sporte | November 17, 2008iGEM is all about synthetic biology, kids. It's the annual International Genetically Engineered Machine competition.
Each team in the IGEM competition has to make something using a kit of biological parts from the Registry of Standard Biological Parts. Teams of students use these parts to design, build, and operate biological systems in living cells.
IGEM began in 2003 with a course at MIT where students made cells blink. Now, this year had:
1200 participants,
84 teams,
and 24 awards.
Amazingly, two of those awards went to a team (UCSF) composed mostly of students from a public high…
sporte | November 16, 2008Hospital cases of methicillin resistant Staphylococcus aureus (MRSA) have risen 33-fold during the past ten years in Washington state, yet our hospitals fail to identify or track cases in a systemic fashion (Seattle Times).
The Seattle Times began a three-part investigative report today describing the rise in MRSA incidence, the consequences for patients, and the failure on the part of our hospitals to take measures to address the problem.
According to the Seattle Times, six out of seven people get MRSA infections at some kind of health care facility. The spread could be contained if…
sporte | November 16, 2008Last spring, in a coffee shop in Berkeley, I saw an amazing thing. It was a cup made from corn. The information on the cup says that it is made from corn, is environmentally sustainable, and 100% compostable.
My fellow ScienceBloggers have written several articles lately about corn in fast food (here, here, and here), but I'm not sure they realized that corn is used for more than fast food. Corn is also used to make the packaging.
The company that made this cup is called Fabri-Kal. The cup is one of many compostable packaging items from Fabri-Kal's Greenware line. Interestingly, although…
sporte | November 15, 2008Poor PZ! Stranded without a working laptop in a strange town! This is the kind of situation that gives me nightmares, so I like to upload presentation materials to the web just in case.
Lately, I've been looking at different methods for doing this to see which ones l like the best.
A few days ago, I tested this with Scribd.
Today, I'm going to see what we can do with Google Docs.
TomJoe said that he started using Scribd because he couldn't share things with Google.
I use Google docs quite a bit, but I haven't tried to share any documents with more than a few people, so I took at look…
sporte | November 15, 2008If you're going to create a new life form (even if it's only digital), Sunday Saturday seems like the best day to give it a try.
Reposted from an earlier year.
Build-A-Virus is a quick, fun, and simple game that was created and put on-line by Bioreliance, now owned by Invitrogen. This game is lots of fun, even when your students are college instructors.
In this activity, you create a new virus by picking different physical characteristics.
The game works like this:
First, you choose whether the virus has an envelope or not.
Next, you choose whether the genome is single or double-…
sporte | November 14, 2008Masha Gessen was faced with a terrifying choice: cut off her breasts, and possibly save herself from cancer, or use them to feed her child.
It was late at night when I walked back to my empty dorm room at the conference. Shivering, I stood on the narrow bed, quickly shut the windows, tore the blankets off the other bed, and wrapped myself up, trying to get warm. Too cold to sleep, I picked up my copy of Masha Gessen's "Blood Matters: From Inherited Illness to Designer Babies, How the World and I Found Ourselves in the Future of the Gene," expecting boredom to lull me into unconsiousness…
sporte | November 13, 2008Well, I had to test Scribd with something. Why not use a document on the Massachusetts Life Sciences Industry?
Scribd is sort of like the YouTube of electronic paper. I found Scribd from TomJoe's post about Life on Mars. His PowerPoint talk is really much more interesting than the life science document that I uploaded as a test, but since you're here anyway, you might as well take a look.
What does Scribd do?
It solves the "waiting for another application to open" problem that I find so frustrating when I want to quickly read (okay, skim) a pdf document that's linked from something on…
sporte | November 12, 2008Is ready for reading at Submitted to a Candid World.
I never thought I'd see the day when a Tangled Bank host would compare PZ Meyers to John McCain, but I admit, it was tastefully done.
sporte | November 12, 2008What skills does a biotechnology technician need to know?
This seems like a simple question, but people have been struggling to define biotech skill standards since the early 90's.
Complicating this question is that many areas of biotechnology require somewhat different skills. Antibody work requires one set, plant or animal tissue culture, another; fermentation, another; manufacturing, another; DNA sequencing, yet another set. Even skills that you might think are universal, like using a microscope, are not. During my years in graduate school, I never used a microscope; I cloned genes…
sporte | November 10, 2008Worldmapper is a web site with 366 maps of the world. These maps however, are not the kinds of maps you've seen in school, with every country shown by size. These maps are cartograms. It's a bit like seeing a cartoon version of a Thomas Friedman book. These maps present a whole new way of visualizing information about the world.
In a cartogram, the size of each country or geographic region is drawn in proportion to some kind of variable. The variable could be population size, number of people who practice a certain religion, incidence of infant mortality, voting patterns, energy use,…
sporte | November 9, 2008Brian Switek, from Laelaps, could probably tell you.
And, if you vote for him in the 3rd Annual College Blogger Scholarship competition, he just might.
He'll tell you why should you vote for him, too, and I agree.
And below the fold, is an inspirational cartoon.
From xkcd.
sporte | November 9, 2008It was a wet and rainy day yesterday, and we have a dissecting microscope, so I decided to see if I could find some tardigrades.
Tardigrade photo by nebarnix
Reposted from Nov. 2006
I went outside and scraped a bit of moss and some lichens off of our deck. Then I put the lichens and moss in a dish. We don't have distilled water in our house, so I added a bit of cool some tap water to the dish. I squeezed the moss and lichens in the water. Then I took a pipette and transferred a bit of the stuff in the water to a plastic petri dish and looked for tardigrades.
Sure enough, I saw one…
sporte | November 7, 2008Over 55,000 people die each year from rabies, a disease that is 100% preventable, according to Dr. Guy Palmer, who spoke last night at the University of Washington.
Dr. Palmer is from the School for Global Animal Health, a group that works towards improving global health through advancing preventative care for both humans and animals. One of the preventative measures is through rabies vaccination.
Image from the CDC Public Library of Health.
Rabies cases can be prevented by vaccinating dogs and other animals that carry the virus like raccoons, skunks, and foxes. The virus itself has a…
sporte | November 6, 2008Before mammals, before dinosaurs, before bacteria, or plants, there was something else; a protocell containing RNA.
The Exploring Origins Project has excellent animations of protocells, a timeline of life's evolution, and best of all- fantastic animations of the RNA world.
You can see how RNA folds, ribozymes (RNA that catalyzes chemical reactions), and learn about the role of RNA when the Earth was young.
BTW- I made this ribozyme image with Cn3D. The RNA is synthetic - made by humans with machines, that is, and this molecule can cut chemical bonds.
sporte | November 6, 2008What kind of dead animals are in your freezer? I used to be skeptical about the whole notion of cloning wooly mammoths. But this recent article in PNAS (1), makes the whole idea seem less far fetched.
Wakayamaa et. al. describe an amazing technical advance where scientists in Japan were able to derive clones from mice that had been frozen for 16 years at -20°C.
I'm guessing that this wasn't one of the freezers with an automatic defrost cycle.
Sure, this demonstration is still a long way from cloning an elephant or related species. Even cat and dog cloning are fairly recent advances…
sporte | November 4, 2008There are tears of joy and relief in my eyes. It's like the most emotional New Year's Eve in my life.
My neighbors are even shooting off fireworks!
Mr. McCain's speech was wonderful. Let's move forward!
Update: I am watching Mr. Obama now on TV with tears in my eyes. I have never been so glad to be an American.
Yes we can, Mr. Obama, yes we can!
sporte | November 4, 2008This quarter, I'm using a wiki with my bioinformatics class and posting sometimes about the things that I learn.
Two things I've been experimenting with are:
Setting up pages for individual students so they can take notes while they're working.
Embedding a Google form into one of my wiki pages for student assessment.
Here's a diagram showing some of the pages in my bioinformatics class wiki site.
Syllabus: I suppose this reflects on my own lack of organization, but I use the syllabus as a dynamic document, making changes and adding information throughout the course. There are links…
sporte | November 3, 2008Want to learn more about Parkinson's disease? See why a single nucleotide mutation messes up the function of a protein?
I have a short activity that uses Cn3D (a molecular viewing program from the NCBI) to look at a protein that seems to be involved in a rare form of Parkinson's disease and I could sure use beta testers.
If you'd like to do this, I need you to follow the directions below and afterwards, go to a web form and answer a few questions. Don't worry about getting the wrong answers. I won't know who you are, so I won't know if you answered anything wrong.
If you have any concerns…
sporte | November 2, 2008I heard some intriguing presentations this week about education in Second Life, but I happen know that there is an open-source, free (?) alternative called "Croquet."
Do any of you have experience with Croquet vs. Second Life? I'd love to hear about it in the comments.
I attended two talks, hoping that someone would compare different platforms, or at least give the audience a chance to ask questions, but no such luck.
I think these multi-user virtual environments are really interesting, but I have some reservations about educational institutions making substantial investments in building…