Wednesday, April 15, 2015

Alternatives to 'genotype' and 'phenotype'

I just posted the following tweet, but realized that it needed a bit more elaboration.


The meanings I want to capture are the following:

'Genotype':  the genetic differences between different people (or other organisms)

'Phenotype':  the differences in traits/characteristics/properties between different people (or other organisms)

This is for a new blurb for Useful Genetics.  Part 1 of Useful Genetics teaches how genotypes differ and how they cause phenotypic differences.  Part 2 teaches how genotypic and phenotypic differences are inherited.

The terms need to stand alone - I'm not looking for analogies to incorporate into explanations of what 'genotype' and 'phenotype mean'.

For 'genotype' I could maybe say 'DNA differences' or 'gene differences', but I can't come up with any way to capture the real meaning of 'phenotype' in one or a few non-technical words.  It needs to not exclude any of the ways that phenotypes differ (appearance/metabolism/behaviour/disease risk etc).

Ideally the words would apply comfortably to both people and other organisms, but it's most important that they apply to people.

Suggestions?



Saturday, April 27, 2013

Useful Genetics, three days in

Four days before our first lectures appear (Module 1: How different are we?), here are the latest stats:
About 1000 students have done our two surveys and the Preparation self-test.  These numbers are quite reasonable - it's well-established that most of the students who register for a Coursera course are just browsing.  We'll be interested to see how the numbers change once the lectures begin.

We're increasingly glad we opened the course a week early.  The night before last some students began reporting that they couldn't download or stream videos, though most students seemed to have no problem.  It took the Coursera engineers about 24 hrs to identify and fix the problem; I'll have to ask them whether it was caused by something that we did incorrectly or just some bug in their system.  But I'm really happy that this happened before the lectures start.  (One of my goals is to set a very positive tone at the start of the course, letting the students see that we're being helpful and responsive, so later they'll not panic when problems inevitably arise.)

There's already lots going on in the discussion forums.  We've inherited a self-titled 'Genetics Gang' from Mohammed Noor's Coursera course Introduction to Genetics and Evolution; they seem knowledgable and enthusiastic so I'm expecting them to be an asset to the course.

The file containing our DNA replication stop-motion animation is gone for good (lesson: don't create important new files inside a Dropbox folder).  I don't know if we'll have time to recreate it, so I guess I should provide an explanation for the students.  Maybe in the next 'announcement', when we announce the availability of the Module 1 materials on Wednesday.


Thursday, April 25, 2013

Useful Genetics is now a real course!

We went live yesterday, a week before our first lectures will be available.  Students are viewing the introductory videos, taking the surveys and self-test,a nd posting on the discussion forum.

Only a few minor bugs:
  • Some students couldn't download the Open Genetics textbook.  We thought this might be because the ualberta server was struggling (though there wouldn't have been that many students) so we put a copy on the Coursera server and the problem went away.
  • Students found an error that had snuck into the grading of one of the self-test questions.
  • Students report that the audio volume is too low on the introductory videos.  We can adjust this for future videos.
It's quite exciting to have real students at last, but I really need to get the next videos prepared and recorded, and the TA and I need to get more quizzes done.

The TA and I spent yesterday morning trying to make a little stop-motion animation of DNA replication, in honour of DNA Day (today).  We'd announced in our introductory email that we were going to do this, and I had the excellent iStopMotion program.  We only got 5 seconds of replication recorded (moving everything around was very fussy and time-consuming), and the animation was pretty rough, but it looked OK and we were going to frame it with cute title and 'The End' animations.  But the recording file that was saved didn't include the images we'd recorded! 

I spent a couple of hours searching for another version of it, sending emails to the TA, troubleshooting the problem by recording different clips and saving them to different places.  This revealed that all files that I saved to a folder in my Dropbox had this problem, but a file saved to another location was fine.  More time invested in composing an email to iStopMotion.  But they responded very promptly, sending me a file that they say will solve the problem.  Here's hoping - we could make a much better recording if we did have to redo the whole thing, but we really can't spare the time.

Tuesday, April 23, 2013

Useful Genetics is about to go live!



It's high time I got back into blogging (I don't know why I stopped).

Our Coursera MOOC, Useful Genetics, goes live tomorrow!  The first set of lectures (Module 1: How different are we) won't be made available for another week (May 1), but we want to make the introductory materials available sooner, both to help students get ready for the course and to give them a chance to complete our introductory surveys before getting distracted by the lecture videos.

In addition to short Welcome and Course Logistics videos, we have three quizzes/surveys:
  •  Community survey: This is a 'tell us about yourself' survey.  The information it provides about student interests and background will help us tailor the course to the students and also be used for later research into teaching strategies.
  • Preparation self-test: This is an ungraded quiz on the background students should bring to the course (we'll be happy with solid high-school-level molecular and cell biology).  Each question has a recommended reading in an on-line high school biology textbook.  We'll also use the data for research into teaching strategies.
  • Genetics Knowledge survey: This is a modified Genetics Concept Inventory.  We're asking students to show us what genetics knowledge they already have, but we expect it will also reveal a lot of misinformation.  Again, the data will be used for research into teaching strategies.
As of today we have about 26,000 students signed up, but participation data from other MOOCs predicts that most of these will fall away within the first week.  We don't regard this high 'drop-out' rate as a failure, but as a reflection of the nature of MOOCs. The openness of MOOCs allows many people to sign up 'just to see', and most of them have no serious plans to complete the course.  Many of the rest will, quite reasonably, take a smorgasbord approach, sampling the materials and taking what they can use.

Because this is a new course, and a new approach to genetics, planning and preparing the lecture videos is an enormous amount of work.  The first and second week's lectures are in the can (well, on the server), but I realized yesterday that the draft material for the next two weeks needs a major overhaul.  Modules 3 and 4 cover how genotypes determine phenotypes, for both simple loss-pf-function mutations and natural genetic variation; I hope to get them all done before May 1.

I'm recording the videos in my office rather than in the video-production studio run by UBC's Centre for Teaching and Learning Technology.  This setup took a very long time to get working properly (many stupid glitches up until a couple of weeks ago) but now it's working OK.  Recording in my office gives the videos the non-slick feel I want them to have, and gives me much more control.  The editing turns out to be quite simple, partly because I'm happy with low production values.

CBC television's main news program, The National, will be doing a feature on MOOCs tomorrow night (April 24) - they recorded a lot of video with us in February so I'm hoping Useful Genetics will get some nice Canadian publicity.

(Now I'm off to write a long-overdue post on my research blog, RRResearch...)

Monday, March 04, 2013

Teaching personal genomics - the commercial issues

(Apologies for the long interval of dead air...)

I'm working on the video lectures for my upcoming MOOC Useful Genetics, and I'm stalled at Module 5, on personal genomics.  I know from our preliminary survey that this is something many students will be especially interested in. 

One factor that makes these videos different from the rest is that I'll be discussing services that are provided mostly by for-profit companies.  When I taught this in my face-to-face class, I found that students were particularly sensitive to this -- when I said positive things about 23andMe's interface, or marveled about how inexpensive genetic testing has become, they worried that I might have a commercial interest in the providers.

Another issue is copyright.  I don't think I can use images from commercial providers' pages without their permission, but obtaining such permissions is likely to be a big pain in the butt.

So I guess the solution is to avoid mention of specific providers, and just discuss the general types of services that are available.  Students will want to know how these analyses work, what kinds of information they provide, why consumers might choose to use such services, how to choose a particular provider, and how to interpret the information they obtain. 

The students can discuss specific providers and their services in the forums.  My job is to provide the information and issues that will help frame these discussions.  I think I'll want to explicitly explain this approach in the overview video for this module.

Saturday, December 08, 2012

First lecture video

Yikes!  I just recorded my first draft of a lecture video, and it's 25 minutes long!  This is twice as long as I want my videos to be.

I don't feel that I covered a lot of material, but I'll see how long the next few are before panicking...

Friday, December 07, 2012

I have a plan (for developing the lecture videos)

Yesterday most of the people involved with UBC's Coursera afforts met to discuss how things were going.  One result of this is that I've changed my plan for preparing the ~60 lecture videos. 

The general plan has been that I'll record the videos in my office, using the built-in camera on my laptop, and a good external microphone and lighting provided by CTLT.  We had set this up using my main office computer (a new MacBook Pro), but switching back and forth between recording and everything else I need to do with that computer was going to be a big hassle.  So yesterday I re-set it up a 5-year-old MacBook Pro that I don't use any more (battery dead, a bit unreliable).

I had been assuming that I'd just start recording some, and then rerecording them as needed to improve the content and the presentation.  But now I think I'll instead try to quickly develop the content (mostly PowerPoint slides) and record them all as voice-over-annotated-PowerPoint, with no video of me (camera off).  Once I've done them all I'll go back through them, deciding what needs changing, what self-test questions to add, and when and where video of me should be added, and then I'll rerecord them with the camera on.

This is good in several ways.  First, it removes the issue of my appearance from the initial development and recording of the lectures - that's the part I was finding most stressful.  Second, the revisions won't start until I have the full set of lectures done - that will help ensure that the whole set is coherent.  Third, it maximizes the amount of recording experience I'll bring to the final recordings.  Fourth, it means that we'll quickly have a full set of lecture videos to help us develop all of the associated material (resource links and the various assessments).  Finally, because the camera will be off, I can move the whole recording setup to a little desk on the other side of the room rather than cramming it onto one side of my main desk.

If I set a goal of doing at least one voice-only video per day, starting today, I should have a full set by early February, maybe sooner.  Revisions will take time, but the re-recording should go fast, because I can probably do a full week's worth in a single day.