3d Molecule Viewer

An excellent 3d viewer for molecules.

An excellent 3d molecule viewer. (The actual app has a lot smoother animations than this.)
An excellent 3d molecule viewer.

In addition to the existing molecules, you can import any number of others if you can find them in one of the right formats (PDB, SDF or MOL molecule definitions): the ligand.info: Small Molecule Meta Database is a good source for SDFs.

Johnson’s Shut Ins

Exploring the natural water works at the Johnson's Shut Ins.
Exploring the natural water works at the Johnson’s Shut Ins.

First off, the Shut Ins are narrower constrictions in the river valley formed when stream flows into an area of harder rock. The hard rock, in this case an old (1.5 billion year old) rhyolite flow, is relatively resistant to erosion, especially the side-to-side erosion that flattens out little flood plains as small rivers meander through the foothills of old mountains like the Ozarks. So the stream only erodes downward through the hard rocks creating a narrow gorge. As they say here: the river’s “Shut In”.

When I told people that I wanted to do a few camping trips this summer, the number one recommendation was the Shut Ins. And I can see why. I took my boys and they had an awesome time.

“It’s like the City Museum. Only real.”
— Overheard at Johnson’s Shut Ins

The Shut Ins are a maze of narrow channels, the old igneous rocks carved smooth by the water and its gravelly bed load over millions of years. A great place for kids to traipse through and explore. I bit like a water-park version of the City Museum in St. Louis.

Rushing water in a shallow channel leads to a deeper pool.
Rushing water in a shallow channel leads to a deeper pool.
Looking down from the cliffs above the Shut Ins, the sets of linear joints in the rocks are quite clear.
Looking down from the cliffs above the Shut Ins, the sets of linear joints in the rocks are quite clear.

The pattern of the channels is largely determined by the jointing in the rocks, because the joints offer easier pathways for water and erosion. There are at least two obvious sets of joints in the rocks, but I would not be surprised if they overlay other patterns given how old the rocks are. As it is, however, the erosion through the joints creates lots of neat little chutes.

Looking along a narrow eroded joint.
Looking along a narrow eroded joint.

Since the Shut Ins are only a couple hours away from St. Louis, they’re a pretty popular tourist attraction.

Population density is high.
Population density is high.

There’s a lot of science that can be done here, however, that would make this a good location for an immersion trip, especially since Elephant Hills State Park (with wonderful spheroidal weathering) is close by. The camping facilities at the Shut Ins State Park are new and quite nice, having been completely rebuilt with some of the $100 million in settlement money from the Ameren power company after the park was flooded by their Taum Sauk reservoir breach in 2005.

The path of the wave from the Taum Sauk reservoir breach created a debris field with huge boulders, and demolished the original Johnson's Shut Ins campground. The Shut Ins themselves are downstream to the right.
The path of the wave from the Taum Sauk reservoir breach created a debris field with huge boulders, and demolished the original Johnson’s Shut Ins campground. The Shut Ins themselves are downstream to the right.

It’s certainly worth the visit.

As the stream exits the Shut Ins it has dredged some excellent swimming pools.
As the stream exits the Shut Ins it has dredged some excellent swimming pools.

Teaching with the Hands

Doug Stowe is an artisan who specializes in making small boxes. He also teaches woodworking and records his thoughts on the melding of education and craftsmanship on his wonderfully reflective blog, Wisdom of the Hands. For example:

In his introductory remarks published in the Teacher’s Hand-Book of Educational Sloyd, Salomon notes the difference between a trained artisan and a teacher. While the trained artisan is focused by necessity on the qualities inherent in the finished product, the teacher must be concerned with the qualities developed within the child. An artisan might step in to make sure the child gets the work right, while the teacher might step back to see that the child learns. In other words, the predisposition of the artisan vs. teacher may be leading in completely different directions.

— Doug Stowe: beyond craftsmanship on Wisdom of the Hands (blog).

I really like the core message here. I’m an advocate for apprenticeship learning: how better to learn to think and act like an experts. But the key lesson for the expert is that students need to be given the opportunity to experiment, and even to make mistakes, in order to learn.

After my own, rough, experiments with making a slide holder, I’d love to take a lesson from someone who knows what they’re doing.

P.S. Hat tip to Karin Niehoff of the Crescent Montessori School for the connection.

Constructing a Wooden Slide Tray

Handmade, 25 slot slide tray.
Handmade, 25 slot slide tray.

To have somewhere to store the slides I’ve been making, I needed a slide storage box. They’re pretty cheap, but they’re also pretty simple to put together with stuff I could, mostly, find around the house: some scrap wood (from an small wooden CD holder tray that I’m not using any more); a small sheet of clear acrylic (from the hardware store); a short piece of sticky-backed, rubber foam for insulating windows (to keep the slides pressed into place so they don’t move in the box); and some craft glue (ModPodge). For tools, all I used were a few clamps and the saw on a pocket tool.

Using the pocket saw was the biggest pain because I had to cut little slots into the wooden frame to hold the slides. Twenty five slides meant 50 slots, and although the wood was soft, the width of the blade was almost exactly the width of a slide, so if the slot was not perfectly vertical the slides would not fit properly and I’d have to carefully saw it a little bigger. The clamps were a big help with the sawing.

The base of the slide tray was put together with scrap wood and the saw on the pocket tool.
The base of the slide tray was put together with scrap wood and the saw on the pocket tool.

Overjustification Effect: Rewards Inhibit Intrinsic Motivation

Kids become less intrinsically motivated to do something when they expect a reward — grades, gold stars, special privileges — for doing them. In fact, when you take away the reward they’ll stop doing things they were previously interested in doing on their own. It’s called the overjustification effect (Lepper et al., 1973; summary here).

There’s been a lot of research demonstrating the effect. An overview of the research in 1995 (Tang and Hall, 1995) found that the effect extends across all age groups.

The primary theory that explains the effect is called Cognitive Evaluation Theory, and is very well summarized here. This theory suggests, however, that extrinsic motivation may not be bad in all situations, because praise and rewards can also server as a useful indicator to a student of their competence.

Grades Nullify the Benefits of Useful Feedback

Grades detract from learning so much that if you give students comments and grades, they tend to ignore the comments and focus on the grades. If you give them comments alone, they’ll actually learn from the comments.

When giving students feedback on both oral and written work, it is the nature, rather than the amount, of commentary that is critical. Research experiments have established that, while student learning can be advanced by feedback through comments, the giving of numerical scores orgrades has a negative effect, in that students ignore comments when marks are also given.

— Black et al., 2004. Working Inside the Black Box: Assessment for Learning in the Classroom in Phi Delta Kappan, Vol. 86, No. 1, September 2004, pp. 9-21.

Stomata of a Basil Leaf

It’s not always easy to see stomata, the pores on the surfaces of leaves that allow plants to breathe. I tried the leaves of pepper and tomato plants with a dissecting microscope to no avail. However, compared to these, the stomata on basil leaves were enormous. They were actually visible on the lowest magnification (6x), but the higher magnification is necessary to make out the detail.

For these pictures, I was lucky enough to have gotten to try out one of Leica’s research grade, digital microscopes (the DMS1000b). Given that I only had a hour or so, I did not take the time to experiment with all the optimization options, however, the pictures turned out remarkably well, none-the-less. In particular, you might note the highest magnification images, labeled 48(d)x, are just digital enlargements from the 48x magnification pictures.

Having the built in camera makes it an awful lot easier to put images into the online microscope app, and I suspect will make focus stacking a lot easier as well. Since this scope is a bit out of the range of my small high-school budget, I really need to figure out a good, solid way of mounting my point-and-shoot cameras on the microscopes I have.

An Online Microscope

Now that I have a new set of microscopes I didn’t think I would actually need to have an online, simulated microscope to show samples. However, I thought having a series of picture that I could scroll through would be useful to illustrate microscopy concepts such as depth-of-field when I talk about them to the whole class. Once I’d created the depth-of-field simulation, I figured it would not be too much extra trouble to put in a few different magnification levels. Now I have this embeddable online microscope simulator.

It’s started off with a single fly wing as a sample, but I’ll be adding to it as I take more pictures.