Sandra Porter
sporte
Posts by this author
November 19, 2007
Sexual 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…
November 19, 2007
Since 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…
November 16, 2007
As 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…
November 15, 2007
DNA 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…
November 14, 2007
Students 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…
November 14, 2007
This 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?
November 13, 2007
The 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…
November 13, 2007
Congratulations 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:…
November 13, 2007
For 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…
November 12, 2007
A 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…
November 12, 2007
I 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…
November 9, 2007
Last 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…
November 1, 2007
Reposted 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…
October 31, 2007
When 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…
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!!!!
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It's easy. Just head on over to one of these pages On…
October 29, 2007
One of the greatest shocks when I started working in industry was the realization that the peer-reviewed paper, the most valuable form of currency in the academic world, was valued so little.
In academics, there is a well-established reward system for getting your work published in peer-reviewed…
October 28, 2007
Metagenomics is a field where people interrogate the living world by isolating and sequencing nucleic acids. Since all living things have DNA, and viruses have either DNA or RNA, we can identify who's around by looking at bits of their genome.
Researchers are using this approach to find the…
October 27, 2007
The simple fact is this: some DNA sequences are more believable than others.
The problem is, that many students and researchers never see any of the metrics that we use for evaluating whether a sequence is "good" and whether a sequence is "bad."
All they see are the base calls and sequences:…
October 26, 2007
We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many of the same…
October 25, 2007
The next time you bite into a crisp juicy apple and the tart juices spill out around your tongue, remember the honeybee. Our fall harvest depends heavily on honeybees carrying pollen from plant to plant. Luscious fruits and vegetables wouldn't grace our table, were it not for the honeybees and…
October 24, 2007
Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?
This quarter, my bioinformatics class, at Shoreline Community College, will be working with chromatograms that were obtained by students at Johns Hopkins University, and graciously made…
October 23, 2007
The NASA Earth observatory has some amazing photos of the wildfires in California. I've put a small version of one image here, but you should go to the NASA site and see the high resolution images. The fires are horrible but the images are fantastic.
October 23, 2007
It's hard to teach bioinformatics when schools work so hard to keep us from using computers.
Anecdotes from the past
Back in my days as a full-time instructor, I fought many battles with our IT department. Like many colleges, we had a few centralized computer labs, tightly controlled by IT (aka…
October 21, 2007
Welcome Bio256 students!
This quarter, we're going to do some very cool things. We are going to use bioinformatics resources and tools to investigate some biological questions. My goal, is for you to remember that these resources exist and hopefully, be able to use them when you're out working…
October 17, 2007
If like me, you were a little disoriented and confused when you visited Second Life and traveled through orientation island, then you may like this.
The Wired Campus (from The Chronicle for Higher Education) led me to an interesting post from the New Media Consortium and a new place to visit once…
October 16, 2007
A few weeks ago, I did some "back-of-the-envelope" calculations to explain to a reader why genome sequencing costs so much.
I estimated that, if JCV's genome were sequenced at the cost advertised by university core laboratories, his genome would cost about $128 million.
That was an estimate, of…
October 15, 2007
This morning Bora and I both gave talks in Second Life. Since this was a pretty new experience for me, I thought I'd share my thoughts on it.
Ever since the days when I watched cartoons on Saturday mornings, I thought it might be fun to be in one. But when I tried it this morning, truthfully, it…
October 14, 2007
I've been reading quite a bit lately about Universities setting up virtual classrooms in Second Life, so when Bertalan Meskó from ScienceRoll invited me to come give a poster, I decided it was time to take the plunge. Besides, I'm going to be teaching an on-line bioinformatics course this spring…
October 14, 2007
October is a month of darkness, mystery, and dread. Only one holiday brings joy in October and even then, October joy is distilled through fear and apprehension. In the early evenings the sun hurries home and once familiar objects loom ominously in the dark. Giant spiders appear out the fog,…
September 26, 2007
For the record: Chlamydia is NOT a virus.
I am bummed. I like the little MicrobeWorld radio broadcasts, and the video podcasts are even more fun.
But I was perusing the archives and I found this:
I could ignore this if it came from a different source, but MicrobeWorld is produced with…