Looking for examples of BAD genetics journalism

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

Here's some more information about the assignment:

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

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

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

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

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

How we define the phenotype is critical

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

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

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

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

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

What I originally said:

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

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

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

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

(Here I'm assuming that the defect in one allele doesn't cause the other allele to be upregulated.  That's a possible answer to part b, though I doubt it was what the questioner was looking for, since this question comes from the first chapter on simple Mendelian inheritance.)
 
We're not told the phenotype of a mutant homozygote, so before considering whether the mutant allele could be dominant to the wildtype allele we need to carefully identify the phenotype in question.  The term 'phenotype' can have different meanings even for a given pair of alleles, depending on what is being observed and how it is being categorized. 

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

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

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

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

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

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

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

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

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

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

Answering a complex problem after discussing it in tutorial

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

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

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

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

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

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

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

All the data

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

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

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

Genetic mapping

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

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

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

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

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

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

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

Genetics problem for tutorial discussion

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

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

This new problem has everything:

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

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

What do you think this fabulous problem is about?

Teaching about 'dominance'

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

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

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

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

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

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

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

Do as I say, not as I do?

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

Global health

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

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

• Small audience but good ideas.

Traditionally:

• rural
• babies and mothers
• infectious diseases
• vaccines

Themes:

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

Who does it:

• community saviours/superstars
• real (Hollywood) celebrities

Changing the perspective:

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

So how should we change our academic programs?

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

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

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

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

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

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

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

The Creative Campus - catalyzing non-routine engagement

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

First speaker:


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

Uptalking!

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

Second speaker:

Curb Program in Creative Enterprise and Public Leadership:

Undergraduate Scholars program (4 years):

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Questions:

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

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

Universities and community colleges need to work together on curriculum.

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

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

Calibrated Peer Review

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

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

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

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

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

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

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

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

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

Using Writing to Improve and Measure Learning in STEM Courses

Objectives in preparing for this workshop:

1.  Share relevant bits of reviews of the literature.

2.  Synthesize findings and understandings.

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


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

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

Myths:

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

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

Promising practices:

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

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

3.  BioTAP:

4.  Calibrated peer review:

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

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

Nothing in Education Makes Sense Except in the Light of Evolution

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

Four main points:

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

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

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

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

Questions:

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

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

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

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

Talk by Reinvention Center Director Pat Turner

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

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

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

AARRGH!!! flowers!

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

What we know about writing in STEM

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

Student writing projects give unsatisfactory results:

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

Why?  

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

We need to change:

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

Techniques to change this:

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

Collaborative writing much better than solitary writing.

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

Video editing project:

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

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

Questions:

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

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

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

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

by Chris Thiess, at the Reinvention Center conference

Designing WtL activities ( minimize work for instructors)

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

Some ideas:

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

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

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

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

The Reinvention Center 2010 National Conference

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


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


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

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

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

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


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

Introductory Genetics ≠ Introduction to Genetic Analysis

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

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

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

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

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

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

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

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

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