sporte | December 1, 2007The grocery store magazine covers all say that home made gifts are big this year. So I thought, some of you might like to channel your inner Martha Stewart and make gifts with a science theme.
I'm here to help to you make a merry mug with one of our favorite molecules. Yep, we're talking caffeine.
1. First, we'll go to PubChem at the NCBI. It's not an exclusive (or even last) resort but there are lots of fancy molecules hanging around, just waiting to be discovered and put onto drinking containers.
2. Now, we'll look for a molecule. I'm going to use caffeine for this example since I…
sporte | November 26, 2007GenomeWeb reports that Rite Aid drug stores on the West coast are now selling kits for doing paternity tests. The kits are made by Sorenson Genomics in Utah.
Sorenson Genomics calls it the "peace-mind-test." Really!
Each kit contains a swab for collecting cheek cells from the inside of your mouth and a container for mailing the sample to the lab.
As far as I can tell, you buy the kit for $29.99, take a sample, fill out the consent forms, and mail the sample to Sorenson along with the $119 lab fee.
Maybe I'm too imaginative, but I'm a little puzzled by some of the information that wasn'…
sporte | November 22, 2007Would you recognize your leftovers when they're magnified? Would you know turkey if you saw it at 40X?
Make a guess and click an image to see the answer.
technorati tags: Thanksgiving, food science, microscopy
Copyright Geospiza, Inc.
sporte | November 20, 2007Which read(s):
1. contain either a SNP (a single nucleotide polymorphism) or a position where different members of a multi-gene family have a different base?
C
2. doesn't have any DNA?
B
3. is a PCR product?
A, B, and C. All of three reads were obtained by sequencing PCR products, generated with the same set of primers.
The quality plots that I refer to are here.
sporte | November 19, 2007The genie is out of the bottle. Personal genomes are not just for Venter and Watson anymore.
Three competing companies, 23andme, Decode, and Navigenics are betting that you want to do a little better than reading your horoscopes and playing with tea leaves. They think that you want to know something about your destiny and take control of your future. And when I look at the 23andme web site, I want it, too. I want it so badly, it makes me drool.
But is it really such an unequivically good thing?
There's been a long-standing debate between companies and at least some scientists and the…
sporte | November 19, 2007Sexual attraction is all in your brain. At least if you're a nematode.
Ricardipus has a great image if you want to see a nematode picture.
I always thought worms were hermaphrodites (both male and female) but the story, as usual, turns out to be a bit more complex. Researchers at the University of Utah have found that worms have definite preferences for one sex or the other. And, if they kill off certain kinds of cells, the preference for one sex or another can change.
From the University of Utah:
"They look like girls, but act and think like boys," says Jamie White, a postdoctoral…
sporte | November 19, 2007Since DNA diagnostics companies seem to be sprouting like mushrooms after the rain, it seemed like a good time to talk about how DNA testing companies decipher meaning from the tests they perform.
Last week, I wrote about interpreting DNA sequence traces and the kind of work that a data analyst or bioinformatics technician does in a DNA diagnostics company. As you might imagine, looking at every single DNA sample by eye gets rather tiring. One of the things that informatics companies (like ours) do, is to try and help people analyze several samples at once so that they can scan fewer…
sporte | November 16, 2007As many of you know, I'm a big fan of do-it-yourself biology. Digital biology, the field that I write about, is particularly well-suited to this kind of fun and exploration.
Last week, I wrote some instructions for making a phylogenetic tree from mitochondrial genomes. This week, we'll continue our analysis.
I wrote this activity, in part, because of this awful handout that my oldest daughter brought home last year. She presented me with an overly photocopied paper that showed several protein sequences from cytochrome C in several creatures. She said she was supposed count the…
sporte | November 15, 2007DNA sequence traces are often used in cases where:
We want to identify the source of the nucleic acid.
We want to detect drug-resistant variants of human immune deficiency virus.
We want to know which base is located at which position, especially where we might be able to diagnose a human disease or determine the best dose of a therapeutic drug.
In the future, these assays will likely rely more on automation. Currently, (at least outside of genome centers) many of these results are assessed by human technicians in clinical research labs, or DNA testing companies, who review these data by…
sporte | November 14, 2007Students at Soldan International High School are participating in an amazing experiment and breaking ground that most science teachers fear to tread.
Soldan students, along with hundreds of thousands of other people, are participating in the National Geographic's Genographic Project. Through this project, students send in cheek swabs, DNA is isolated from the cheek cells, and genetic markers are used to look at ancestry.
Genetic markers in the mitochondrial DNA are used to trace ancestry through the maternal line and markers on the Y chromosome can be used to learn about one's father.…
sporte | November 14, 2007This structure is called a "kissing loop" and I find that name just a bit odd, given the source of the structure.
Now, here's the puzzle: Why would I say that the name "kissing loop" is ironic?
sporte | November 13, 2007The Wired Campus has an interesting article on nursing students at Tacoma Community College. In John Miller's class, the students practice interviewing patients in Second Life.
This sort of activity, of course, is one that could be carried out in a classroom, but I can see the advantages of having student interview other "people" who are for the most part, strangers. It will be a different and valuable experience.
sporte | November 13, 2007Congratulations to George Cachianes (who I've written about before), his amazing students from Abraham Lincoln High School, and collaborators at UCSF!
These students, from a public high school no less, placed in the top 6 finalists, along with only one other US team. The other top teams were: Peking University (China), University of Science and Technology (China), University of Paris (France), University of Ljubljana (Slovenia), and UC Berkeley. I'm really impressed that these public high school students managed to beat students from MIT, Stanford, Harvard, Caltech, and Princeton, but…
sporte | November 13, 2007For many years, I had my biotech students do projects where each group of students would analyze their own data, in addition to all of the data gathered by the class. I would draw a table on the white board and each group would enter their data. At the end of the class, all the groups would copy all the results into their notebooks, then analyze them in Microsoft Excel.
This worked pretty well, but it wasn't perfect. There were always cases where one group would be really slow, or someone had to leave early, or I needed to use the board and couldn't.
And, this method certainly wouldn't…
sporte | November 12, 2007A few weeks ago, I asked if you, dear readers would be able to tell the difference between a computer scientist and a serial killer. Now, I've seen the crowds at the UW computational biology seminars and I've also seen pictures of serial killers in the newspaper. I don't think it would be easy to tell the difference if you had to rely on looks alone.
I also wondered if some people might be better at this than others.
A surprisingly large number of people (290!) completed the survey. Most people did pretty well and guessed correctly for 6-8 photos. I think this is a little better than…
sporte | November 12, 2007I had some strange notions when I made the jump from working at the lab bench to teaching at the white board. I thought good teaching meant interesting lectures. And I was completely unaware that people actually conducted research in science education. If I had been asked about education research, I would have replied that it was largely anecdotal, probably limited to sociologists and primary grades, and as far as I was concerned, useless.
And, honestly, to me it was useless.
I never saw any of science education articles or journals. No other instructors every discussed them and…
sporte | November 9, 2007Last year I wrote about an experiment where I compared a human mitochondrial DNA sequence to primate sequences in the GenBank. Since I wanted to know about the differences between humans, gorillas, and chimps, I used the Entrez query 'Great Apes' to limit my search to a set of sequences in the PopSet database that contained gorillas, bonobos, chimps, and human DNA.
A week ago, I tried to repeat this experiment and...
It didn't work.
All I saw were human mitochondrial sequences. I know the other sequences match, but I didn't see them since there are so many human sequences that match…
sporte | November 1, 2007Reposted from Halloween 2006.
Since Ben shared his family's taxonomy of candy types, and it's Friday, after all, I thought I'd share some of things that we do with candy around our house and describe some fun things that you can do with candy at home.
Materials and methods. First, you need some candy. My husband and I used to get our candy fix from our kids, but only one of our children goes trick or treating these days. She's good, though. She works the blocks like a political volunteer a week before the election, hitting all of her friends' houses and the commercial district besides…
sporte | October 31, 2007When purified, it glows with an unearthly light. You can't go "chemical free" and try to escape it. It's part of our bones and it forms the backbone of our DNA. A tool for good, a tool of war, essential for gardening, and infamous as a pesticide; phosphorus is truly an amazing element. Amazing too, are the stories about it's discovery and our history with using it. Many of the stories in The 13th Element by John Emsley (2000, John Wiley & Sons), from the alchemist's bench to the murderer's kitchen, are well-suited to reading on a Halloween eve.
From the nightmare inspiring stories…
sporte | October 30, 2007 I missed my chance to get my own DonorsChoose challenge together, but that doesn't mean that you have to miss your chance to contribute and, of course:
WIN FABULOUS PRIZES!!!!
WIN FABULOUS PRIZES!!!!
WIN FABULOUS PRIZES!!!!
It's easy. Just head on over to one of these pages On Being a Scientist and a Woman (Her teachers still need $83) or
The Questionable Authority (His teachers need $88), or A Blog Around the Clock and click the right links.
You know you want to.