At higher magnifications, microscope lenses will only be able to focus on layers within your specimen. You could take a series of images with different focal planes and stack them together, but without a camera mounted on the microscope, getting images to line up right for focus stacking is quite the challenge. The alternative is focusing in and out until you get a feeling for the three dimensional shape of the specimen.
Since I don’t have a camera mount I’ve created an html5/javascript page that simulates focusing in and out of a sample. It’s embedded above, but a direct link is here.
You can use the knobs to the right of the image to adjust the focal plane. You should be able to see hairs on the top and bottom of the transparent wing.
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.
This app lets you drag and drop electrons, protons, and neutrons to create atoms with different charges, elements, and atomic masses. You can also enter the element symbol, charge and atomic mass and it will build the atom for you.
Note, however, it only does the first 20 elements.
Here’s a neat little video, which holds the Milky Way (galactic-centric) steady as the Earth rotates relative to it.
For comparison, here’s the original video by Stephane Guisard and Jose Francisco Salgado, showing the geocentric view of the sky moving:
It is always revelatory to see things from unexpected perspectives. Brian Swimme was amazed by the immensity of it when he first truly recognized that he was standing on a planet that was rotating through space orbiting the Sun.
I’ve always been struck by the opposite point of view. To think that if you hold still enough, and think about it a bit, from one point of view you could be the central reference point for the entire universe, with everything else moving relative to you: the Earth still beneath your feet; the Sun (almost) orbiting around you; and the planets arcing through their epicycles.
Orbits of the inner planets viewed from the Earth (a geocentric perspective). Paths plotted using Gerd Breitenbach's neat little applet.
Paths of hurricanes in 2010. The North Atlantic hurricane season was the 3rd most active on record. Visualization from NOAA's excellent Historical Hurricane Tracks interactive map.
Forest fires in the Amazon. Image from NASA.
Jeff Masters has an impressively detailed post laying out the argument that 2010, with its record setting snowstorms, droughts, heatwaves, flooding, hurricanes, etc, had the most extreme weather since 1816, the year without a summer.
Looking back through the 1800s, which was a very cool period, I can’t find any years that had more exceptional global extremes in weather than 2010, until I reach 1816. That was the year of the devastating “Year Without a Summer”–caused by the massive climate-altering 1815 eruption of Indonesia’s Mt. Tambora, the largest volcanic eruption since at least 536 A.D. It is quite possible that 2010 was the most extreme weather year globally since 1816.
The Genetic Science Learning Center (which I’ve mentioned before) has a wonderful slider-bar animation that shows the differences in scale from what we perceive (a grain of rice or a coffee bean) down to the scale of cells, molecules and finally a carbon atom.
The smallest objects that the unaided human eye can see are about 0.1 mm long. That means that under the right conditions, you might be able to see an ameoba proteus, a human egg, and a paramecium without using magnification. …
Smaller cells are easily visible under a light microscope. It’s even possible to make out structures within the cell, such as the nucleus, mitochondria and chloroplasts. [my example] … The most powerful light microscopes can resolve bacteria but not viruses.
To see anything smaller than 500 nm, you will need an electron microscope. … The most powerful electron microscopes can resolve molecules and even individual atoms.
–Genetic Science Learning Center (2011, January 24) Cell Size and Scale. Learn.Genetics. Retrieved June 13, 2011, from http://learn.genetics.utah.edu/content/begin/cells/scale/
