Middle and High School … from a Montessori Point of View
The rapid, snow-melt driven, flow in the creek has receded a little, but it managed to clear out most of the dead leaves that have carpeted the stream bed since the fall. Now that the rocky bottom is exposed, hopefully, we’ll be able to see some more of the benthic fauna that’s been invisible for the last few months.
Update: I stumbled across this nice beginner’s guide to pond microbes that makes me thing these microbes are Gastrotrichs.
The Gastrotricha World portal has more information, as does the EOF and micrographia.
A video of a gastrotrich is down below.
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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.
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 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.
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.
Update 4: Now you can embed the nucleobase color patterns into other websites. Like so:
DNA Writer A: https://earthsciweb.org/js/bio/dna-writerA/
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 |
I’ve also posted the code to GitHub: https://github.com/lurbano/dnaWriterA with instructions on how to adapt the sequence.
Adam Cole has an excellent NPR article on some fascinating researchers who are storing data — text files, web pages, sonnets — on DNA.
This should be a interesting introduction for middle-schoolers to the idea of DNA as a means of storing and transferring information. The question I hope to get is, “How did they do that?”
The salamanders themselves don’t do photosynthesis, but they host symbiotic algae that do.
Spotted salamanders, too, are in a long-term relationship with photosynthetic algae. In 1888, biologist Henry Orr reported that their eggs often contain single-celled green algae called Oophila amblystomatis. The salamanders lay the eggs in pools of water, and the algae colonise them within hours.
By the 1940s, biologists strongly suspected it was a symbiotic relationship, beneficial to both the salamander embryos and the algae. The embryos release waste material, which the algae feed on. In turn the algae photosynthesise and release oxygen, which the embryos take in. Embryos that have more algae are more likely to survive and develop faster than embryos with few or none.
Then in 2011 the story gained an additional twist. A close examination of the eggs revealed that some of the algae were living within the embryos themselves, and in some cases were actually inside embryonic cells. That suggested the embryos weren’t just taking oxygen from the algae: they might be taking glucose too. In other words, the algae were acting as internal power stations, generating fuel for the salamanders.
–Marshall (2013): Zoologger: The first solar-powered vertebrate in New Scientist based on Graham et al. (2012).
Charles Darwin and colleagues attempted to vegetate the barren, volcanic Ascension Island with plants from botanical gardens around the world. Essentially, it was an experiment in transforming. And it worked. Howard Falcon-Lang has the details at the BBC.
This nice little video combines a bit of physics, chemistry, and biology as it discusses how bubbles form in champagne: the gas is carbon dioxide; carbon dioxide forms from the fermentation of sugars by yeast — it’s a byproduct of the reaction that produces alcohol; the bubbles form at tiny flaws or bubbles in the glass (so you can put in tiny flaws to control where the bubbles form); the bubbles rise because the gas is less dense than the liquid around it; and the bubbles expand as they rise because the pressure of the liquid becomes less and less the closer to the surface you are.