MolView is a great site for drawing molecules and rendering them in 3D.
MolView: Website for Drawing Molecules
Category: Natural World
John Snow: How to be a Scientist
These three excellent, short videos on John Snow’s life and work on cholera do a nice job of describing what makes for good science–careful observation; good notes; creative analysis of data, etc. They should make a good “spark your imagination” introduction to biological science.
They also have an excellent explanation of all the ‘lies’ and liberties they took in the making of the video.
Chessboard Project
For our annual fundraiser’s silent auction, I made a chess board. The structure was made of wood–I learned how to use dowels to attach the sides–but the black squares were cut out of the material they use for matting the borders of pictures. My student drew “cheat sheet” diagrams of each of the black squares in bright gel pen colors. The squares were laid on a white grid and the entire top epoxied with a clear glass-like coat. We also made two sets of chess pieces with the 3d printer (rounds versus squares).
It turned out quite well.
Gene Transfer from Algea to Sea Slug
One of my students wanted to figure out how to make animals photosynthesize. Well, this article indicates that sea slugs have figured out how eat and digest the algae but keep the algal chloroplasts alive in their guts so the sea slug can use the fats and carbohydrates the chloroplasts produce (the stealing of the algal organelles is called kleptoplasty). To maintain the chloroplasts, the slugs have actually had to incorporate some of the algae DNA into their own chromosomes–this is called horizontal gene transfer and it’s what scientists try to do with gene therapies.
More details here.
The Wind Right Now
Windyty shows beautiful animations of the current wind patterns around the world.
Limiting Chemical Reactions
Figuring out the limiting reactant in a chemical reaction integrates many of the basic chemistry concepts including: unit conversions from moles to mass and vice versa; the meaning of chemical formulas; and understanding the stoichiometry of chemical reactions. So, since we’ll need a number of these, I wrote a python program to help me design the questions (and figure out the answers).
Program examples come zipped because they require the program file and the elements_database.py library:
Baking Powder and Vinegar (Common Molecules)
Limiting_component-Common.py: This has the baking powder and vinegar reaction limited by 5 g of baking soda. It’s nice because it uses a few pre-defined “common molecules” (which are defined in the elements_database.py library.
You enter the reactants and products and the program checks if the reaction is balanced, then calculates the moles and masses based on the limiting component, and finally double checks to make sure the reaction is mass balanced.
Limiting_component-Common.py
from elements_database import *
import sys
print "LIMITING REACTANT PROGRAM"
print
print " Determines the needed mass and moles of reactants and products if reaction is limited by one of the components"
c = common_molecules()
'''Create Reaction'''
rxn = reaction()
# Add reactants (and products)
# Use rxn.add_reactant(molecule[, stoichiometry])
# molecule: from molecule class in elements_database
# stoichiometry: integer number
rxn.add_reactant(c.baking_soda,1)
rxn.add_reactant(c.hydrochloric_acid,1)
rxn.add_product(c.carbon_dioxide)
rxn.add_product(c.water, 1)
rxn.add_product(c.salt)
'''Print out the reaction'''
print
print "Chemical Formula"
print " " + rxn.print_reaction()
print
'''Check if reaction is balanced'''
balanced = rxn.check_for_balance(printout=True)
'''Calculate limits of reaction'''
if balanced:
rxn.limited_by_mass(c.baking_soda, 5, printout=True)
Outputs results in the Results table (using scientific notation):
LIMITING REACTANT PROGRAM
Determines the needed mass and moles of reactants and products if reaction is limited by one of the components
Chemical Formula
NaHCO3 + HCl --> CO2 + H2O + NaCl
Check for balance
---------------------------------------------
| Element | Reactants | Products | Difference |
---------------------------------------------
| Na | 1 | -1 | 0 |
| H | 2 | -2 | 0 |
| C | 1 | -1 | 0 |
| O | 3 | -3 | 0 |
| Cl | 1 | -1 | 0 |
---------------------------------------------
Balance is: True
Given: Limiting component is 5 g of NaHCO3.
Molar mass = 84.00676928
Moles of NaHCO3 = 0.0595190130849
Results
------------------------------------------------------------------
| Molecule | Stoich.*| Molar Mass (g) | Moles req. | Mass (g) |
------------------------------------------------------------------
|NaHCO3 | 1 | 84.0068 | 5.952e-02 | 5.000e+00 |
|HCl | 1 | 36.4602 | 5.952e-02 | 2.170e+00 |
|CO2 | -1 | 44.0096 | 5.952e-02 | 2.619e+00 |
|H2O | -1 | 18.0156 | 5.952e-02 | 1.072e+00 |
|NaCl | -1 | 58.4418 | 5.952e-02 | 3.478e+00 |
------------------------------------------------------------------
* negative stoichiometry means the component is a product
Final Check: Confirm Mass balance:
Reactants: 7.1701 g
Products: -7.1701 g
--------------------------
= 0.0000 g
--------------------------
General Example
If not using the common molecules database, you need to define the components in the reaction as molecules yourself. This example reacts magnesium sulfate and sodium hydroxide, and limits the reaction with 20 g of magnesium sulfate.
Limiting_component-General.zip
The main file is:
Chem_Exam-limiting.py
from elements_database import *
import sys
print "LIMITING REACTANT PROGRAM"
print
print " Determines the needed mass and moles of reactants and products if reaction is limited by one of the components"
# create reaction
rxn2 = reaction()
# Add reactants (and products)
# Use rxn.add_reactant(molecule[, stoichiometry])
# molecule: from molecule class in elements_database
# stoichiometry: integer number
rxn2.add_reactant(molecule("Mg:1,S:1,O:4"))
rxn2.add_reactant(molecule("Na:1,O:1,H:1"), 2)
rxn2.add_product(molecule("Mg:1,O:2,H:2"))
rxn2.add_product(molecule("Na:2,S:1,O:4"))
'''Print out the reaction'''
print
print "Chemical Formula"
print " " + rxn2.print_reaction()
print
'''Check if reaction is balanced'''
balanced = rxn2.check_for_balance(printout=True)
'''Calculate limits of reaction'''
if balanced:
rxn2.limited_by_mass(molecule("Mg:1,S:1,O:4"), 20, True)
# print out masses
print "Masses Involved in Reaction"
print " Reactants:"
for i in rxn2.reactants:
#print "rxn", i
print " {m}: {g} g".format(m=i.molecule.print_formula().ljust(10), g=i.mass)
print " Products:"
for i in rxn2.products:
#print "rxn", i
print " {m}: {g} g".format(m=i.molecule.print_formula().ljust(10), g=-i.mass)
This program is slightly different from the common molecules example in that, at the end, it prints out masses calculated in a more easily readable format in addition to the other data.
Masses Involved in Reaction
Reactants:
MgSO4 : 20.0 g
NaOH : 13.2919931774 g
Products:
MgO2H2 : 9.69066512026 g
Na2SO4 : 23.6013280571 g
When I have some time I’ll convert this to JavaScript like the molecular mass example.
Molar Mass of Molecules
Calculate the molar mass of a molecule:
The notation for the chemical formula is a little funky: you put the element symbol and then the number of atoms separated by a colon; each element/number of atoms pair are separated by commas, so sodium chloride (NaCl) would be “Na:1,Cl:1“.
This will have to do until I can write something to parse the regular chemical formula notation.
On the plus side, you can link to a specific molecular mass calculation by adding the formula to the url. So magnesium chloride (MgCl2) can be found with this url:
https://soriki.com/js/chem/chem_db/molecular_mass.html?formula=Mg:1,Cl:2
She’s got (a) heart: Duck Dissection
Dissection time is always interesting in the middle school classroom. Some kids start off a little squeamish, but there are always a few who pitch right in. All of the class were working on different organisms–microscopic algae (desmids), insects, plants, etc.–but I set up the dissection table in the middle of the room. With all the other tables facing inwards, everyone who wanted to got a chance to see the internal organs as they were carefully, but triumphantly, traced and extracted. It spreads the enthusiasm, and gives the other students a heads up as to what will be expected.
One student brought in a duck that her father had shot. She was familiar with cleaning hunted fowl, so had no qualms about the dissection. The duck was a great specimen, because the internal organs were large and easy to identify.
She, and most of the rest of the class, had dissected a sheep’s heart in elementary school. This time, however, they got to see how the heart was connected to the rest of the body. We got to talk about why smaller organisms, like ducks, could get away with two chambered hearts, while larger ones need four chambers.
Indeed, the tracing of the artery leading out of the heart lead us to compare of the color of the duck’s lungs–so red they were almost black–and the fish’s gills, which were also a deep red. And that, in turn lead to a discussion of how organisms ingest the gasses they need to survive: microbes through diffusion; insects through spiracles and trachea; mammals through lungs. Tomorrow we’ll talk about how the surface area to volume ratio changes with size.