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.
Mrs. D. recommended this nice little article on “flipped teaching”, where students get lessons from videos (usually at home) and spend their time in class working on problems and getting help from peers and their teacher. Sounds a lot like Montessori. In middle school, for example, where you get a short lesson at the beginning of the week and spend the rest of the time working on projects and assignments.
Pushing the video out of the classroom can, potentially, be a useful step, especially for those students who can work independently. I’ve been trying it a little with the Khan Academy videos, but I need to organize it a bit more.
Influence Explorer is an excellent resource for assessing data about money in politics.
The website Influence Explorer has a lot of easily accessible data about the contributions of companies and prominent people to lawmakers. As a resource for civics research it’s really nice, but the time series data also makes it a useful resource for math; algebra and pre-calculus, in particular.
