the operating system at the Raspberry Pi website’s download page.

Installing

As of this writing, I’ve been using balenaEtcher to install the operating system on the SD Card.

balenaEtcher is free and pretty easy to use. Hopefully, your computer has an SD card port, if not you’re going to have to find an adapter. Just plug your SD card into your computer and run Etcher, it will ask you to:

Select Image: Which is the Raspbian file you downloaded
Select Drive: Which should default to the SD card you plugged in (check the size of the drive to make sure)
Flash: Which writes the Operating System files to the SD card, making sure everything is in the right place.

You may see some warnings pop up about Unrecognized Files Systems or similar. You can just close those windows.

When the flashing is done, don’t take the SD card out of your computer (or put it back in if you have) just quite yet. We’re going to set it up so the Pi can automatically connect to the WiFi, which will make it easier to talk to.

Setting Up WiFi

You’re going to have to edit some files on the SD card to give the Pi the information about the WiFi situation so that it can automatically connect. This is most useful if you’re not going to plug in a keyboard and monitor and just want to control the Pi from your computer (more on how to do this later). If you do want to go the keyboard and mouse route, you can just plug the SD card into the Pi, power it up, and set up the WiFi like you would normally do on your laptop.

To edit the files I use Atom on Windows or TextEdit which is built in on Mac. These programs should allow you to easily save files as plain text, without any of the fancy styling that will create errors when the Pi operating system tries to get the information from the files.

WiFi

Create a new file called: “wpa_supplicant.conf” (based on these notes) containing:

ctrl_interface=/var/run/wpa_supplicant GROUP=netdev
update_config=1

network={
 ssid="networkID"
 psk="password"
}

But you have to change:

networkID to the name of the WiFi network you’re trying to connect to
password to the password for the network

If you need to connect to multiple networks (home and school for example) you can add another network command on a new line after the first one:


network={
 ssid="otherNetwork"
 psk="otherPassword"
}

Save this file to the boot directory of the SD card.

ssh

ssh allows you to remotely connect to your Pi’s operating system. This means that you can use your laptop to control the Pi (however you’ll be using command line commands).

Create an empty file named “ssh” and save it to the boot directory of your SD card.

USB connection

You should be able to find your Pi on the network (I use an app on my phone called Fing) and ssh in. However, to do most of the setup, especially if the Pi has trouble connecting to the WiFi (or you can’t find it on the network), you’ll probably want to set up your pi so you can plug it into your computer’s USB port and control it from the computer. Based on the notes from Adafruit, do this:

Open the file “config.txt” which is in the SD card’s boot directory, and add this as the last line in the file:

dtoverlay=dwc2

Save the file then:

Open the file “cmdline.txt”, find the word “rootwait” and, after it, insert the phrase:

 modules-load=dwc2,g_ether

You should end up with something that looks like “…=yes rootwait modules-load=dwc2,g_ether quiet…”:

Connecting to your Pi

To talk to your Pi’s Operating System you should be able to connect your Pi’s USB port to your computer’s or connect over WiFi. Either way you’ll need to use an ‘ssh’ program.

Windows: I use putty. Install the program and run it. Then you’ll need to enter:

Host Name: raspberrypi.local
Password: raspberry

Mac: I use the built-in Terminal (In your Applications->Utilities folder). Type in the command (don’t type in the “>”):

> ssh raspberrypi.local
Use the password: raspberry

If you go the WiFi route, you’ll need to find your Pi’s IP address and use that as the Host Name.

Update and Upgrade

Once you’re ssh’d in, and are connected the internet, you can update and upgrade the operating system. Type in the commands (without the “>”).

> sudo apt-get update
> sudo apt-get upgrade

The “sudo” means you’re giving yourself permission to run commands that could potentially mess up your system. The program you’re running is called “apt-get” which connects to the internet repositories with the latest updates and upgrades to your operating system and programs, and then downloads and installs them. The options “update” and “upgrade” specifically tells the “apt-get” program what you want it to do. Downloading and upgrading may take a while.

Enable Interfaces

You’ll also want to check that the interfaces to the GPIO pins are enabled, so you can build circuits and control them. Notes on this are here.

First check that your tools are installed and updated with the commands:

> sudo pip3 install --upgrade setuptools
> sudo apt-get install -y python-smbus
> sudo apt-get install -y i2c-tools

Then Activate the Interfaces. You’ll run the command “raspi-config” and then use your keyboard to tab through the windows to activate the I2C and SPI interfaces. These are just two different ways for the Pi to talk to the devices you plug into it.

> sudo raspi-config
---- Interfacing Options
-------- I2C
------------ Yes
---- Interfacing Options
-------- SPI
------------ Yes

To get this all up an running you need to reboot the Pi:

> sudo reboot now

For the OLED displays

To control the little OLED displays we have, install the adafruit-blinka, and OLED libraries:

> sudo pip3 install adafruit-blinka
> sudo pip3 install adafruit-circuitpython-ssd1306

Tornado Server

The tornado server allows us to create webpages on the Pi that we can connect to over WiFi that can be used to control devices connected to the Pi. Install tornado using:

> sudo pip3 install tornado

Now restart everything and we can get to work.

> sudo reboot now

Human Migration over the last 125,000 years

Video by Tobais Friedrich out of the University of Hawaii. It’s based on a recent paper that suggests that the large fluctuations in climate over the last 120,000 years opened and closed green corridors that allowed multiple pulses of migration out of Africa.

He has some other excellent earth science scientific visualizations.

Math Flowcharts

Flowchart in progress. Showing topics being covered in basic statistical graphing. The topics they are working on at the moment are highlighted in yellow. The worksheets attached to each topic are linked on the left side in the highlighted area.

To help students track their progress in math we’ve started requiring them to map what they’re doing on flowcharts. Right now, they’re doing it on paper, but we’re working on getting it to be all electronic.

Tracking with the charts helps them see how what they’ve done fits into the bigger picture. It allows them to be able to go back up the chart to previous topics if they need to review, and look forward to what comes next (and to work ahead if they would like).

The image above shows a sample what a student’s flow chart would look like while they are working on a subject (statistics in this case). The topics they are working on at the moment are highlighted in yellow. The worksheets attached to each topic are linked on the left side in the highlighted area. Links to references (Khan Academy for example) are linked on the right–there are only a few on right now (see the Mean topic on the upper right of the flowchart).

The topics on the flowchart can be expanded (using the green button on the top right of each topic) to show more detail.

Expanded window for the topic "Mean". — Expanded window for the topic “Mean”. Detail on the topics is a little sparse at the moment as we’re focusing on setting up all of the flowcharts first.

At the moment, I’m uploading the flowcharts that we’re currently using up on the website myself. Students can use the website to get worksheets and links to references, but if they mark what they’re doing on the webpage it’s not saved. We’re currently working on making it possible to create and edit flowcharts on the website itself. After that, we’ll be setting it up so students can log in with their school accounts and track their progress electronically. One ultimate goal is to map the entire upper school curriculum with these flow charts so a student might be able to track their work all the way from 7th to 12th grade.

Video: From a Single Cell to an Alpine Newt

Becoming from Aeon Video on Vimeo.

Watch a single cell become a complete organism in six pulsing minutes of timelapse. A film by Jan van IJken (www.janvanijken.com).

More on this video: aeon.co/videos/watch-a-single-cell-become-a-complete-organism-in-six-pulsing-minutes-of-timelapse
Watch more on Aeon: aeon.co/video
Subscribe: vimeo.com/aeonvideo

An exceptional timelapse of the developing of an Alpine newt by Jan van IJken

How to make a Boxplot in R

Guest post by Grace Appell.

What is a Boxplot?

A box plot is a graph that helps you to analyze a set of data. It used to show the spread of the data. In it you use five data points: the minimum, the 1st quartile, the median, the 3rd quartile, and the maximum.
The minimum is the lowest point in your data set, and the maximum is the largest. The median is the number in the middle of the data set when you have the number lined up numerically.
For example if your data set was this:

 5, 6 ,11, 18, 12, 9, 4

First you would put them in order lowest to highest.

4, 5, 6, 9, 11, 12, 18

Your median would be 9, because it is the middle number. The minimum would be 4, and the maximum would be 18.
The first quartile would be 5, the median of the numbers below 9, and the third quartile would be 12, the median of the numbers above 9.
So the data you would use in your boxplot would be

(4,5,9,12,18)

The boxplot would look like would look like this.

What is R?

R is a software program that is free to download that you can use for calculating statistics and creating graphics.
Here is their website: https://www.r-project.org/

Boxplots in R

In R you can create a boxplot by using this formula.

> Name of data set <- c(minimum, quartile 1, median, quartile 3, maximum)
> boxplot(Name of data set)

First you have to name your data set. In our project where we analyzed the number of times people repeated their Shakespeare lines that they performed, I used the name Macbeth. So the formula looked like this:

> Macbeth <- c(1,9,18,48,93)
> boxplot(Macbeth)

Using this data set, your box plot should look like this

Making 3D Periodic Tables

Ms. Fu’s chemistry class were given a project to make 3d periodic tables based on the properties of the elements. A few groups went with Makerspace options, using the new vinyl cutter and laser.

3d Periodic Table showing electronegativity. Laser cut.

Periodic Table relief based on ionization energy. The blocks on this one have 1.5 inch square bases. The colors for the different regions use stains including tea (assam) and blackberry juice extracted from berries from the canes on campus.

The part that took the longest was marking all the columns for cutting. A worthwhile assignment would be to write a program to automatically make the cut-marks in an svg file that can be etched with the laser.

Periodic Table column heights based on density. Laser cut.

Paper columns and vinyl cut lettering on this periodic table.