Wednesday, March 29, 2006

Carnival time

Carnival of Education is up on Right Wing Nation.

Tangled Bank is up on Island Of Doubt.

Carnival of Homeschooling is up on Why Homeschool.

Technorati Tag: teaching-carnival

Sunday, March 26, 2006

Teaching Biology Lab - Week 3

This week we had a busy lab, which means I did not have time for much inpired talking like I did last time. We did some exercises together as a group, while some other exercises were set as stations arund the room and each student did them alone, at their own time.

First, the students used the staining technique they learned last week to find out what kinds of organisms live on their fingers. They saw bacteria from store-bought colonies last week. This week they saw their own cocci and baccili. They also saw quite a lot of molds (and I placed on other microscopes some ready-made slides of Aspergillus, Rhizopus and Pennicilium for them to compare).

Of course, their first reaction is "Yeeew!" and comparisons who had dirty fingers and who did not. This was a nice entry for me to talk about all the symbiotic microorganisms that live on our body, as well as those that live inside of our bodies, mainly in the digestive system. I told them about the initiative to make the Human Genome Project complete by adding the complete sequqnces of all the microorganisms that live inside of our bodies. Without them, we are only half-human. They have co-evolved with us for millions of years and have taken on a number of roles that we are incpabale of doing ourselves, from defense to absorption of some vitamins. Also, it is useful to think of the bacteria in our intestines as an ecosystem. If you get sick and take lots of antibiotics, the bacterial flora is wiped out. Just like an island after a volcanic eruption, there is an orderly succession process that follows. There are species that come first and pave the way for the introduction of other species etc. Over time, the ecosystem changes a number of times until it reaches the mature, balanced stage.

The second big exercise was an experiment that tested essentially two things: 1) which of the three possible catalysts (sand, MnO2 or catalase) is the best at breaking down hydrogen peroxyde into water and oxygen; and 2) what intercellular conditions need to be met for catalase to work properly. Each test tube was a model of a cell. Just like in Week One, when we moved a salt-lake into a rubber hose, this week we moved a cell into a glass test-tube. That way, we can control all the factors one at a time and eliminate the complexities of the real world.

Manganese Dioxide actually worked too well - I think the students put too much in the tube! Sand was pretty slow. Catalase worked great this time around (last time it sat outside the fridge for a couple of days and got stale because nobody told me it has arrived!).

Catalase worked well on room temperature in water at pH=7. It did not work at all at pH=3 and pH=10, which I connected to the mechanisms of pH control I talked about at length last week (when I was talking about homeostasis and rheostasis, I used calcium control and pH control as two examples of processes where the limits are so narrow, there is no daily rhythm at all). Hot water denatured catalase (which is an enzyme, thus a protein). In ice-cold water, there was no reaction at first, but as the water warmed up to room temperature we could observe the reaction (oxygen forming bubbles).

Then I explained in quite a lot of detail what happens in the mitochondria, i.e., starting with food being digested and broken down to glucose, glucose being broken down via glucolysis and Krebs cycles, the electron transfer cascade from one cytochrome to the next with the final recepient being oxygen, and the resulting production of ATP. AS no machine is 100% efficient, there is some wobble in this mechanism as well, resulting in production of free radicals, one of which is hydrogen peroxyde. Free radicals are implicated in cell damage and perhaps the process of aging. Catalase is the enzyme that neutralizes free radicals and protects the cell from damage.

As every machine that transforms one form of energy into another is less than 100% efficient, some of the energy gets lost, mostly in the form of heat. Heat generated by the mitochondria in this process is what warms up our bodies and keeps our core body temperature more or less constant. Hormones, like thyroxine, can modulate the efficiency of the electron transfer, thus modulate the amount of heat produced by the cells in out body, thus controlling thermoregulation.

In the second half of the lab, students went around the lab and got familiarized with various types of plants, including mosses and ferns. They worked as a team to identify tree species from small disks. They made slides from leaves of Zebrina (a terrestrial plant) and Elodea (an aquatic plant) and found stomata in the former but not in the latter, and we discussed how stomata work and why a submerged plant would not need to have them.

We got a Venus flytrap to close its leaves (trick: do not use a pencil or a needle - use the corner tip of a paper towel) and discusssed the mechanism by which the leaves close at such a high speed.

Finally, the students looked at a number of animal specimens laid out in jars (mostly filled with alcohol, only a few in formaldehyde). Their job was to identify at least the Phylum for each specimen, which was, in some cases quite hard. If they managed to do that, they should also have tried to go down the taxonomic levels and try to identify the Class, Order, Family, Genus and perhaps even species (that last one was possible in only a couple of specimens, e.g., flunder and snapping turtle). This is an exercise I like a lot because it gives me an opportunity to give little tidbits about various animals, to tell some cool stories (e.g., how it was discovered here in NC, at Greensboro College, that sponges actually move along the surface), and to dispell some myths that people tend to have about some kinds of animals. This also reinforces the evolutionary message of the course - all those things are related and we explored their exact relationships. Homework: a worksheet - answering ten questions about vertebrate evolution.

Previously in this series:
Teaching Biology To Adults
Teaching Biology Lab - Week 1
Teaching Biology Lab - Week 2

Technorati Tag: teaching-carnival

Thursday, March 23, 2006

On Teaching Science

EducationWonks found an excellent article written by a student about science education in elementary schools and beyond:
Light a fire under students for math, science programs :

Upon reviewing the major points of the bill, however, I failed to find a specific focus on improving science and mathematics education in grades K-6. The bill seems to be geared toward secondary school students - those in junior high and high school - and even college students.

However, interest in science truly begins at the elementary level. A key component of improving the number of American scientists and engineers is igniting interest at a young age and nurturing that interest throughout a child's education.

Educational television can help to interest a child in a subject. When I was young, I watched "Bill Nye the Science Guy" and "Magic School Bus," and I learned much from those shows that I remember and utilize today. High school science teachers often use "Bill Nye the Science Guy" in their classrooms because it is such an excellent resource.

Currently, educational television leans toward multicultural education. While multicultural education is indeed extremely important, a balance should exist. A greater number of fun and educational science shows should appear.

Even if children enjoy math and science when they are young, they may lose or ignore that interest in junior high because of the enormous peer pressure to be "cool." If educators could find a method to make science "cool" and socially acceptable, I believe that many more students would pursue the subject.

Teenagers tend to believe that scientists are social pariahs who are concerned only with their work. Adults should strive to dissuade them from this perception by demonstrating that scientists and engineers are indeed normal human beings.

In addition, illustrating the application of classroom learning to real-life situations would more fully engage a young teenager. Instead of simply learning formulas and doing simple labs, science teachers should demonstrate the widespread effects and applications of their subject. Some teachers are already adept at this, but some are not. Students need applications to which they can relate.

Recently, the government has focused on improving standardized test scores. While that is certainly a worthy pursuit, better test scores will not increase interest in math and science. Politicians and government officials should instead attempt to develop a true interest and involvement in science and math among young people.

Careers in science and math are certainly not ideal for everyone. We shouldn't attempt to force young people into such careers. However, students may miss out on something they truly enjoy if their science education comes solely from a textbook, which I'm sure many would consider quite dull. In order to increase the number of math, science and engineering majors in the United States, we first have to infuse students with an enthusiasm for the subject.

Yes, yes, yes...

(cross-posted on Science And Politics)

Technorati Tag: teaching-carnival

Wednesday, March 22, 2006


Carnival of Education #59 is up on The Education Wonks.

Carnival of Homeschooling is up on PHAT Mommy.

Technorati Tag: teaching-carnival

Tuesday, March 21, 2006

Teaching Biology Lab - Week 2

When teaching the lecture portion of the course, I naturally have to prepare the lectures in advance, and each lecture has to cover a particular topic. This makes biology somewhat fragmentary and I try to use various strategies to connect one lecture to another, one topic to another, one area of biology to another, and especially each area of biology to evolution, as it is the unifying principle of all biology. As I have written before, I often use diseases, especially my favourite (what - you don't have a favourite disease?) - malaria.

On the other hand, teaching the lab is a great opportunity to introduce mini-lectures that appear almost like streams of consciousness, touching on several different topics in succession, veering off on tangents, yet actually serving as unifiers - demonstrating how evolution, ecology, physiology, behavior, genetics etc. are all connected. Teaching adults makes this even easier because they do not expect me to be a Perfect Human Being, and are capable of laughing with me. I can also use more real-life examples and they are not squeamish to talk or hear about sex.

In my lab yesterday, I did something like that. But I had a great starting point - the jigsaw puzzle excercise that I have described before here (also here, and check a long discussion thread here). I kept talking on and on and on. Here is, roughly, what I said and what the students said:

"A-ha, I see what all of you are doing first - turning all the pieces right side up. You know that each piece has a dull grey side and a colorful side. You also know that the colorful side is much more informative than the grey side. The grey side gives you only the information about shape, and even that only as a mirror image, while the other side also gives you information about color and pattern. You knew to do this because this is not, for any of you, a new excercise. You've all done jigsaw puzzles when you were kids and now you are doing them again with your own kids. This, as far as solving puzzles, gives you experience and prior knowledge. If you think of science, this is an equavalent of 6 or 8 or 10 years of grad school. You have background knowledge, you have experience, and you have perfected the use of the puzzle-piece-flipping technique. It is like being really good at using a microsope, something that you learned last week and will again use later today.

So, what are you doing first? Looking at the pieces - that is observation. You still have absolutely no idea what the Big Picture is going to be, but you are looking for a good starting point, so you are soaking in all the information that you can glean from all the jumbled pieces on the table. So you are taking prior knowledge and using it to make sense of observed phenomena.

What are you doing next? You are trying to put some pieces together. Those are experiments. Every time you pick up two pieces and try to put them together you are testing a hypothesis - that the two pieces will fit. Most of the time your experiment fails at the first try, so you try again by rotating the pieces a little bit at a time and trying again. If it does not work, you drop the pieces and leave them for later, as obviously you need additional information. If it works, you publish your findings in a scientific journal and move on to the next hypothesis.

I see that different people have different approaches. Some look for edge pieces and try to put them together. Others are looking for any two pieces that may have shape, color and pattern similar enough that they may fit together, yet others are looking for key pieces - those with most interesting pieces of information, like an eye or a nose.

This is just like personal styles of different scientists. Some start with easily gleaned information - the edges - and systematically build on it, piece by piece. They know that this approach is slow and tedious, but will certainly, over time, build the whole picture. Others do something more risky - go for the most interesting information although it is difficult to study it or to place it in a broader context. They are more likely to fail, but if they get it right, the returns on the investment are enormous - they have figured out what the big picture is going to be without doing all the detailed boring work.

Does anyone already know what the big picture is going to be? No? Any hints and hunches so far? Perhaps a chicken over here, but you are not sure. So, this is still a hypothesis and not yet a theory. The same here with deer? OK.

Do you ever try to force a piece in its place although it does not fit and keep it there?

I do.

A-ha. But later, once you find the correct piece that fits there, will you stubbornly resist removing the right piece?

No, I'd replace it.

Good. That is just like scientists work. Sometimes you tentatively accept wrong data because they serve as place-holders - they help drive the future research. And although everyone is aware that the data are flawed, everyone tolerates it until better data come along.

We seem to be missing a piece!

What piece?

A corner piece. Actually, all corner pieces.

Good. It took you about 10 minutes to discover that. I guess there was nobody here who always starts a jigsaw puzzle by looking for corner pieces. Do you really need the corner pieces in order to figure out what the big picture is?

No, not really...

Correct, the key information is unlikely to be at the periphery. But, you are humans, so it drives you nuts that the corner pieces are missing, so here they are - you can have them.

But, those are not our corner pieces they are theirs!

That's fine. I made sure when I bought the puzzles that the pieces have exactly the same shapes. You can use the wrong corner pieces as place-holders. They fit by shape, although they do not fit by color and pattern. By putting them in, it can help you add a couple of more pieces together. But in the end, you will not be happy with semi-correct data and will put a lot of effort into solving that problem. Perhaps, as science is collaborative, international, and does not recognize borders, you can negotiate with the other group to exchange the corner pieces later on in order to get a more perfect picture. It is like sharing data or sending each other laboratory reagents, or publishing all your findings in reputable journals for all to see.

In the same vein, I could have ruined some pieces by removing the colorful top layer. You would have only shape to work with as there is no more color or pattern to it. You would still be able to fit it into the puzzle and although it may look ugly and incomplete, it would help you build the rest of the puzzle by adding more pieces to it, and it is unlikely to affect the Big Picture. This is equivalent of incomplete data. You can reconstruct a piece of history from an ancient manuscript although it is partially burned. You can reconstruct the evolutionary history of a particular group of organisms by working with an incomplete fossil record - after all, there are other puzzle-pieces supporting your theory, for instance the data from genetics, embryology, comparative anatomy and physiology, etc.

Any ideas yet what the big picture is going to be?

We are going to have a bird - not the chicken as we first thought, but more something like a duck, as well as a cat, we think...

We thought at first it was going to be a deer, then we thought for a while that it was going to be a squirrel, now we are back to deer.

OK, so you have changed your minds over time. How easy or hard was it for you to change your minds?


Good. So, you did not have a great emotional need to stick to your first guess and, once new information came in - when you placed a number of new pieces, you adapted your thinking to fit the new information. How sure you are that it is going to be a deer? Or a cat and a duck?

Pretty sure.

100%? Do you think it is possible that you may change your mind again as you place more and more pieces.

Perhaps, but unlikely.

OK, so now you have moved from the hypothesis stage to the theory stage. You are quite confident that you have a correct solution for the whole puzzle, although you are still missing many, many pieces and some modifications of the theory are still possible without changing the main gist of things.

Ha! Now this was interesting! You just put together an eye piece together with a nose piece and both to a group of green grass edge pieces. This is a relatively small amount of work: just two pieces being put together and placed in the context of the whole theory, but it is huge in terms of information content. This is something you would publish in a major journal, like Science or Nature or Journal of American Medical Association. On the other hand all those green edge pieces, as many as you have already put together after a lot of tedious work, as important they are for building the whole picture, are just not that interesting - they say little about the Big Picture or if your theory is correct. That is kind of stuff you would publish in the American Journal of Green-Grass Jigsaw-Puzzle Research - a lower-tier journal for sure.

Putting together pieces that fit well with your theory is sometimes called "normal science". Putting in the pieces that result in your changing your mind on what the Big Picture is going to be is sometimes called a "paradigm shift". So, you work within a paradigm that it is a squirrel and keep looking for pieces that have squirrel-like properties and putting them in, until you run out of such pieces and it looks less and less likely that it is a squirrel. Then, you find a couple of pieces that persuade you that you were wrong and that the Big Picture is the deer. You have experienced a paradigm shift, and now you are going to do some normal science within the new paradigm - adding more and more pieces with the assumption that it is going to turn out to be a deer.

We have a paradigm shift right now! It is not an adult deer but a fawn!

Great. It is a pretty big change. Although a fawn is technically a deer, there is a difference that is important in the description of your theory. You are now going to call it the Fawn Theory instead of The Grand Theory of Deer. Sometimes theory changes a lot, sometimes a little. Even if you think that the piece that will fill this hole is going to be just grass, if it turns out that it also contains a little flower, this is change in the theory. It does not overturn the whole theory - it is still going to be a fawn, but it will be a change in details. It is like adding sexual selection and neutral selection to the natural selection - the theory of evolution is not overturned - it just gets more detail and sophistication.

How about now? Do you think there is a possibility that adding another few pieces can make you completely change your mind on what the Big Picture will be? No? You are completely sure that you are correct although so many pieces are still missing from the puzzle? You would place it at 100% now? Yes? OK. But you, if you were a scientist, would never say that out loud, because, technically, this may happen no matter how sure you are. In well-supported theories, like relativity, plate-tectonics or evolution, chances of overturning the whole theory are practically zero, but it is considered bad form, philosophically incorrect, to state that a theory is Truth with capital T. Every new piece of the puzzle just confirms that all of life on Earth evolved out of a single common ancestor. Every new piece confirms that natural selection is the major mechanism of evolutionary change. Not a single piece of new information is at odds with those notions and have not been for the past 150 years of thousands and thousands of scientists looking really hard.


What happened?

It is not one fawn - we have two! It was kinda hidden in one of the corners so we missed it at first.

Great. So, you get to keep the original theory of the fawn and get to add a second fawn. It is like keeping natural selection but adding sexual selection into the theory, something that Darwin himself did a couple of decades after he published the Origin of Species.

OK, how much your understanding of the whole picture changed since you just started the puzzle? A lot? Well, the science changes the same way. Theory of evolution from 1860s is not the same as the theory of evolution in 1900s, or the theory of evolution of 1940s, or 1960s, or today. We cannot use Origin of Species as a textbook today because so many details are different. Darwin got many details wrong, and in cases in which he got things correctly, he did not have much supporting evidence - his puzzle was based on too few puzzle pieces which we now have. But what Darwin got right was the Big Picture. He said it was going to be a Duck and the Cat and we still agree that it is a Duck and a Cat, although we now also known which flowers are growing around them and that the cat is very young and grey and looks like it may be an Abyssinian and the duck is also very young - just a duckling really and it is yellow and really cute. Darwin was right, but our knowledge is much more complete.

Also, if I was going to be really mean to you I would have also removed all the edge pieces. That way, you can never finish your puzzles, just like the work of science is never finished - there are always more details to uncover and more hypotheses to be tested. Also, no scientific theory lives in isolation. If I left the edges out, you would be able to connect one whole puzzle to the next puzzle to the next puzzle. A century or two ago, it was easy to ditinsguish what was biology, what was astronomy, what was physics, or chemistry or geology. Today, we know so much, the borders between disciplines are blurred. We have physical chemistry connecting physics and chemistry, biochemistry spanning biology and chemistry, biophysics in-between biology and physics - it's all connected. Not to mention how much one field uses the techniques developed by another field or is based on the knowledge developed by another field.

Now quit doing the puzzle.


What? Why groaning? I bet if I asked you 15 minutes ago you would have had no problem quitting. You, just like all scientists, are kids at heart. At the beginning you may have wondered what on earth are we doing playing jigsaw puzzles in college, but now you really like doing it. Fine, you may continue and finish the puzzles. Happy? Just like scientists, more you know about something, more you want to know. It is so hard to get scientists to retire - many work until the day they die. There is always another experiment to do, another hypothesis to test, another piece of information to collect. More you know, more you realize how much more there is to know, and more you want to learn more. It is a positive feedback loop...wait, do you remember what a positive feedback loop is? You all have had lecture portion of the course at some point in your careers. Can anyone give me an example of a positive feedback loop from human physiology - the way the human body works?

When you cut yourself, the way the blood clots and makes a scar.

Excellent, that is a very good example. The cut makes a molecule act on another molecule which energizes another molecule and that molecule may recruit more copies of the first molecule so the whole process works faster and faster over time. Let's make a more general description of a positive feedback loop. A process A triggers a process B which, in turn, triggers process A again. Moreover, it multiplies over time as A may trigger 10 instances of process B which in turn trigger 10 instances of process A each, so very soon you have both processes happening thousands of places simultaneously. Does anyone know any other examples of positive feedback loops in the human body?

[expectant looks]

OK, here's one. Breast-feeding. You all have children so you should know this one. When a baby is hungry it latches onto the nipple. There are receptors in the nipple that sense that and send a signal to the brain - more specifically the part of the brain that you may remember from the lectures called the posterior pituitary gland - which secretes a hormone called oxytocin - no, not Oxycontin, that is what Limbaugh is taking. Oxytocin makes the milk glands eject milk. The baby gets the milk and is prompted to suckle on the nipple some more which releases more oxytocin which releases more milk which makes the baby suckle more etc etc the process reinforces itself until the baby is not hungry any more and quits eating. How about another example? Also has to do with babies?

[blank stares]

OK, giving birth is a positive feedback loop, too. When the baby is ready to be born it signals the mother, which makes the uterus contracts. At that moment you know the baby is coming that day and you get in the car and go to the hospital. That first contraction of the uterus pushes the baby down a little bit. That movement stretches the uterus a little which results in release of more, again, oxytocin, which makes uterus contract again, which pushes the baby a little bit more out, which stretches the uterus more, which tirggers release of more oxytocin, which makes the uterus contract again....over and over again, faster and faster, until the baby is completely out. Good, how about another example? It also has to do something with babies. Anyone? Come on - you all have children - you should all know this outside of biology class, just from real life!

[eyes glazed over]

OK, here it is. It is making babies. Sex is a positive feedback loop. Just like doing the puzzle, it is easy to stop at the beginning, and much harder farther along you go. More you do it, more you want to do it and faster you go, until the orgasm in the end.


All right. Right off the top of my head I cannot think of another example of a positive feedback loop in the human physiology. Those are really rare. Most of the events are negative feedback loops. Can anyone give me an example?

Walking. It is loosing and regaining balance. You lean forward and you catch yourself from falling by stepping out.

Good. That is a pretty good example. Pretty much every time something goes away from the optimum, there are mechanisms that bring it back to the optimum. Put more formally, an event A triggers an event B which supresses the event A. For instance, if a hormone surges, there will be mechanisms that inhibit further synthesis and release of that hormone.

This whole concept of negative feedbcak loops keeping everything in the body at an optimum is called homeostasis and it can be depicted like this:
Let's say you exercise or go out in the hot sun. Your body temperature rises. As a response, you start sweating, perhaps lower your metabolic rate, there are changes on the sub-cellular level that we will discuss next week, you wil also try to find a shade and drink something cold. Thus, there are biochemical, physiological and behavioral mechanisms that will drive your elevated body temperature back towards its normal level. Likewise, if you go out in the cold and your temperature starts dropping, your metabolism gets cranked up, you shiver, you put on more clothes, go inside, light up the fireplace and drink hot chocolate - again biochemical, physiological and behavioral mechanisms that will drive the temperature back up to the optimum level.

Now, all this is correct, but this graph is correct only if the X-axis spans time in the range of minutes, e.g., from 0 to 60 minutes for the whole length of the graph. How does it look like if the X-axis spans 24 hours? It looks more like this:
This does not mean that homeostatic mechanisms do not work very well - they do. It just shows that the optimal values - those defended by the homeostatic mechanisms - are not static. They are dynamic. They change predictably over the course of the day. For instance, your body temperature is lowest just before dawn and highest in late afternoon. On the other hand your cortisol levels in the blood are the highest early in the morning, preparing your body to wake up and seize the day! This controlled dynamic change in optimal values is called rheostasis. The daily rhythms are called circadian rhythms and there is a small area at the bottom of the brain which contains a few thousand brain cells that act as a clock, a circadian clock, which acts a relay - telling other parts of the brain and other parts of the body when - over the course of a single day - to raise and when to drop the optimal values of whatever processes they govern.

[Update: Here I spent some more time describing two functions that do not show rhythms - blood levels of Calcium are constant and blood pH is constant because the optimal values have an extremely narrow range. I talked about parathormone here, etc.]

Let's take a break now. Please break down the puzzles and put them in these boxes here. By the time we come back, the slides you prepared first thing this morning will be dry and we can stain the bacteria and look at them under the microscope. This is obviously not hypothesis-testing. You are just learning a technique - how to flip the puzzle-pieces right side up so you can make observation of shapes, colors and patterns of...bacteria. Once you know how to do it, you can go on and make your own further obeservations and make predictions and test hypotheses. We'll do that, too. You will press your thumbs on the agarose in these petri dishes that I poured this morning and next week we are going to see what kinds of critters live on your fingers.

Finally, at the end today, we are going to dissect owl pellets. By using the charts I give you, you will try to figure out which pellet comes from a Northwestern owl and which one from a Southeastern owl. Your homework will be to explain the results and the methodology you used to figure it out and then, next week, we will talk about this some more."

And that is what we did. Wow - what a roller-coaster. From philosophy and sociology of science (no need to critique Kuhn at that level of instruction), through various areas of physiology to circadian rhythms, just to be continued with some microbiology and ecology in the second half of the lab. This is so much fun!

More in this series:
Teaching Biology To Adults
Teaching Biology Lab - Week 1
Teaching Biology Lab - Week 2
Teaching Biology Lab - Week 3

Technorati Tag: teaching-carnival

Friday, March 17, 2006

Education-related carnivals

The latest edition of the Teaching Carnival is up on The Salt Box.

Carnival of Education - Issue #58 is up on Education Wonks.

Carnival of Unschooling - the third edition is up on Atypical

The latest edition of the Carnival of Homeschooling is currently on Common Room.

Technorati Tag: teaching-carnival

Thursday, March 16, 2006

Teaching Molecular Biology to people who are afraid of it

Afraid of the dense terminology of molecular biology? Don't despair! David Ng came to the rescue with a clear, easy and beautiful cartoon guide to DNA replication, over on The Science Creative Quarterly.

I may use it next time I teach the lecture portion of the Intro Bio course (in May). I hope that transcription and translation will come soon - in time for that.

Technorati Tag: teaching-carnival

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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Wednesday, March 01, 2006

Freshman Science Course

Rob the Dirty Liberal has some interesting and thought-provoking ideas about a college freshman science course - or how one can be designed: University Science Education: A New Approach. What do you think?