Saturday, January 26, 2008

What we did in school today (well, yesterday)

Friday's BIOL 121 class wasn't a lecture at all.  Instead I took advantage of the personal response system (PRS, clickers) to have students spend the 50 minutes working through a particular kind of genetics problem.  The clickers let me give students points for correct answers and also let all of us see where the difficulties were.  (If this course had the tutorials it deserves, this kind of activity would be done there, but that's not an option.)

This let the students build their own understanding of how the alleles (versions of genes) an individual has are passed into the gametes they produce.  Having this process clear is essential for our next step, understanding how the alleles of the two parents determine the genetic properties of their offspring.

The problems we did were designed to take us through increasingly complex situations.  The complexities arise from several factors.  We began by considering alleles of a single gene, then moved to alleles of two different genes.  We also began by considering the results of a single meiosis, which I could demonstrate by labeling and moving around transparent coloured strips on the overhead projector, and then moved to considering the pooled results of the many meioses that produce, for example, sperm.  With two genes we also had to take into account whether they were located on different chromosomes or on the same chromosome, and, if the latter, whether there could be a crossover between them.

I wanted students to work through these problems using paper strips as model chromosomes (they can write the allele names on the strips, move the trips through meiosis, and then look at which alleles end up in which gametes).  Some students did this, and the expressions on their faces showed the discoveries they were making.  But many students clearly felt that working with model chromosomes was unnecessary, and that they could solve the problems either by just thinking about them or by drawing chromosomes in their notebooks.  Sadly, repeatedly getting the wrong answer didn't seem to change this attitude.

I thought these were very simple problems, and yet most students initially got them wrong. This is where the clicker technology really reveals its value. I think I now need to figure out how to tabulate the students' answers so I can share them with other instructors of this course. I think they may also not realize how difficult these concepts are for students.

Although we didn't actually deal with a situation where a crossover did happen, I would like students to be able to deal with this, at least at the level of a single meiosis.  But we'd have to spend at least a bit of class time on it.  Maybe I could demo it with the transparent strips, and then give it as a clicker question for the next class.

Saturday, January 19, 2008

Paper chromosomes

It's late on Saturday, and I just snuck down to the administration area, pilfered some sheets of coloured paper from the Microbiology Dept, and ran them through a shredder belonging to one of the secretaries. Now I have a big cardboard box full of skinny strips of coloured paper to take to Monday's class.

Why? Because on Monday my students will need to learn how mitosis works, which I hope will prepare them for Wednesday and Friday, when they'll need to come to grips with meiosis. By using paper strips as pretend chromosomes, they'll be able to model what chromosomes actually do. Because the strips are coloured, they'll be able to keep track of chromosomes of different types, or with different histories. And because the strips are paper, they'll be able to write the names of alleles onto them.

In the following weeks we'll be doing genetics. I think that most students find genetics difficult primarily because they don't understand meiosis. One reason for this is that they usually encounter it as a series of 'stages', artificially frozen images of what is really a continuous process. Each stage has a name to be memorized, as does each feature of each image. Students have a hard time connecting these static stages with the genetic consequences of meiosis. Watching an animation of the process (even the lovely ones our textbook company has provided) isn't much help.

By encouraging the whole class to use these paper strips simulate mitosis and meiosis for themselves, I hope they'll more easily remember what these processes accomplish. By then having them repeat the simulations with chromosomes labeled with their alleles, I hope they'll come to see how Mendel's 'Laws' are simply an inevitable consequence of what the chromosomes do in meiosis.

Students often mistakenly think that activities like this are babyish, and that as university students they should put away such childish pastimes and settle down to the serious business of learning from books. But I tell them that we're at the frontiers of our abilities here, so we need to use every resource we can to help us understand. This includes a lot of drawing coloured pictures and playing with bits and bobs.

Wednesday, January 09, 2008


The university bookstore has run out of our textbook, as has the nearby discount textbooks store. This may be because they know that a new edition will be used next year and don't want to get stuck with copies they can't sell. Or it may just be incompetence.

The classroom DVD player has epilepsy, or maybe it's Parkinson's disease. Now I recall, it was misbehaving last year too. I've emailed Classroom Services asking for a permanent solution - I suggested taping it shut, with a note telling instructors to use the computer's DVD player instead.

The only way to format short-answer answers to quiz questions in our Blackboard/Vista course management system is with Perl 'regular expressions'. But there is absolutely no support for using these. Not in my 800-plus page Vista manual, not from our part-time Faculty of Science Vista support person (she's doesn't know anything about them and in any case is swamped with other faculty's requests for help) and not from Blackboard, who just point vaguely to web sites offering support for Perl programmers. I do have a Perl for Beginners book, and it has a whole chapter introducing regular expressions, but nothing in there explains why Vista insists on giving students 2/1 for a correct answer. (Yes, it knows the question is only worth 1 point but nevertheless awards 2 points.)

But the students seem pretty good - they had interesting and thoughtful ideas about whether natural selection could happen to snowflakes! Today I gave them some very big ideas to chew on, about the origin of 'life' (of entities that naturals election could act on), and on Friday I'll reprise these to help the students fit them into their world-view.

Sunday, January 06, 2008

Why is it so hard to clearly explain what 'chromosome' means?

I'm polishing up some of the material I'll present in classes #4 and #5 of my intro biology course. I think class #4 is OK. It introduces DNA, chromosomes and genes, although 'introduces' is hardly the right term for something the students will have been learning about about since grade school. In this class chromosomes are just DNA molecules big enough that they have lots of genes, and different chromosomes have different sequences and different genes. But it gets a lot more complicated in class #5.

Class #5 is about how DNA and genes and chromosomes vary. It first introduces the evolutionary concept of homology - defined as similarity because of descent from a common ancestor. Then we take the previous class's introduction to chromosomes etc. and consider the relationship between our paternal and maternal sets of chromosomes, and why we refer to them as 'homologous'. I push the idea of these being different versions of the same chromosome, but students often find the whole business confusing, which puts them in deep trouble when we move on to meiosis and genetic analysis.

Part of the confusion arises because chromosomes are physical things but they are also conceptual categories of things. Two particular DNA molecules in a particular cell in your body (e.g. in the skin cell closest to the tip of your left index finger) are chromosome 13s, but we can also refer to 'your maternal chromosome 13' (of which there are as many as there are cells in your body, about 10^10) and to 'human chromosome 13' (2 x ~10^10 x ~7x10^9). And these are far from identical.

Students need to think about the differences between the versions of human chromosome 13, as well as what unites them, and this isn't easy. This point in the class will be a good place (one of many) to emphasize the importance of variation in biology. For first-year students, having to think about variation and diversity will be new, and it's one of the big things that separates biology from the physical sciences (see Why biology is harder than physics).

Maybe I can give them a sketch that moves out from the single cell to the human population. Let's see what I can pull together from Google Images.

HapMap for beginners?

This year I'm going to use the human polymorphism map (the HapMap) as part of the framework for thinking about genetics and evolution in my first-year biology course. I haven't done this at all before, but I can see a lot of places where it would fit naturally. Most of the other instructors in this course seem to be content to teach the standard Mendelian genetics, but I think students need to learn about the modern resources and issues that the popular media will expose them to.

Classes start tomorrow, but we won't get into the HapMap until next week, when we start talking about DNA and genes and genomes and chromosomes. Monday these will be introduced, and Wednesday we'll consider how they vary. Then on Friday we'll consider how human variation corresponds (or doesn't) to conventional views about human races.

In some ways using the HapMap will mean moving the level of understanding up a notch, but in other ways it may help students make sense of what their genes and chromosomes are.

Friday, January 04, 2008

My recent provocative post on Why biology is harder than physics has been discussed by both Philip Johnson on Biocurious (critically) and Larry Moran on The Sandwalk. (favourably). One commentor on my post, Fred Ross, then complained that I was misusing the term 'complex'.
It's also a pet peeve of mine that biologists insist on calling their organisms "complex," a very specific, technical term which I have never seen justified in biology. They are complicated, but I have seen no evidence that they are complex. There are problems of graph theory that are complex, but the graphs that biologists insist on writing down of protein interaction and genetic networks aren't sufficiently well posed to take any difficult mathematical problem that appears in them seriously.
This is a timely point as I've been thinking quite a lot lately about words that, like 'complex', have both an everyday meaning and one or more specialized meanings. Evolutionary biologists have been fumbling with this problem as it arises for the word 'theory'. When we speak of 'the theory of evolution' we are using the work in a very special philosophy-of-science sense, but creationists then criticize evolution as being 'just a theory', using the term in its everyday sense and counting on the general public not knowing the difference.

One context where such words create big problems is for students learning science. In biology we have words like adapt, assort, base, segregate, phase, message, membrane, sex. Two colleagues even wrote a whole article about many meanings of the one word 'cross' ("The crosses genetics students have to bear"). The teaching fellow associates with my Biology 121 course has been compiling a list of such words, and I'm going to ask my students to start collecting them for their own learning.

But I've also started putting out feelers about such words to linguists and educators, wondering if they have insights into how our brains (and our students' brains) deal with such words. I'm even wondering if we might get together a workshop of researchers in different disciplines to try to clarify the issues they raise.