Saturday, December 17, 2011

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 and Tony Griffiths).  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.