sporte | August 22, 2008The Periodic Table of Videos from the University of Nottingham has 118 short YouTube clips about the elements. Wired Campus recommended the Sodium clip (below). I liked it, too. It's not quite as funny as Mentos in Diet Coke, and but it's still cute and the narrator has a haircut like Gene Wilder in Young Frankenstein.
H/T: Wired Campus.
sporte | August 22, 2008Two teenagers, Kate Stoeckle and Louisa Strauss, carried out their own science project over the past year. They visited 4 restaurants and 10 grocery stores and gathered 60 samples of fish and sent them off to the University of Guelph to get sequenced.
I like this story. One of my former students did a project like this for the FDA years ago, sampling fish from the Pike Place Market and identifying them with PCR. He was an intern, though. Here we have students identifying sushi on their own!
Quoting the New York Times article:
They found that one-fourth of the fish samples with…
sporte | August 21, 2008One of the things that drives me crazy on occasion is nomenclature. Well, maybe not just nomenclature, it's really the continual changes in the nomenclature, and the time it takes for those changes to ripple through various databases and get reconciled with other kinds of information. And the realization that sometimes this reconciliation may never happen.
One of the projects that I've been working on during the past couple of years has involved developing educational materials that use bioinformatics tools to look at the isozymes that metabolize alcohol. As part of this project, I've been…
sporte | August 15, 2008Vaccines work by stimulating the immune system to respond to a specific thing. Most of the vaccines we use are designed to prime the immune system so that it's ready to fight off some kind of disease, like whooping cough, polio, or influenza. Some vaccines can have more specialized functions, like stimulating the body to attack cancer cells, kill rogue autoimmune cells, or prevent pregnancy. We'll look at what they do in later posts, for now, let's look at the kinds of things that can be used as vaccines.
It's an amazing assortment. Even more amazing is that these items don't all work in…
sporte | August 14, 2008A long time ago, I saw a movie called "The Other Side of the Mountain." The movie told the story of Jill Kinmont, a ski racer who contracted polio and lost the use of her legs. I was sad for days for afterward, but also relieved to know that Jill Kinmont's fate wasn't going to be mine. I wasn't going to wake up in an iron lung after a ski race, and neither were my friends, because most of the children in my generation had been vaccinated against the Polio virus.
This image shows a polio survivor learning to walk. The image comes from the CDC Public Health Image Library
We were lucky.…
sporte | August 14, 2008Every year people adopt pet dogs, cats, birds, and other creatures and take them to their local veterinarians for all the usual vaccinations and exams. The usual vaccinations protect your pets from diseases like rabies, distemper, Feline Immunodeficiency Virus, and Feline Leukemia. But it's not just pets that get protected by vaccines. Agricultural creatures: fish, chickens, sheep, cows, pigs, and horses receive vaccines and increasingly, wild animals are getting vaccinated, too.
One example comes from the National Center for Ecological Analysis and Synthesis. They are looking at ways to…
sporte | August 13, 2008if you take this survey.
Wanna change the world? Make it possible for everyone to talk about science in a normal conversation? Do you have ideas for improving science literacy?
Seed is interested in your ideas. Answer the survey and share your thoughts. And I've seen the MacBook Air. It's beautiful.
UPDATE: if you had trouble accessing the survey, try it again. It will be open until Friday, August 15th, 11pm EST.
sporte | August 12, 2008write your Senators and Representatives about saving the Endangered Species Act.
But, first read what Mike Dunford has to say. Mike describes the changes that the Bush administration has proposed in great detail and consequences for wild animals. Greg Laden has posted on this, too.
sporte | August 12, 2008Ancestry tests aren't just for humans anymore. We went to Petco this weekend to buy dog food and found brochures for doggy DNA testing. Now, those of you with dogs of uncertain parentage need puzzle no longer. According to Petco, their SNP test (what is a SNP?) can identify over 100 different breeds and they'll tell you which breeds are represented in your dog and whether your dog's breeding is mixed (or pure).
The brochure from Petco also claims that knowing something about your puppy's parentage could be helpful in understanding their behavior and potential health risks. That's probably…
sporte | August 11, 2008The first lab mouse I touched had soft white fur and a light pink tail. It looked cute enough to snuggle and take home as a pet and I was smitten. I slipped my hand into the cage, thinking the mouse would respond like my pet gerbils or my brother's pet rat. As my hand closed around its belly, that sweet little mouse sunk its teeth deep in my thumb. I screamed and shook my hand, smashing the mouse on the cement floor and killing it in an instant.
It's been many years now since I've been doing anything with mice or rats. There's much more oversight these days, as DrugMonkey has been…
sporte | August 10, 2008It justs gets weirder and weirder.
moar funny pictures
You can find more of the story and more puppy pictures here.
H/T to Jennifer - one of erv's commeters.
sporte | August 9, 2008Instead of enjoying a sunny summer day today, or partying with SciBlings in New York, I'm staring out my window watching the rain. Inspiration hit! What about searching for August?
Folks, meet the HFQ protein from E. coli. I found this lovely molecule by doing a multi-database search at the NCBI with the term 'August'.
HFQ is a lovely protein with six identical subunits, that's involved in processing small RNA molecules and is homologous to some eucaryotic proteins that work in RNA splicing (1).
Do you see the blue loopy regions in the center of the structure? Those are positively…
sporte | August 8, 2008A few weeks ago, I wrote about a paper in Science(1) that I read on a connection between a mutation in the dopamine D2 receptor and the genetics of learning.
Only, it turned out that when I looked at the gene map...
the mutation mapped in a completely different gene.
I presented the data here and wrote a bit about my surprise at finding this mistake and even greater surprise at seeing this same mistake perpetuated by others.
Now, I have some updates to the story.
The folks at the NCBI responded quickly and added annotations to both the DRD2 and the ANKK1 citations in the Gene database.
Now…
sporte | August 7, 2008"Did you know," my friend whispered, "that the Humane Society funds terrorists?"
I was stunned. What? That's crazy! I've adopted pets from there. No way! How could those be the same people??
My friend and I were suffering from "brand confusion." In business, this happens when different companies use similar names for their products in order to confuse the marketplace. In the animal rights movement, brand confusion is used to misdirect the funds that would otherwise help groups who do genuine humanitarian work.
As I learned in "The Animal Research War" by P. Micheal Conn and James Parker…
sporte | August 7, 2008Leave it to those wacky Korean cloners. In December, scientists from Gyeongsang National University gave us fluorescent kitties. Now, we have cute little puppies!
These aren't the first cloned pets on the market, we have stores that sell glowing fish. But these clones have a bit higher price tag. For $50,000 Bernann McKinney got 5 new "Boogers" from RNL Bio; "Booger McKinney," "Booger Lee," "Booger Ra," "Booger Hong and "Booger Park." That's $10,000 a Booger!
Still, who can resist these cute little boogers? I have a picture of the puppies below the fold and as you can see, they're…
sporte | August 6, 2008When female bloggers get death threats for comparing a Batman movie to a poor business plan, and friends can have their lab fire bombed for doing plant genetics, it's sometimes a little scary to step into the fray and take a stand on controversial issues.
But that's the point. We have to speak out. Scary or not, unless we speak out against the animal rights terrorists who firebomb people's homes and harass researchers, we will lose any chance to save our loved ones from diseases like cancer, HIV, Alzheimer's, or many others.
Let's think about just one of these.
According to an article from…
sporte | August 6, 2008Microbiologist develop some strange habits when it comes to food.
Some take a fatalistic approach. They reason that microbes are everywhere, we're going to die anyway, we might as well eat dirt and make antibodies. You know these people. They quote things like the "10 second rule" when food drops on the floor, tell you we're all getting asthma because we're too obsessed with cleanliness, and let their dogs wash their dishes.
Eeew.
With a few possible exceptions, I'm in the other camp.
I'm the one who freaks out if the cover is left off the salad dressing during dinner. I brush my…
sporte | August 6, 2008This the third part of case study where we see what happens when high school students clone and sequence genomic plant DNA. In this last part, we use the results from an automated comparison program to determine if the students cloned any genes at all and, if so, which genes were cloned. (You can also read part I and part II.)
Did they clone or not clone? That is the question.
But first, we have to answer a different question about which parts of their reads are usable and which parts are not. (A read is the sequence of bases obtained from a chromatogram file.)
How does our data get…
sporte | August 5, 2008start all over again.
MDRNA Inc., a Puget Sound area company formerly known as Nastech, announced on Monday that they'd be laying off 23 people including their president and chief business officer. This might not sound like a lot, but according to Joseph Tartakoff, from the Seattle PI, this brings the total number of layoffs up to 145 since November.
These events present a challenge to those of us who teach in biotech programs or biotech-related fields. Nastech, the predecessor to MDRNA had been around for over 20 years. Who would expect a 20+ year company to shed three quarters of it's…
sporte | August 5, 2008This the second part of three part case study where we see what happens when high school students clone and sequence genomic plant DNA. In this part, we do a bit of forensics to see how well their sequencing worked and to see if we can anything that could help them improve their results the next time they sequence.
How well did the sequencing work?
Anyone who sequences DNA needs to be aware of two kinds of problems that afflict their results. We can divide these into two categories: technical and biological.
Technical problems are identified using quality values and the number of bases…