Category: Natural World

DNAi: History of genetics and manipulating DNA

DNA. (from Wikipedia)

DNA interactive is another great resource for studying the history of genetics and how we manipulate and use it today (recommended by the indispensable Anna Clarke). They have lesson plans and nice pages on the modern techniques used to work with DNA.

Image from the DNAi webpage on gel electrophoresis. Electrophoresis is a bit like chromatography which might make for a good demonstration.

I have not done much with genetic sequencing myself and I found the website interesting and informative. I have, however, written programs to get and work with the GenBank database, which is not that hard since they have some easy tools to work with. I would love to figure out how to get a sample sequenced and then run it through GenBank to identify it. It would so nicely integrate the curriculum, using a practical exercise to solve a problem (like what species are on the nature trail), while using the same tools and resources that scientists use, and tie wonderfully into the short stories in Mirable.

CellsAlive: Cell model

Interactive cell model from Cells alive!

Another good interactive cell model, similar to the Teach.Genetics‘ Flash app I posted about earlier, can be found at CELLS alive. I first used the CELLS alive website two years ago and I like it because, while it has a much simpler picture than Teach.Genetics’, it has a nicely linked glossary of terms. The glossary is, however, a little technical, but it’s a nice exercise (and not terribly difficult) for students to decipher the basic information that they need.

Inside a cell

Looking inside a cell. From Teach.Genetics.

Teach.Genetics has a bunch of “Print and Go” pdf lessons on their site, but also have a really neat interactive page where you can look inside an animal cell. What’s really neat about this flash app is that you can move around a little, round window as you scan through the cell membrane. You can also take the membrane away to see everything inside the cell at once, but that takes away the challenge.

When you use the little window you have to piece together what everything inside the cell looks like by memory. For a student new to the parts of a cell this might be a bit of cognitive overload, but once your somewhat familiar with the pieces, this makes for an interesting challenge.

The Teach.Genetics site and materials are free for educational use.

Teach.Genetics: Family trees

Handy Family Tree exercise from Teach.Genetics.

Dealing with genetic traits and family trees can be kind of tricky sometimes, particularly with early adolescents who are still learning about personal boundaries and have the potential for sharing too much information. One alternative to delving too deeply into personal family histories is to stress the less invasive traits. Anna Clark has had some success (and the students liked it) using the Handy Family Tree, from the University of Utah’s Teach.Genetics website.

John Wyndham's The Crysalids. (via Powell's Books).

I also discuss some of the thornier issues when we do the John Wyndham book, The Chrysalids. It can be an uncomfortable book, but has the emotional separation of fiction.

Teach.Genetics is a great resource. They have a number of “Teach and Go” exercises like this one, and some interesting interactive applications. I’ll post more as I browse more through their website.

Making pectin

Extracting pectin for making jelly does not seem to be that hard. Sam Thayer has a nice little article on how to get pectin from apples. The blog Spain in Iowa, has some nice pictures and video of how they extracted pectin from apples and what the result should look like when you test it by putting a teaspoon of pectin into a teaspoon of rubbing alcohol. Almost immediately (but leave it in for a minute), the pectin should jell in the rubbing alcohol and you should be able to pull it out using a fork.

Basically, all you do is chop up the apples, cook them for a long time over low heat till they’re broken down, and then strain out the liquid produced. Since I have access to a lot of green apples that won’t be used for anything else, I tried the process myself. Using a pot full of apples I produced a lot of liquid; way more than I could ever use, but the process seems to work fairly well.

One 8 quart pot of apples produced 8.75 cups of liquid. I’d planned to use the home-made pectin in my currant jam, but testing the currant juice showed that it had just as much, if not more pectin than my boiled apple residue. I guess I’ll save the apple pectin for future use.

Ideally, Student Run Businesses should sell goods or services that are worth the value paid. While I appreciate that there is some value to the sympathy of friends and family, it is nice when customers believe they’re getting a good deal even without that. One direction I try to direct the students is toward making things from scratch, because it adds so much to the experience. Then they can have the extra value of using natural, perhaps even organic, ingredients and satisfying Michael Pollan’s rules for good eating.

In Defence of Food by Michael Pollan

My students have not yet tried jam or jelly-making, but if they do natural pectin would be great.

Jam algebra

I’d like to minimize the sugar content of the jam in order to see the most of the currant’s tartness. According to the FAO, you need to have about 60% sugar concentration in the final jam for good preservation. I’ve squeezed the currants and produced quite a bit of juice. I need to find out how much sugar to add.

To figure out how much sugar we need to add, based on the mass, we need to define our terms. Let’s say the amount of sugar is s, the amount of jam is j and the total mass, the sugar plus the jam, is t.

So the total mass is going to be:

(1) t = s + j

Since the amount of sugar needs to be 60% then:

(2) s = 0.6 t

If we substitute the first equation (1) into the second (2) we’ll have just one equation we can solve to find the amount of sugar:

(3) s = 0.6 (s + j)

Now we solve for the amount of sugar, s. Start by expanding the right hand side of the equation (distributive property):

(4) s = 0.6 s + 0.6 j

Next, isolate s on the left hand side of the equation by subtracting:

(5) s – 0.6 s= 0.6 s + 0.6 j – 0.6 s

Which gives:

(6) 0.4 s= 0.6 j

Now, get rid of the coefficient on the left hand side by dividing through:

(7) 0.4 s / 0.4 = 0.6 j / 0.4

To get:

(8) s = 1.5 j

So to have the right amount of sugar, I need to add one and one half times as much sugar as I have juice. So, if I have 2.0 kg of juice, then:

s = 1.5 (2.0 kg)
s = 3.0 kg

3.0 kg of sugar is a lot of sugar! However, if we boil the jam, some of the water in the juice will evaporate. Therefore, if we know how much sugar we want to add in we should be able to calculate how we need to evaporate to get the right ratio. More evaporation should also lead to a more concentrated flavors in the jam. Hmmm …

Well, I have a scale.

Jam tectonics

Boiling jam will often create a froth that floats on top, much like the granitic continental crust floats on the Earth’s mantle. Also like the boiling jam, the mantle convects (even though the mantle is not liquid).

Convection in jam.

The darker red areas in the image are where the convection cells in the boiling jam reach the surface and push the froth away. It’s a bit like the bulge in the Earth’s crust that occurs beneath hot-spots and the mid-ocean ridges.

Model of convection in the Earth's mantle (image from Wikipedia)

Origin of life lab

ENSI has a set of great labs that can be used all the way from the middle school to the university level. They deal with the nature of science, the origin of life, evolution and genetics/DNA. (Thanks again Anna Clarke for the link.)

Amoeba (image from Wikipedia). This image is part of a neat video of amoeba movement.

I’m thinking that the Creating Coacervates lab, the only one on the origin of life section, might fit into my orientation cycle plans. Coacervates are small, microscopic blobs of fat (lipids) that look like, and have many of the same properties as cells, amoebas in particular. They can be produced with simple chemicals. One of the key things I’d like to start the year with, is the idea that:

complex life-like cell-like structures can be produced naturally from simple materials with simple changes. Flammer, 1999.

These abiotic blobs can be compared to the protozoans in a water droplet sample while we learn how to use the microscopes. It also ties into the Miller–Urey experiments that produced amino acids using electricity and simple compounds: water, methane, ammonia and hydrogen gas. The Miller-Urey experiments will pop up later when we read Frankenstein.