A modern genetics problem

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!")

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?

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

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

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):

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

 Written Answer Questions:

1. Should any topics be cut from the course material?  Most said no.
2. Were any topics missing from the course that you wish had been covered? Most said no.
3. 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

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):

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

 Written Answer Questions:

1. Should any topics be cut from the course material?
2. Were any topics missing from the course that you wish had been covered?
3. 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:

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

Focus group?

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

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.