Classic Digital Bio
sporte | September 28, 2010Theo chocolate is situated in a neighborhood called Fremont, in the city of Seattle, in the former Redhook brewery. I used to consult for Redhook in my microbiology days, when I had access to a -80°C freezer and a proper microscope, so the building has a comfortable feel and some pleasant memories.
These days the bar is gone and the aromas are more like roasting coffee than brewing beer. Most of machinery, though, is surprisingly similar. The equipment is very much the same as the equipment you'd find in many kinds of biotech manufacturing facilities. There are giant scales, fermenters,…
sporte | December 24, 2007This wasn't in the lab, but it was an accident, and it was funny later on.
Normally, I wouldn't think twice about storing bacterial cultures in a refrigerator. After all, bacteria on a petri plate, inside of a plastic bag, are kind of stuck. They can't get out of the plates, and even if they did, they certainly can't crawl out of a plastic bag.
I thought soil bacteria, on agar plates, were mostly harmless.
I was wrong.
When my husband was finishing graduate school, he brought home some agar plates that he had streaked, with different Streptomyces species, so that he could photograph them…
sporte | December 18, 2007How do you go about researching a genetic disease?
This multi-part series explores how digital resources can be used to learn about Huntingtin's disease. Reposted and updated from the original DigitalBio.
A bit of backgroundAlice's Restaurant is a movie with an unforgettable song that mostly revolves around Arlo Guthrie hanging out with his friends. Somewhere in the movie, the conversation turns to Woody, and someone asks the question that no one wants to touch. Does Arlo's girlfriend know about Huntington's? ...dead silence... Now, I did see the movie quite a few years ago, so my memory…
sporte | October 18, 2006Reposted from the original Digitalbio.
About a decade ago, I took a fascinating summer course at the UW on bioethics. We read about the Nuremburg trials and the Geneva conventions. We learned about horizon problems and eugenics. And we discussed lots of challenging scenarios with genetic testing, autonomy, family relationships, and the problems faced by people seeking to have children, trying to get insurance, or looking for a job.
So naturally, when I started a biotechnology course for non-science majors (Biotechnology and Society) at our community college, I used many of those examples…
sporte | October 11, 2006No one in a life science-related industry or research lab, in Western Washington, is safe at this time of year.
Surely, you're joking!
No, seriously, there are teachers and science enthusiasts everywhere looking to sign you up! And don't call me "Shirley."
Sign me up?
That's right, it's time to prepare for the
BIOTECH EXPO
This is the Western Washington version of the science Olympics! Those science enthusiasts are out scouting for anyone who does something related to science or a life-science industry to act as an advisor (sort a mentor with a lower committment level) to high school…
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 4, 2006Awhile back Chemical & Engineering News published a fascinating article called "The Secret Life of Plant Crystals" with some wonderful photos of calcium oxalate crystals. Special cells (called "idioblasts") produce these crystals, with shapes that are unique to each type of plant.
Even though 75% of flowering plants make these crystals, no one knows why they make them and in fact, their functions may be as diverse as their shapes. Some crystals look sharp and dangerous, like thistles or thorns, suggesting that they function to defend a plant from hungry herbivores. Other crystals are…
sporte | September 26, 2006Razib inspired me to share some of the story behind why white people are considered derivatives.
Reposted from the Classic Digital Bio.
No red herrings, here! Lamason et. al. found a single gene that controls human skin color while studying pigmentation in zebra fish (1).
These zebra fish had an unusual golden color that turned out to be an important clue. Lamason and collaborators found that the golden zebra fish lost their normal color because of a mutation in the slc24a5 gene. When the zebra fish have the mutant form, they produce fewer melanosomes.
A short language lesson
Fewer…
sporte | September 19, 2006Modified from the original post.
Playing around with molecular structures is one of the more entertaining activities that you can do with digital biology. I've become totally entranced with molecular structures, both because they're a fascinating art form and because every structure has its own story.
I learned this because I ended up writing 69 different structure stories for the "Exploring DNA Structure" instructor guide. This was never in my original plan but my friend Charlotte Mulvihill wrote to ask me about the functions of different structures. I blithely replied that sometimes the…
sporte | September 13, 2006Reposted and slightly modified from Classic DigitalBio.
Some people say that science takes the magic out of everyday life.
Not me!
I've learned some things by reading Science (1) that might give some people nightmares, especially young children. Remember that scene in "The Wizard of Oz" when the trees get ticked off and start hurling apples at poor Dorothy?
Real plants do defend themselves.
Those "Wizard of Oz" trees would really defend themselves by giving poor Dorothy a tummy ache
Pardon me a moment while I apologize to enforcers of precise scientific language.
Okay, okay, real apple trees…
sporte | September 11, 2006A long time ago, I saw a Star Trek episode where the crew encountered aliens who lived at a different frequency. I may have this backwards, but I think the aliens moved so quickly that no one knew they were there. And until problems struck, our heroes were happily oblivious to the existence of the others.
The Plants In Motion movies remind me of that episode.
Since plant movement occurs much more slowly than movements we can easily observe, we tend to think that plants don't move. These movies prove that idea wrong. Filmed with time-lapse photography, these short movies show seeds…
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 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 4, 2006It 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 time to be thinking about antifreeze. Antifreeze proteins, that is. Antifreeze proteins help keep pudgy yellow meal worms from turning into frozen wormsicles and artic flounder from becoming frozen flat fish.
Funny, but I would have thought that one antifreeze protein would…
sporte | July 26, 2006Trade publications; such as catalogs, technical bulletins, and web sites; are a valuable source of information for students in biotechnology-related courses. Not only do catalogs and technical publications provide current information, but they also contain a wealth of useful facts and physical constants that biologists need on-the-job. Further, using catalogs in the classroom mimics the way that science is carried out in the real world. In the research lab, scientists and technicians often rely on catalogs, technical bulletins, and web sites, for quick and useful information.
I probably…
sporte | July 24, 2006A few years ago, the General Biology students at the Johns Hopkins University began to interrogate the unseen world. During this semester-long project, they study the ecosystems of the Homewood campus, and engage in novel research by exploring the microbial ecosystems in different sections of the campus. Biology lab students gather environmental samples from different campus ecosystems, isolate DNA, amplify 16s ribosomal DNA by PCR, and check their PCR results by gel electrophoresis.
DNA samples are next sent to the university's Genetic Resources Core Facility , where scientific staff, in…