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What's that stuff?
Category: Classic Digital Bio
Have you ever wondered about Cheeze Whiz? why new cars have a distinctive smell? or what makes golf balls so springy?...
Posted by Sandra Porter at 11:08 AM • 4 Comments •
Discovering Biology in a Digital World
My thoughts on biology, teaching, life, and exploring the living world via the digital one. Only my opinions are represented by these postings, they do not represent the viewpoints of any funding agency or Geospiza, Inc.
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I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (Geospiza Education).
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- Workforce shortages in biotechnology, part I. Why is this a problem?
- Would your class like to clone and sequence plant genes?
- You tell 'em Arnold!
- The Genetic Nondiscrimination Act (GINA) is passed by the House
- The snake rescuer
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- Comparing mutant and wild type structures
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- Sandra Porter on The Genetic Nondiscrimination Act (GINA) is passed by the House
- Josh on The Genetic Nondiscrimination Act (GINA) is passed by the House
- Sandra Porter on A beginner's guide to making a phylogenetic tree
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- Miles on You tell 'em Arnold!
- Sandra Porter on Workforce shortages in biotechnology, part I. Why is this a problem?
- PA on Workforce shortages in biotechnology, part I. Why is this a problem?
- Sandra Porter on Workforce shortages in biotechnology, part I. Why is this a problem?
- PA on Workforce shortages in biotechnology, part I. Why is this a problem?
- TomJoe on Would your class like to clone and sequence plant genes?
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August 31, 2006
August 29, 2006
Birth of a Hummingbird
Category: Classic Digital Bio
The 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...
Posted by Sandra Porter at 1:00 PM • 1 Comments •
August 28, 2006
Butterfiles, birds, and worms
Category: Classic Digital Bio
One 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...
Posted by Sandra Porter at 12:00 PM • 0 Comments •
August 25, 2006
Digital Biology Friday: All mutations are not alike
Category: Digital Biology Fridays
Like 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...
Posted by Sandra Porter at 8:10 AM • 2 Comments •
August 23, 2006
Just a Box of Rain
Category: Ask a Science Blogger
We 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...
Posted by Sandra Porter at 12:52 PM • 2 Comments •
Using HIV to prove some points about evolution, part IV
Category: HIV/AIDS
Did 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....
Posted by Sandra Porter at 10:06 AM • 0 Comments •
August 22, 2006
Sequencing a Genome: the video
Have 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?...
Posted by Sandra Porter at 11:00 AM • 0 Comments •
August 21, 2006
Using HIV to prove some points about evolution, part III
Category: HIV/AIDS
In 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...
Posted by Sandra Porter at 10:00 AM • 0 Comments •
August 20, 2006
A lovely Sunday in the garden
Category: Announcements
August 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...
Posted by Sandra Porter at 3:21 PM • 1 Comments •
August 19, 2006
Using HIV to prove some points about evolution, part II
Category: HIV/AIDS
Let the experiment begin....
Posted by Sandra Porter at 11:35 AM • 0 Comments •
August 18, 2006
Digital Biology Friday: Monkeying around with mitochondrial DNA
Category: Digital Biology Fridays
The 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....
Posted by Sandra Porter at 3:43 PM • 2 Comments •
August 17, 2006
Too funny to ignore
Category: Humor
Chad 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...
Posted by Sandra Porter at 1:36 PM • 1 Comments •
Using HIV to prove some points about evolution, part I.
Category: HIV/AIDS
When 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...
Posted by Sandra Porter at 11:59 AM • 2 Comments •
August 15, 2006
Fat Footballers Face Fleeting Future
Category: Miscellany
Folks 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...
Posted by Sandra Porter at 4:48 PM • 2 Comments •
August 14, 2006
No, I don't worry about AIDS anymore
Category: Ask a Science Blogger
But that hasn't always been true. When I was in college, I had part-time jobs drawing blood from patients in the university hospital and as a phlebotomist at local plasma center. Plus, I was a volunteer EMT on an ambulance crew. Needless to say, I saw plenty of blood. And those were the days when no one wore gloves. We...
Posted by Sandra Porter at 4:40 PM • 4 Comments •
August 11, 2006
Digital Biology Friday: How similar are apes and humans?
Category: Digital Biology Fridays
During these past couple of weeks, we've been comparing mitochondrial DNA sequences from humans and great apes, in order to see how similar the sequences are. Last week, I got distracted by finding a copy of a human mitochondrial genome, that somehow got out of a mitochondria, and got stuck right inside of chromosome 17! The existence of this extra...
Posted by Sandra Porter at 1:14 PM • 5 Comments •
August 10, 2006
It's never too late for Bio::Blogs
Category: Announcements
Bio::Blogs#2 is been out for a few days but it's certainly not out of interesting ideas and things to read. There is some interesting stuff about Brisbane. Queensland looks like a lovely place and much different than my mental images of Australia. Sorry, but when I picture Australia, I get a strange image of a cross between Babe, old Mad...
Posted by Sandra Porter at 9:00 PM • 0 Comments •
Waxing lyrical about that stuff in our ears
Category: population genetics
It's hard sometimes when you're out of synch with the rest of the world. While my fellow ScienceBloggers have been obsessing about breasts, I've been really amused by the genetics of ear wax. Eh, what's that you say? Yes, it's true. Back in March, when Nature Genetics published this paper from Yoshiura (and friends), this bit of fun just went...
Posted by Sandra Porter at 2:30 PM • 3 Comments •
August 9, 2006
Biotechnology cleans my clothes
Category: molecular structures
One of the commenters on a previous post, pointed out that proteases have pretty diverse structures, even though they also share a common function. What else could I do? I had to take a look. I found structures for chymotrypsin (from a cow) and subtilisin (from a soil bacteria, Bacillus lentus) and used Cn3D to see how they compare (below...
Posted by Sandra Porter at 12:50 PM • 3 Comments •
August 4, 2006
Digital Biology Friday: Hey, who moved my DNA?
Category: Digital Biology Fridays
Last week, we decided to compare a human mitochondrial DNA sequence with the mitochondrial sequences of our cousins, the apes, and find out how similar these sequences really are. The answer is: really, really, similar. And you can see that, in the BLAST graph, below the fold. A quick glance shows that the ape with the most similar mitochondrial sequence...
Posted by Sandra Porter at 1:39 PM • 3 Comments •
Anti-freeze for winter weather
Category: Classic Digital Bio
It seems kind of funny to be thinking of anti-freeze at the moment, with heat waves blanketing the U.S., but all this hot weather makes me miss winter. And so I decided it was time to re-post this from the original DigitalBio. Winter is coming soon, my bike ride to work was pretty chilly, and it seems like a good...
Posted by Sandra Porter at 11:38 AM • 5 Comments •
