sporte | May 18, 2007tags: plants, bioinformatics, sequence analysis, viruses, fungi
Quick synopsis: A type of grass grows in Yellowstone National Park in hot (65° C), unfriendly soil. How the plant manages this feat is a mystery. What we do know, is that the grass can only tolerate high temperatures if it's been infected by a fungus, and the fungus has to be infected by an RNA virus. In the paper describing this discovery, the researchers provided the GenBank accession numbers for the viral sequences. I decided to see if I could find out more about the proteins and what they do. Read part I, part II, and part…
sporte | May 17, 2007Dave says that your drinking container reveals your philosophical side.
Janet, being a teacher, only uses mugs that she gets as free gifts.
At Geospiza, I use the communal mugs that I find in the cupboard. Most of these mugs seem to come from now-defunct biotech companies who handed them out at meetings. One of my all time favorites, though, is a really cool mug that I got from Betty Kutter with a picture of phage T4 and a map of its genome. The pictures are getting worn away, but I still like the mug.
At home, I drink out of these:
"
One of these mugs was a gift. I made the…
sporte | May 11, 2007Do you want to learn how to use some cool biotechnology and bioinformatics methods in your college or high school class?
If you're on the East coast, the best place to go is the Fralin Biotechnology Conference at Virignia Tech, July 18-21st.
(Yes, it's the same Virgina Tech, and that's why I waited to post this announcement).
There's something for everyone at this conference. For beginners, there's a pre-conference Biotech Boot camp where you can learn to run gels and clone genes. For instructors with more experience, there are great talks, new techniques to test, and plenty of…
sporte | May 10, 2007tags: moose, bioinformatics class, willows, plant genes
PZ's morning post about a bear killing a moose in someone's yard (they do live in Alaska, after all), reminded me that it's time to make an announcement about our upcoming course.
No, no, no! We're not going to kill any moose on the premises. We're going to learn about the moose and its food, not the moose as its food.
But, if you take the course that precedes ours, you might get to see some moose, and you might get to see some bears eating salmon.
The class before ours is entitled "Ecology of South Central Alaska " and they have…
sporte | May 10, 2007tags: crows, intelligence, birds
We don't have the sorts of wild kingdom experiences in Seattle, that they have in Alaska, but we do see nature taking its course, from time to time, right out on our city streets.
This morning, while walking the dog, I heard a gawdawful noise coming from around the corner. Naturally, the dog and I had to investigate.
We found two crows playing tug-of-war with a dead rat.
One crow had a tight grip on the rat's tail, the other crow had its ear. Together, when they flew, the rat was outstretched between the two crows, it almost looked like they were trying to…
sporte | April 21, 2007If you've ever looked at an evolutionary tree, contemplated phylogeny, cladistics, or the like, you're probably aware that Joe Felsenstein is one of the leaders of the pack.
And you will certainly enjoy, this interview that Blind Scientist has posted.
I wouldn't advise reading the interview to learn about doing phylogenetics, but you will learn a bit about the social anthropology of the field. Felsenstein does a wonderful job of supplying historical context to phylogenetic arguments and filling in the missing details.
A phylogenetic tree is a kind of model or hypothesis that's put forth…
sporte | March 31, 2007Science labs are not for all people.
I've always enjoyed teaching lab courses, so some of you might find it strange that I agree with some of the comments from Steve Gimbel and fellow Sb'ers on the questionable benefits of laboratory courses in introductory physics. But you see, I wasn't very impressed with the undergraduate physics labs that I took either. And with a little reminiscing, it's pretty easy to pick out example labs where the kindest description is "time-waster."
This wasn't true of all my lab courses. My biochemistry and microbiology lab courses were phenomenal, and, it's…
sporte | March 26, 2007It's dyscalculia.
The curse of math instructors everywhere.
A few years ago, students at the community college, where I taught, petitioned to have math removed from the list of courses that were required for a degree. Part of the reason, they argued, was that one student claimed that he shouldn't have to take math because he had dyscalculia.
(Dyscalculia is like dylexsia, except that it makes it harder for people to do arithmetic. )
The math instructors argued that they weren't going to eliminate requirements for a "fictional disease."
Now, it appears that miscalculations do have a…
sporte | March 14, 2007From NWABR:
Would you like to integrate ethics into your science classroom, but aren't sure which topics to address or teaching methods to use?
Do you feel that ethics is important to include in science education, but feel uncomfortable with your own lack of background knowledge?
Have you observed how students' motivation to learn content increases when science is discussed within its social and ethical context?
Come to the Ethics in the Science Classroom workshop and learn more!
Who is this for? Secondary Science Teachers
Program dates: July 16-20, 2007 (participants may arrive July 15…
sporte | March 13, 2007Blogging from the NW ASM branch meeting, part II
Yesterday, I wrote about the some of present (and future) methods that are (or will be) used in clinical labs to identify pathogenic microbes. In these next two posts, I want to describe the talks I attended on antibiotic resistance, from Xuan Qin and Fred Tenover (CDC), and some new things that I learned.
How do bacteria survive when their human hosts take a lot of antibiotics?
Children's Hospital (Seattle) routinely sees about 200 children with cystic fibrosis. Cystic fibrosis is a genetic disease that only appears when you have two copies…
sporte | March 12, 2007It looked like just any other rainy Saturday morning in the Pacific Northwest, but no, this Saturday was a day for microbiology. Reluctantly, I crawled out of my warm bed and headed over to the University of Washington to attend a meeting of the Pacific NW branch of the American Society for Microbiology (ASM).
My goals for this venture were diverse. Of course, I wanted to go hear some good science and see some old friends. But I also wanted to learn more about what microbiologists are actually doing these days, out there in the wild.
In my world, since all we hear about are nucleic acid…
sporte | March 11, 2007I don't often play these meme games but since none of the other female SciBlings have jumped on the bandwagon, and I've read at least as much science fiction as some of the other Scibs in the game (PZ, Mark, Afrensis, Orac, Joseph, Bora, and John), I just had to join in.
First, for the record, I think whoever came up with this "The Most Significant SF & Fantasy Books of the Last 50 Years, 1953-2002" overlooked some truly wonderful authors. I'll share some of my favorites in a little bit.
How did I get started reading SF?
When I was a child, we lived in a house with a crawl space…
sporte | March 10, 2007It must be spring. Summer course announcements are popping up everywhere and this site is no exception.
Last Friday, I posted an announcement about our summer bioinformatics course in Alaska, June 27-29th.
This week, I have a couple more conferences to announce. Naturally, I'll be at both of them, leading hands-on workshops for college and high school teachers in using the technology.
Today, I want to tell you about the Bio-Link Summer Fellows Workshop, June 4th-8th Berkeley, CA
I became involved with Bio-Link ten years ago when I was running the biotechnology program at Seattle…
sporte | March 9, 2007Registration has opened a bit late this year, but it's always tricky when large programs change hands. The Chautauqua Short Course program for College Teachers is no different. In fact, as far as I know, we may still be waiting for the National Science Foundation to make a final decision on funding.
Still, summer is rapidly approaching and I know many of you are making plans for attending summer workshops and squeezing in a bit of vacation time.
That's why I think you might like to consider learning bioinformatics in Alaska.
Yes. I did write "Alaska."
Anchorage, Alaska.
Dr. Linnea…
sporte | March 8, 2007
Maybe a little squid told him that tomorrow is PZ's birthday.
Happy birthday PZ!
The fish and I wish you 50 more!
sporte | February 21, 2007Grasses at Yellowstone National Park are able to grow temperatures (65°; C) that would toast most living things.
Step right up! Watch original research, as it happens, on the web!
I'm going to use bioinformatics to see if I can find that answer to the puzzle of heat-tolerant plants.
Previous parts:
Part I. The research
Part II. An introduction
Today: Part III: An inordinate fondness for hypothetical proteins
After today, we will have:
Part IV: Did we get lost in translation?
(I will add the link after it's posted)
Let's begin
Sigh.
It always happens when I have homework to grade.…
sporte | February 17, 2007How do microbiologists determine which microbe caused a disease?
As Tara has eloquently described (I, II), we are covered with bacteria and other microbes. A reasonable question then, is when we get sick, how do we which little devil deserves the blame?
In many cases, pathogens (disease-causing organisms) are identified by a common series of steps, known as Koch's postulates. Robert Koch described these steps in 1876 when he used them to prove that Bacillus anthracis was the cause of anthrax. During the past century, his steps have been used successfully many times.
Koch's steps are…
sporte | February 17, 2007 Yes, yes, I know Darwin Day was Februrary 12th. Nevertheless, the Alliance for Science is sponsoring an essay contest in Darwin's honor and, if you're a high school student you can still celebrate by writing an essay.
And if you're a high school teacher, and your student wins, you win $$ for buying lab supplies.
Okay, I suppose it's only us geeky bloggers who consider writing an essay to be a kind of celebration.
If the sheer joy of celebrating Darwin Day by writing an essay, doesn't pique your interest, there are prizes.
Write an essay on the topic: "Why would you want your doctor to…
sporte | February 16, 2007It's not too late. You can do research on cool topics, get paid, and even live in Las Vegas for the summer. If I were a student, I'd go.
The University of Nevada, Las Vegas is still taking applications for students to come do research in the desert.
The microbiology faculty at UNLV and the Desert Research Institute have received NSF funding for a summer Research Experience for Undergraduates (REU) program in Environmental Microbiology. This grant will provide students with the opportunity to work on a research project for a 10 week period with a faculty mentor.
Students will receive a $…
sporte | February 16, 2007Sometimes I think the field of biology suffers from collective amnesia. Like the girl in the movie "50 first dates," we discover things over and over and every time we find something, we forget that it's ever been found before. This is especially true if a phenomenon has been discovered in a biological subfield, like microbiology or virology.
Over 26 years ago, microbiologists found that Bacillus subtilis uses different DNA signals (alternative promoters) to control the expression of genes related to development (1).
Now, it turns out that this phenomenon is widely employed in the human…