If evolution is wrong...

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

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

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

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:

1. 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?"
2. 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

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

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

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

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

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

(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

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:

1. Why I've chosen to teach first-year classes
2. Problems ("Challenges"? "Goals"?)
   
3. Solutions - principles
4. 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

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?

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

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

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

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

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...

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)

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

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...

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?

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

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

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

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

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

HapMap for beginners?

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

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

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

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

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

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?

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

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

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?

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

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.

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• 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?

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

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

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 !?!

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

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.