RRTeaching

A modern genetics problem

2011-12-17T13:18:00.000-08:00

This problem was on the final exam of our new Fundamentals of Genetics course. It's an example of what I'd like our students to be able to do.

(10 points) The ideogram above shows a normal child’s genome, with her chromosomes coloured by 23andMe to show the results of genotyping her DNA and the DNAs of her maternal grandparents. Blue segments indicate blocks of alleles shared with her maternal grandmother, and white segments indicate blocks of alleles shared with her maternal grandfather. Hatched segments could not be analyzed because they have too few SNPs.

a. (1 point) What genetic process is responsible for these blocks of alleles?

b. (2 points) When and where did this process occur?

c. (2 points) What property of the child’s maternal chromosomes 11 and 14 is unexpected? Why is this property unexpected?

d. (4 points) Suggest two different kinds of events that could explain this unexpected property. Give rough estimates of the probabilities of the events you propose.

e. (1 point) The black triangles above some chromosomes show the locations of SNPs linked to effects on nose shape. What do these predict about the child’s appearance?

What genetics should all our students learn? ("Stop, we're teaching the wrong stuff!")

2011-12-17T11:39:00.000-08:00

Several years ago I was asked to take charge of developing a new second-year 'fundamentals of genetics' course, to replace our program's long-standing third-year course (a legacy from David Suzuki). So I put together a committee of genetics instructors (profs, sessionals, a TA), and we developed a new set of learning objectives and an ordered list of topics to be covered (a syllabus). The committee then disbanded , leaving me to implement its work, first as a small pilot class (last winter) and then as a regular course (just finished).

We thought we had been quite radical, because we'd made a very big change in how our course would teach the two big concepts students needed to master - how genotype determines phenotype and how genetic information is inherited. Traditional genetics courses start with Mendel, and, following in Mendel's footsteps, use analysis of crosses to reveal all the basic concepts of classical genetics; this is Suzuki's 'Genetic Analysis' approach. Our new syllabus began not with Mendel but with three weeks about how genotype determines phenotype (no crosses yet), followed by two weeks just about how inheritance works (leaving phenotypes out entirely) Only then would it introduce Mendelian genetics, and then use the standard genetic analysis framework to teach the more complex concepts.

It wasn't until I started to teach the pilot section that I realized we'd been much too conservative. We'd simply assumed that the goal was to teach students the standard 'classical genetics' concepts. But what we should have done is first thought long and hard about what students should be learning in a modern 'fundamentals of genetics' course. That is, what genetics facts and concepts will our students actually use, not just in later courses but in the rest of their lives?

Way back, the answer was that students needed to learn genetic analysis, for two reasons: First, analysis of how phenotypes are inherited in crosses used to be the most powerful tool for understanding how organisms work. Even if students weren't going to go on to do this analysis themselves, as biologists they needed to understand how it was done. And following in the footsteps of the great geneticists was thought to be the best way to learn it. Second, genetic analysis is hard, and learning to do it trains the mind in rigorous thinking. Genetics students' experience at solving complex genetic problems was expected to make them better at solving all kinds of problems, in everyday life as well as academia.

Although genetics has changed dramatically, this motivation has largely been left unquestioned. Although I didn't buy the 'following in the footsteps' part, I accepted the rest. But the importance of classical genetic analysis to biology is shrinking day by day, displaced by powerful molecular methods. Worse, improved understanding of students' learning suggests that most genetics students pass their exams using pattern-matching rather than the general problem-solving skills we thought they were developing.

So, what should today's biology students take away from a 'fundamentals of genetics' course? What will they use in later courses? What will they use in the rest of their lives? Are there other concepts that every educated person know about?

So here's a partial list of learning objectives for a modern course in the fundamentals of genetics. Yes, I know these aren't all phrased as actions students should be able to do, they aren't in a sensible order, the list is incomplete, and the syntax isn't even consistent. PLEASE give me suggestions for improvement in the comments.

Students should be able to detect basic errors in news coverage of genetics stories.
Students should be able to understand why a genetic test or sequencing aids medical diagnosis and treatment.
They should understand how genetic differences affect health risks.
Which genetic principles apply to all organisms.
The extent to which the differences between individuals (humans and other species) are due to differences in their genes.
How the phenotypes of diploid organisms are affected by interactions between different versions of a single genes, and between different versions of different genes.
How offspring inherit genetic information from their parents (how meiosis and mating work).
How genes and genomes change over the generations and over evolutionary time.
At a simple level, how control of gene expression leads to differentiated phenotypes (a special case of gene interactions).
They should be able to think about ethical and societal issues arising from genetics.

Twitter in the classroom?

2011-09-05T09:01:00.000-07:00

The big 'Fundamentals of Genetics' course starts on Wednesday, and I'm going to try letting students ask questions in class with Twitter. Of course they'll still also be able to ask their questions the old-fashioned way, by raising their hands, but Twitter has some nice features.

I'll tell students that, if they have a question about what I'm saying, they can post it to Twitter with the hashtag #biol234. When it's time to pause for questions, I'll display the #biol234 Twitter feed on the screen for everyone to see. Maybe I'll give us all a minute to read the top questions, and then I'll answer them, integrating answers to different questions where this makes sense. And then I'll ask for verbal questions.

Students in the class can follow the #biol234 feed on their smartphones and laptops, and can 'retweet' questions that they think important. Questions that are retweeted will rise to the top of the feed list. The lecture room has two screens, so I plan to use one for the powerpoint slides from my laptop and a second for internet content from the built-in podium computer. (This screen will be blanked when I'm don't want students to attend to it.) One web tab will be the Twitter feed, ideally set so only the top 5 or so questions are visible.

Other features and concerns?

Students can also use Twitter to answer simple questions posed by other students.

Students who want to contribute will need to have Twitter accounts as well as smartphones or laptops. This is good - I don't want questions to be posted anonymously, as this can lead to silliness and unpleasantness.

Students won't be disadvantaged by not participating. If they don't bring laptops or smartphones to class, or just don't want to use them for this, they'll still see the Twitter feed and and my responses.

Won't students who follow the #biol234 feed on their smartphones/laptops be distracted? Well, they'll be distracted from watching me, but at least they'll be thinking about the material.

One thing I really like about this is that it will help shift the focus from answers to questions.

If this works well I'll need to shorten the presentation parts of my classes, to allow more time for the questions, but this is something I'd want to do anyway.

I don't know anything about Twitter apps, but I suspect that the Twitter web site isn't the best interface for what I want to do. I'll probably ask the students for suggestions, but I'd appreciate any suggestions from readers.

Teaching evaluations

2011-07-07T17:07:00.001-07:00

Results of student survey: no need to have a focus group

2011-04-23T09:31:00.000-07:00

I've analyzed the preliminary results of my student survey. It provides some ideas of ways the course could be improved, but my focus-group experts agree that it doesn't raise any issues deserving focus-group investigation.

What they said:

Agree/disagree (~Likert scale):

I had the necessary background for the course. Most agreed
The readings and reading quizzes prepared me for the lectures. Neutral
The iClicker questions were not challenging enough. Most disagreed
The Genetics in the News slides took too much time away from course material. Neutral
The homework increased my comprehension of the lecture material. Most weakly agreed
The tutorials helped me learn to solve genetics problems. Most agreed
Having two mini-midterms and a midterm was too much testing. Most disagreed
The course grade was based on too many different components. Most disagreed
The workload was much higher than for other courses. Neutral
I feel prepared to deal with genetics issues that may arise in my life. Most agreed

Written Answer Questions:

Should any topics be cut from the course material? Most said no.
Were any topics missing from the course that you wish had been covered? Most said no.
A pizza-lunch focus group will be held later this month; all students are welcome to attend. Please mention below any specific issues that should be raised then. Below is what they said:

Workload, discrepancy between difficulty of lecture material and what was tested (in tutorials, reading quizzes, midterms, etc.)
The tempo of the class. The first half seems like a review, and all the new stuff are in the second part.
Methods of assessing learning in this course.
No specific issues.
How much we liked the format of the lectures -the methods in which we tried to prepare for exams
Mini-Midterm format. I think that the midterm was a fair examination however, the second mini midterm had a multiple choice question that had about 9 choices and was worth about 6 marks. I felt I did good on the rest of the exam but still didn't get a great mark because of 1 MC question.
How to study for the final. Every test has been a different format, what to expect.
I would like to suggest ways to make homework more helpful in preparing us for the exams. Also, maybe investment
into custom booklets with some notes and problems sets like Bio 201.
They are too little guidance in this course
Tested materials --> what to expect in midterms/exams weren't very clear
Overall structure of how the course will be run next year. Textbook assignment and readings. Better formatting for the meiosis/mitosis content from the beginning of the year - personally I am still fuzzy, even though the concepts were stressed to be very important.
I think going over online homework and reading quiz questions in class would help. Or perhaps explanations for the answers could be posted online because there are still questions that I don't understand. I also think the amount of work this course requires should be re-evaluated. The amount of reading is quite heavy and having two quizzes (homework and reading) PLUS peerwise PLUS tutorial each week is a lot.
How this course and its changes (234 vs. 334) related to other courses, such as Biol 335.
How to study genetics
I think that the easiness of this course should be covered. I felt that this course reviewed a lot of material and didn't cover that much new material.

Ranking the course components:

Many components of this course contribute to the final grade. Please try to rank them according to how valuable you found them, taking into account your learning gains and the amount of time you invested in them. For example, an activity that took a lot of your time but resulted in little learning would score low.

Tutorials High
Peerwise questions Low
SNP report Low
Calibrated Peer Review Low
Online homework High
Reading quizzes No consensus
Studying for midterms No consensus
Attending lectures High

Only 21 of the 38 students have completed the survey so far. That's certainly enough to go on, but I'll reanalyze the responses after the final exam marks have been posted (that's the last time the students will give any thought to the course).

The focus group plan

2011-04-12T11:36:00.000-07:00

OK, I've consulted with the local experts. They had excellent advice on how to proceed, and will be able to run the focus group for us if we decide it's what we need.

The first step is to analyze the responses from my student survey. The survey questions are pasted below - for the purpose of the focus group the most important question was the one asking for topics for a focus group. Once I've consolidated the responses I'll send them to the local experts and we can decide whether issues were raised that should be considered by a focus group. For a one-hour group we only want two or three such issues, and maybe one in reserve.

An ideal focus group would be about 6 students, and as few as three would be OK, so I think we can safely schedule it in May rather than before the final exam. (And we do have money for pizza in the course budget.)

Survey Questions:

Agree/disagree (~Likert scale):

I had the necessary background for the course.
The readings and reading quizzes prepared me for the lectures.
The iClicker questions were not challenging enough.
The Genetics in the News slides took too much time away from course material.
The homework increased my comprehension of the lecture material.
The tutorials helped me learn to solve genetics problems.
Having two mini-midterms and a midterm was too much testing.
The course grade was based on too many different components.
The workload was much higher than for other courses.
I feel prepared to deal with genetics issues that may arise in my life.

Written Answer Questions:

Should any topics be cut from the course material?
Were any topics missing from the course that you wish had been covered?
A pizza-lunch focus group will be held later this month; all students are welcome to attend. Please mention below any specific issues that should be raised then.

Ranking the course components:

Tutorials
Peerwise questions
SNP report
Calibrated Peer Review
Online homework
Reading quizzes
Studying for midterms
Attending lectures

Focus group?

2011-04-09T09:23:00.000-07:00

I've been advised that the best way to collect useful feedback from the students in my genetics pilot course is to have a focus group. This initially seemed like a great idea (book a room, order pizza, tell the students), but I'm gradually realizing that implementing it will be difficult. Several issues need to be dealt with.

First, I don't even know what running a focus group involves. I expect that the discussion would need to be coordinated, and some record of the discussion kept. This might just be notes, but an audio or video recording would be better. But if a recording was made, then someone would have to later go through the recording, pulling out the important information. And if there's no recording, would the person who is coordinating the discussion also be able to take the notes, or would a separate note-taker be needed? How much expertise is needed to coordinate the discussion - can the needed skills be picked up in 5 minutes, or is formal training desirable?

Second, who is available to do this (call them the 'facilitator')? To get uninhibited discussion the facilitator shouldn't have been involved in teaching the course or grading the students. The person who recommended having a focus group initially suggested having the course TA run it. This would be only slightly better than having me run it, and the TA quickly pointed out that she was not an appropriate facilitator.

There are other instructors who I could ask to act as facilitator, but I have no idea (1)how much work I would be asking of them; (2) whether this would be considered a personal favour or part of their job; (3) whether any of them have whatever skills or experience a facilitator needs. Might there be a Faculty of Science teaching/research person who could do this? Should I contact our Centre for Teaching, Learning and Technology for help?

Third, I also don't know when we should hold the focus group. I was initially thinking that we should do it in the week before the final exam. The exam is scheduled for April 28, the very last day of the three-week exam period. But the TA thought we should have it in May - she says many students will still be around. And do we want to ask students to sign up for this, or just run it as a drop-in group?

Finally, who pays for the pizza? Is there a special fund for course-development activities, or should it come out of the course's photocopying/petty cash budget?

I think I had better turn this post into an email to the person who suggested a focus group and to the head of the teaching-research group, so I can get their advice.

Classes are over

2011-04-07T09:39:00.000-07:00

Yesterday was the last lecture of the genetics pilot course. I combined a review with specific everyday cases where knowledge of genetics would be useful, all framed as 'a friend or family member asks your advice, because you're now the genetics expert'.

Now I just need to prepare a final exam (and a sample final), and pull together as much feedback as possible to use in preparing for September. I've given the class an on-line survey, and they'll do the usual post-course teaching evaluation, but we're also going to have a focus group in the week before the final, with pizza.

Planning next year's tutorials

2011-04-01T07:14:00.000-07:00

The other day I sat down with my favourite pedagogy expert to discuss how to improve the tutorials for the new genetics course. I'm quite happy with the problem-solving component of the present tutorials, but they still need a component that develops students' reading-interpretation and connection-making skills. We came up with a plan that I think will work well.

Any plan has to deal with the big practical problems. First, students much prefer activities that they see as directly useful, and activities that will improve such fuzzy and poorly defined skills as reading-interpretation and connection-making fall far below activities that will directly improve their grade. Second, most of the students are very anxious about speaking in class. Third, even experienced and skilled teaching assistants are understandably reluctant to impose tutorial activities that the students don't like. Fourth, many of our teaching assistants will be inexperienced and unskilled.

Under the new plan, students will spend the first part of each tutorial analyzing one or two short readings taken from textbooks. They won't have to do any extra preparation for this, as the material they'll be analyzing will be part of the preparatory readings recommended for that week's classes (motivated by the weekly Reading Quiz). They should see the analyses as directly useful, because the texts (and associated figures) will be about topics they need to master to pass the course.

In each tutorial, about 30-45 minutes will be spent on activities using these readings. These are 2 hour tutorials, and the rest of the time will be spent working on a complex genetics problem (described in the last paragraph below). They'll first work in pairs or small groups with a clear goal, such as

'Identify a question you'd like to ask the author of this paragraph.'
'What are the important differences between the information presented by the paragraphs from two different textbooks?'
'How does the figure clarify the text? What potential confusion does it clear up?'

Then the ideas from the groups will be discussed by the class. I think that students are more comfortable reporting what their group came up with than describing their own ideas directly. They could either form groups on their own, or the groups could be pre-assigned by the TA.

In the first few weeks of the class, the TA will then use one of the two texts to demonstrate one way to diagram the relationships of ideas in a text (one week hierarchical diagrams, another week flow charts, another week concept maps). The students will then individually create this type of diagram for the other text they've been analyzing, and hand this in. In later weeks the TA demonstration won't be needed, and the students can diagram the text in any way they like. The TAs will mark the diagrams out of 2 points (1 for any attempt, 2 for something good), and return them to the students at the next class..

My pedagogy expert and I considered ways to let the students also look over what other students had done. We didn't decide on anything, but later I came up with something that might be good. The TA could hand the marked diagrams to random students (not to their authors). Each student gets a minute to look over the diagram they've been handed before finding its author and giving it back to them. This will be an ice-breaker, a minute of chaos that will get students talking and help them meet each other. If we wanted to designate the pairs or groups that will discuss the new assigned text (rather than letting students pick their friends), returning the diagrams could also assemble the groups - each report could be given to another member of the designated group. One other possibility we discussed was having the TA choose one diagram from each tutorial and give photocopies to all the students.

Because the students should see this text-analysis process as valuable and non-threatening, the TAs should be comfortable leading it. In the weekly TA meeting we'll prepare them by going over the readings with them, pointing out ways to help students develop their ideas. We'll also show them how to teach the diagram-creating activity. We'll make sure they know how to do the marking very quickly, without worrying about details.

A note about the problem solving part of the tutorials: We've developed a complex genetics problem for each tutorial. Students get the introductory information and one or two relatively simple questions ahead of time, and are expected to hand in the answer(s) at the start of the tutorial. After the text-analysis, they spend the rest of the tutorial working through this problem in groups (mostly at the chalkboards) and discussing the answers to the questions it poses. Finally the chalkboards are erased and the students are given a sheet with one or two of these questions, which they answer and hand in. As with the text-analysis activity, the TAs are given lots of preparation for this problem-solving activity and for grading the answers (again 1 point for any attempt, 2 for a good answer). The intent is that the TA meeting will fully prepare the TAs for their tutorials, and that the grading will not take more than one hour for each tutorial.

Once classes end next week, we're going to spend time developing the materials we have into a draft set of TA materials for each week.

A lecture about the genetics of behaviour

2011-03-28T18:54:00.000-07:00

I let the students in my genetics-pilot class choose a topic for me to teach about, and they chose The Genetics of Behaviour. The class comes up next Monday (the second-last class of the term), so I need to get to work on it. Of course I know nothing about this, but that's not a big problem - I can certainly learn.

The problem is that all I've found is various individual studies that connect particular behaviours with particular genotypes. All very well, each reasonably good science about an interesting behaviour, but essentially just a series of anecdotes. What I'm hoping to come up with is a lesson, or a take-away message, or some unifying principle.

What form might such a principle take? That behaviour is a biochemical phenomenon? That it isn't? That we still have free will? That we don't? That nature and nurture interact to determine behaviour, as everything else?

Maybe I should start the class by raising the big questions (after I start preparing for the class by finding out what these are). What is consciousness? No, too big. Do we have 'free will'? Also too big. In fact, I think both these questions should be better handled by saying "What do we want the words 'consciousness' or 'free will' to mean?" After we've settled on clear definitions we'll be in a better position to answer questions about them.

So I won't start with such big questions. How about 'What can genetics teach us about why we behave the way we do?" A bit vague. Should I pick one behaviour that's been well studied and report on the findings? Not if it's a boring behaviour like the ability of rats to remember the location of an underwater platform. What about all those Drosophila vegetable mutants (rutabaga, cabbage, turnip, dunce)?

Sexual behaviour is much more interesting, especially to college kids. And it's where natural selection/sexual selection has probably acted very strongly, but in complex ways. Maybe the genetics of sexual orientation - review the studies, tell them whether there is any good data at all? Wikipedia looks like a good starting point, but it tells me that there's very little good data, certainly not enough to base a whole lecture on.

What about human pheromones? The whole question of whether we pick our mates partly because they have different HLA alleles than we do. All those T-shirt-sniffing experiments are thought to be detecting genetic differences. And there's that ocytocin study, and lots of sleazy marketing. And then I could end with the new Drosophila study showing that the smells being used for mate choice can come from bacteria which come from the food source...

The 'calibration' part works!

2011-03-15T07:46:00.000-07:00

My students have finished their Calibrated Peer Review assignment, and now I'm discovering the wealth of instructor resources for interpreting the outcomes and correcting discrepancies.

First is a Student Results page, listing each student's total score on the assignment (text plus reviewing activities), the points earned by the text they submitted, and their Reviewer Competency Index. The latter is a measure of how well they reviewed the three calibration texts, and is used to modulate the ratings they assigned to the three student submissions they reviewed. From this screen you can click on any student's name to see all the details of the scores they assigned and received.

Next is a Problems List page. This again lists the students, this time flagging in red any problems the system noted with their assignment. Students who failed to complete the calibrations on time are flagged and their Reviewer Competency Index is zero. Reports that were reviewed by only a single student, or not reviewed at all, are flagged. So are reports that received discordant reviews (discrepancies exceeding a pre-set tolerance) , and reports that were reviewed by students with very low Reviewer Competency Indexes.

Only two reports had seriously discordant reviews, and rather than being evidence of problems with CPR, both of these demonstrate how well the CPR system works. The first was a very good report that received one very low score because the reviewer had given too much weight to very minor flaws. But because this reviewer had also performed badly on the calibration reviews, they had a low Reviewer Competency Index and this poor review didn't drag down the good report's score. The second problem report also had one very low score and two good scores. But this time the low score was from a very competent reviewer, and when I read the report I discovered strong evidence of plagiarism, which would certainly justify that low score. (The other two reviewers evidently assumed that the professional writing was the student's own work.)

The third set of resources are on a Tools page. Here you can change deadlines for individual students to allow them to submit after the original deadline has passed (I've done this for one student), change student's ratings and scores, and have the whole assignment remarked to incorporate adjustments you've made to a Reviewer Competency Index. You can also download the complete texts of submissions and evaluations. You can even access the system as if you were any one of the students (this gets you a caution that any changes you make will appear to have been made by the student).

Overall I'm very pleased with the CPR system. I've only encountered a few minor problems: One is that many of my students earned low Reviewer Competency Indexes. I suspect this is because I had so many calibration questions about specific details of the submissions. Several students had minor problems submitting the various components by their deadlines. I think these were mostly because they overlooked a final step needed to complete the submission. The text-only interface didn't seem to cause many problems - some students had trouble with the word limit (because HTML tags are counted as words), but only one student's submission had text-formatting errors.

Now it's time to start spreading the word around campus about this new resource. Hopefully there'll be enough interest that UBC will decide to purchase it once our free trial ends.

Peerwise let my students write their own midterm problems!

2011-03-12T18:19:00.000-08:00

(Of course they didn't know it at the time!)

The students in my introductory genetics pilot class have had weekly Peerwise assignments all term. In alternate weeks they either had to either create at least one multiple-choice genetics problem suitable for an open-book exam (i.e. not based on memorization) or to answer and critique at least two problems previously created by other students.

I had used Peerwise a couple of years ago in a first-year class. Each student only had to create one question and critique four. I had found their questions to be full of confusions, poorly written and lacking important information, but the critiques were quite good.

This time, my students have told me that they don't mind answering the problems other students have posed but find creating their own to be quite difficult. The first problems I had looked at hadn't been very good. But last week I started going through their more recent problems, looking for ideas I might use in creating problems for the upcoming midterm, and I was pleasantly surprised by the high quality of many of the problems they had developed.

I was so impressed by the students' questions that I decided to use them for the midterm, rather than writing my own. I downloaded a range of questions to consider - some of them were very good but much too difficult for a 45-minute midterm. I had thought that the good questions might have all been written by one or a few students, but when I checked their usernames I found that 16 of the 17 questions had been written by different students; this means that most and maybe all students are creating good problems!

I used 14 questions for the exam - most of them I was able to leave unchanged, but some required minor editing for clarity. The students must have recognized their own questions, but I haven't seen anything on the course discussion board to suggest that they've realized that they collectively created all the questions on the exam. I'll tell them on Monday.

The CPR site counts html tags as words...

2011-02-24T08:54:00.000-08:00

The instructions for my Calibrated Peer Review assignment specified that the reports should be between 300 and 500 words long. And a nice feature of the CPR assignment setup is that it polices this - the instructor specifies the acceptable word range for submissions, and submissions that are too short or too long are not accepted. But a problem has arisen because the CPR submission form only accepts plain text, and needs HTML tags even for paragraph breaks.

Of course very few of my students will be familiar with HTML tags (it's a bit shocking that I'm more web-savvy than most of them). I thought I had solved the formatting problem by giving them a link to a web page where they could paste in their formatted text (from a Word document) and have it converted to HTML, which they could then paste into the CPR submission form.

But the CPR form counts the HTML tags as words and, for students who have meticulously formatted their reports in Word, this adds hundreds of pseudo-words that push it way over the word limit.

So I've raised the CPR word limit to 1000, but warned students that their final submission (after CPR is complete) will still have to be no more than 500 words.

CPR almost ready to go, surpasses all expectations

2011-02-18T08:40:00.000-08:00

The Calibrated Peer Review assignment for my genetics class is almost ready to go, thanks to lots of work by our Faculty of Science technical support person working with the Centre for Learning, Teaching and Technology (or is it 'Teaching, Learning and Technology...?).

The legal indemnification issue has been resolved; apparently it arose due to a misunderstanding between the two parties about which university was meant by the phrase "the University". The software has been installed into UBC's elearning system, and the course has been created.

Setting up the student accounts turned out to be a bit of a hassle. The local CPR setup needs to be told, for each course, the names and IDs of the students who are entitled to create user profiles. In principle this info should be uploadable from the class list for the course, but for some reason it had to be entered manually (by the tech person, not me). This problem will need to be resolved by September, as we'll have >400 students in the course then. (Note added later: In my Instructor view I see a page for uploading students from a class list file; I don't know if this is what wouldn't work for the tech. Later: this problem has been solved.)

The students have been sent emails telling them to set up their user profiles (just password, email address and secret question/answer) and complete the introductory tutorial and pretest, and several have already done so. Once they have an account they must agree to the CPR Terms of Use; this requires them to promise to abide by UCLA's Student Conduct Code! (I couldn't check out the code because the link to it is broken.)

The tutorial and pretest are an excellent feature. The tutorial takes students through ten pages of information about the different steps of a CPR assignment. The pages are very clear, with good diagrams and illustrative screen shots. Once the student has been through the tutorial they take a pretest to check that they've understood how the CPR process works, with 12 Yes/No questions. The pretest isn't graded, but the system records that the student has completed it.

At this point students are ready to begin their assignment. Unfortunately mine can't do this yet, because a setup problem won't let me import the assignment information from its home on the CPR Central website at UCLA. I've finished creating all the assignment components (learning objectives, instructions for the students, calibration essays, review questions, answers and feedback to review questions for each calibration essay). The local CPR interface asks me if I want to activate a new assignment, and then asks for my CPR Central userID and password so it can connect to the assignments I have there. But it can't make the connection.

The support tech had her CTLT tech working on this problem yesterday (Later: they're waiting to hear back from the UCLA tech). If it's solved today (and no other bugs surface) I'll be able to tell the students to submit their drafts by the Sunday midnight deadline. If it persists I'll have to extend the submission deadline again, and push back the dates for completing the various stages of the assignment. Fortunately I set up the original dates to have the final polished submission due several weeks before the end of term, so moving to a later deadline won't be a big problem.

Over all I'm very impressed with the high quality of the CPR resources and interface. Every step has been very straightforward and easy to understand, and the supporting materials for both instructors and students are very well designed. (Of course, the technical people may think differently...)

email to a textbook rep

2011-02-15T20:25:00.000-08:00

Dear textbook rep,

I haven't received the brand-new textbook yet (author's name and title redacted), but today I did get the Instructor's Media CD for it, and I've been through all the sets of slides. I'm afraid it's not at all what we're looking for.

Because the title promises a genomics approach, I was hoping for a text that presented the basic principles of genetics in the context of our new spectacular information about human and other genomes. Instead it's yet another old-fashioned Genetic Analysis textbook, with no modern genomics at all!

The first chapter covers molecular biology at a high-school senior/Intro Bio level, and is followed by the standard four chapters teaching classical genetics (Mendel and single-gene inheritance, mitosis and meiosis, linkage and mapping, chromosome structure and behaviour. All the same material that's been taught since the 1960s, with the odd snippet about gene function, such as the molecular defect in Mendel's wrinkled pea allele. Then a series of more molecular chapters (DNA replication, bacteria and their viruses, gene expression, gene regulation), all still very classical in the information they present.

Chapter 10 claims to be about genomics. But what does it contain? The same old molecular cloning and genetic engineering methods, supplemented with explanations about how microarrays work and how a germ-line transformation is done. The only genomics is the genome of the bacterium Mycoplasma genitalium, published 15 years ago! No human examples at all, just flies and fish and rice.

Then more standard chapters with the standard material present in every other textbook: development, mutation and DNA repair, cell cycles and cancer, classical population genetics, classical quantitative genetics.

Students taking an introductory genetics course don't need to learn how to clone genes, they don't need to know what Mendel did, and they certainly don't need to understand how a Southern blot is done. Even professional geneticists never do Southern blots any more!

More than anything students need to understand their own genomes. They need to know how inheritance works, and how genes affect phenotypes. They need to understand natural genetic variation, in their own and other species. These concepts aren't particularly difficult, except maybe when they're embedded in the baggage of classical genetic analysis.

I'm quite disappointed, as I was hoping that this would finally be a textbook we could use. But I guess I'll continue to make do without any assigned textbook.

I'm attaching a copy of the lecture schedule for this course, just in case you know of any other textbook that might take a more modern approach.

Rosie

Comparing the midterm results

2011-02-13T15:23:00.000-08:00

Here's a graph comparing how each student in my pilot genetics course did on the first and second mini-midterms. The first tested their understanding of the relationship between genotype and phenotype, especially in diploid organisms. The second tested their understanding of how alleles are inherited through meiosis and mating. The material on the two tests did not overlap at all. Both were 25-minute, open book, and mostly multiple choice and short answer.

The blue dashed line separates students who did better on the first midterm (dots above the line) from students who did better on the second (dots below the line). Although many students did worse on the second one, 14 of the 38 did better.

The two dots in the lower left square are students who failed both tests. The single dot in the upper-left pink square is the student who failed the first test but passed the second. The ten dots in the lower-right pink square are students who all passed the first midterm but failed the second (some very badly).

We've just entered the marks for each question, but I'm starting to think that the dataset is too small to allow any more useful generalizations.

Interpreting a grade distribution

2011-02-12T08:21:00.000-08:00

Yesterday my genetics students wrote their second 'mini-midterm'. This was a 25-minute quiz on the material we've covered in the last two weeks. Everything went smoothly, the papers are graded, and the grades are posted along with the answer key. But I don't know how to interpret the grade distribution. Here's the histogram:

The quiz was open book, with five questions that were designed to require some thoughtful analysis but be very easy to mark (grading 38 papers took four of us about 30 minutes). The questions weren't too difficult - 3 students earned perfect scores, and most had finished before the time was up. They also weren't too easy - 12 students failed, and the mean score was only 15.8/25 (62%).

We expect grades on most tests to give a 'normal' distribution - the bell-shaped curve. The curve may be skewed to the right if the exam was too easy, or to the left if it was too hard. A bimodal curve (with two humps) usually means that the students fall into two groups - those who have acquired some key skills and those who haven't.

But the grade distribution for this quiz looks flat to me, not really a curve at all. It's flat all the way from 12% to 100%, with no more scores close to the mean than elsewhere. I've never seen a grade distribution like this before and I don't know how it should be interpreted. I can find technical descriptions of this shape in the context of a normal distribution (it's 'platykurtic') but I can't find any consideration of what this would imply about either students' abilities or the design of the test.

Maybe I'll ask my colleague in Curriculum Studies...

CPR update

2011-02-12T07:54:00.000-08:00

The original plan for our Calibrated Peer Review assignment was that students would submit their draft assignments by last night. Next week is Reading Week, a mid-term break with no classes or assignments due, so this would give them have a week off before doing their three calibration reviews (one week) and their reviews of three student submissions (the next week).

But getting the CPR system up and running at UBC is taking longer than I had hoped, so I've set back the due date until next Sunday (at the end of Reading Week).

I had anticipated that there might be problems't getting the CPR software to work as intended, and had set the original the due date with the plan that it could be changed. However the problem isn't software implementation at all, but the legal license agreement between UBC and UCLA.

The agreement includes an 'indemnity' clause that (I think) protects UCLA from the consequences of anything bad that UBC might do. But UBC's lawyers have provided a standard indemnification clause that isn't as sweeping as the one UCLA specifies. Any changes to this could require months (years?) of back-and-forth between the legal counsels for the two institutions.

The new version of CPR (CPR4) is the first one to have a local component installed on the user's computers - the previous versions all ran entirely on the UCLA system and were remotely accessed by students at other institutions. So I was concerned that UBC might be the first foreign user, and that all the legal bugs still had to be worked out.

Luckily my UCLA contact assures me that there should be no legal problems, so the local installation is proceeding. With luck, we'll get all the bugs out next week and be ready for the students next weekend.

How to solve genetics problems

2011-02-09T08:12:00.000-08:00

Calibrated Peer Review is 'developmental' for instructors as well as students

2011-02-05T14:02:00.000-08:00

I've set aside the original plan of having the students in my new genetics course write letters to the editor about genetics reporting errors, because finding suitable errors turned out to be too difficult for them (but thanks for the suggestions). The new plan (they voted and chose it) is that they will instead write short reports titled 'My Favourite Human SNP'. This looks like it will work well both for this small pilot class and for the ~500 students we expect in September, because the pool of SNPs with associated phenotype information is large and growing fast. The assignment still has the benefit of letting each student choose their own topic, and of being very suitable for Calibrated Peer Review (CPR).

I've already posted on our course-management system a page of instructions to the students about what is expected in this assignment, but now I'm creating the assignment within the CPR system. Although the CPR interface for the students is run locally (i.e. at UBC) under the new CPR4 system, assignments are generated centrally on the CPRCentral server at UCLA. This allows the central server to maintain consistency (all authors have to use the same structure) and to provide a library of past assignments that any instructor may use or adapt.

In principle I could have adapted one of the many existing assignments from the CPR library, but none of them were suitable. Instead I'm writing my own from scratch, using some of the library assignments as models. Now I'm working through the surprisingly many steps of creating an assignment from scratch, using the detailed Authoring Guide that CPR provides. This turns out to be much less daunting than I had expected, and much more enjoyable and educational (for me).

The first step is choosing a title and descriptive information for the assignment. Because all assignments are put it the open library for others to later adapt, it's more important that this title be informative for future users than that it be the best title for the students. A suggested student title can be included in the explanatory notes. The assignment is also given a topic area (mine is Biology - Genetics), keywords, and a user level (mine is Lower-division undergraduate). This information is used by other instructors but I don't think it's seen by the students.

The next step is writing explicit Learning Goals for the assignment. I hadn't done this for an assignment before, so thinking through what I wanted the students to learn (guidelines are provided) helped to educate me about the value of setting such goals as well as providing the students with clear expectations (students see these at the top of the assignment page).

Writing the Learning Goals was the first place where the lack of formatting power raised its ugly head. The CPR interface accepts only plain text with or without html codes (e.g. you have to manually insert
wherever you want a line break). I expected this to be very frustrating but the combination of a nice page of html tags and my kindergarden-level html skills let me format lists of points and boldface headings without a hitch. However I anticipate that most of the students will have more difficulty with this - at a minimum they'll have to put in the line breaks. (Yes, I know paragraph breaks are better, but if you don't have any idea how html tags work, line breaks are easier to understand.) I'll need to create a short example page for them on Vista showing how to do this. They can also just use a web page I've found that lets them paste their Word-generated text into a box that converts it to HTML.

The next steps create the resources the students should use to carry out their assignment (to generate the reports that will be assessed by their peers).

I. Guidance for Studying Source Materials: This tells students how they should gather the information and understanding that will go into their report. It has two parts, some text describing the source materials (handouts, textbook, articles, etc) and then some hyperlinks to web pages. Here I just used modified text from the first part of the instructions I'd already posted for my students. I didn't initially notice the second part of this section, so I hand-coded the hyperlinks into my text section - that worked fine.

II. Guidance for Writing Your Text: This tells students what their reports should say and how this should be presented. Here I used modified text from the second part of my posted instructions.

III. A 'writing prompt'. This appears above the text entry box and gives the student specific instructions about format and text entry.

Now comes the big task of preparing the 'calibration essays'. Three of these are required; each student will evaluate these using the series of rubric questions that you create in the next step. One calibration essay is tagged 'high quality', one 'middle quality', and one 'low quality', but they can differ along several axes, with the caution that students will have a hard time evaluating the content of an essay with too many writing errors. I had already decided on the SNPs I would write these about, but they're only about half done right now so I'll write more about these later.

The next step is creating the series of questions that students will use to evaluate the essays. The interface makes this quite easy; it lets you specify what kind of answer is expected (yes/no, none/some/many, A/B/C (where you specify what A, B and C mean), and whether the student is expected to enter some text in a box. I had some questions in mind from the original instructions I'd given the students, and I thought of more while I was working on the calibration essays. Now I have 17 questions, which I suspect may be too many, even though most of them are very simple: "Does the report contain spelling errors? (none/some/many)"; "Does the report say how common the phenotype of interest is? (yes/no)". I'll no doubt refine these once I'm into the next step.

The final big step is, for each evaluation question, designating the correct answer for each of the three calibration reports and writing a brief explanation of why this is the correct choice in each case. This is going to take a while, and I can't begin until I finish writing the calibration essays. But I'm looking forward to it, because I can see how valuable it will be.

So the above is a lot of details - what's the big picture? UBC's learning technology people agreed to set up this CPR trial because they saw CPR as much more 'developmental' for the students than our existing peer-review options (iPeer and the peer review component of Turnitin). I agree, but I'm finding that the experience of creating the assignment is also developmental for me - I'm being gently led through a series of steps that greatly improve the learning experience I'm providing for my students, with instruction at each step so I see both why the step is valuable and how best to implement it.

Looking for examples of BAD genetics journalism

2011-01-29T06:20:00.000-08:00

The students in my introductory genetics class have an unusual assignment - each of them has to find an error in the reporting of genetics and write a letter to the editor about it. They're not very skilled at finding examples of such errors (and I'm afraid I haven't given them much time), so I'm asking the twitterverse for help. If you've recently wrung your hands about some egregious error in the reporting of some advance in DNA or genetics research, we'd be very grateful if you would post a link (or other identifying info) in the comments.

Here's some more information about the assignment:

The students are asked to find somewhere in the media where an incorrect statement is made about a genetic topic. This could be in a tabloid, newspaper or magazine, on television, or in a news-media online source. (General blog posts are not eligible, though media-affiliated ones are.)

These students are only part-way through their first genetics course, so the error needs to be pretty basic. Examples I've given them include

describing genome sequencing as 'cracking the genetic code'
describing a bacterium with arsenic in its DNA as 'a new form of life'
credulously reporting about the predicted effect of what turns out to be an imaginary gene
claiming that gene A causes behaviour B, when it only slightly increases the probability of the behaviour.

The students write a draft letter to the editor (polite, concise, in correct English), and then do a complex peer review of each others' drafts, using Calibrated Peer Review (CPR). (UBC's Centre for Teaching, Learning and Technology is setting this up for us on a trial basis, as nobody here has used it before.) They then polish their letter, submit it for final grading, and (we hope) also send it to its destination.

The present class is only 40 students, but if this assignment works well (and the CPR works well) we'd like to run it for 500 students next Fall. This would lead to a barrage of letters to the editor complaining about the poor quality of their genetics coverage, and might even lead to an improvement in future reporting.

How we define the phenotype is critical

2011-01-27T09:14:00.000-08:00

The post-doc and I are discussing the following genetics problem, taken from a textbook:

Q. For a certain gene in a diploid organism, eight units of protein product are needed for normal function. Each wild-type allele produces five units.

a. If a mutation creates a null allele, do you think this allele will be recessive or mutant*?

b. What assumptions need to be made to answer part a?

*Note: I don't know what the word 'mutant' means here, since we already know that the allele is mutant. I suspect it's an error so I initially ignored it.

What I originally said:

The mutation is not recessive to the wildtype allele, because the heterozygote has a different phenotype than the wildtype homozygote. I don't think this conclusion requires any assumptions other than the usual definition of recessive.

However the postdoc and others have been arguing that mutation should be interpreted as dominant. This requires interpreting the word 'mutant' as an error where 'dominant' was meant, which is not unreasonable.

What I say now (after quite a bit of thinking):

First, we're told that the mutant allele is a null allele, so the heterozygote is expected to have half the normal amount of protein (5 units instead of 10) Since 8 units are needed for the normal phenotype, the mutant heterozygote will not be normal. So the mutant allele certainly is not recessive.

(Here I'm assuming that the defect in one allele doesn't cause the other allele to be upregulated. That's a possible answer to part b, though I doubt it was what the questioner was looking for, since this question comes from the first chapter on simple Mendelian inheritance.)

We're not told the phenotype of a mutant homozygote, so before considering whether the mutant allele could be dominant to the wildtype allele we need to carefully identify the phenotype in question. The term 'phenotype' can have different meanings even for a given pair of alleles, depending on what is being observed and how it is being categorized.

For example, if a pigment is being observed it could be treated qualitatively (red/white; red/pink/white; present/absent) or quantitatively (how much pigment is present). Phenotypes are usually treated qualitatively in genetics textbooks, with quantitative phenotypes segregated into a special chapter. But most real phenotypes have gradations, and the observer must decide whether to treat them qualitatively (with 2, 3 or more categories) or qantitatively.

Qualitative categories are usually chosen to reflect the underlying genetic effects. For example, an observer might initially categorize flower pigment as red/white, and later realize that the 'red' category should be divided into 'red' and 'pink' because this better explained how the colours were being inherited. If a gene were later discovered that modulated pigment production, the observer might then treat pigment quantitatively.

The problem posed above doesn't give us explicit guidance about whether this phenotype should be treated qualitatively or quantitatively. Normal is presented as an ordinary word, not flagged as a special term by quotes or italicization, so we could certainly interpret it quantitatively. However it could be meant qualitatively, although we're not given any clues to what the categories would be (normal/abnormal? normal/abnormal/severely abnormal?).

If the phenotype is to be treated quantitatively (with 'normal' just taking its ordinary English meaning), then the mutant homozygote is expected to have a more severe abnormality than the heterozygote, so the allele would not be dominant.

But the postdoc argues that it's just as reasonable to treat the phenotype qualitatively with two categories, 'normal' and 'abnormal', and I agree that under this definition the mutant allele would be considered dominant.

However I think that requiring the phenotype to be defined this way is tantamount to making this a 'trick question', because this definition implies that the person posing the question deliberately ignored whatever information might be given by a more nuanced definition (one that considered possible differences between the mutant homozygote and the heterozygote).

Because the wording of the question doesn't favour this interpretation over any other, we should go for interpretations that are more reasonable - qualitative with more than two categories, or quantitative.

Would it be OK to say that the mutant is dominant because the heterozygote and mutant homozygote really do have identical phenotypes under more nuanced definitions (i.e. that they are equally abnormal)? No, because this would require a biologically unreasonable explanation for the dominance - either the null allele in the heterozygote must completely prevent expression of the normal allele, or the presence of two null alleles in the homozygote must allow them to produce 5 units. The former is very unlikely though not impossible, and the latter is inconsistent with the meaning of 'null allele'.

Later: I've heard back from the person who wrote this question. He indeed meant 'dominant' rather than 'mutant, and his intended answer agrees with that of the postdoc - that all non-normal phenotypes should be lumped together into the 'abnormal' category, which would make the null allele 'dominant'.

I think this is both scientifically bizarre and pedagogically misleading. It reinforces the erroneous assumption that alleles must be either dominant or recessive, and requires a very improbable explanation to be treated as typical. Either question a should give a third option (recessive, dominant or neither) or the question should be framed with "What is wrong with this question?". Question b can be deleted.

Answering a complex problem after discussing it in tutorial

2011-01-25T05:59:00.000-08:00

My genetics students are complaining about the way I've designed the tutorials. I have them spend the first part of each two-hour tutorial in a structured discussion of the topics covered by the past week's classes, and the second half working on a complex genetics problem. It's this second part that's generating the complaints.

They're given the problem in advance, and are asked to print it out and make a preliminary attempt at it before tutorial. I've told them that this attempt can be quite superficial; it's only worth 1 point (out of 5). They turn in this attempt at the start of tutorial, and are given a blank copy of the problem to work on. The students then work on the problem in groups of 3-4 at the chalkboards. (This classroom is in the old math building so it has lovely chalkboards filling three walls.) Different groups then explain to the class their suggested answers to the different parts of the problem, and students discuss these answers. They also discuss how the problem might be adapted or modified for use in different settings, for example, changing the organism so it can be reused on a test, or making part of it into a shorter stand-alone problem. (In future we'll try to get them to also explicitly discuss what is needed for a good written answer to the problem, but they're not ready for that yet.)

All this seems to be OK with them. But the final step is for each student to write out a careful answer to the problem they've been discussing, as if this was an exam setting. These answers are handed in and marked; they're worth 4 points. At present the group work is left on the chalkboards while students are writing their answers, but I've told them that in a few weeks we'll start erasing the boards before they write their answers.

Students are complaining that this is a waste of their time, that they don't learn anything by having to write answers after they've already seen how the problem should be answered, and that they would learn more by spending the time in additional discussion. I disagree - I think that observing the right answer doesn't lead to much learning, and that having to apply what they've just observed by creating a written answer adds a lot.

In tomorrow's lecture I'm going to show them some data that might help them see the value in this. It's from a paper that just appeared in Science (Karpicke and Blunt). In both of the two studies they describe, the authors had students spend 5 minutes reading a half-page of text about a biological topic, and then consolidate what they'd read in various ways. The students were then asked to predict how much they would remember a week later. A week later they were tested on each topic.

In the first study the students either (i) did nothing more, (ii) reread the text three more times, (iii) spent 25 minutes making a concept map with the text, or (iv) tested their recall immediately by writing about it for 10 minutes, then reread the text, and retested their recall. In the second study the students either (v) spent 25 minutes making a concept map or (vi) tested their recall, reread the text, and retested their recall. In the first study each student read only one text and was tested a week later with a short-answer test. In the second each student was given two texts, one learned with a concept map and one with recall testing, and these were tested a week later using either a short-answer test or a concept map (in randomized combinations).

In both studies the students predicted that they'd remember more with the non-testing methods, but in the post-tests they always scored substantially higher when they had consolidated their reading by testing their recall. Here are edited versions of their graphs:

All the data

Part of the data, that I'll describe to the students

I'm going to show my students this study in tomorrow's lecture, and I'm going to give them two conclusions: First, people are not very good judges of how much they've learned. (So my students should realize that their opinions of how much they learn by different tutorial activities may well be mistaken.) Second, testing oneself is an excellent way to learn. (So my students should realize that having to develop a written answer after a discussion is a valuable way to reinforce what they've discussed.)

This will take a few minutes that I could otherwise spend talking about mitosis but I think learning how to learn is more important. The students have a mini-midterm coming up on Friday, so they should be fairly receptive to ideas about how to learn. I don't expect that this new data will convince them all that my tutorial design is good (that's why I wrote 'should' above instead of 'will') but at least they'll realize that I'm not just doing it to to be mean.

Genetic mapping

2011-01-22T07:39:00.000-08:00

In yesterday's course meeting for my new second-year genetics course (which I'm now thinking of as "21st Century Genetics"), I mentioned that the syllabus doesn't include the classical technique of genetic mapping. The others were shocked!

My students will learn how meiosis works. They'll learn about segregation and independent assortment. I've never really seen clear explanations of the meanings of these widely used terms, but segregation means that each daughter cell gets one version of the two homologous chromosomes (never two or none), and independent assortment means that which version of each pair a particular cell gets is random and independent of the version it got of each other pair. They'll learn how crossing-over between parts of a pair of homologous chromosomes makes new combinations of the alleles.

The students will learn how to find out if genes are linked (close enough together on the same chromosome that their alleles aren't randomized by meiotic assortment and crossing-over). They'll also learn that the frequency of crossing-over between any two genes gives a rough estimate of how far apart they are. They might even learn how to compare these frequencies to tell which gene is in the middle of a group of three linked genes (maybe as a homework problem). BUT, they won't learn to use three-factor crosses to determine 'map distances'. (Here's a web page with a fill-in-the-boxes version showing how such mapping analysis is done.)

Why not? Because they won't have any use for this skill. Even if 1000 students take the course each year, I would be very surprised if even one ever needed to map genes using crosses, except as an exercise in an old-fashioned upper-level genetics course.

Here's a page arguing that even real geneticists didn't do this - that the idealized three-factor mapping cross was largely an exercise for students. I don't think that's necessarily true, but it's certainly true that real geneticists rarely do this any more. Genetic mapping in general, and mapping by three-factor crosses in particular, is fast becoming an archaic technique. If one of my students should ever find that they need to do this (and I'm having a hard time coming up with an example where they would), there are lots of textbooks to show them how.

I think that the main reason genetics courses have always included three-factor mapping is that (i) this used to be how accurate gene maps were made, and (ii) this provides a tidy way to test whether students understand the consequences of crossing-over.

I think I will teach the students the difference between a physical map and a genetic map of a chromosome, and I'll expect them to be able to explain why the two kinds of map might not be identical - because recombination frequencies are influenced by DNA sequences (chromosomes have hotspots and cool spots), and because the data from the crosses may have flaws (low numbers, phenotypic problems that limit detection of recombinants). But I won't expect them to be able to do the mapping.

Genetics problem for tutorial discussion

2011-01-15T06:36:00.000-08:00

The postdoc and I just created an excellent genetics problem for the pilot section of my new course.

The problem needed to get students thinking about how changes to genes affect phenotype, but it couldn't involve crosses because they won't be doing those for another couple of weeks. That rules out just about all the problems in the textbooks.

This new problem has everything:

haploinsufficiency
dominance
repressor gene
activator gene
natural polymorphism
important human diseases
screening of newborns
problems important in developing countries
amino acid substitutions
isoelectric focusing to detect changed protein charge
mixed-allele dimers
differences in protein levels
developmental regulation
interactions between fetus and mother at the placenta
suppressor mutations (mitigating the deleterious effects of another mutation)
natural selection in human populations
mutations that are very well characterized (DNA, RNA, protein, function)
genome-wide SNP analysis
a mutation that's lethal when homozygous but beneficial when heterozygous
new research in a high-profile journal (Sept. 2010 paper in Nature Genetics)
students label subunits in tetramers
students predict bands in gels, for different genotypes and developmental stages
students predict protein levels through human development (draw lines on graph)
students diagram regulatory interactions between genes, for different genotypes

But it's still straightforward enough for second-year students who are just beginning to learn genetics (no crosses, no matings, no trees, no pedigrees).

What do you think this fabulous problem is about?

Teaching about 'dominance'

2011-01-08T18:26:00.000-08:00

In my new genetics course I'll soon be teaching about how genotypes determine (or influence) phenotypes in diploid organisms. For these Week 3 classes I want to give the students some reading material, both to read before the lectures and as a study reference for material covered in class. But there's nothing suitable in any of the genetics textbooks I've looked at, so I need to create it myself. Below I'm going to try to work out how best to present this and to design the reference I'll have them read.

The Week 2 lectures (= this week), will discuss natural genetic variation, how mutations generate this variation, and the phenotypic consequences of genetic differences in haploids and homozygous diploids. In the last of these lectures I want to consider the differences caused by standing genetic variation as well as lab examples. And here I should raise the issues we'll deal with next week, explaining that diploidy complicates the relationship between genotype and phenotype, and that the next week's classes will all focus on building a solid understanding of this relationship in diploid organisms.

Somewhere (in the Friday Week 2 class or in the Monday Week 3 class) we'll need to consider that there are different kinds of phenotypes. Some are strictly qualitative - presence or absence of an antigen or blood type, presence or absence of a disease - but many are best treated as quantitative, especially when we consider natural variation. These include obvious things like height and hair colour, and less obvious things like about of an enzyme or metabolite present in a cell or bodily fluid.
I'll also need to introduce the idea of 'risk' as a quantitative phenotype - this is best done in the context of natural variation and genomics.

The first Week 3 class will just be about interactions between alleles of single genes. I'll start with some of the same examples I used the Friday before, asking students to predict the phenotypes of individuals heterozygous for mutations whose homozygous phenotypes we've already established. These should include intermediate phenotypes, 'both-type' phenotypes, and dominant/recessive phenotypes, and genes with more than two alleles.

The existing terminology is terrible, since everything is described in terms of dominance, whereas dominance and recessiveness are really only two extremes of the range of heterozygous effects. The problem is maintained by the practice of beginning genetics courses with Mendel, and of introducing all the important concepts with dominant/recessive allele pairs and the A/a allele representation. Only long after students learn this (mainly by rote) are they told about genes with more than two alleles and about 'Variations on Dominance' (Introduction to Genetic Analysis), 'Modifications of Dominance Relationships' (iGenetics), or 'Complications in the Concept of Dominance (Genetics: Principles and Analysis). These books, and all the other genetics textbooks I've seen, present 'co-dominance' and 'incomplete dominance' or 'incomplete dominance'

Oh, and in the preceding Friday class I also need to raise the important issue of how we name alleles - when the A/a convention is appropriate and when it isn't. I'll tell them that its usually only appropriate for made-up examples in classrooms, because genetics researchers have different conventions for the real organisms they study. (There's no point teaching students these conventions, because they are not only arbitrary but are different for different organisms.) I'll also tell the students that I will only use the A/a convention for alleles known to be dominant/recessive to each other, and that they should be careful to only use them it they are confident that this is the case.

I really wish we had good terminology for the different kinds of effects. I don't want to use 'codominant' and 'semi-dominant' (or 'incompletely dominant'), but the only alternative is to describe the actual relationship in each case. Maybe I can at least standardize the words I'll use in this course: 'blended' for a heterozygote phenotype that's halfway between those of the homozygotes, 'both phenotypes' for co-dominance.

Do as I say, not as I do?

2010-11-13T12:57:00.000-08:00

Very few of the speakers at the Reinvention Center conference have applied any insights into teaching and learning into their presentations. We get the same talking heads, and today a bad powerpoint.

Global health

2010-11-13T12:45:00.000-08:00

Note: This session turned out to be a presentation about how and why to develop courses and programs in global health, not about how to bring global health issues into ones own courses, as I was expecting. She didn't give us any outline or goal for the talk at the beginning, so it took me a while to figure this out.

Aha - she (Heather Wipfli, USC) starts by asking us to write definitions.

Small audience but good ideas.

Traditionally:

rural
babies and mothers
infectious diseases
vaccines

Themes:

We (the rich) help others (the poor)
Help needed by helpless innocents, not prostitutes
fix and move on

Who does it:

community saviours/superstars
real (Hollywood) celebrities

Changing the perspective:

We are all getting older.
Chronic diseases (cancer, cardiovascular, asthma, diabetes) kill most people even in low-income countries.
Epidemiology is changing
Global warming and environmental issues
Urbanization increasing but megacities not like NY and LA.

So how should we change our academic programs?

Need to shift student perspectives from medicine to global health. Many universities have graduate programs in global health (mostly MSc and MPH), but the number of associated undergraduate programs is increasing rapidly.

Geoffrey Rose: "Sick individuals arise from sick populations."

Every factor is interrelated with many other factors and various levels, from domestic to international.

Mexico (70% overweight, 28% obese) consumes 665 servings of Coke per capita per year.

Students are highly motivated by these issues. How can we integrate this into our courses?

Change of topic: using electronic games to teach. The Redistricting Game (teaches about political boundaries).

For genetics: discuss (have them suggest/investigate) gene-environment interactions that apply to immigrant populations.

The Creative Campus - catalyzing non-routine engagement

2010-11-13T11:21:00.000-08:00

Still at the Reinvention Center conference, Steven Tepper and Elizabeth Long Lingo, speaking after lunch.

First speaker:

Stupid jokes by a speaker (topic=creativity) who admits that he has too many slides. Now he's reading his slide to us. Now a slide with a table full of 4-digit numbers... And another... Dorky animations, annoying music.

Uptalking!

A Master of Fine Arts degree may give transferable skills for the aestheticization of everyday life (IKEA, Apple, Target toaster).

Second speaker:

Curb Program in Creative Enterprise and Public Leadership:

Undergraduate Scholars program (4 years):

ability to invent
expressive agility, to convince
dexterity to develop and implement their ideas
ability to critically examine.

Learning inside and outside the classroom (Zemsky follow-up)

2010-11-13T08:48:00.001-08:00

Language requirements aren't later used - if students have to study a language, we should offer special sections of upper-level courses for students who speak that language. e.g. German history for students who had studied German.

Integrate junior-year study-abroad outcomes into senior courses.

How to assess the real important outcomes??? Maybe look at what the GRE does - what do the individual questions assess. Some successfully assess context, not facts.

Why do students who did well in high school fail even at community colleges?

Students won't do well on a test unless they have a stake in the test. Must make the test results important to the student.

Why do student advisors (profession advisors, not faculty) like the course smorgasbord system? Because it makes their lives easy?

Bob Zemsky: Mission-sensitive and market-smart universities?

2010-11-13T05:52:00.000-08:00

Bob Zemsky is Chair of the Learning Alliance for Higher Education and author of Making Reform Work, which was written in response to the disappointing outcome of the Spelling Commission (I don't know what this is).

People have been trying to reform higher education for decades (read "A Nation at Risk"), and Zemsky seems to have been involved in higher ed policy since the 1970s. But I don't know where this speech is going...

Maybe about the still-unresolved need to integrate the courses and the faculty into a well designed coherent curriculum. This problem, clearly identified 25 years ago, hasn't been solved. Will it ever be? The "money bet", a Las Vegas term referring to the most probable expectation, is that no, it won't (because it hasn't in 25 years).

But maybe, he says, this is the moment when the money bet is wrong. The recession means that the public money isn't coming in to the public universities as it used to. It's also sending the public universities more students (teach more with less), and the extra students are not as well prepared as the usual ones.

The other force for change is what we're finally learning about learning. Read "The Art of Changing the Brain". Learning is physical changes in the brain, not just philosophical and metaphorical. For example, neurosciences tells us that we can't tell students to forget what they already know - instead we have to start by having them tell us what they already 'know'.

We need to learn from the for-profit institutions (the interesting ones, not the sleazy ones): Why are they succeeding? Unlike us, they put real money into courses at the front end, and the people who teach don't own the curricula. Thus their transfer system works seamlessly, whereas ours doesn't. Professional Masters degrees are becoming a big target for them. Practical problems of the public universities: too many students don't finish, and teaching costs too much.

"It's the curriculum, stupid!" Not under-enrolled courses but over-enrolled students. Students graduate with 145 credits in programs with 120-credits. What's wrong? Consider Oshkosh University. It gets 1/3 of their students from community colleges, but the credits don't transfer to the courses they need (not even the 'general education' requirements. The curriculum requirements are driven by inter-departmental turf wars and by what faculty want to teach, not by what the students need. Faculty and departments need to stop being independent contractors; "we have to return to collective action."

We need to get rid of the curricular smorgasbord, even though both the students and the faculty like it. Students don't connect the learning from different courses, and neither do we.

How to end the era of faculty as independent contractors? He likes collective action by the faculty rather than profit-driven corporate-style decisions.

Questions:

Undergraduate programs in engineering have better curricula, better faculty teamwork and good learning 'closure' at the end of the program, and might be good models (build on what is working). Also architecture, nursing, and small business schools. But Arts and Sciences faculty find these models distasteful. And we talk about distribution requirements rather than outcome requirements.

Funding shortfalls have led administrations to push financial problems on to faculty, treating them even more like independent contractors.

Universities and community colleges need to work together on curriculum.

Liberal Arts doesn't easily give 'closure' because it doesn't aim to prepare students for specific jobs, but to make them ready for a changing job market. But the job market is for health and business services now, so maybe we should prepare our students for this.

Faculty complain that this would take choice away from students. But students aren't really ready for these choices, and the real faculty concern is that choice is being taken away from them.

Calibrated Peer Review

2010-11-12T19:26:00.000-08:00

I had dinner with Arlene Russell of UCLA, the creator of Calibrated Peer Review (CPR). With Calibrated Peer Review, students evaluate the written assignments submitted by several other students (their peers), and simultaneously gain a deeper understanding of the assignment's requirements. For several years I've wanted to use this tool in my classes, but until now there have been logistic and legal obstacles - we can't send private student info out of the country, and UBC's instructional technology can't figure out how to run CPR here.

Each student first submits their own answer to written assignment. They are then given a grading rubric and three 'calibration' submissions to review. These submissions were prepared by the instructor; the first two have carefully chosen errors typical of those on which grading is to be based, and the third is a fully correct example. The student evaluates each of these calibration submissions according to the points specified by the rubric, providing brief explanations for their decisions. They then assign each submission a grade out of 10.

The students are then given feedback on their evaluations. If the evaluations were poorly done they're given a second try (the instructor specifies how closely the student evaluation must match their expectations.). The quality of the evaluations will be taken account of in the next step, evaluation or real submissions from other students, with a poor calibration decreasing the impact of the grades they give to their peers' submissions.

Once the deadline for calibration evalutations is passed, each student is given submissions by three other students. They use the rubric to evaluate them, again providing comments to justify their evaluation and giving a grade. After they've done all three they are also asked to evaluate their own submission.

Once all the reviews are done, each student gets their grade (the mean of the four grades given by the three peers and themself). Students also get to see the reviews submitted by the two other reviews of the submissions they reviewed, giving them a better sense of how good their evalutations were.

The grading of the whole project is critical to its success. Arlene recommends that only 20% of the total assignment+review activity be allocated to the actual assignment grade. 30% is given for their performance in the calibration activity (how well their assessments matched those specified by the instructor), and 30% for their performance in assessment of their peer's work (how well each of their assessments matched those of the other two reviewers). The final 20% is for their assessment of their own submission - if they gave a grade too different from those of the three other reviewers, they get zero. This is to prevent students from unfairly inflating their own grade.

What does the instructor need to do? Basically, design the assignment and create the calibration submissions and the grading rubric. A number of premade assignments are available to be used or modified, or just used as guides for creation of a new one. The instructor also needs to deal with problems that arise, especially defaulting students and inconsistent grading.

What would I use CPR for? The letter-to-the-editor assignment. The students would submit their draft letters for review, and then improve their draft based on both the feedback they've gotten from their peer reviewers and the experience they've gained by evaluating other submissions. I could allow lots of time for this, maybe having the initial submissions due just before the Reading Week break, and the calibration and peer-reviews done in the two weeks after the break. This would leave the students a week or two for their revisions, with the final submissions due at least two weeks before the end of term. Ideally the students would get their graded letters back before the end of term, and would then be encouraged to submit them to the editors or producers responsible for the error.

After more conversation, over breakfast: The 'calibration submissions' need to be carefully designed to allow students to learn to identify the errors. For example, if a biology submission contains both biology errors and writing errors, the student will have a hard time disentangling these. Instead we might provide one calibration submission that is biologically correct but might contains a few or small writing errors (this would have a grade of 8-10), one that is well written but contains significant biological errors (grade of 6-8) and one that is well written but contains more biology errors (grade of 4-7). Distribute the important errors across the three submissions, rather than combining them in one really bad example.

Using Writing to Improve and Measure Learning in STEM Courses

2010-11-12T13:12:00.000-08:00

Objectives in preparing for this workshop:

1. Share relevant bits of reviews of the literature.

2. Synthesize findings and understandings.

3. Delineate the research questions that must be addressed in future studies.

Julie Reynolds: What we know about writing-to-learn in STEM.

WtL deepens conceptual understanding, reveals deep misconceptions. Acculturates students into our disciplines. Increase retention?

Myths:

?STEM faculty don't care about writing?
?Writing isn't integral to STEM - is a last minute add-on? (We mislead students about this.)
?It's the English dept's job?
?A department needs only a few writing-in-the-discipline courses?
?More writing assignments are all that's needed? No, objectives and task-prompts are commonly misaligned.

Students only learn to write science by having to write science. They benefit from being asked about the writing (see that they're learning writing). From writing in many courses, for many genres and audiences.

Promising practices:

1. Lesh translation model (constructivist): give students multiple modes of learning.

2. Project- and problem-based learning? Give students real-world goals - something useful to others.

3. BioTAP:

4. Calibrated peer review:

5. Jing as a tool for providing high-quality feedback with minimal work.

Now I think we're going to break into groups...

Nothing in Education Makes Sense Except in the Light of Evolution

2010-11-12T12:32:00.000-08:00

A talk by David Sloan Wilson at the 2010 National Meeting of The Reinvention Center. (David Sloan Wilson blogs about evolution at ScienceBlogs. I don't remember much about the content, but I do remember that I disagreed with it.)

Four main points:

1. Evolutionary theory integrates all of biology. Darwin's theory transcends disciplinary boundaries. So evolutionary biologists already are thinking interdisciplinarily. (But only within biology.)

2. It can do the same for all human-related subjects. Well yes, because humans are products of biological evolution, and everything we do has some sort of biological base. But academics outside of biology, and even many within, think of human affairs as having little to do with biology. Ed Wilson's Sociobiology book as a landmark - everyone up in arms at an attempt to apply biological thinking to human activities. Evolutionary ideas are not reflected in higher education, except in biology.

3. Can it integrate undergraduate education? To the extent that learning and culture are biological properties, yes. His new initiative = EVOS. Objcctive is to teach evolution to all students, early (Evolution for Everyone" optional first year course open to all). An EvoS seminar series and associated course directed at a wide audience. The topics certainly would qualify as 'sociobiology'.

4. Can learning about evolution make students smarter? He thinks so (he's collecting the data), because a few basic principles are repeatedly applied to a diverse array of subjects.

Questions:

"Everyone knows that life is a cycle. Is evolution cyclic?" A very tactful answer, emphasizing that evolution is not linear or goal-directed, and ignoring the claim about life being a cycle.

How to deal with the fear of many in social sciences that application of evolutionary theory to human affairs may provide very distasteful (politically incorrect) answers? He tactfully avoids dealing with the issue by slithering to the value of evolution as a toolkit for understanding human nature.

What about how humans have evolved to interact with technology, and how we and technology will coevolve?

A asked a question but didn't really make my point well. I want to know about the evolution of learning, and what that tells about how to teach.

Talk by Reinvention Center Director Pat Turner

2010-11-12T10:53:00.000-08:00

This was an informal lunchtime talk by the new director, Pat Turner of UC Davis, who's also in charge of undergraduate studies at UC Davis. She mostly talked about her undergraduate experience, especially the perspective of someone from a family with no background of higher education. She reminded us that many students choose a university with no understanding of the distinctions that we academics think so important.

One caution she gave us is that, because most people think all universities are basically the same, the bad experience of a student with, for example, a for-profit institution, may cause all the people in their circle to expect similar problems with any university.

Students also come to university with no understanding of how universities work either (she thought that you became a professor after years of proving yourself as a high school teacher). I had a lot of the same misconceptions.

AARRGH!!! flowers!

2010-11-12T08:35:00.000-08:00

I just discovered that this blogger format makes all the bullet points into little flowers! OK, I found a better (cleaner) template.

What we know about writing in STEM

2010-11-12T08:33:00.000-08:00

Greg Bothun, U. Oregon: (at the Reinvention Center conference)

Student writing projects give unsatisfactory results:

book reports, factoids
Reliance on authority, not experiment
poor organization
not fluid presentation.

Why?

students are taught to be factoid-driven.
no motivation for reflection (takes too much time)
Organizing takes time
students think in bullet points.

We need to change:

Students perceive writing as irrelevant to their goals.
Students perceive writing as a reporting task, not as a synthesis tool.

Techniques to change this:

Open-ended assignments don't work.
Give out-there essay topics - topics that are so vague and cosmic that they can't get the answer from Google or Wikipedia ("Did humanity lose its soul in the industrial revolution?") But how to grade???
Allow creative presentation as 'writing'. Make them write poetry about the topics!!! Newspaper article? Work in a group to prepare a flyer for a target audience.
Carrots? Republication on blogs with high readership.

Collaborative writing much better than solitary writing.

Collaborative lab reports.
Reports as consultant agency -
Write a flyer (wind power example from a student team; could we do this in Genetics?).
Group oral presentations (asking for persuasive arguments, not factoids)
Video.

Video editing project:

"Your 15 min video will be shown at halftime in the superbowl, to get audience to change how they make decisions."

(Oops, missed the last part because I was trying to find out why my tweets aren't showing up.)

Questions:

Copyright issues for videos: He doesn't worry about.

Slacker management? Let the groups manage this informally. Asking students to grade each other's contributions doesn't work (not mature enough). Asking for a one-page summary outlining what each student contributed, and saying that grades will be individually adjusted only in extreme situations.

Or have them use Blackboard etc, then you can just look at their individual online contributions.

Workshop on Writing to Learn (WtL) in the STEM Disciplines

2010-11-12T08:04:00.000-08:00

by Chris Thiess, at the Reinvention Center conference

Designing WtL activities ( minimize work for instructors)

Limit the need for grades
Make writing integral, not an add-on.
Use peer response/review
Use digital tools (e.g. blog posts) to multiply real audiences, expose students to writing by other students, to speed feedback.

Some ideas:

Writing as a tool that helps students achieve their own goals.

Regular, in-class activities, one-minute task, writing about an idea from the class.
Help students learn to take better notes.
Prompts that build-in assessment criteria - think about how the assignment can prompt students to do the things you will want to assess.
Make draft/feedback/revision the norm for important writing. Could we do this in presenting the assignment to them??? (i.e. we revise the poorly explained assignment in response to their feedback???) Ask him.

Measuring WtL: (He is addressing both how we assess the students' writing and how we assess the effectiveness/payoff of the WtL activity.)

Tools for assessment of activity effectiveness: surveys, focus groups, discourse analysis, student portfolios and reflective essays.

The Reinvention Center 2010 National Conference

2010-11-12T06:59:00.000-08:00

I'm in Washington DC at the 2010 National Conference of a group called The Reinvention Center, a national consortium of research universities established in 2000 and inspired by the Boyer Commission report, Reinventing Undergraduate Education: A Blueprint for America's Universities (1998).

There's about 200 people here, almost all from major American universities. Many people who run innovative programs in the humanities and sciences, and there are lots of vice-presidents and deans and program directors. The sessions are strongly focused on what needs to change and how.

The first talk has just ended. Bernadette Gray-Little is Chancellor of the University of Kansas, so her talk was focused on the changing forces acting on research universities - how students view us, how donors view us, the risks of the necessary changes to become more entrepreneurial.

"The Kenmore model: As courses and other educational resources become increasingly available on-line, will universities become retailers for educational products we have not created and do not control?"

The proportions of minority students are shifting - disproportionate numbers are going to for-profit institutions (mostly online). Partly this is due to better marketing - the for-profits advertise that they offer students more flexibility and maybe less debt, but the student experience is very different.

The questions are great. The man beside me is asking about the role of ethics in these changes. Will we risk becoming like WalMart, doing wrong to make money? She doesn't, of course, have answers, just cautions.

We like to think about the research experiences that students can get, but most students don't because there aren't enough places in faculty labs for them. So how do we scale our advantages? I'm sitting beside a woman who runs an HHMI- and NSF-supported program that puts 500 freshman students (at U. Texas Austin) into research labs, in groups mentored by full-time postdoctoral teaching fellows.

Introductory Genetics ≠ Introduction to Genetic Analysis

2010-11-05T18:49:00.000-07:00

(The ideas in this post aren't well-organized - I'm still struggling to sort them out.)

I'm finally doing what I should have done ages ago - reading the Prefaces to genetics textbooks. This is where the authors explain what they are trying to accomplish - what the book is trying to teach.

Reading the Preface to the genetics text always used at UBC (Introduction to Genetic Analysis) clarifies why I think it's wrongheaded. The goal is to teach students how to do genetic analysis, i.e. how to use genetic methods to find out about biological processes. (Duh, I shouldn't be surprised, that's what the title says too.)

The framework of IGA has always been explicitly historical, which is (or at least was) sensible. Students of course need to learn how inheritance works before they can use genetic analysis, and in this framework they're taught this by learning about the classic genetic-analysis experiments that were used to discover the mechanisms of inheritance. By seeing what was learned about inheritance from generations of geneticists studying the results of crosses, students learn both the principles of inheritance and the methods of genetic analysis.

Because this textbook has been so successful (it's now heading for the 10th edition, 35 years after the first), all the other genetics textbooks have adopted its historical Mendel-first framework even when teaching genetic analysis is not the main goal (or only one of them).

But the role of genetics has changed. Genetics is no longer a specialist topic, taught to the best and the brightest students, used by elite biologists. Rather it's everywhere in our lives - the media (every day, in both discussions of genetics and in analogies ("the DNA of music", "the DNA of advertising"), the doctor's office, the elementary schools. And genetic analysis itself relies much less on crosses, and more on combinations of mutant-construction, DNA analysis and phenotype analyses. All of these are more easily taught outside of the context of crosses.

Given this, I think that the primary goal of a modern introductory genetics course shouldn't be to teach genetic analysis, but to give a solid understanding of how inheritance works and how it applies to a broad range of important issues.

Unfortunately, for most students, this goal isn't achieved by courses that emphasize genetic analysis, especially with the standard historical approach. One problem is that the students have changed. Now most biology programs require a course in genetics, so the student base is much broader and more diverse. Their background has also changed. They've already been taught about DNA and Mendel's 'rules'. But I think the biggest problem is that the historical approach makes understanding the basic principles more difficult than it needs to be. Early in the history of genetics, genes were a 'black box', and researchers used genetic analysis to gradually pry the box open. Now the box is wide open, but we still start teaching it as a black box. This encourages students to treat genetics principles as factoids to be memorized and regurgitated.

I'm also reading the Preface to Sturtevant and Beadle's 1939 Introduction to Genetics. They don't take a historical approach at all, rather they have chosen 'to give a natural order that simplifies the presentation.' They start with chromosomes, introducing sex chromosomes as explaining why there are equal numbers of males and females, and then follow a sex-linked mutation (bar) through crosses where the mutation is either present on the male's sole X or on both of the females Xs. Because bar+ is NOT dominant to bar-, the phenotypes make sense (the heterozygous genotype gives an intermediate phenotype). In a later cross using the sex-linked white locus they introduce dominance, and make the point that dominance is a relationship between alleles (they say that w+ is dominant to w-). They also introduce human pedigrees quite early. Surprisingly, autosomal inheritance and Mendel's work aren't introduced until Chapter III, after Chapter II has discussed sex-linked inheritance and the segregation of chromosomes in meiosis.

Helping students learn when no textbook is assigned

2010-11-04T07:59:00.000-07:00

Yesterday I met with a colleague who has given a lot of thought to how students learn from textbooks. I wanted her advice because my new genetics course won't have an assigned textbook - instead students will be expected to use a textbook of their own choosing (I've provided suggestions) in conjunction with other materials. These resources will be used as reading assignments to be completed before each week's classes and as study materials that reinforce and clarify the lecture material.

Not having an assigned textbook will be a new experience for these students, and for me at this level. I'm doing it because a suitable textbook doesn't exist, but I think I can also use the experience to help students build valuable skills that will be useful in other courses and in the rest of their lives. They'll improve their abilities to gather information from various sources and to integrate this information both across sources and across topics.

Helping students find appropriate readings:

My colleague said that one key will be to give students very explicit guidance about where to look for information. The resources I suggest can probably be organized as 'levels', with level 1 resources being places to start, with the goal of getting a big-picture overview of the topic. For example, for the week that will focus on meiosis, I might recommend that they begin with Wikipedia or an introductory biology textbook (even a high-school biology book), and read with the goal of finding out what function meiosis accomplishes that mitosis doesn't, and why this is important. I'd recommend that they then move on to more specialized level 2 resource such as whichever genetics textbook they have and any specific readings I've provided, and read with the goal of finding out how meiosis accomplishes its function. There might also be level 3 readings - places to go for details. And I'd like to include other materials than text, such as expert and beginner animations and movies found on YouTube.

For each level's reading goals, students should also be given one or two study questions to answer. For example, a level 1 question about meiosis might ask why meiosis only happens in the cells that make eggs or sperm, and a level 2 question might ask about the differences between the chromosome pairs seen in mitosis and those seen in the first and second stages of meiosis. The students' ability to answer these questions will be tested in weekly on-line reading quiz due each Sunday midnight (before the week's classes); the questions in the quiz should be very similar to the study questions they'll have been given.

She also emphasized the importance of giving students tasks and activities they need to accomplish using their reading, to help them focus and to stop them from just passively absorbing the factoids. It would be good to be able to assign students to 'reading groups', with each group given a different component they had to sort out and somehow present to the other groups. But I think organizing this and finding time for it would be too big a challenge, both for me and for the students.

I will use one technique I have used in the past with my first-year classes. One question of each week's reading quiz will ask for the student for a question about the readings that they would like to have answered in class. This (I hope) nudges them to pay attention to identifying the things they don't understand, rather than just comforting themselves with the things they (think that they) do understand. This might even help them to regard discovering things they don't understand as progress rather than as failure.

Helping students interpret and connect what they've read:

My colleague also suggested a way to use part of each tutorial to get students (i) explicitly analyzing what they learned from the readings and (ii) making connections between the material for different weeks. (We have the luxury of a 2-hr tutorial each week.) It's very low-tech, relying on flip-chart sheets and coloured pens.

Each week the tutorial starts with a blank flipchart sheet and a specific pen colour. Let's assume that this tutorial is happening in the third week of classes, when the lectures are addressing topic C. The TA asks the students for important points about topic C that they learned from the readings they've just done, and writes these on the flipchart (red ink). The TA also asks them for important words they've learned, and maybe other things too. Then the TA puts up the topic B flipchart sheet (green ink) from the previous week's tutorial (there won't be a topic A flipchart since there were no tutorials in week 1). Now the students are asked to make connections between the two sheets, and the TA uses the green pen to annotate the points on the topic C sheet with the relevant point numbers from the topic B sheet.

As the course proceeds this organizing and connection-making activity will become increasingly complex; it will probably take half an hour in each tutorial, sometimes more. Students will be told (over and over) that this connection-making activity is especially critical for success in this course, because we're separately introducing the two major genetic phenomena (how genes control phenotypes and how genes are inherited) and then asking students to connect them and work with the combination for the rest of the course. And that it's also extremely valuable in other contexts.

If we also encourage students to use this part of each tutorial to share information about the sources they found useful and the problems they experienced using them, this will help all the students (and us) discover the best kinds of resources to try. We might even be able to photograph the flipchart sheets after the tutorials and post them online for students' (and our) future reference.

I'll have to check out the room assigned for our tutorials, to see if this can work. OK, here it is, Math 103. Wow, do we ever have chalkboards! Lots of opportunities to have students work through problems on the boards. And lots of space to tape up flipchart sheets.

Helping students improve their writing skills:

My colleague also reminded me that, next fall, many of my students will have been working on their academic writing skills as part of a first-year 'seminar' program . My course will include a small writing assignment (see Don's brilliant idea), and she's going to send me a document that spells out the writing goals the students were working towards in this program. That will let me explicitly build on their first-year experience.

What do I want in a genetics textbook?

2010-10-31T09:54:00.000-07:00

I'm trying to complete a questionnaire about a genetics textbook (for its publisher), but it's hard because my objections to it (and all the other genetics texts on the market) are so cosmic in scale. I started trying to write a few paragraphs that summarize what I think is wrong and what should be done. But now I think I should write a more substantial article, that I would submit to Genetics or to Nature Reviews Genetics. Below are some sentences:

Genetics textbooks teach students to manipulate meaningless symbols and numbers according to what appear to them to be an arbitrary set of rules.

It's pure wishful thinking to believe that most students in an introductory genetics course can come to understand how inheritance works by walking in the footsteps of Mendel and Morgan.

Nor will they learn how genes affect phenotypes by following genetic symbols through crosses that obey apparently arbitrary rules.

Nor does the ability to manipulate genetic symbols according to a set of rules show that they understand anything about how inheritance works or genes affect phenotypes.

Nor des the ability to apply technical terms to pattern-recognition images show that they understand anything about what meiosis accomplishes or how it does it.

The ability to put genotype symbols into a Punnett square doesn't mean students understand meiosis and mating.

The ability to decide whether to use an uppercase or lower case letter for an allele doesn't mean students understand anything about how allele combinations determine phenotypes.

Students naturally (wisely) treat meiosis as a pattern-recognition challenge, and think dominance is an intrinsic property of certain alleles, perhaps caused by some mysterious kind of epigenetic modification.

If evolution is wrong...

2010-10-20T19:38:00.000-07:00

I'm working on a one-page handout to be given out at an upcoming talk by a young-Earth creationist. I think I've discovered a new slant on the 'why evolution must be true' arguments:

Evolution is as true as gravity:

Not only is evolution fully consistent with the other principles of science, if it were false they would also have to be false.

If evolution is wrong:

· Probability must be wrong. If weak effects of genetic differences don’t accumulate over many generations, we must not understand the cumulative effects of recurring rare events.

· Geology must be wrong. If we don’t know how to date fossils, we must also not know how to date rocks.

· Biochemistry must be wrong. If biochemical pathways didn’t evolve, then metabolism makes no sense.

· Microbiology must be wrong. If viruses don’t evolve, we shouldn’t keep getting colds and the flu.

· Genetics must be wrong. If natural selection doesn’t happen, mutant genes must not be passed on to offspring.

· Physics must be wrong. If evolution hasn’t happened, we must not understand the laws of thermodynamics.

· Pharmacology must be wrong. If lab animals aren’t our relatives, our drug tests must be giving the wrong results.

· Ecology must be wrong. If we don’t know how species change, we must also not know how species interact with their environments.

· Agriculture must be wrong. If the plants and animals we eat didn't evolve by natural selection, we couldn't have improved them by artificial selection.

With young college students (my target audience) I think this may be quite a powerful argument for evolution. Basically, if they believe that scientific research has gotten evolution all wrong, they have to also suspect all the other parts of science and technology that their lives depend on.

But I don't think I've done a very good job with the particulars. I find it hard to twist my mind around the consequences of discarding things I'm confident are true, and I'd welcome any suggestions for improvement.

Here's the second part of the handout:

Evolution is as important as life:

As individuals and societies, we are now making decisions that will have profound consequences for future generations.

· How should we balance the need to preserve the Earth’s plants, animals, and natural environment against other pressing concerns?

· Can we preserve endangered species without changing them?

· Should we alter our use of fossil fuels and other natural resources to enhance the well-being of our descendants?

· To what extent should we use our new understanding of genes to alter the characteristics of living things?

· How can we prevent bacteria from becoming resistant to our antibiotics?

Unless we understand evolution we will not be able to make these decisions wisely.

I think this is also not very well done. I lifted most of it from the conclusions of the National Academy of Sciences 88-page report on Science, Evolution and Creationism. If this doesn't get rewritten I'd better remember to credit them in a footnote.

Don's brilliant idea

2010-10-07T16:28:00.000-07:00

I was just meeting with some genetics textbook editors and the colleague that I'll be teaching the new genetics course with. I had been saying that I want to include a writing component in the assignments, and he had described an essay assignment he had used with an advanced class.

Later we were griping about the quality of news reporting of genetics issues, and he had the brilliant idea of requiring each student to write a 'letter to the editor' correcting some incorrect genetics information that they had read in a newspaper, magazine or blog, or heard or seen in a broadcast. Each student would be expected to find their own information to correct. We could incorporate peer review, so the authors would have to revise and improve their draft letters. The TAs would mark the letters, and the students would be strongly encouraged to then send them to the offending writer or editor.

What a blast! Hundreds of letters sent, complaining about specific errors in science journalism.

Thinking about textbooks

2009-08-04T06:06:00.000-07:00

In preparation for this morning's meeting of the genetics-revision committee, each committee member has reviewed one of the candidate textbooks. I had prepared a checklist of content and presentation issues to guide this, but it was a quick-and-dirty list and I now realize that I overlooked some big issues.

I realized this because I spent yesterday afternoon reviewing the textbook I'd taken on, and yesterday evening reviewing the first (draft) chapter of a new genetics textbook. I filled in my checklist for the former, and sent the publisher a lot of detailed comments on the latter, but now I think I need to add to my checklist and send a second email clarifying the big issues.

One is the difference between information and science. I really like the first-year textbook I've been using (Scott Freeman's Biological Science) because of its explicitly scientific approach. Each topic is introduced as questions: What do we (students and researchers) want to understand? What are the hypotheses? How have they been/are they being tested? Neither genetics textbook I reviewed does this. Instead they present lots of information, but as facts and history, not science.

The history aspect is a big problem. Classic experiments are described in detail, but it's not at all clear why students should know these. The strongest original evidence that DNA carries genetic information came from two now-famous studies. Both textbooks explain these well, but doing so requires explaining a lot of technical details about the experimental systems used (pathogenic bacteria and bacterial viruses) that does nothing to advance students understanding of DNA's function. If we just wanted to convince students that DNA does carry the genetic information, there are many simpler experiments available now, such as transforming bacteria with a plasmid carrying an antibiotic resistance gene. If we want students to learn history, we need to know why.

Another problem is telling the students why particular information is being presented, how they are expected to use what's in the chapter. The draft first chapter I read was densely packed with information on an enormous range of topics: the history of genetics, the structure of DNA, how gene expression works and how it is regulated, how evolution happens, the first organisms, how evolutionary relationships are inferred from DNA sequences. The authors' Prospectus indicated that they think students will already know a fair bit of this, but the students aren't told how they should use this information. Is it meant to be a review? Will they need to know this in order to understand the following chapters?

The techniques students are taught are strangely archaic. Nobody does Southern blots any more, or scores restriction-fragment-length polymorphisms! Instead, modern genetic analysis is based on direct determination of DNA sequences. The technologies that do this are complex, but analysis using sequences is (should be) much more intuitive for students to understand than the indirect methods we used to rely on. I can appreciate how an old textbook such as IGA might be conservative in the methods it describes (laziness, partly, and lack of imagination) but this is inexcusable in a completely new book.

Results of the textbook meeting

2009-06-18T09:14:00.000-07:00

Yesterday's meeting with the textbook rep clarified several tasks (listed below in no particular order):

1. The textbook publisher could create a composite textbook for us, made up of chapters taken from two or more different sources. But this may be more suitable for a survey course than for one that gradually builds expertise The rep will find out whether instructors have used 'composite' textbooks for courses like ours, and if so will put us in touch with the instructors.

2. The textbook rep will find out about on-line genetics activities provided to students with the various textbooks. And we will go through the activities she discovered in one of the textbooks, to find out how suitable they would be for our students (we want interactive activities, where students have to make decisions about what to do and predictions about what will happen).

3. I will dig out our old autotutorial genetics material to see if some of that could be repurposed for this new course.

4. We will look more carefully at the available textbooks, to determine what might be suitable. In particular, is there a textbook that would be OK if it were supplemented with one or two chapters from other sources, or with a week or two of material we have written specifically for our course?

5. We will prepare an email to the authors of existing genetics textbooks, explaining the approach we want to take and asking if they know of any suitable textbooks or other resources. (We'll also give this to the rep.) Here's a draft for us to start with:

Dear genetics textbook author,

We are planning a new genetics course for second-year biology majors, but we haven't been able to find any textbook that uses the approach we think best (described below). So we're contacting the authors of respected genetics textbooks to ask if they might know of something suitable.

After many years of teaching genetics, we feel that understanding the core of genetics has three main components. First, students must understand meiosis and its genetic consequences - how parental genotypes give rise to gamete genotypes, and how random gamete fusion creates offspring with new combinations of parental genotypes. Second, students must understand how genotypes produce phenotypes - how genes and proteins work, the role of environmental variation, how changes to DNA sequences change gene activities, and how, in diploid organisms, different alleles of the same or different genes interact to produce phenotypes. (This last point is perhaps the most important: students need to understand the molecular basis of dominance and epistasis.) Finally, once students have some mastery of both inheritance and phenotypes, they must learn to put these together to understand how phenotypes are inherited.

We have been unable to find any textbook that takes this approach. Traditional (Mendel-first) texts throw students in at the deep end, asking them to start applying Mendelian principles without any explanation of their causes. Even the simplest Punnett square implicitly requires students to figure out parental genotypes from parental phenotypes, to predict the gamete genotypes and proportions these parents will produce, to predict the offspring genotypes and proportions that random fusion of these gametes will produce, and to predict the offspring phenotypes from these genotypes. It's not surprising that students cope by blindly memorizing rules and patterns. Later chapters in the textbooks do teach meiosis and gene action, but most students treat these explanations as independent facts to be memorized, and never really make the causal connections between them and the rules and patterns they began with. (If you doubt this, try asking students why we see dominance.)

DNA-first textbooks give students all the facts of molecular biology before introducing Mendel, but students are unable to use this information to predict phenotypes because the text spent no more than a paragraph on the critical issue of what happens when two different alleles are present. And meiosis is again treated largely as patterns to be recognized, with no emphasis on using it to predict gamete genotypes.

Here's what we think is missing from the textbooks we've examined:

Material that teaches students to predict gamete genotypes from parental genotypes. This needn't be a chapter in itself, but the basics should be introduced when meiosis is introduced, and extended when each new complication is brought up. For example, when crossing over or chromosome rearrangements are taught, students should also be taught how to predict the gamete genotypes that crossovers and rearrangements will produce. This teaching needs to be accompanied by appropriate problems. For example: "A man has genotype a1 a2 b1 b2. What gametes will a single meiosis produce? What gamete genotypes will the pooled products of many meioses contain, and in what proportions?"
Material (probably a chapter) that teaches students about the causal relationships between diploid genotypes and diploid phenotypes, explicitly incorporating the molecular basis of each effect. (Haploids could also be in such a chapter.) What if one allele produces a functional enzyme but the other produces no enzyme at all? What if one allele of a repressor gene is defective?

We really don't want to write our own textbook, or even our own supplementary chapters. Might you know of any textbook that takes the approach we're looking for. Or perhaps just a chapter or other written material that could fill in the gaps we see?

Thanks very much in advance for any suggestions,

Preparing for a meeting with our usual textbook rep

2009-06-17T14:30:00.000-07:00

The Genetics planning committee (or whatever we are) is about to meet with a textbook rep to discuss options for getting a textbook that fits the kind of course we want to teach.

I'll set aside for now the issue of whether we want a textbook at all. I think we need a set of required readings (and maybe activities) that we expect students to complete BEFORE they come to class. These could be chapters of a standard textbook, a collection of chapters from different textbooks that a publisher has put together for us, stuff we wrote ourselves, or ???

Why a typical genetics textbook isn't suitable:

Our approach to teaching genetics seems very sensible to us, but it's certainly not the one most courses take. Genetics courses and textbooks usually start either with some combination of Mendel's discoveries, meiosis and DNA/gene expression, introducing the basics of what's called 'transmission genetics'. They may do Mendel first, or DNA first. Students learn to predict phenotypes of offspring from phenotypes of parents, and vice versa. To do this they need to have memorized 'Mendel's laws'. In this context our current understanding of molecular biology and meiosis is presented as explaining what Mendel found.

We instead want to separately teach the two components of transmission genetics. We will thoroughly teach how DNA sequences determine phenotype, building a solid molecular foundation for such concepts as ploidy and dominance. Separately we'll teach how DNA sequences are inherited (meiosis, gamete fusion, chromosome reassortment and crossing over, etc.). Only once both components have been solidly established will we combine them to teach about the inheritance of phenotypes.

But we can't find a textbook that does a proper job of teaching how genotype determines phenotype. This deserves at least one full chapter, maybe more, but textbooks usually gloss over it, assuming that students who understand how DNA makes RNA makes proteins and what proteins do will automatically grasp the implications for phenotypes, especially in diploids.

So maybe the solution is to use a standard textbook but somehow create this anomalous chapter ourselves, or find it somewhere outside of the usual textbooks.

Improving the match between objectives and assessment

2009-04-15T07:31:00.000-07:00

Yesterday one of the biology instructors presented to the rest of the first-year instructors the results of an analysis she'd done. She wanted to find out whether the 'learning objectives' we developed and are trying to follow match what we actually assess in our midterms and final exams. The issue wasn't so much about their content as about their level of difficulty, which she scored using the 'Bloom's Taxonomy' scale.

What she found was that our exams ask more of our students than they would expect from the learning objectives we give them. Even our multiple choice questions are quite challenging, mostly requiring a lot more than simple regurgitation of factoids. This is good in that we're assessing learning at the level we want, but bad in that we're not telling students the truth about our expectations

The cause of the discrepancy is that we are all relatively new to writing learning objectives. When we wrote them (as a committee) we focused more on content than on what we wanted our students to be able to do with the content. We knew enough to use 'performance' verbs like describe, list, and explain rather than 'state' verbs like know and understand, but we needed to also use words like predict, interpret and deduce.

The instructor fixed the objectives for us - she went through all of them (about 50!) and rewrote them to reflect what we are actually assessing.

Word-cloud of the 3491 questions about biology

2008-10-22T12:20:00.000-07:00

Here's a Wordle analysis of the 3491 questions posed by my Biology 121 students last year:

And here's a different representation:

Ideas from a creationist

2008-09-22T14:07:00.000-07:00

Last night I went to a talk by a creationist, 'Professor' Walter J. Veith, chair of the Department of Zoology at the University of Western Cape, South Africa. It was part of a two-night series called "The Genesis Conflict", with two talks each night (creationists must have a lot of stamina). I couldn't find out who sponsored it, though collection baskets were passed and a lot of people put money in them. There was a big poster at a bus shelter in Tsawwassen - I took a photo of it which I'd like to put here, but I'm afraid I haven't figured out how to access photos that I took with my iPhone (I can copy them to my laptop but then I can't find them).

Veith's mini-biography on the flyer says, inaccurately, that he served for many years as chair of the Zoology Dept. at the University of the Western Cape in South Africa. Apparently he only served for a few months, after which the department pushed him over into the Physiology Dept, where his anti-evolution ideas would be less problematic (see this archive). He's been retired since 2003, and has lots of tapes and DVDs for sale. His current affiliation is Seventh-Day Adventist. Over the next two weeks he's giving another series of 10 talks on the topic of "Reformation Rekindled", which appear to be about how the true spirit of the Protestant Reformation has been squelched by the wicked Roman Catholics.

This talk was titled "The Genes of Genesis". His premise was the old canard that the requirements for life are far too improbable to have arisen by chance, so we must instead infer the hand of a designer. He began by calculating the odds of 300 nucleotides assembling in the right order to encode a specific 100-amino acid protein (2^300 = 1-^127). He then pointed out that this was far larger than the number of particles in the universe, and asked "You decide, chance or a designer?"

He put this question to the audience each time he added another requirement for life onto his list (ribosomes, chaperonins, regulatory proteins,multicellularity, differentiated cell types, biochemical pathways, chromosomal rearrangements, sexual reproduction...). He was quite glib, throwing in enough technical terms and genial explanations to impress the non-scientific audience. He didn't make any other points, just kept pushing the numerical improbability of the origin of life/animals/people.

I especially enjoyed this because I explain the resolution of this 'paradox' in the very first class of BIOL 121. If it were true that 'life' couldn't get started evolving until a fully functional microbial cell had arisen by chance alone, then the origin of life would indeed be a big paradox. But it's not true. We can set aside the issue of that we mean by 'life', and just consider how much chance is required to produce something that natural selection can act on. Before the catalytic properties of RNA were discovered, only entities with RNA-directed protein synthesis machinery were thought to have the heredity and variation needed for natural selection, and these really are much too complicated to arise by chance. But now we know that RNA-like molecules can, in principle, catalyze their own replication. This means that evolution could have gotten started by the chance production of a single relatively simple molecule. Improbable maybe, but not nearly as improbable as a designer.

I think I can improve this BIOL 121 class by introducing it with a description of Veith's talk. This will bring home to the students that

I tried to stick around for the second talk ("Creation to Restoration"). Judging by the first few minutes, it was going to be about how the animals in Eden (vegans all) became nasty carnivores and parasites and pathogens. He had lots of just-so stories ready to go, beginning with how Eden's snakes transformed their salivary glands into venomous fangs, and how roaches in Hawaiian caves evolved eyelessness in 8 months. (The latter appears to confound colonization of Hawaiian lava tubes with Australian cave cockroach evolution.)

When I came out I was pleased to find a flyer from the local Humanists Society tucked under each windshield.

What they learned in kindergarden

2008-07-31T10:42:00.000-07:00

I had breakfast with a kindergarden teacher, and we discovered some similarities in our jobs.

In both kindergarden and first-year university, students are learning to function in a new environment. They must discover what's expected of them before they can do what we expect.

In both kindergarden and first-year university, some students are very reluctant to speak up, because they don't feel intellectually safe (they're afraid of saying the wrong thing). We need to find ways to build their confidence, not in being right but in the value of not (yet) understanding. This problem is much worse in university than in kindergarden. That's probably because learning how to do new things is what young children do (they're used to succeeding), whereas high school somehow shifts their focus to being concerned about failing to learn at the expected rate or under the given circumstances.

Teaching Philosophy, Take Two

2008-07-27T14:44:00.000-07:00

(Yes, this is a completely different organization that I tried in Take One)

Why I chose to teach first-year students: Most faculty prefer to avoid teaching introductory courses, but in many ways this is the most important teaching of all. First, it fills a more urgent need - the inability of the general public to approach the world scientifically is much more critical than the supply of new professional scientists. Second, it has more impact - first-year students are more open to new ideas. Third, it's more interesting - first-year courses deal with the big questions in biology, and teaching them pushes me way out of my area of expertise. Below I describe some specific issues that arise, and my approaches to them.

Learning how to teach: Like most academics, I initially planned to teach the way I wished I had been taught, but soon realized that what would have worked for future faculty didn't work for the great majority of students. I then sought out pedagogical expertise, especially from a colleague in the Faculty of Education with whom I still meet regularly. This exposed me to many innovative ideas, a number of which I've implemented. But I also realized that, although most of these ideas sounded good on paper, few had ever been critically tested. The example of the physics Force Concept Inventory convinced me that chances to teaching strategies need to be grounded in rigorous evaluation: science faculty should apply to their teaching methods the same requirements for evidence that they apply to their science. My involvement with the Carl Wieman Science Education Initiative is now enabling me to begin contributing to this evidence,in the form of a very well controlled experiment testing the effect of written homework on both students' writing skills and understanding of biological concepts.

Teaching how to learn: Most first-year students' biggest problem is that they don't yet know how to learn. Despite much excellent teaching in high school, they expect university biology to consist largely of applying their demonstrated memorization skills to more advanced facts. Because these skills have served them well in the past, students are very reluctant to replace them with what they see as more risky approaches. To help them experience "not understanding" as a necessary stage in learning rather than as failure, I award marks for posing questions about each week's reading material. To help them see the value of cooperative learning, I encourage students to consult their neighbours before answering in-class questions. To help them learn about how they learn,I also explicitly explain the pedagogical issues underlying different class activities and assignments. To help them learn that understanding is more valuable than rote memorization, all my tests and exams are open-book.

Teaching science as a process: Initially, first-year students think of science as a body of facts generated by specialists, an attitude that can't be changed by simply telling them "Science is a way of knowing". To demystify science, and to help them begin to see themselves as beginning scientists, I incorporate new research results into course work, and have students use the same tools for their homework assignments that researchers use for their research (e.g. HapMap, News & Views articles, and text and figures from recently published papers). Many students also earn 15% of their course grade by reading and reviewing a research paper of their own choice.

Reinforcing relevance: Students view course work as unrelated to their real lives, needed only for the test and perhaps for more advanced courses. To help change this, the homework activities have been carefully designed to focus on issues the students care about: cancer risk, the environment, human diversity. Many students earn 15% of their course mark for community-service learning projects in inner-city schools. By receiving course marks for what they consistently describe as a "life-changing experience", students learn that the university values their ability to help their communities.

Teaching philosophy

2008-07-25T11:28:00.000-07:00

It's time to write a new 'Teaching Philosophy' section for my CV, so I though I'd work on it here.
I think there should be four headings:

Why I've chosen to teach first-year classes
Problems ("Challenges"? "Goals"?)
Solutions - principles
Solutions - what I'm doing.

1. Why I've chosen to teach first-year classes: The inability of the general public to approach the world scientifically is much more important than the supply of new professional scientists.

2. Goals: A. Increase students' confidence in their ability to learn at the university level (to learn as scientists). B. Help them see the broad relevance of their learning. Not just the relevance of the material I'm teaching them, but that their having learned it makes a difference to more than their grade in the course (in their lives and what they can do for the rest of the world). C. Get them comfortable with not-understanding, as not a failure but a necessary prelude to understanding. D. Get them comfortable with working collaboratively. E. Convince them that rote memorization has little or no role in university learning. Help them transition from rote memorization to real understanding.

3. Solutions (principles): A. Scientists have been very slow to apply to their teaching methods the same requirements for evidence that they apply to their research. Where possible, make changes supported by evidence (preferably from peer-reviewed sources. Work to generate evidence. B. We can't blame high-school science teachers for the misconceptions our first-year students arrive with - we're the ones who taught those teachers.

4. Solutions (what I'm actually doing): C. Giving only open-book midterms, exams, quizzes. Giving students choices - letting them modify what they take on and how they are assessed. Talking about the learning process - explaining why topics are presented in certain ways. Using clickers (I pioneered this in Biology 121). Providing opportunities for students to consult with each other in every class. Running a research project on the effect of written homework. Asking that they learn to pose their questions in writing. Incorporating the latest research into the course - exposing students to appropriate research papers from the start. Regularly consulting with a colleague in the Faculty of Education whose expertise is in biology education. Providing a community service learning option - this is the most popular component of the course. Giving homework assignments that are relevant to issues in health and ecology. Explicitly incorporating material that will prepare them to deal with creationism. Giving marks for asking questions, not just for providing answers.

I should be doing more of this

2008-07-17T07:32:00.000-07:00

An article by Martha Kinney in today's Inside Higher Education explains how the military's training methods can be applied in the college classroom. The basic points are: make expectations explicit, have students crawl, then walk, then run, and be thick-skinned enough to seek out informed criticism of your teaching methods.

She points out that college instructors may apply this conscientiously to the content of what they teach, and yet completely fail to use it in teaching the skills they want students to build. For me, the big difficulty is that I need to clarify for myself exactly what skills my class will develop (not just "I want them to be able to think like scientists."). Perhaps focusing on understanding how scientists write would be best (following on my recent conversation with a colleague in the English Department) - this would let us build both writing skills and interpretation skills.

Showmanship for teachers?

2008-06-29T15:26:00.000-07:00

A post on BoingBoing a few months ago prompted me to order Magic and Showmanship: a handbook for conjurers, by Henning Nelms. This book isn't about how to do conjuring or 'magic' tricks, but about how to incorporate drama, suspense, human interest etc. into performances in order to make the tricks much more compelling to the audience.

My hope is that some of this advice will also apply to teaching. If even a little bit rubs off on my classroom persona, the students will find my classes more interesting and, I hope, find the material easier to remember.

Learning to think/write like a scientist

2008-06-06T09:12:00.000-07:00

Yesterday I had a very interesting conversation with a colleague in the English Department. Her research concerns the interactions between reading, writing and disciplinarity. In her role as Associate Dean of Arts she's been working to improve the usefulness of the Arts courses that Science students are required to take. I had thought she might be a good source of advice about interpreting the 'homework project' data, but it was other ideas that got me excited.

We talked about how students make the transition from (a) their high-school relationship to science ('science' is a body of facts I am learning) to (b) seeing themselves as practitioners of science ('science' is how we learn about the world). Reading and writing in the discipline can be a big help with this transition. But it's important that what is read be genuine scientific writing, not writing for students. We talked about how to help students understand the language styles and conventions of research papers (I think her word would be 'genres'), and how this can help them understand how science works. I am going to adopt her practice of taking a paragraph from a research paper and working with students in class to pull it apart and understand what it is communicating, and how. I can use paragraphs from the research papers used in the homeworks, which will also help students see how the homework material is indeed closely tied to the course goals.

We also talked about helping students shift their emphasis from answers (what are the facts?) to questions (what do we want to find out, and how can we do that?) My course's textbook does this very well, but I haven't really tried to reinforce it by what happens in class. I told her that the most successful change I'd made this past year was having students pose questions about the textbook readings (see 3491 questions about biology). Next year I'm going to expand on the question-posing, both in class and in the homework assignments.

This colleague has also, in her capacity as Associate Dean, hired some post-doctoral fellows to work on student writing issues. I'm hoping we can set up a collaboration, using them and perhaps our science teaching fellows, that will enrich the experience for everyone.

Problems with Blackboard Vista

2008-05-13T16:52:00.000-07:00

In previous years my courses used versions of the WebCT course software, but this year they were 'upgraded' to the Vista platform; WebCT has been bought out by Blackboard, so this is a Blackboard system.

Some new 'features' of Vista have worked very well (for example creating and giving homework to sub-groups of students), but others (and some old stuff) have not. I've been keeping a list of the issues that our local tech support people didn't solve, hoping that someone would someday ask me about problems I've experienced. But nobody's asked, so I'm posting the list here (Mainly so I can throw out the sheet of paper it's written on).

First a complaint about the technical support. The problem isn't the support people, who do their best, but the way UBC allocates resources. Years ago UBC decided to transfer funds and responsibility for computer support to local units (Faculties and Departments), rather than providing it centrally for everyone. I don't know whether this was driven by budget issues (dreams of 'cost recovery' were in the air) or by the hope that local support would better suit user's needs, but the consequences for university-wide resources such as Vista have been disastrous. Instead of having a central support group with experts available when we need them, we have many dispersed department-level support people, each working part-time (ours is only available after 4pm) providing support for a system they haven't been able to learn in depth. Worse, each answer they provide is only available to the individual who asked the question. Because there is no discussion board individual users have no way to learn from answers given to anyone else.

So here's my list:

I can't connect to Vista with Safari on my office computer. I can connect with Safari at home, and with Firefox in my office, but when I try to connect with Safari I get the message that I already have a connection and can't have two. And yes, I've emptied the Safari cache, and tried quitting Firefox.

When I do connect with Firefox, I get several problems that I didn't get before I upgraded to Leopard.

First, every time I connect I get 'Code not verified' security warnings (two). I can't find any way to stop them appearing.

Second, when I try to upload files to Vista from my computer, I get a warning that a Java applet isn't working and that I will have to use a more cumbersome method.

Third, when I download results from quizzes, all of the question marks, percent symbols, and single and double quotes in students' answers have been replaced by 'Unicode' codes (e.g. ''' replaces every '?').

Other problems may not have anything to do with using Leopard:

For a while I couldn't upload student marks for one segment of the course. I'd get a 'System exception' error, which apparently just means that for unknown reasons Vista has failed to do what was asked of it.

When I click on View Submissions for an assessment in the Assessment Manager, sometimes I'm taken to the submissions for that assessment, and sometimes I'm instead taken to the submissions for whatever assessment the Manager feels I should be looking at. No rhyme or reason that I can detect.

Sometimes the settings for quiz questions appear to have been reverted, even though I'm quite sure I set them up correctly.

The system claims that it will show me the number of times individual students have read discussion board posts, but the numbers it provides are obviously very wrong.

I've had lots of other problems that our local support person was able to solve, but not these.

Homework project progress

2008-05-02T10:35:00.000-07:00

Grades are in (and so far have generated remarkably little student angst), so now the homework project shifts from teaching to research. I see that I haven't posted about this project here, so here's a link to a post about it on my research blog, RRResearch. Basically, my ~400 introductory biology students were split into two homework groups - one group got homework with multiple-choice questions to answer, and the other had to provide written answers (one sentence to one paragraph in length).

I'm working with a teaching fellow in our university's Carl Wieman Science Education Initiative (CWSEI); we're addressing two questions. First does having to generate written answers and explanations improve students' understanding of course content? This will be assessed by comparing the scores of the two groups on different parts of the final exam. Second, does the homework writing, and the feedback they get, improve students' ability to write clear and correct sentences and paragraphs? This will be assessed by scoring the quality of their writing on written-answer exam questions and on other components of the course. For most of the writings we'll only be looking at basic errors in grammar, spelling, punctuation, syntax etc.

Now that the exams have been graded we have the data to answer the first question. I've just done some preliminary mean-calculating and graphing, but I'm not going to describe the results here yet, partly because these results need careful checking (I could have made yet another Excel error), and partly because I need to first discuss research-blogging issues with my teaching fellow partner in this project.

We can't answer the second question yet because the students' writing hasn't been scored. Luckily we don't have to do this ourselves; the CWSEI has given us funds to hire assistants to do this. The assistants will be Biology grad students, but we need to first check that the students we hire have good enough English skills to catch all of the students' errors. Our first idea was to put together a small set of error-filled student writing and ask potential assistants to grade it with the rubric that was used for grading the homework answers. We've now polished the rubric to make it better for this new purpose. But in the meantime we realized that we probably weren't the first researchers needing to assess basic writing skills,a nd that our research would have more credibility if we assessed our assistants using tools that had been previously validated. So this morning I called our Writing Centre, which provides a number of non-credit courses to improve students' ability to write in various contexts (Language Proficiency Exam, term papers, etc.). The helpful director suggested I call the English Department's first-year program, which she thought had a test they had previously used to assess potential tutors. I'm waiting to hear back from them.

3491 questions about Biology

2008-05-01T17:21:00.000-07:00

One innovation this year was intended to build students' abilities to ask questions. Before each week's lectures the students had to complete a brief multiple-choice reading quiz (usually about 5 questions) based on the assigned readings for the week. This year the last question on each quiz (worth 1 point, like the others) asked

Please give one question about this week's material that you would like to have answered in class.

To earn the point your question must be stated as a question in correct English (e.g. "How do birds fly?", not "how birds fly" or "I want to know how birds fly.").

The writing was initially bad, but both the writing and the quality of the questions quickly got much better, and I started posting each week's questions on the course web site for students to read, and using some of them in class.

Now I've assembled all of the questions, unedited, into a single Word file titled "3491 questions about Biology", which I'm going to email to the other instructors teaching this course. I'll also post it on my own web site; here's a link.

Still here...

2008-04-23T09:16:00.000-07:00

How ironic that teaching diverted the attention I was going to put into my teaching blog. Classes are over and my final exam is on Saturday afternoon.

Yesterday afternoon I attended a "LEAD Meeting", one of 8 sessions organized by the Vice President Academic (in charge of education at UBC) to find out what faculty think should be doe to improve education. He's hoping to get short-term funding for what appears to be a pedagogical 'surge', and wants us to tell him what needs to be done. That is, he wants to invest as-yet-unidentified resources into interventions that will produce a long-term and stable improvement in teaching (and learning) at UBC without requiring any increase in long-term funding.

LEAD stands for Lasting Education, Achieved and Demonstrated; apparently they spent a lot of time coming up with this. Here's what I suppose is the mission statement:

"A central goal to the UBC LEAD initiative is to enable faculty members to create and maintain a rewarding teaching and learning experience. Through a series of LEAD Meetings involving more than 300 UBC faculty members, we seek to learn from our experienced educators the building blocks of a lasting education, and how the university community could further empower and enrich these experiences."

Unfortunately (but not surprisingly) all we came up with was platitudes like "Encourage creative thinking", "Prepare students for the future", and "We need to learn how to change learning as well as teaching". The leaders seemed very happy with this, and I gather that the previous groups did the same.

I don't know why the people behind this initiative decided to waste our time with such poorly informed and undirected meetings. It was a bit like asking a gathering of philosophers how they thought the universe ought to work, based on their day-to-day experiences with reality. There's a lot of data out there on how learning works and how teaching can be improved, and one of its major themes is that we instructors can't trust our intuitions and feelings.

What we did in school today (well, yesterday)

2008-01-26T04:51:00.000-08:00

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.

Paper chromosomes

2008-01-19T18:05:00.000-08:00

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.

Frustrations...

2008-01-09T20:18:00.000-08:00

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.

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

2008-01-06T18:09:00.000-08:00

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?

2008-01-06T17:03:00.000-08:00

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.

2008-01-04T21:55:00.000-08:00

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.

How to teach Hardy-Weinberg equilibrium

2007-12-31T08:23:00.000-08:00

Over on the Gene Expression blog there's a discussion about how to explain Hardy-Weinberg equilibrium. Commentors are claiming that it's best explained mathematically rather than verbally. I'm posting a comment arguing that the best explanation is pictorial. Because I don't think I can put the picture in the comment I'm putting it here.

And here's the text of the comment I posted:

The best way to describe (and teach) Hardy-Weinberg Equilibrium is neither mathematically nor verbally but graphically, using a drawing that's like a Punnett Square with allele frequencies replacing the alleles. I've posted an example on my teaching blog.

Viewed this way, HWE is so obvious and so intuitive that there's no need for ps and qs at all. (And there never was any need for the apparent complication of q, as it's just 1-p.) The sides of the square are simply labeled with the actual allele frequencies, and the areas they create are the genotype frequencies in the next generation.

Of course math will be needed to deal with the deviations from HWE produced by selection and other factors, but starting with this graphical explanation helps beginning students see how simple and inevitable HWE is. (My freshman class on this is titled "The incredible tedium of Hardy-Weinberg equilibrium".)

Why biology is harder than physics

2007-12-26T04:38:00.000-08:00

Beginning university students in the sciences usually consider biology to be much easier than physics or chemistry. From their experience in high school, physics has math and formulae that must be understood to be applied correctly, but the study of biology relies mainly on memorization. But in reality biology is much more complex than the physical sciences, and understanding it requires more, not less, brain work.

Biological processes of course are consequences of physics and chemistry, which is why we require our biology students to study the physical sciences. But organisms are also historical entities, and that's where the complexities arise. The facts of physics and chemistry are constant across time and space. Any one carbon atom is the same as any other, and today's carbon atoms are the same as those of a billion years ago. But each organism is different. That's not just a statement that fruit flies are different from house flies. Rather, each fruit fly is different from every other fruit fly alive today, and from every other fruit fly that ever lived, and it's the differences that make biology both thrilling and hard.

The differences have several causes and consequences. One cause is that biology depends on past history, because descendants are not identical to their ancestors. This is true at all scales, and the fundamental reason is that the process of genetic inheritance is not perfect. The DNA sequences we inherit from our parents are never identical copies of their DNA - instead they contain copying errors. So every copy is slightly different, even between two siblings. We are all mutants. These differences also accumulate over the generations, like in the party game Americans call "telephone" and the British call "Chinese whispers".

The second cause is natural selection, which shapes the accumulation of differences, favouring those that improve survival and reproduction and making it harder for disadvantageous differences to persist over the generations. And because most natural selection arises from interactions with other evolving organisms rather than with the relatively stable physical environment, the changes are rapid.

The result is that all biological systems are diverse at all levels. Even high school students are used to the idea of 'biodiversity', meaning the dramatic differences between different species of plants and animals. But the diversity is much more ubiquitous. Within each multicellular species, every individual is genetically different; every fruit fly is genetically different from every other fruit fly. The invisible bacteria turn out to be much more diverse than anyone would have thought. Bacteria isolated from natural environments are so different that even the individuals we would have considered the same species turn out to have about 10% of their genes from unrelated sources. In lab cultures, bacterial mutation rates are high enough that a single ml of culture will contain millions of different genotypes.

Even genetically identical cells are not functionally identical. When a cell divides its molecules are randomly distributed between the two daughters; because 'randomly' does not mean 'evenly', these daughters will have inherited different sets of the proteins and RNAs that carry out their functions. And even if the two cells had identical contents, these contents would still have different interactions - repressors bump into cofactors at different times, DNA polymerase slips or doesn't slip at different points in its progress along a chromosome. Understanding the how and why of biological phenomena thus requires us to consider historical and ecological factors that are many orders of magnitude more complex than those of physical systems.

The critical word is probably 'population'. Biologists rarely try to define it, but they use the term everywhere to refer to similar but not identical organisms or cells (or even molecules) that interact in some way. 'Population thinking', the realization that species are populations, not pure types, is said to have been key to Darwin's insight that members of a species undergo natural selection. And population thinking is probably what makes biology so much more complex than the physical sciences.

Of course we can't consider all of the differences all of the time, so at different levels of study we biologists try to pull out the factors that we think will matter most. Molecular and cell biologists work with populations of molecules, but they keep everything else as identical as possible. Developmental biologists study how cells become different, but they use pure-breeding lines and clones to ensure that the genetic properties of their organisms are as identical as possible. Ecologists pay attention to the big differences between species, but under conditions where they can ignore the differences between the individuals of each species.

I don't think population thinking is addressed in high school biology. We can't really blame their teachers, because the issues probably were never made clear to them either. Instead high school teachers pass on the facts they remember from what they themselves learned at university. The result is that their students enter university expecting their biology education to consist mainly of memorizing lots of new facts.

We instructors want our new students to start focusing on understanding complex processes and interactions, between entities that are themselves populations of diverse and somewhat unpredictable entities. We're thus asking them to set aside all the learning strategies that worked well for them in high school biology, and to learn in a new way. To students this probably seems the height of foolishness, and they're understandably reluctant to take the chance. So one big challenge, for instructors and for our students, is to find ways to ease this transition. We need to give students confidence that deep understanding will bring better grades than will rote memorization, and that saying "What I don't understand is..." is not an admission of failure but the essential first step to this understanding.

Can we do a Genetics reading assignment?

2007-11-12T17:53:00.000-08:00

The New York Times is publishing a series of very good articles (11 so far) under the heading The DNA Age, about the social and personal implications of DNA sequencing. I'd like to find a way to require all of my BIOL 121 students read and think about at least one of these articles.

How could this work? I'd tell them they need to choose one of the articles to read, and that they will be asked to write a paragraph about what they've read, in response to an article-specific question I'll post. They'll be encouraged to discuss their chosen article with other students, face to face or on the WebCT discussion board, but will need to compose their own paragraph answers. To discourage copying I can have them submit their paragraphs to Turnitin as well as in answer to a WebCT quiz question. I don't know yet what kind of questions I'd ask them.

Marking this would require some extra grader hours - I'd give them a strict word limit for their answers but even marking 400+ 50-word paragraphs will be a big chore. More generally, I'd like to shift at least 5% and maybe 10% of the course mark from the midterm and final to in-class and homework activities. I guess it's time I read up on ways to incorporate peer evaluation into such activities and assignments. I'm getting hold of a book by Eric Mazur called "Peer Evaluation"; I hope this will help me shift much of the marking burden onto the students (who will learn an enormous amount by doing it).

I think peer-marking is one of the things that our new WebCT-Vista system is supposed to facilitate. I hope it's not too hard to use.

The first day of class

2007-11-12T17:30:00.000-08:00

I've been thinking about changing what I do on the first day of classes. In past years I've basically done a fast information-dump about the course and then dived right into content (shaking them up with the role of natural selection in the origin of life).

But this year I'm hoping to shift all of the classes in this course to less information-delivery by me and more thinking and doing by them. And it's important do actually do this on the first day. So I'm going to be asking them for input on what they hope to get from the course.

I also think that my default expectations have been shifted by spending the past 6 months developing learning objectives for the first-year biology courses. Learning objectives need to be stated as actions the students should demonstrate ("can do X, can explain Y, can interpret Z", not just states we want them to achieve ("understands X, knows Y"). I'm going to tell the students this, in the context of introducing the existence of learning objectives, and then I'm going to ask them to write down for me, not what they want to learn or understand or know by the end of the class, but what they want to become able to do.

I expect this will take some prompting, so I'll give them some examples: "I want to be able to explain to my parents why my sister has Down syndrome"; "I want to breed healthier Siamese cats"; "I want to help save polar bears from global warming"; "I want to help develop an AIDS vaccine". These goals are rather lame and/or unreasonable, but their only purpose is to stimulate the students to think of other ones.

I'm hoping this activity will accomplish several things. It will give me feedback that I can use in later classes. It will give them a chance to influence the course. It will require them to write. They will be encouraged to discuss their responses with other students (I'm not sure yet how best to do this). Most importantly, they'll experience (not just be told) that they are expected to do things in class, not just sit passively and watch me.

How to teach about dominance

2007-11-06T13:37:00.000-08:00

Yesterday the team of people teaching BIOL 121 had our second meeting to discuss our new learning objectives. One issue that hadn't been included in the list of objectives is dominance. I added it to the list on our Instructors' Blog, stated as follows:

Students should be able to define dominance as a particular relationship between the effects of two alleles; dominance is said to exist when the phenotype of the heterozygote is the same as that of a homozygote for one of the alleles (the 'dominant' one). They should also be able to explain that dominance usually results when a single copy of the normal allele is sufficient to give the normal phenotype when combined with a defective allele, and to predict phenotypes when given such information.

Students find this very difficult, I think mainly because they are encouraged in high school to blindly accept "Mendel's Rules", and think of dominance as resulting from some mysterious gene inactivation process. At the meeting I put forward the way I have been trying to teach this concept. I was (slightly) mortified to discover how many assumptions my explanation relied on (assumptions fortunately not shared by my colleagues), so I've been trying to build a better explanatory framework, using ideas they raised.

Here are the figures I would use. The first three figures would be introduced at the end of the first class about how genotypes determine phenotypes (yes, I know that's an oversimplification that ignores the massive effect of environment in real organisms...).

Figure 1: Introduce lactase and lactose intolerance:

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Figure 2: Show a graph of how lactose digestion depends on the amount of lactase:

Students may need to be told that each tube contains the same amount of lactose.

(I don't know if students should be told that this is fake data.)
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Figure 3: Show the questions I'll ask about this information at the start of the next class.
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Here are the figures I would show at the start of the next class:

Figure 4: Show the first question again.

Students could be asked this question first, before being given the guidance suggested on the next figures.
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Figure 5: Remind them of the graphed data.

I've made the original graph pale, and superimposed on it the labels and numbers appropriate to thinking about the amounts of lactase in adults.
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Figure 6: Add bars showing how much lactose would be digested by each amount of lactase.

Students could be guided by asking them how high these bars should be.
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Figure 7:

Now we're back to the original question. After the guidance all students should be able to see that adults with 5µg/ml lactase digest lactose almost as well as adults with 10µg/ml lactase.
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Figure 8:

This question is intended to connect their understanding of genotypes to phenotypes. The answers should be: 0 = -/-, 5 = +/-, 10 = +/+.
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Figure 9:

The +/- heterozygotes have almost as much ability to digest lactose as the +/+ homozygotes. So they will be lactose-tolerant, and we will describe the + allele as being dominant to the - allele.

This is a lot of figures. Ideally the students would have the time to try to figure most of the steps out themselves; the figures are my ideas of the steps their thinking should take.

This lesson should also build the idea that dominance and recessiveness are not properties of alleles in isolation, but properties of relationships between pairs of alleles.

I usually tell students to ignore confusing terms like 'partial dominance' and 'incomplete dominance' and 'co-dominance', and to instead just describe any other interactions between alleles and phenotypes using more informative descriptions such as 'blending' (e.g. many pigments) or 'both phenotypes are present' (e.g. blood types A and B).

The numbers on the graphs are made-up data. Real human lactase assays are usually normalized to the ratio of sucrase to lactase, which is too confusing to present here. But here's a nice graph showing how lactase levels decline and sucrase levels rise in rats (from a page by R. Bowen at Colorado State).

What does 'memorize' mean?

2007-10-20T10:26:00.001-07:00

Last night I had a conversation with some faculty friends about teaching. We reached the common point where some of us were saying that students shouldn't have to memorize lists of facts, and others were saying that students need to know the facts before they can begin to think about what they mean. One of us made the important point that the word 'memorize' may mean different things to different people, and different things in different contexts, which (slowly) got me thinking about how we can be more clear.

We all want our students to remember the facts we think important. When we complain that students are memorizing rather than learning (student readers of this blog should note that we are just as likely to be blaming the teachers as the students for this), we mean to distinguish 'rote memorization' from our more-or-less vague concept of 'real learning'. Maybe we could speak of 'remembering without understanding' and remembering with understanding'.

I'll use the cell-division process of meiosis as an example. Students are often expected to be able to define meiosis, name the stages of meiosis and reproduce the textbook illustrations of these stages. But students can accomplish this by rote memorization or as part of a richer remembering. A student who 'really understood' meiosis might be able to explain how the consequences of meiosis differ from those of mitosis and what role this difference plays in reproduction. They might be able to draw steps intermediate between the defined stages, or move paper chromosomes to simulate the entire process. They might be able to explain the physical forces and interactions that bring about the different stages, and how the genetics principles called 'Mendel's rules' are a consequence of what happens to chromosomes in meiosis.

I'll try another example, brought up by a botanist who teaches students about how the different parts of plants transport water and nutrients. Students could simply rote-memorize the names of the structures (phloem, xylem, cambium, stomata, root hairs...) and be able to reproduce textbook definitions and drawings of them, complete with labels of the substances transported and the directions of flow. Or they could also be able to explain why plants need root hairs, why some substances move up the phloem and others down the xylem (or vice versa?), which parts of this transport consume energy and why other parts don't.

Of course a student could have used rote memorization to remember all this information. And we often test students' learning in ways that can be satisfied by rote memorization, probably because this is much easier for us to assess than is deeper understanding. Our Physics colleagues have been discovering that tests that they thought were assessing understanding were in fact being passed by rote memorization. Students could 'plug and chug' - getting the answer to a question of a recognized type by inserting numbers into a memorized formula. When physicists began to assess students' understanding by putting the phenomena into new (simpler and more familiar) contexts where formulas weren't useful, they discovered that the students could no longer answer the questions. So now Physics faculty are leading the way in devising ways to measure genuine understanding, and using these measures to identify and change weaknesses in their teaching.

In Biology we of course do try to test understanding, not just memorization. We do this by asking such questions as "Would anything go wrong if a cell started meiosis with three copies of one of its chromosomes?" or "Would a plant growing in a greenhouse on Mars need the same number of root hairs as one growing under identical conditions (light, water, nutrients, atmosphere) on Earth?" One reason that I give only open-book exams is to discourage myself from asking questions whose answers can simply be looked up in the book.

One big question for Biology faculty is whether our students should be asked to rote-memorize some information before they develop their understanding of its importance, or whether the remembering should only be built up (and assessed) as part of the understanding. I favour the latter. I have been thinking that some of my colleagues disagree, but this may be only because we've meant different things by the word 'memorize'.

Skill-Development Objectives for First-year Biology Courses

2007-10-04T16:51:00.000-07:00

These objectives were developed by the sub-committee we put together at the end of August. We did it in only 2 meetings!

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Understanding of the scientific process:
Given a suitable description of an experiment, students should be able to identify the hypothesis or question being addressed, the experiment’s design, the possible outcomes of the experiment, the observed results, and the conclusion.

For first-year students, examples from the textbook or from everyday life are likely to be most appropriate.
Students should also be able to identify situations where the experimental design and/or results mean that no conclusion can be made.

Communication skills:
Students should be able to construct a logical and clearly expressed argument supporting a statement.

A Short Guide to Writing about Biology (Jan. A. Pechenik) is an excellent resource for writing assignments. Instructors may choose to require their students to obtain it and use it as a framework for one or more assignments.
Some instruction should be provided in class, possibly with examples of better and worse writing, but the actual writing can be done outside of class and assessed with WebCT, through the Help Centre or by peer review.
Students should also be given experience in verbal communication and group work by having opportunities to explain a concept to another student or small group of students.

Study skills
Students should be able to make effective use of textbooks, including the table of contents, glossary, end-of-chapter summaries, figures and diagrams, and study questions.

Students benefit from practice in constructing hierarchical summaries of information provided in textbooks and in lectures.
Interpreting an unlabelled diagram is a good exercise.
A textbook-based scavenger hunt for information is a good in-class exercise that could be done multiple times on different topics.

Societal context of science:
Students should be able to identify scientific issues relevant to societal problems, and societal issues arising out of scientific advances.

Instructors may wish to choose one issue relevant to course material for in-depth consideration by the class, or have students consider a number of issues throughout the course.
It is important that students gain experience in discovering the issues themselves, rather than simply learning about issues presented by the instructor.

Should undergraduates learn to read scientific papers?

2007-09-27T13:17:00.000-07:00

Over at the biology blog Sandwalk, Larry Moran triggered a discussion of whether or not undergraduates should be encouraged to read and evaluate scientific papers. He thinks they're not ready for this challenge, but a number of the people commenting think differently. Here's my contribution:

Students in my first-year biology classes have an option of reading a scientific paper and writing a report on it; this replaces 15% of midterm+final exam marks. I provide a list of papers by local authors that aren't likely to be too technical, but they can select a different paper if they like. I don't vet their paper choices, and give them only a small amount of guidance.

Those who choose to do this find it very challenging, often telling me that "I had to read the paper six times before it started to make sense!". But they also find it very rewarding; they're proud to have accomplished this difficult task, and feel that the experience will give them an advantage over other students in future courses.

Our courses need 'process' objectives

2007-08-29T09:36:00.000-07:00

Last spring a group of faculty (including me) put a lot of effort into developing detailed descriptions of the curricula of our first-year biology courses. Along with this we developed a list of about 30 learning objectives - abilities we wanted our students to acquire by taking these courses.

Recently we realized that, although we had done an excellent job on the scientific content of the courses, we had overlooked the need to explicitly describe the more general abilities we want our students to acquire. This category would include advanced reading and writing skills, the ability to interpret and design tests and experiments, and such learning skills as the ability to identify the gaps and confusions in their understanding (I think Dick Cheney called these "unknown unknowns").

So on Friday a sub-group of us are sitting down to begin developing these objectives for our first-year classes.

Preparing for Reading Week projects

2007-08-08T12:31:00.000-07:00

I just had a meeting with the people looking after UBC's Learning Exchange, to discuss the arrangements that will let students in my classes participate in Reading Week projects. In these projects the students will spend their week off working as part of groups enhancing the experience of children in schools located in Vancouver's poorest communities (mainly the "downtown east side").

The biggest issue for me is to be sure the projects my students do include some biology, because I want to give academic credit for this work. The nature of the projects is driven mainly by the teachers' knowledge of their students' needs, and by the interests of the graduate students who coordinate the projects, but it should be possible to make sure our projects have a biology component.

Purple hair !?!

2007-07-23T19:48:00.001-07:00

Lately I've gone back to tinting my hair interesting colours. We'll see what the students think when I start teaching again in January.

Preparing students to teach evolution

2007-05-23T13:45:00.000-07:00

I just sent an email off to some faculty in the Faculty of Education, asking if they'd meet with me and a colleague to discuss how we are preparing (mostly failing to prepare) our students to teach evolutionary biology. These future teachers will be in the front ranks, defending evolutionary science against the 'war on biology' being waged by the Christian and Muslim fundamentalists. We can't complain about how they do this job if we haven't done our best to prepare them for it.

Rank, reward, filter...

2007-04-30T10:07:00.000-07:00

I'm about to submit the final grades for my freshman biology course, which prompts some thinking about why we give grades (rather than e.g. pass/no credit).

A "pass/no credit" system accomplishes one of the functions of grading. It filters out the students who are not prepared to proceed to the next stage in their education program (or their like). When students complain (beg for special consideration), I often argue that "I've given you an 'F' for your own good", and I encourage them to think about other career plans than medical school (or Pharmacy, which is big here).

But when I fail students in their first year of university I'm also motivated by the benefits to other members of the university community. That's the filtering function - part of my responsibility is to prevent unprepared students from going on to more advanced courses. Such students are a tremendous drag on teaching; both the instructor and the other students pay a heavy price if the level of instruction has to be lowered to accommodate students who should never have been allowed to enroll.

The other functions of grading won't be satisfied by a "pass/no credit" system. One of these is ranking the students who have passed. Our university uses student grades to assign priority in registering for next year's courses. So students with good grades have first choice of the often-limited places in the courses they want, and students who have just scraped through have to put up with what's still available when are finally allowed to register.

Another function of grading is giving the best students the marks that get them scholarships and other benefits. It's not enough that a student is top of the class - if the top mark is only a B this student won't make the local equivalent of the Dean's List. With a class of 400 (well, two classes of 200), I want to give the top ten or so students A+s, even though my tough final might have left them with what would otherwise be an A-.

One final issue is consistency of grading in a big course with sections taught by different instructors. The different instructors may have to compromise our individual grading philosophies a bit to ensure that students in different sections are treated comparably. So I'm waiting for the course coordinator to give me the OK to click the "submit grades" button.

Not "hot"

2007-04-26T19:23:00.000-07:00

My sense of responsibility to my students prevents me from reading what they're saying about me on RateMyProfessors.com until AFTER I've submitted their final grades.

Oral exams

2007-04-17T12:08:00.000-07:00

One of my grad students is about to defend his PhD thesis, which got me thinking about oral exams. Most undergraduate students never experience an oral exam, but they're the best and I think fairest way to assess a student's understanding.

Usually the examining committee has several members, who each ask the candidate a series of questions. The goal is to find out the limits of the student's understanding, and the strength of oral exams is the flexibility of the questions. So when the student easily answers one question, the examiner responds with a harder question on the same general topic. If this is answered well, the next question will be even harder. Any question the candidate can't answer defines one boundary of their knowledge. The examiner responds by changing topics, again starting with an easy question and moving to harder questions if the student's answers are good, until another boundary is reached.

So taking an oral exam is a scary experience. No matter how well or how badly you are doing, you'll still spend a substantial fraction of the time dealing with questions you find very challenging, and you probably will be unable to answer some questions. But knowing that this is supposed to happen to even the best students can save you from panicking when it happens to you.

Gender bias in students' expectations

2007-04-06T18:22:00.000-07:00

I'm still seething over a couple of postings an anonymous student made to the discussion board for my freshman biology course. I had asked a colleague (Dr. X) to give two lectures, in exchange for three I had done for him earlier in the term.

I've already responded on the discussion board to the implication that when I'm not lecturing I'm resting (see posts below), but here I want to point out the implicit gender bias in this student's expectations.

The student views Dr. X's research work as more important than his teaching responsibilities. (I had told my students he was doing botanical research, but in fact he was accompanying his wife on a trip combining her research with a vacation for them both.) The student assumes that of course I should make sacrifices to support this work.

On the other hand, although I run a much larger research program than Dr. X, I am seen as only a teacher. And in addition to teaching, I'm judged on how deeply I appear to care about my students.

These different expectations are one of the many reasons women faculty have a hard time. Students make excuses for male faculty (who they see as having more important things to do than teach), but expect women faculty to be substitute mothers, sacrificing any other goals to take care of their students. On Wednesday the students will do their teaching evaluations, and I expect as usual to be criticized for insufficient nurturing.

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Here are the discussion board posts:

From an anonymous student:

I felt really bad for him. He was just given a package of slides and then tried to teach from there. I thought a lot of people were really disrespectful. Like if you went the monday lecture and found him insanely boring, why did you come to the one on wednesday just so you could talk the whole time and then make a huge scene by leaving early?

My response:

Hi everyone,

Dr. X normally teaches another section of Biology 121. He taught
these two classes for me because I had taught three classes for him in
late February, while he was in Thailand.

He did not have any prepared material that he thought would be suitable
for my students, so I provided him with copies of the slides I used last
year, thinking that he could use them as a framework to develop two
classes on sustainability. I did not expect him to simply show my
slides, and I apologize for any problems with the classes he taught.

Dr. Redfield

From another anonymous student:

Its quite rediculous that she asked Mr. X to teach for her although she helped him
teach 3 classes. Mr. X was away for a reason, but dr. Redfield is just taking a
break and not being responsible for our class. Just so dissappointed.

(I deleted this post, and last night a new one appeared - same sentiment and same spelling error so probably the same student.)

I actually disagree on that. Some parts were interesting, but this teaching skill was not good. Dr. Redfield's teaching method was really better and have the skill to actually crab your attention! However, I am quite dissappointed that she wasn't able to teach our class. She taught Dr. Xs class because he was away to Thailand, but now he is taking over her class while she is resting. This really shows that she is very unresponsible for our class. She is a good, interesting and smart prof, but maybe she needs to care more.

And here's my response.

!!! RESTING???

Pardon the 'shouting', but I've been working night and day, holidays and
weekends, on this course; just check the dates and times of my
Discussion Board postings. Since my last lecture to you I've taken
exactly one day off (yes, it was a weekday, but I worked on all of the
weekend days).

If my lectures are interesting it's because of the work I put into them.
For example, I've spent part of the Easter weekend working on
Wednesday's final lecture. This is a lot of work because I've decided
to replace about half of what I had prepared with material from the new
IPCC Report on climate change. I'll be spending much of today on it too.

I also spent part of the Easter weekend compiling and posting the PRS
marks. This including tracking down the errors students had made in
entering their student numbers so they would get the marks their answers
have earned.

I spent part of it analyzing and posting the Reading Quiz marks. This
included going back over the original 'opt-out' quiz to find those
students who had never realized that if they weren't going to take the
quizzes they needed to actively opt out. (About 15 students had marks
of zero; I discovered that they had not opted out but never taken a
quiz, so I opted them out retroactively.)

I spent part of it reading and responding to Discussion Board postings.

I spent part of it working on the final exam.

I spent part of it reading reports of students' projects.

And I spent part of the weekend doing an experiment in my research
laboratory. Today (Easter Monday) I may even find time to analyze the data.

At the end of February I took valuable time away from preparing my grant
proposals to teach Dr. X's classes, so that he could spend an extra
week in Thailand. We agreed in advance that he would repay this favour
by lecturing to my classes, freeing me to catch up on other
responsibilities.

I realize that students don't have many opportunities to see the work
their professors do outside of class. But 'resting' is the last thing
we have time for.

Dr. Redfield

Last class: teaching evolution

2007-04-05T17:46:00.000-07:00

I won't be teaching evolution in this class. Instead I want to address the problems raised by the sophisticated war being waged against evolution by Christian and Islamic fundamentalists. Nobody else I know covers this in their biology classes, but we can't just blame the high-school teachers for doing an inadequate job of teaching evolution, when we're the ones responsible for teaching the next generation of teachers.

Last year I taught this in the middle of the term, at the end of the Evolution section, but this year I've moved it to the last class. I'm also going to cut down on the mass of examples of fronts in this war, both to allow more time for introducing the resources available for biology teachers, and because we need to allow time for end-of-term teaching evaluations.

It's important to not put all the blame on the Christians. The richly funded Islamic fundamentalist group operating under the name Harun Yahya is not well known in the West, but they produce an enormous amount of very slick anti-evolution propaganda.

Playing fast and loose with the curriculum?

2007-03-23T17:11:00.000-07:00

One of the weaknesses of the course I teach is also one of the reasons I like teaching it.

The curriculum revision committee I'm on has been discussing ways to maintain coherence between different sections of this multi-instructor course. Right now we have two courses to compare to. One of these, the one I'm presently teaching, has five or six different instructors, each teaching their interpretation of "Ecology, Genetics and Evolution". I kid you not, that's the full detailed curriculum.

I like teaching it because I can pick and choose freely among possible topics. So, for example, I've taught my students nothing about behaviour and almost nothing about DNA replication, but quite a lot about our local environment and about HIV in Canada and Africa. And in some ways this is good for the students, as I teach them the things I'm enthusiastic about. But, from the perspective of the goals of the Biology Program this is not a good situation, as different students learn very different things and sometimes learn nothing at all about some important topics. All sections do use the same excellent textbook.

The other first year course has the opposite problem. Instructors and students all use a common 200 page set of photocopied course 'notes' instead of a textbook. Coherence between different sections is thus not a problem (except if an instructor runs out of class hours before getting to the final topic). For inexperienced instructors this is a good thing, but there is little opportunity for experienced instructors to control what they teach. So it's hard to work up much enthusiasm.

So one goal of this committee is to come up with a curriculum document that's sufficiently specific to ensure that the important topics are covered, but sufficiently flexible to allow instructors to feel they control what they're teaching.

Are clickers worth the hassle?

2007-03-20T15:30:00.000-07:00

I've spent most of the last 24 hrs wrestling with the software that goes with the Personal Response System (PRS) 'clickers' I have my students using in class. This is the third time I've assembled all the marks the students have earned for the answers they've given to the questions I've posed in class and posted the combined marks on WebCT. This time I think I've finally gotten it right. (Thank you, students, for your patience.)

The software isn't that bad, though it's a bit clumsy. Now I better understand how it works, it all seems quite straightforward. But getting myself to this point would have been easier if my university provided better support for instructors using PRS in their classes. The fuss I made about this last year produced some talk of a PRS Users Group, where we could help each other, but that seems to have been vaporware.

But I do think using clickers is worth the trouble. It enables me to push the students into doing 'active learning', rather than passively absorbing whatever I tell them. I really like to see the students talking with each other about what the answer should be.

'cumulative' exams

2007-03-06T07:38:00.000-08:00

Students often ask me whether the final exam for my course will be 'cumulative', testing material covered both before and after the midterm. The alternative is that the final only tests material taught after the midterm.

I understand that some professors do give non-cumulative final exams, but I find it hard to think of a situation where this would be appropriate. In my courses, we build ideas onto other ideas. I select a particular order of topics (e.g. genetics then evolution then ecology) for precisely that reason. By first studying genetics, we develop the genetic underpinnings needed to understand evolution, and by understanding evolution we can better appreciate issues relevant to ecology. The exam questions I like best are the ones that ask students to pull together concepts taught in different parts of the course.

Telling students that material covered before the midterm won't be needed for the final is tantamount to telling them to forget that material - it's not even valuable enough to remember for another 6 weeks, much less beyond the final exam.

Researchers as teachers

2007-03-01T21:03:00.000-08:00

I've been away from blogging for the past month, as I've been focused on getting two research grants submitted by a March 1 deadline. Yes, that's today, and they're both done.

I've been neglecting not only this blog, but also the students in my classes, as a consequence of caring more about my research than about my teaching. I originally wrote 'as much about my research', but that's not true - I do care more about research than teaching. But I'd like to think that caring about research makes for a good teacher, maybe better than someone who cares only about teaching.

Being taught by scholars (researchers in the science or humanities or whatever) is one of the supposed benefits of studying at a real university rather than at a college where the faculty have little or no time or facilities for scholarly work. The benefit is (should be) that the teachers are people who DO research. We care deeply about intellectual work, about scholarship, and we can communicate about the process from our ongoing experience. Active research also keeps us at the frontiers of knowledge, and gives us the perspective to make value judgments about what's in the textbooks.

The down side of this is that we're unlikely to be as dedicated to teaching as our non-researcher colleagues (at UBC, 'sessional lecturers' and 'instructors'). I, for example, have been skimping on my teaching responsibilities for the past couple of weeks, to get my grant proposals done.

But this isn't because we don't care about learning. I, and every researcher I know, care much more deeply about learning than the great majority of our students do. We LOVE learning - it's our favourite thing in the whole world. But we love learning as a concrete activity, experienced most rewardingly in the research we do, not as an abstraction. So it shouldn't be surprising that we value our own learning activities (our research) more than the learning activities of our students.

Too easy or too hard?

2007-02-03T08:50:00.000-08:00

We spent yesterday's class working very slowly through one genetics problem, and now I can't decide whether what we did was way too easy or too hard.

I wanted the students to appreciate how best to approach genetics problems. Normally this would be done in tutorials, but the university administration has decided that this course doesn't need tutorials (1500 first-year biology students! (not all mine)), so I did it in class. Using clickers makes this possible, because students are participating, not just watching.

The problem was a complex one. To solve it students needed to combine information from three different crosses, so we worked through each cross in turn, considering possible hypotheses and testing them against the data. I wanted to emphasize that doing the analysis slowly made the logical steps easier to appreciate, but I fear we went too slowly through the first parts. Almost every student got the PRS questions right, which indicates that we probably should have been spending less time on these issues. And we didn't really get to the last part of the problem, which is both the most difficult and the most rewarding - not getting to the answer leaves the students hanging, and leaves them with the most difficult part.

And, based on comments from students after class, most students will find finishing the problem harder than it should be because they missed the significance of information I gave them about why the problem would interest a scientist. They don't understand how two genes can both affect one phenotype, in this case that the genes each code for an enzyme that produces a pigment (pink and blue respectively) and that the pigments mix to produce the purple wildtype flower colour.

So I'm going to have to spend part of the next class providing this explanation, which means less time to spend on pedigrees and sex chromosomes and aneuploidy.

Why posting the solutions isn't the solution

2007-01-28T19:03:00.000-08:00

Students always ask me to post the answers to the questions I give them, but I'm reluctant to do so. This makes them unhappy, as they sincerely believe that seeing the right answers is a good way to learn. But I think that seeing the answers often just gives a false sense of confidence.

Say you first try to do the problem without looking at the answer. Because you know the answer is available, you don't spend a lot of time on it. Instead you try do the problem quickly.

If you're able to come reach an answer, you don't spend a lot of time trying to decide whether the answer you've come up with is right, you just check your answer against the posted one. If it agrees with yours, you pat yourself on the back and go on to the next problem. If it doesn't, you look at how your answer differs from the correct one, say "I see how it's done; I won't make that mistake again", and go on to the next problem.

If you can't reach your own answer, you look at the posted one, say "I see how it's done; I'll be able to do it right next time" and go on to the next problem.

Using my "going to university isn't like going to the tanning salon, it's like going to the gym" analogy helps explain why this doesn't really teach you how to solve the problem. Looking at the correct answer is like watching a trainer show you the right way to do squats. You know you need to practice doing them correctly, so you do lots more squats, matching your moves to those the trainer showed you. If you just say "OK, I see" and go on to do bench presses, your squats won't improve.

But you can't go back to the same genetics problem again and learn to do it right, when you already know the answer. Working back from the answer is very much easier than working forward through the forest of possible answers. You need to build the skills that let you evaluate the candidate answers you come up with, testing each one against all the information you have.

It's comforting to think that seeing how a problem is done gives you the skills to do it. But it doesn't. Instead it gives you a false sense of security that can hold you back.

(next time - why going slow teaches you to go fast.)

colour-coding

2007-01-27T08:00:00.000-08:00

A student pointed out on the course discussion board that I'd not used colours consistently in drawing chromosomes. I apologized for the confusion and tried to clarify it in a response.

But then I raised the issue directly in class yesterday, pointing out that on Monday I'd coloured the two chromatids in a pair differently (dark ad light blue), but on Wednesday I'd coloured them the same shade of blue but coloured their homologs pink. And the transparent strips I used to demonstrate meiosis had the three different chromosomes from one parent green, whereas those from the other parent were blue.

And I then told them that I was about to use yet a different colour coding in yesterday's class, with the homologs the same colour (maternal distinguished from paternal by a wavy line drawn on them) and the different chromosomes (those with completely different genes) different colours.

The class had been given strips of coloured paper to use as their won chromosomes in solving our first genetics problems, and I told them to pay attention to the colours they used, with the goal of having the colours a guide to the relationships between the chromosomes they were representing rather than a source of confusion.

The most important thing isn't that they get the colours right, but that they learn to think about what colours will be least confusing, and more generally about how to represent the factors that matter in any given problem. It's this thinking that leads to the most learning.

Acting out

2007-01-23T13:51:00.000-08:00

Yesterday in one of the two classes I teach, I had some volunteers come the front of the class and model the process I had just explained. Why is this worth doing, given that it's time-consuming and chaotic?

One reason is that it's just one more way of presenting information. Different ways work better for different people, and when a point is important I try to present it in as many ways as possible.

But there's a better reason for using students to model it. We're social animals. Almost from the day we're born, we find watching people to be more interesting than watching anything else. So, although many students will probably forget how I slid the model chromosomes around on the overhead projector, they'll remember the girls tied together at the front of the room, being tugged back and forth by boys with the yellow ropes and then released by the boy with the scissors. And maybe they'll remember that what happened to the girls is what happens to chromosomes.

What should biology students learn?

2007-01-20T10:08:00.000-08:00

Our Biology Program has just been awarded a big 5-year grant (from the Carl Weiman Initiative) to improve how biology is taught. One issue that came up at our first meeting was "What should we be teaching our students?"

Students reading this may be horrified to realize that this is an open question. Surely professors decide what they should teach before they start to teach it! Well, we do try, but deciding what should be taught is a complicated problem and one we have no training for.

We university professors tend to teach a combination of what we learned as students and what we've learned since. This is bad for two reasons.

First, every time we learn something new and important we're tempted to add it to the curriculum, so the amount of information we're trying to teach keeps increasing. Most of us realize this, and keep trying to cut back on the information overload, but we never go as far as we probably should.

Second, the things we learned aren't necessarily the things our students should learn, because we were far from being typical students. Many of us were uber-geeks, and we were all the kind of students who go on to be university professors. But most of our students are nothing like we were. Their futures are likely to be much more diverse than ours, and many will have no direct connection to science at all.

There's another problem. We don't feel competent to teach many of the things we would like to teach, because we have no good ways to assess whether our students have learned them. We want to teach our students how to read critically, how to think creatively, how to write clearly. We want our students to really understand complex principles and processes, not just parrot back textbook explanations. But we don't know how to assess these abilities.

The Weiman Initiative grant will give us resources to develop the assessment tools we need. But that only addresses the second problem. First we need to decide what to teach. And these decisions need to be made in collaboration with our students.

We know what biology you need to learn if you're going to be a biology professor or a high school biology teacher, and some of the biology you'll need if you become a physician, dentist, or other medical professional. But many of you will go on to careers that have nothing to do with biology. So we'd like you to tell us how you might use your biology education when you're raising a family, or working in the family business, or selling real estate, or building furniture.

You can post comments to this blog entry, or if you're in my Biology 121 classes you can post them on the course's WebCT Discussion Board.

Finding the balance with clicker questions

2007-01-18T09:23:00.000-08:00

Designing good clicker questions is tricky. I want them to be challenging enough that the students have to think quite a bit, but because correct answers count for marks, I want most students to get them right most of the time.

Usually I let the students discuss each question with each other before they answer. One way to improve both the benefits of the consultations, and the proportion of the answers that are correct, might be to first present the question not for marks, asking students to answer without consulting their neighbours. Then show them the range of answers (?) without indicating which is correct. Then ask them to consult their neighbours before answering again, this time for marks.

I have a couple of little books about using clickers in the classroom (gifts from the textbook rep). One is specifically about science teaching - I'll see what suggestions it has.

Ancestors

2007-01-12T18:30:00.000-08:00

What we did:

1. Thought about how to infer properties of ancestors, when we know the properties of the descendants and the phylogenetic tree that connects them. This can be seen as learning to think as scientists, rather than as learning what scientists have found out.

2. Considered properties that might be shared by all cells. Not surprisingly, many students hadn't yet learned to include Bacteria and Archaea in their thinking about life. I wonder if the students who have taken Biology 112 were the ones who had?

3. Considered how the first cell could have evolved. It's difficult to be very specific, given how little scientists know about this, and difficult to be very thought-provoking, given the little exposure many of the students have had to molecular biology.

What we didn't do:

1. Use the clickers. The PRS software froze up when trying to create a PRS 'lesson' within PowerPoint even though it had worked fine on my computer this morning. To make matters worse, it also worked fine after class, when I tried to demonstrate the problem for the technician from Classroom Services. I suspect it was due to some changed setting on the podium PC that had returned to its default when I rebooted the computer. I'll come in on the weekend and check that Monday's questions are going to work.

2. Spend enough class time on student-thinking problems. I think this will be easy once we're into real genetics, but for next week I'll see if I can come up with a few thought-provoking ones.

big pictures

2007-01-10T16:14:00.000-08:00

We tackled a number of very big issues in today's class. Probably too many, as none of them got the level of development they deserve.

The clicker questions didn't work. This was my own fault; I had assumed (hoped) that deleting the PRS logo from a slide would delete the associated clicker question, but instead it just created a mismatch between the questions and the slides that sent the PRS software into a tizzy. So we did the science questions by shows of hands, which was fine.

In both classes students raised a point I hadn't anticipated, that phylogenetic trees usually have the deepest branches on the left. I wonder if they learned that in high school. I'm pretty sure this isn't an explicitly-stated convention, but it is commonly done.

Learning about and with clickers

2007-01-09T06:28:00.000-08:00

We didn't do anything with clickers in the first class, but I want to have some clicker questions in the next one, and to spend a bit of class time on the mechanics. So this requires two kinds of preparation.

First, I need to have a series of steps that get students started with clickers, because close to half said they hadn't used them before. 1. How to program your student number into your clicker. 2. How questioning works. 3. How answering works. For this I need to have a few very easy sample questions, and to allow time that would otherwise be spent on the science.

And there should be have at least one interesting thought-provoking clicker question about the science we're doing. This can come at the end of class, but I should allow at least a few minutes for it.

The pedagogical challenge is to move one or more concepts from lecture-style presentation, in which I tell the students the concept, to question-plus-thinking presentation, in which I raise the question, students evaluate possible answers, then I tell them the answer. The latter takes a lot more time, but gives much more real learning. So this is another pedagogical problem - because I need to spend less time lecturing on other concepts to create time for thinking about the most important ones.

Why have a 'teaching blog'?

2007-01-04T07:13:00.000-08:00

Classes start on Monday, and I've put a link to this blog on the BIOL 121 WebCT homepage (only open to students), so curious students from my classes are likely to start visiting this blog. I doubt that any of their other profs have teaching blogs, so I'd better explain what I'm trying to accomplish here.

This is where I'll be reflecting a bit about my goals for the course. I'll discuss what I'm trying to accomplish in each class and the logic behind the different things I'll ask students to do. I'll probably also consider how to deal with problems (both practical and pedagogical), and now to improve approaches that are not working as well as I'd like.

I'm making it easy for students to read this blog because I'm a big believer in open information. People who study teaching often write about 'meta-learning' (learning about the process of learning) and argue quite convincingly that students who are encouraged to think about how they learn will learn better.

The comments are open (anonymous comments are allowed), and I'll always read them though I probably won't directly respond. Students who want responses should post their questions on the WebCT Discussions Board; I'll create a 'topic' there for posts about this blog, and allow anonymous posting.

And no, the blog material won't be on the exam.

Papers for students to report on

2007-01-03T08:53:00.000-08:00

One of the Biology 121 project options is writing a report on a peer-reviewed scientific paper. Students are free to choose any paper that interests them, but I'm providing a list of suitable papers as well.

It's nice if the papers are by local researchers, so I've emailed my colleagues asking for suggestions of papers they've written that might be suitable. The paper shouldn't be overwhelmingly technical, which rules out a lot of molecular biology papers, but this course isn't about molecular biology so that's OK. And they shouldn't be too long. And they should be sufficiently well written that students can understand what the research question was and why it's interesting.

When I discussed their papers with last year's students, many said "I had to read my paper five times before I started to understand it!" But they weren't complaining - rather they were proud that they'd eventually mastered such difficult material, and felt that this new skill would be a big help in their future courses.

Preparing for January

2006-12-29T17:51:00.000-08:00

I pulled up last year's detailed course outline to start deciding what to cut and what to rearrange.

Given the shorter term this year, and the timing of the mid-term break, I think I'll move more of the fundamental evolution material into the first two weeks. This will give us a solid grounding in evolutionary principles and processes before we get into the nitty-gritty of genetics.

That will also let me schedule the midterm in the last class before the break, before we get into the technicalities of how natural selection works. And I'll be able to cut a week from last year's post-midterm material on evolution, leaving us enough time to get into sustainability and ecological principles.

But the above assumes that I'll still teach the same content, just crammed into fewer classes. That's not what I want, so I still need to work on cutting factoids to give more time for thinking. And on the classroom activities (clicker questions) that get us all thinking and discussing, rather than just transmitting information.

What to cut?

2006-12-22T07:03:00.000-08:00

The powers-that-be have left us with only 12 weeks of classes this term, rather than the usual 13. This is probably due more to the dates that various holidays fall on, rather than to a fiendish scheme by the bean-counters to give the sudents 10% fewer classes for their tuition dollars. But it means that I need to cut 10% of the content from my classes.

I actually want to cut more than that, because I'm hoping to have students spending more of their class time thinking and less time than copying down things I tell them. This means I need to come up with thought-provoking classroom problems and activities, but also means I need to eliminate even more of the 'lecture style' content.

Cutting content is hard. What criteria should I use to decide what students don't really need to know about? Which of the lovely PowerPoint slides I slaved over last year should I consign to the trash? Should I cut the cool new frontiers of science stuff, or some of the classic concepts? Should I just not bother to teach the parts that everyone forgets right after the exam? Do I cut the hardest concepts, or the time I spend reminding students of the basic principles?

To make this even harder, I want to include more about ecological sustainability this year. I fear that this means some genetics will have to go.