Saturday, July 09, 2016

Genetics News 2 readership

Thanks for clicking on the link in the Genetics News email.  By visiting this page you've told the Useful Genetics staff that you read the July 9 (Part 2) edition.

Feel free to leave a comment below if you'd like to help us make these emails better!

Thursday, July 07, 2016

Genetics News readership for Useful Genetics Part 1

Thanks for clicking on the link in the Genetics News email.  By visiting this page you've told the Useful Genetics staff that you read the July 8 (Part 1) edition.

Feel free to leave a comment below if you'd like to help us make these emails better!

Control post

Nothing happening here folks.

Wednesday, April 20, 2016

Post-Oreskes thoughts

I haven't posted anything here for ages.  But I teach about climate change now (see here), so RRTeaching seemed a better place for this than PPResearch.

Last week Naomi Oreskes gave a public lecture in downtown Vancouver about her research into climate change denial.  This post was originally going to be about what I came away from the talk with, but now it's expanded into a 'Here's what I think about anthropogenic climate change' statement.

So here's what I think:

Almost everyone in North America (and probably much of the rest of the world) falls into one of two camps:
  1. People who aren't doing anything to prevent global warming because they either deny the climate-change science or think technology will save us from its consequences.
  2. People who are taking token actions to prevent global warming, and wringing their hands about the other camp.
 Camp 1: The deniers: Ultimately, people who cast doubt on the science behind climate change (or believe those who do), do so because they don't like the actions that the validity of the science implies.  They may argue that these actions would infringe on personal freedoms, threaten democracy and destroy jobs, but the bottom line is that they don't want to give up the good life that fossil fuels let us all lead.

The techno-solution group: Many people, including some who accept climate-change science, are predicting that the free market will male lifestyle changes unnecessary - that entrepreneurs will develop cheap practical technology that either replaces fossil-fuel energy or removes the unwanted CO2 from the atmosphere.  It could happen, but almost certainly not without nuclear power.

Camp 2: Those of us who accept climate-change science shouldn't feel smug, because we still haven't given up the good life that fossil fuels provide.  Sure we recycle, we occasionally bike or take the bus (if it's not inconvenient), and maybe we drive a hybrid car.  Maybe we vote for candidates who promise to institute a carbon tax.  Maybe we even pay for carbon-offsets when we fly.

But given the massive scope of the problem, these are tokens.  Literally: they mark us as 'good' people, but they have no significant impact on the problem.  We are deluding ourselves when we think that our individual actions will make much difference.  Not even if everyone in developing countries followed our example.  Not even if everyone in the world followed our example.

Some people are doing more:  Some of my UBC colleagues are doing their best to make the issues clear to the public - unfortunately this mostly serves to shift people from Camp 1 to Camp 2.  (I'm doing this in my Human Ecology course.) But some are also working to provide the government with solid advice about the best options.  For one example, see this report: Acting on Climate Change. In principle this could encourage government action that really could make a difference, but in practice I think the obstacles (social, political and especially economic) are too high.

So what do I think is going to happen?

Probably not the worst-case scenario, but a lot worse than the 2 °C people have been hoping for.
The worst-case scenario is that the we don't stop returning fossil-fuel carbon to the atmosphere until we run out of fossil fuels - until we've burned everything that could possibly be extracted and burned.  This would be much worse than the IPCC's worst-case 'business as usual' scenario ('RCP 8.5'), because RCP 8.5 assumes that we decide to leave some fossil fuel unburned. 

Here's a discussion of the burn-everything consequences. Global average temperature would rise by about 16 °C; polar temperatures by about 30 °C.  Much of the planet would be uninhabitable, and much of the rest would not be suitable for growing food.  So we'd be crowded and starve, unless we had already gotten too depressed to reproduce.

Most researchers assume that the short-term effects of increasing CO2 will be sufficiently horrible that governments (?) will impose drastic measures before we run out of fuel.  Maybe, maybe not.
But we're certainly not going to turn things around before we hit a 2 °C increase in global temperature, and probably not until we're well on our way to much higher temperatures.

Take Canada as an example:  We burn a lot of fossil fuel, and not just to keep warm and transport goods across our big cold country. The biggest greenhouse-gas producing category (25%) is production of the oil and natural gas that we sell to others or use ourselves.  (This latest data is 2013.)
And we're likely to keep burning a lot.  The latest report came out in February (Canada's Energy Future 2016; download here).  They conclude:
Total energy use in Canada, which includes energy use in the energy production sector, grows at similar rates in all EF 2016 cases, and GHG emissions related to that energy use will follow similar trends.
They developed energy-use predictions for six different scenarios.  In addition to the 'reference' scenario, they consider the implications of not building any more pipelines, of higher and lower natural-gas prices, and of high and low exports of liquefied natural gas.  Note that these are all market and distribution factors, and that these, not individual behaviours, are what determine how much energy Canada will use in the next 25 years.

Sadly, even market factors don't make much difference.  The different coloured bars below represent energy-use predictions for the different scenarios.  They all predict the same thing - a modest INCREASE in energy use over the next 25 years, a bit higher if natural gas prices are high.
At the Paris conference last fall, our new Liberal government committed to the 'Intended Nationally Determined Contribution' made by the Conservatives last spring,
"Canada intends to achieve an economy-wide target to reduce its greenhouse gas emissions by 30% below 2005 levels by 2030."
That sounds pretty good (though note that the level we're reducing from has been raised from the 1990 levels originally used).  But it's not where the Energy Report says we're headed.

There's nothing in the government's plans, nor in the behaviour of Canadians, to suggest a different future. ("Spend $300 million on new technology!"  "Have a conference with all the provinces!" "Engage the public!""Include indigenous peoples!")

Of course Canada is only a small player in global emissions, 1.6% of the total for 2011.  But we're supposed to be the good guys, at least now that the Liberals are back in power.  European countries are certainly doing better than us, but I doubt that we'll see any better reductions by the USA, or China, or Russia, or India.

People aren't going to change:  It's a waste of time to bemoan the behaviour of others, or to say that we need to eliminate greed or corruption or self-interest.  Anthropogenic climate change is the Tragedy of the Commons writ on a (literally) global scale.

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.


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...)