The universal pH indicator turns red for acids and blue for bases.
Ms. Wilson’s chemistry class did a beautiful electrolysis experiment by mixing a universal pH indicator into the salt solution. The indicator changes color based on how acidic or basic the solution is; we’ve used this behavior to show how blowing bubbles in water increases its acidity.
Changing colors of universal indicator show how blowing bubbles acidifies water (light green-second beaker) from neutral pH (dark green-third beaker) standard. For comparison, the first beaker (red) is acidified while the last beaker (blue) is made alkaline.
In this experiment, when electrodes (graphite pencil “leads”) are placed into salt (NaCl) water and connected to a battery, the sodium (Na) and chloride (Cl) split apart.
NaCl –> Na+ + Cl–
The positive sodium ion (Na+) migrates toward the negative electrode, where it gets an electron and precipitates on the electrode as a plating. This is called electroplating and is done to give fake gold and silver jewelry a nice outward appearance.
Similarly, the water (H2O) also dissociates into hydrogen (H+) and hydroxide (OH–) ions.
H2O –> H+ + OH–
Hydrogen bubbles forming at the negative electrode.
The positive hydrogen ions (H+) go toward the negative electrode where they get an electron from the battery and are liberated as hydrogen gas (when they bond to another hydrogen you get H2 gas). However, releasing the positive hydrogen ion, leaves behind hydroxide ions in the area around the positive electrode.
The opposite happens at the positive electrode, with hydrogen ions left behind in the solution.
Since acidity is a measure of the excess of hydrogen ions in solution (H+), the left behind hydrogen ions make the solution near the positive electrode acidic, which turns the indicator solution red. The OH– left near the negative electrode make the solution basic, which shows up as blue with the indicator.
If you gently shake the petri dish you end up with beautiful patterns like this:
Swirls.
And this:
After the electrodes have been disconnected.
Note: if the solution is mixed completely the hydrogen and hydroxide ions react with each other to make water again, the solution neutralizes, and becomes uniform again.
Note 2: This is an experiment that I should also do in physics. It should be interesting for students to see this experiment from two different perspectives to see how the subjects overlap.
I’ve collected a set of aquatic plants for our fish tank for the middle school students to be able to look at their cells under the microscope. A few are from the store, like the Eregia densa I’ve used in the past, but we’ve also grabbed some algae from the creek, and Mr. Woodbury brought in some algae specifically for our two resident tadpoles.
I was checking out at the creek algae under the microscope when I came across these two microbes. They both were motile and seemed to be surrounded by cilia, but I really don’t know what they are.
Environmental Science students have been working on a wide range of term projects. They’re required to use real data. Some are using the long term weather, climate and socioeconomic records from national and international data repositories. Others are collecting their own measurements — the ability to connect temperature, pH, and conductivity sensors to the new calculators have proven invaluable.
One project that I’ve been particularly happy that someone has taken up, because of its potential future use, has been to assemble a specimen collection cataloging the vegetative biodiversity in the area around the creek. With the help of TFS parent Scott Woodbury, who works for the Missouri Botanical Gardens, she’s collected, identified, and preserved dozens of specimens. She’s also compiled them all into an online phylogenetic tree (using mind42) that should serve as a wonderful reference for future class and student projects.
We covered the Millennium Development Goals in Environmental Science this past quarter. However, the big outstanding question was how close have we come to meeting any of the goals. Health Intelligence hosts an excellent, interactive map for tracking progress on the Millennium Development Goals.
DNA Writer: Translate text into a DNA code (and back again) using a simple lookup table.
I created this little DNA Writer webpage after seeing the article on scientists recording one of Shakespeare’s sonnets on DNA, I was inspired to put together something similar as an assignment for my middle-school science class to demonstrate how DNA records information. With the website to do quick translations for me, I’ll give each student the translation table and a simple message in DNA code and have them figure out the message.
Update: I’ve adapted the code to add a two to five letter sequence of non-coding DNA to the beginning and end of the message code. There’s also start and stop code as well.
The DNA sequence (or RNA in this figure) can be broken down into groups of three nucleotides called codons. Each codon codes for a specific amino acid, so the order of codons gives the sequence of amino acids in the proteins created by the DNA strand. Image by TransControl via Wikipedia.
The DNA Writer code uses a simple look-up table where each letter in the English alphabet is assigned a unique three letter nucleotide code. The three letters are chosen from the letters of the DNA bases – AGCT – similar to the way codons are organized in mRNA. Any unknown characters or punctuation are ignored.
Also, with a little tweaking, I think I can adapt this assignment to show how random mutation can be introduced into DNA sequences during transcription. Maybe break the class into groups of 4, give the first student a message as a nucleotide sequence have them copy and pass it on to the next student and so on. If I structure this as a race between the groups, then someone’s bound to introduce some errors, so when they translate the final code back into English they should see how the random mutation affected their code.
UPDATE: Non-Coding (junk) DNA: I’ve updated the code so that you have the option of adding a short (2-5 character) string of non-coding DNA to the beginning and end of each sequence.
A more personalized and printer friendly format for output.
UPDATE 2: Personalized and Printable output: Since I’m using the DNA writer to give each student a personalized message, I’ve created a button that gives “Printer Friendly Output” which will produce an individualized page with the code, the translation table, and some information on how it works, so I can print off individualized assignments more easily.
UPDATE 3: You can now get a color coded version of the sequence.
Ravenclaw’s DNA sequence color coded, and translated back to English.
In constructing the codon-to-english conversion table I had to decide if I wanted to go with the standard coding (e.g. letting GTC which codes for alanine represent A) or make up a random encoding.
I opted for the random approach for a number of reasons, but the primary one was that multiple codons can code for the same amino acid. GCT, GCC, GCA, and GCG all code for alanine. This would not necessarily be a problem, except that if we respect all of the multiple encodings, we run out of codons to represent things like numbers and punctuation. A secondary reason is that U is used to represent the 21st amino acid, selenocysteine, but its codon is the same as the stop codon (Croat, 2012) and its addition to the protein chain depends on not just a single codon in the sequence.
I’ve created a hybrid option: dnaWriterA which respects the standard lettering as much as possible (based off of the inverse DNA codon table on Wikipedia). In the table below, the bolded sequences are the ones that have been reassigned.
Letter/code
Amino acid
Codon
start
ATG
stop
TAA
space (” “)
GCA
.
GGA
A
Ala
GCT
GCC
GCA
GCG
B
Asn or Asp
AAC
C
Cys
TGT
TGC
D
Asp
GAT
GAC
E
Glu
GAA
GAG
F
Phe
TTT
TTC
G
Gly
GGT
GGC
GGA
GGG
H
His
CAT
CAC
I
Ile
ATT
ATC
ATA
J
TTG
K
Lys
AAA
L
Leu
CTT
CTC
CTA
CTG
TTA
TTG
M
Met
ATG
N
Asn
AAT
AAC
O
AGG
P
Pro
CCT
CCC
CCA
CCG
Q
Gln
CAA
CAG
R
Arg
CGT
CGC
CGA
CGG
AGA
AGG
S
Ser
TCT
TCC
TCA
TCG
AGT
AGC
T
Thr
ACT
ACC
ACA
ACG
U
AGA
V
Val
GTT
GTC
GTA
GTG
W
Trp
TGG
X
AGC
Y
Tyr
TAT
TAC
Z
Gln or Glu
CAA
CAG
GAA
GAG
0
AGT
1
GCG
2
GGG
3
CTG
4
CCG
5
CGG
6
TCG
7
ACG
8
GTG
9
GAG
Codons mapping to letters/codes used in the dnaWriterA version. The bolded sequences are the ones that have been reassigned.
