Sunday, March 12, 2006

Teaching Biology Lab

Yesterday I had my first class of the semster of the BIO Lab at the community college. This is the first time with a new syllabus, containing some new excercises.

At the beginning, we took a look at some cartoons, as examples of Inductive and Abductive Arguments, or, in other words, as examples of the way scientists think and work, which I used to explain why scientists never state "this is the Truth", but always sound a little less decisive. I also used it to explain the scientific definition of "theory" as opposed to the common usage of the word. I went through several theories (gravity, relativity, plate tectonics, etc), and ended with the Theory of Evolution, which - I stated with the authority of the Instructor-Who-Knows - is one of the best supported theories of all science.

One of the cartoons, the one described here, is titled “Dick should not drink the coffee.”:

Frame one: three people sitting at a counter with coffee cups.
Frame one: the person on the left takes a sip of coffee.
Frame two: the person on the left drops the cup and looks sick and drops the cup, the person on the right takes a sip of coffee.
Frame three: The person on the left keels over, the person on the right looks sick and drops his cup.
Frame four: Person on the right keels over, the person in the middle looks curiously at the contents of his coffee cup.

The second cartoon, named "The fellow stole the purse", had three frames:
Frame one: A room with a table, a purse on the table and a clock on the wall showing 5 o'clock
Frame one: A guy passes by the table and notices the purse
Frame two: The guy looks left and right (pretty shiftily). The time is 5 o'clock.
Frame three: The room is empty, the guy is not seen, the purse is not on the table, the clock shows 5:05.

The third cartoon, "Spot chased a cat":
Frame one: A man is walking a dog on a leash through a pretty meadow. The sun is shining.
Frame one: A text bubble points to somebody outside of the frame saying"MEOW!"
Frame two: The man has a surprised look on his face. He appears to be falling. He has just let go of the leash. The dog is gone from the frame. Someone outside the frame is saying "ARF! ARF! ARF!"

The students really jumped on this, showing what alternative hypotheses were possible to explain what we saw in the cartoon, but that would point to the titles being inaccurate. For instance, in the first cartoon, we are not 100% sure that the liquid in the cups (all three, or any one of them) is really coffee. We also do not know whose name is Dick.

In the second cartoon, we do not actually see the fellow taking the purse, so it is possible that he did not take it. Five minutes is sufficient time for someone else to come by and ake it. Perhaps the time difference between the frames two and three is not five minutes but 12 hours and 5 minutes, or 24 hours and 5 minutes, or even years apart. Perhaps the guy picked up the purse because it is his, or belongs to someone he knows, or because he works there and will put it in the "Lost and Found" office.

Likewise, in the third cartoon, we do not know whose name is Spot: the dog, the man, the cat or someone else? Again, we are not sure if the time difference between the two frames is just seconds (the cartoonist convention) or much longer. Perhaps the time is even going in reverse! Perhaps the cat was chased by another dog, and the dog from the cartoon chased the other dog. Perhaps somebody or something else said "Meow" - a dog, a person, a squirrel, a machine... Perhaps it is a monster mutant giant cat from the sci-fi channel that chased and grabbed the dog!

I used the cartoons to emphasize a couple of points:

First, that seeing something happen is not neccessary for making correct conclusions. We never see the coffee, or the act of picking up the purse, or the cat. Likewise, in science, we can infer information about events that happened far away (as in billions of miles away deep in the cosmos), about events that are too small for us to observe (e.g., atoms and subatomic particles), and about events that happened in the past (e.g., burning of Rome, or Big Bang). Likewise, we need to use inference to figure out what happens at timescales that are too short (microseconds, e.g., events at the atomic scale, activity of a neuron, etc.), or too long (millions and billions of years, as in plate tectonics and evolution).

Second, that we use background knowledge (cartoon conventions, what substance is usually found in coffee cups, how do English-speaking people transcribe noises made by dogs and cats, how to read the time off the clockface, the fact that usually dogs chase cats and not the other way round, etc.) to inform our analysis.

Third, that although the alternative hypotheses may be correct, they are all less likely than the one stated in the title, because all the alternatives require either unusual events, or thinking up additional players - which got me to the rule of parsimony and how it is used in science.

Finally, if we do additional research of such situations in real life, we may be able to put a number to the probability that the title is accurate versus the probability that any alternative hypothesis is correct, ie., we can use statistics.

Once we were done with the cartoons, we did two related excercises, both involving solving a crime scene mystery. Although nobody witnessed the murder, we could figure out who the killer was because we could match the hair samples and blood samples to one of the suspects (and not to the other suspects or the victim). Both of those excercises come in easy-to-do kits from Ward's and take about two hours to do them both. All along, as we were doing these, I was going back to the cartoon excercise and reminded them of some of the prinicples, e.g., parsimony, the lack of necessity for actually observing an event in order to correctly infer what happened (a canard often invoked by creationists - "nobody observed evolution in action", which actually is not true, and even if it was it does not matter, as there is plenty of evidence to infer that evolution occured before and is occuring right now, at time-scales longer than what we can usually pay attention to), etc.

In the second portion of the lab, we did an experiment with brine shrimp (Artemia salina). Usually this is done with larval brine shrimp and the students count the numbers of shrimp under the microscope. However, years ago I realized that adult shrimp work just as well, are easier and quicker to count and easier to get (I do not need to hatch and raise them myself in advance of the class - I just buy a dollar worth of them and a quart of water in a local fish store, sufficient for 5-6 racing tubes).

This is an excercise in which nature is brought into the lab. As a salt lake, brimming with brine shrimp, evaporates in summer, many aspects of water quality change, e.g., temperature and pH. Brine shrimp detect the changes and swim towards the deeper recesses of the lake, somewhere in its center, where they mate, lay eggs and finally, once the lake is completely gone, die. The eggs can survive compete dehydration for quite a long time. When the first rains of fall appear, about half of the eggs hatch, counting on the lake re-establishing itself again. However, this may be a mistake - a sporadic mid-summer shower that does not fill the lake. Thus, about a third of eggs hatch after two cycles: dry-wet-dry-wet. Finally, the remaining 1/6th of the eggs requires three such cycles. This way, no matter what strange pattern of weather occurs in any given year, the shrimp are highly likely to repopulate the late in fall (or the little "Sea Monkey" containers you buy in toy stores - that is what this animal is).

The point of the excercise is to tease out the factors, one by one, and figure out what do the brine shrimp really cue onto - something that cannot be done in the lake itself (though the students wanted to go to a field trip right away, what with the 80 degrees weather outside!).

The students filled clear plastic tubes (about half-inch in diameter) with the shrimp and water, closing the tube with rubber stoppers on both side and trying not to have air bubbles remaining in the tubes. They attached each tube to a yard stick using clamps at 0 inch, 12 inch, 24 inch and 36 inch markers (the first and the last are very ends of the tube). The clamps were left loose so the brine shrimp could feely swim through the tubes, and the tubes were laid horizontally on the desks.

We let the tubes sit for a while to allow the shrimp to equalize their densities along each tube (it is hard, due to the cumbersome way of injecting the water+shrimp into the tubes by syringe, to get them equalized to begin with). Then, we left one tube as a control, in one we added some acid on one end, in one we added some base on one end, in one we covered one third of the tube with a Ziploc bag filled with very warm (but NOT boiling hot!) water, and on one we placed a Ziploc bag full of ice on top of one third of the tube. We gave the shrimp about 30-45 minutes to swim weherever they wanted, then screwed down the clamps (to prevent the animals from moving from one segment of the tube to the next) and counted the numbers of animals in each segment, writing the data on the whiteboard.

In advance of placing the treatments, the students stated their hypotheses - where are the shrimp going to swim? The data confirmed their expectations: the shrimp swam away from the heat (as the shallow water in summer would be), towards the cold (but remaining at the edges of the ice-bag, not under it - that was too cold even for the bottom of the middle of the lake!), away from acid and away from base (again, away from the edges where much more decomposition is likely to occur as the fish and other animals and plants start dying).

They correctly pointed out to the factors that may have affected their data (e.g., the placement of tubes in relation to the ceiling lights). Then I gave them a little spiel about the neccessity to repeat this a number of times and do the statistics in order to be confident about their findings. Repetition can also control for some of the other factors, by filling the tubes from the left in half of the cases and from the right in half of the cases, while always applying the treatment on the left end of the tube; by placing the tubes in different relations to the lights (or somehow manipulating the lighting conditions in the room to be more evenly spread), etc.

In addition to these treatments, we also did another test. Brine shrimp are diurnal migrants. During the day, they swim down towards the bottom (away from sunlight) - this is negative phototaxis, i.e., running away from light. During the night, they swim towards the surface, toward the moonlight - positive phototaxis.

The intensity of light tells them if it is day or night. The circadian clock tells them if it is time for negative or positive phototaxis. What we do not know is, if the swiming "up" and "down" is aided by gravity, or by the direction from which the light is coming. In other words, when they see light, and the clock tells them to swim towards the surface, do they swim towards the light no matter where it is, or do they swim "up", no matter where the light is?

By placing a tube in a horizontal position, we eliminated gravity as a factor. Placing one end of the tube directly under the ceiling light and covering the other end of the tube with a stack of pices of black screen (and just a couple of pieces of screen on the middle segment), we built a light gradient. The shrimp swam towards the dark, telling us that they new that it was daytime, and that they do not need informaiton about gravity for diurnal miration, but do direct phototaxis: swim towards the light wherever it may be.

More next week, as the course progresses...

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