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 | September 6, 2006How can you win a nerd contest if you don't dress the part?
Last year, I started a shop at CafePress to help distribute lab materials and fund my adventures in science education. Part of the fun has been making molecular merchandise to help show everyone that molecular models are beautiful, in their own special way, and help people engage in random acts of science education.
Here are some of my suggestions for molecular wearables that can help you explain why science is fascinating to people that you meet in the grocery store or the coffee shop.
Kissing DNA. Unfortunately, the DNA…
sporte | September 6, 2006Do you ever imagine the presidential advisors doing the Basil Fawlty silly walk, looking crazed and confused, and quoting John Cleese whenever there's been a bad day in the Middle East?
I do. And this mental picture makes me think the title of Chris Mooney's book (The Republican War on Science) will surely keep it out of the top ten volumes on the White House reading list.
Nevertheless, I'm looking forward to reading it and to hearing Chris talk when he tours the country and elaborates on the story. If you'd like to hear him in person, or get your copy signed by the author, the schedule is…
sporte | September 5, 2006Ole and Lena's hot dish on a stick probably is explosive if you like to ride on a tilt-a-whirl afterwards. But what do you do if you're far from St. Paul?
Never fear.
There is more to life than hot dish.
I've always known that there were fun chemistry experiments that could be done with peeps, especially in the spring, but I never realized that so much fun could had with candy and soda pop.
In this article, the Disgruntled Chemist tested the explosive properties of different kinds of soda products when combined with minty items like Mentos or peppermint gum. These results are way more…
sporte | September 4, 2006or, better yet, enjoy the fine selection of summer carnivals.
In no particular order, we have:
Bio::Blogs#3
Hosted this month by mndoci (aka Depak Singh) at business|bytes|genes|molecules, Bio::Blogs is a carnival of articles at the intersection of biology and computation. If you are interested in life science informatics, digital biology, computational biology, or any spin-off, thereof, check out the reading material. And, definitely consider sending me a link if you've written anything on the subject that you'd like to submit for next month's edition. Send submissions to digitalbio at…
sporte | September 1, 2006If we compare sections 1, 2, and 3, we see that section 2 matches very well in a number of different samples, and that there are differences between the sequences in sections 1 and 3.
We also learn something about the people who did the experiment.
At first it appears somewhat odd that there are many matching sequences that are all shorter than the genome and all the same length.
What's up with that?
It turns out that information doesn't have anything to do with the fraction of the genome that matches our query. These short segments are PCR products. They're the same size because the PCR…
sporte | August 31, 2006Have you ever wondered about Cheeze Whiz? why new cars have a distinctive smell? or what makes golf balls so springy?
Chemical and Engineering News, published by the American Chemical Society, has a wonderful section that you will certainly appreciate.
"What's that stuff?" is a collection of entertaining stories about the stuff we encounter in everyday life. Each article combines chemistry with history and fun facts in a way that entices the reader to stay awhile and read every one.
Since the stories are written for non-chemists, they make a perfect companion to chemistry courses ranging from…
sporte | August 29, 2006The fall soccer season is well underway and the Hummingbirds soccer team is kicking everything in sight. The hummingbirds in these two series of photos are much quicker, considerably smaller and certainly cute.
A friend sent me this link since I manage the Hummingbirds soccer team. Hopefully, the person who posted these shots of baby hummingbirds will leave them up for awhile.
My husband told me about this page at Nature Photography with other truly incredible hummingbird photos. There are some great photos of hummingbirds in mid flight plus some pics of hummingbirds sitting quietly at bird…
sporte | August 28, 2006One of most wonderful things about the Internet has been the emergence of research projects that involve the general public. Universities like Cornell, Kansas University, and the University of Minnesota, to name a few, have established web sites and on-line databases that encourage both students and amateur biologists to participate in biological field studies. Not only do these projects extend the potential for good science by collecting more data, they give visibility to the research process and allow the public to take ownership and contribute to the store of scientific knowledge.
Monarch…
sporte | August 25, 2006Like biology, all bioinformatics is based on the idea that living things shared a common ancestor. I have posted, and will post other articles that test that notion, but for the moment, we're going to use that idea as a starting point in today's quest.
If we agree that we have a common ancestor, then we can use that idea as a basis to ask some interesting questions about our genomes. For, example, we know that genomes change over time - we've looked at single nucleotide changes here and here, and we've seen that large chunks of DNA can move around here.
So, it's interesting to consider…
sporte | August 23, 2006We heard quite a bit about rainforest destruction in the 80's and 90's. Even the Grateful Dead joined the efforts to raise awareness and gather support for rain forest preservation. In the past, the Dead stayed away from political activism because (quoting Jerry Garcia):
Power is a scary thing. When you feel that you are close to it, you want to
make sure that it isn't used for misleading. So all this time we've avoided
making any statements about politics, about alignments of any sort.
But the Dead decided deforestation was too big of an issue to ignore and held a press conference at the…
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 22, 2006Have you ever wondered how people actually go about sequencing a genome?
If they're sequencing a chicken genome, do they raise chickens in the lab and get DNA from the eggs? Does the DNA sequence come out in one piece? Why is there so much talk about computers? What are Phred, Phrap, and Consed? What is the Golden Path?
Wonder no more!
You too, can take a virtual tour of the Washington University Genome Center.
I found this really excellent series of short videos that follows two genetics students, Libby and Bryce, as they meet on the bus to the Genome Center and learn about all the steps…
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 20, 2006August is the time when gardens look their best. Fruit becomes showy, flowers abound, and plants are large and plentiful. Mendel's Garden #4, currently blooming at The Inoculated Mind, is no exception. Evolgen pointed this out, so I had to go take a look.
I enjoyed this trip through the experimental garden at UC Davis. It's a nice change to see someone with a scientific bent planting such a spicy garden. It was interesting to learn about how genetic engineering saved the papaya industry in Hawaii and the strains of flood-resistant rice.
Karl's own gardening experiences were…
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…
sporte | August 18, 2006The past few Fridays, we've been comparing human mitochondrial DNA with the mitochondrial DNA of different apes.
We started doing this here, where you can find directions for getting started.
And, we've found some interesting things.
In this installment, we found that humans have practically an entire mitochondrial genome stuck in chromosome 17.
Last week, we found that human mitochondrial DNA is more similar to that of chimpanzees than to gorillas. We found that 90.6% of the bases in human mitochondrial DNA match bases in the Bonobo chimp and 90.7% match bases in the Chimpanzee.
This…
sporte | August 17, 2006Chad Orzel posted a cute bit about True Lab Stories: The Party Game. I like these things because, yes, they make it clear that those of us who do science put coffee cups on top of our cars and drive off, just like everyone else. For those of who are thinking about careers in science, you don't always have to be brilliant, what you need is perseverance.
I can share one story from the lab where I was a graduate student.
One day, one of our visiting scientists came to me with a thermometer.
"It's not working!" he said.
I was skeptical, but I took a look.
The thermometer was really dirty…
sporte | August 17, 2006When can a really bad virus be used to do something good?
When we can use it to learn.
The human immunodeficiency virus, cause of AIDS, scourge of countries, and recent focus of ScienceBlogs; like humans, evolves. As one of my fellow ScienceBloggers noted, few biological systems demonstrate evolution as clearly as HIV. In this series, I'm going to guide you through some experiments on HIV evolution that you can do yourself. You won't even have to put on any special clothing (unless you want to), wash glassware or find an autoclave. And, you don't need to any UNIX commands or borrow a…
sporte | August 15, 2006Folks have been enthusiastically commenting around the clock on the possiblity of using prisoners in clinical trials.
Meanwhile, Thomas Hargrove has analyzed obesity and death rates in the National Football League. He suggests that those pharmaceutical companies with anti-obesity drugs might be better off taking a look at Monday night football. Or, at Monday night football players. He found that 56% of the players in NFL are obese, with offensive tackles weighing in at an average of 313 lbs.
From Mark Uehling, Bio-IT world:
Some of Hargrove's data came from a retired pollster, David…