classroom activities
sporte | August 17, 2007One time I was watching a football game on TV and they had a short quiz, called "You make the call" or something like that, and you had to watch a play and pretend to be a referee. A short video clip showed football players falling over each other. Then you were three possible calls that a refereee might make and asked to chose which was correct. After the commercial, the announcer would tell you which choice was right and explain why it was correct. I suppose this was a trick to make us watch the commercials, but I thought the game was kind of fun.
My SciBling "Mike the Mad" had a great…
sporte | July 30, 2007Amateur astronomers unite! The pros want your help!
image from Astronomy Picture of the Day, Credit: NASA, ESA, A. Aloisi (STScI / ESA), Hubble Heritage (STScI / AURA) - ESA/Hubble Collaboration
I learned about this from the Washington Science Teachers Assocation.
Galaxy Zoo and the Sloan Digital Sky Survey are looking for your help in sorting out different galaxies. It's a cool opportunity for anyone to go where few non-astronomers have gone before and help do real science at the same time.
What does this involve?
Go to the Galaxy Zoo, peruse their tutorial, and learn how to pick…
sporte | July 27, 2007I've had some requests for some more molecular puzzles since the last one that I posted (see A DNA puzzle ). One person liked it so much he even blogged about it.
So, here's one for you to chew on over the weekend.
This puzzle is a variation of an activity in Exploring DNA Structure, a CD/lab book that I made (with funding from the NSF) and used for some educational research.
tags: DNA structure, DNA , molecular structure, biochemistry
Any ideas?
sporte | July 16, 2007BLAST is a collection of programs that are used to compare sequences (DNA, RNA, or protein) to larger collections of sequences that are stored in databases. I've used BLAST as a teaching tool for many years, partly because it's become a standard tool for biological work and partly because it's very good at illustrating evolutionary relationships on a molecular level.
A few months ago, the NCBI changed the web interface for doing BLAST searches at their site. I wrote earlier about changes that I made to our animated tutorial in response to the new BLAST. Now, I want to mention some of the…
sporte | July 12, 2007By now, many of you have probably seen the the new BLAST web interface at the NCBI. There are many good things that I can say about it, but there are a few others that caught me by surprise during my last couple of classes.
tags: blast, BLAST tutorial, science education
Because of these changes, and because I'm giving a workshop for teachers on BLAST at the Fralin Biotechnology Conference in Blacksburg, VA, next week, it seemed like a good time to update our animated BLAST tutorial at Geospiza Education and save myself some trouble.
I originally created the BLAST for beginners tutorial to…
sporte | May 27, 2007An introduction to our Alaskan NSF Chautauqua course and a pre-course assignment.
I don't know how well this will work, but I thought it might be interesting this year to experiment with blogging about our course and sharing some of our experiences with the rest of the world. Here's your chance readers, if you'd like to do some of the assignments, you are very welcome to follow along and give it a try.
tags: plants, Alaska, NSF Chautauqua courses, bioinformatics, sequence analysis, evolution, wound inducible genes, moose
I'm not likely to get all the assignments or course info posted on-…
sporte | May 11, 2007Do you want to learn how to use some cool biotechnology and bioinformatics methods in your college or high school class?
If you're on the East coast, the best place to go is the Fralin Biotechnology Conference at Virignia Tech, July 18-21st.
(Yes, it's the same Virgina Tech, and that's why I waited to post this announcement).
There's something for everyone at this conference. For beginners, there's a pre-conference Biotech Boot camp where you can learn to run gels and clone genes. For instructors with more experience, there are great talks, new techniques to test, and plenty of…
sporte | February 17, 2007 Yes, yes, I know Darwin Day was Februrary 12th. Nevertheless, the Alliance for Science is sponsoring an essay contest in Darwin's honor and, if you're a high school student you can still celebrate by writing an essay.
And if you're a high school teacher, and your student wins, you win $$ for buying lab supplies.
Okay, I suppose it's only us geeky bloggers who consider writing an essay to be a kind of celebration.
If the sheer joy of celebrating Darwin Day by writing an essay, doesn't pique your interest, there are prizes.
Write an essay on the topic: "Why would you want your doctor to…
sporte | January 19, 2007The American Society for Human Genetics is sponsoring the second annual DNA Day Essay contest. If you are a high school teacher here's your chance to combine an interesting assignment along with a contest.
This year's essay questions are:
If you could be a human genetics researcher, what would you study
and why?
In what ways will knowledge of genetics and genomics make changes
to health and health care in the US possible?
The rules are here at GenEdNet.org
I also have an animated tutorial at Geospiza Education that might be of some help. The tutorial is titled Allelic Variants of Human…
sporte | January 12, 2007The bioinformatics classes that I teach use web services and web sites as much as possible, but I still find that it's helpful to have programs on our classroom computers. Here is a list of my favorite desktop programs for those of you who might want to add some bioinformatics activities to your biology courses.
Why not use the Web?
Before going on, I should probably explain, why we use desktop programs, we have so many things available on the web. We do use the web whenever we can. Web services are nice because you can shift the computation burden to someone else's computer. (I think this…
sporte | January 10, 2007I was frantically getting ready for class when I happened to glance out the window. What did I see? Big fluffy white flakes rapidly falling from above. You can't say we weren't warned. The newspapers have been predicting snow since Monday. It's just, well, unusual. And Seattle is never prepared to deal with it.
Even the kids aren't looking too happy about it, though. By this time of the school year, they've caught on that every snowday has a price. And, they will pay that price IN JUNE. Already the last day of school has been postponed until the 25th of June.
Who knows? The kids…
sporte | October 13, 2006In last week's episode, your assignment was to think of an interesting plant trait and find a description about a gene, related to that trait, by searching PubMed.
Since coming up with an interesting trait might be a challenge for some people, let's think about how to approach this step.
Picking your trait. If you're having a hard time thinking of a trait, it might be helpful think about where plants grow, why we grow plants, and why it might be hard or easy for plants to grow.
Some of the environmental factors that affect plant growth are: climate, soil composition, nutrient…
sporte | October 10, 2006Why is an eye, an eye and a nose, a nose? Why do different cells create different kinds of tissues when all the cells in a single organism start out with the same set of instructions (aka DNA)?
Head, Shoulders, Knees, and Toes is a learning activity that helps students discover, for themselves, that certain genes are expressed in some tissues but not in others. My goal here, as part of our NSF-funded project, is to show how students can learn biology by doing science with bioinformatics tools.
If you already know all about ESTs, you might want to jump ahead and read about the activity. If…
sporte | October 5, 2006Many of you might take this for granted, and I know it seems amazing today, but I when first started teaching, our access to scientific literature was pretty limited. I could go to the UW and use Grateful Med to search Medline, but we didn't have anything like it at my college and web browsers, like Mosaic, had yet to be invented. So, when I first started giving workshops for teachers on biotechnology and the world of the web, many were quite surprised to find out about the PubMed database.
Since PubMed is (to me) one of the best resources to ever come along, I think we should explore it a…
sporte | September 15, 2006Today, we're going to look for rainbows in double-stranded DNA and see what they can tell us about DNA structure.
First, we're going to get a structure for a double-stranded molecule of DNA and open it in Cn3D.
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If you want to do this at home and you haven't already downloaded a copy of Cn3D, you may want to read these instructions and get a copy. These directions also show how to download and open the structure. It's pretty simple once you've given it a try.
Hide a strand
Next, we're going to hide one of the strands. To do this, look in the menu bar for the Show/Hide menu and open…
sporte | September 8, 2006Why do I love Cn3D? Let me count the ways.
What does Cn3D do? (Hint: say "Cn3D" out loud).
Seriously, Cn3D is a program that draws lovely pictures of molecular structures by using experimental data from techniques like X-ray crystallography and nuclear magnetic resonance spectroscopy. Surprisingly (to some), and in contrast to many bioinformatics programs, Cn3D is really easy and fun to use.
Have you ever used programs like MS Office? Using Cn3D is at least 10 times easier.
An added benefit is that you don't have to try and find old copies of Netscape or other bits of obsolete software…
sporte | September 7, 2006No biology course is complete these days without learning how to do a BLAST search.
Herein, I describe an assignment and an animated tutorial that teachers can readily adopt and use, and give teachers a hint for obtaining the password-protected answer key.
Development of the tutorial and the activity were supported by funding from the National Science Foundation.
This is reposted from the the original DigitalBio blog.
This popular activity, designed to accompany the BLAST for beginners tutorial, has been updated to incorporate student comments and teacher requests. Originally developed for…
sporte | August 23, 2006Did HIV become resistant to Atazanavir because of a genetic change?
Was that genetic change inherited?
Did HIV evolve?
Can we explain why genetic changes at specific sites might help HIV escape the effects of the drug?
Let's find out.
All of the sequences in the image below (except for the first) come from HIV strains that were isolated from patients who took Atazanavir and no other protease inhibitors. All of the strains of HIV from patients were resistant to the drug.
If an amino acid is different from other strains, the color at that position is changed. Since we see different…
sporte | August 21, 2006In which we see the results and come to our own conclusions.
If you want to let other people tell you what's right and what's wrong, they will surely do so. Turn on the TV and hordes of happy actors bounce around, only too happy to help you purchase the right deodorant. Open your e-mail and everyone wants to share the best on-line pharmacy and investment guide.
Ugh.
I prefer making my own decisions, thank you very much.
So, I want to give you a chance to look at the data and decide for yourself, if the data show HIV protease sequences changing over time.
Let's see the results.
We're…
sporte | August 19, 2006Let the experiment begin.
We're experimenting with HIV in this series. And yes, you can try this at home!
If you want to see where we've been and get an idea where we're going, here are the links.
Part I. Meet HIV and learn how we're going to use it look at evolution. An introduction to the experiment and a link to a short flash movie on HIV.
Part II. Instructions for doing the experiment.
Part III. Look at the sequence results.
Part IV. Look at protein structures and see if we can explain why the experiment worked the way it did.
Let's move onward.
1. I made a data set of amino acids…