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The snake rescuer
Snake in your yard? Call the snake rescuers.Posted on May 1, 2008 2:07 PM • 10 Comments •
Discovering Biology in a Digital World
My thoughts on biology, teaching, life, and exploring the living world via the digital one. Only my opinions are represented by these postings, they do not represent the viewpoints of any funding agency or Geospiza, Inc.
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I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (Geospiza Education).
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- Workforce shortages in biotechnology, part I. Why is this a problem?
- Would your class like to clone and sequence plant genes?
- You tell 'em Arnold!
- The Genetic Nondiscrimination Act (GINA) is passed by the House
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- Miles on You tell 'em Arnold!
- Sandra Porter on Workforce shortages in biotechnology, part I. Why is this a problem?
- PA on Workforce shortages in biotechnology, part I. Why is this a problem?
- Sandra Porter on Workforce shortages in biotechnology, part I. Why is this a problem?
- PA on Workforce shortages in biotechnology, part I. Why is this a problem?
- TomJoe on Would your class like to clone and sequence plant genes?
- Sandra Porter on Workforce shortages in biotechnology, part I. Why is this a problem?
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environmental education:
Mapping polymorphisms in 16S ribosomal RNA
In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions. We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and determined that the mixed bases mostly likely come from different...Posted on April 17, 2008 8:00 AM • 2 Comments •
Biologists hunt Washington cougars - and make a video
Conflicts between predators like cougars and coyotes and human companions like pets and small children are becoming more common as people move into areas that used to be wildlife habitat. The Seattle Times has a great story this morning about biologists in Washington who are studying cougars to learn if cougars and people can coexist. The biologists think most of...Posted on March 16, 2008 11:42 AM • 0 Comments •
Exploring OpenOffice: what did we learn?, part I
I think all of us; me, the students the OO advocates, a thoughtful group of commenters, some instructors; I think many of us learned some things that we didn't anticipate the other day and got some interesting glimpses into the ways that other people view and interact with their computers. Some of the people who participated in the challenge found...Posted on March 13, 2008 6:42 PM • 0 Comments •
Little monarchs, little monarchs, where are your trees?
Your canopy is disappearing, you're likely to freeze. NASA's Earth Observatory reports that over 1,110 acres of forest were illegally logged, during the past four years, in the Monarch Butterfly Biosphere Reserve in central Mexico. Monarch butterflies travel here from all over the United States and Canada. Images from the Ikonos satellite tell us though, that future migrating butterflies are...Posted on March 11, 2008 10:04 AM • 5 Comments •
The NASA Earth Observing System and dealing with all that data
The NASA Earth Observing System is an incredible resource for both science and education. One of the amazing things about it is all the different kinds and quantities of data are assembled together into pictures that even grade school kids can immediately comprehend. How do they do it? Each of the EOS satellites delivers a terabyte or more of data...Posted on March 10, 2008 9:31 AM • 0 Comments •
Digital Biology Friday: A microbiology blast puzzler
Here's a fun puzzler for you to figure out. The blast graph is here:...Posted on March 7, 2008 12:28 PM • 2 Comments •
Bacterial metagenomics on the JHU campus: analyzing the data, part III
This is third video in our series on analyzing the DNA sequences that came from bacteria on the JHU campus. In this video, we use a pivot table to count all the different types of bacteria that students found in 2004 and we make a pie graph to visualize the different numbers of each genus....Posted on February 26, 2008 10:47 AM • 0 Comments •
Bacterial metagenomics on the JHU campus: analyzing the data, part II
What do you do after you've used DNA sequencing to identify the bacteria, viruses, or other organisms in the environment? What's the next step? This four part video series covers those next steps. In this part, we learn that a surprisingly large portion of bioinformatics, or any type of informatics is concerned with fixing data entry errors and spelling mistakes....Posted on February 26, 2008 10:19 AM • 0 Comments •
Bacterial metagenomics on the JHU campus: analyzing the data, part I
For the past few years, I've been collaborating with a friend, Dr. Rebecca Pearlman, who teaches introductory biology at the Johns Hopkins University. Her students isolate bacteria from different environments on campus, use PCR to amplify the 16S ribosomal RNA genes, send the samples to the JHU core lab for sequencing, and use blastn to identify what they found. Every...Posted on February 26, 2008 10:14 AM • 0 Comments •
Digging up the dirt on campus bacteria: how do we know if we have good data?
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 culprit that's killing the honeybees. We're also trying to find out...Posted on October 28, 2007 2:24 PM • 0 Comments •
Metagenomics, biomes, and dirt: separating good data from bad
Sequencing the dirt: see how it's donePosted on October 27, 2007 7:00 PM • 0 Comments •
Playing in the dirt: metagenomics on the JHU campus
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 principles....Posted on October 26, 2007 2:20 PM • 0 Comments •
Making discoveries in the open: doing digital biology with the class
Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?...Posted on October 24, 2007 4:05 PM • 0 Comments •
Grants for kids to study beetles
Charles Darwin was so fascinated by beetles he paid people to help him build his collection. The Coleopterists Society and the Smithsonian Institute want to help kids explore the wonders of beetles, too. They're providing grants for kids, in grades 7-12 to work on beetle biology. Applications are due by November 15, 2007....Posted on August 23, 2007 3:00 PM • 1 Comments •
Hot plants and viruses, part III: An inordinate fondness for hypothetical proteins
How do plants grow at 65°C?Posted on February 21, 2007 6:19 AM • 2 Comments •
If you can't stand the heat, get infected!
Are viral and fungal infections always a bad thing? Maybe not if you're a plant. In fact, if you're a plant trying to grow in the hot (65° C) soils of Yellowstone National Park, you're going to need all the help you can get....Posted on February 6, 2007 4:10 PM • 1 Comments •
Do Science in Las Vegas: Undergraduate Research Opportunities in Environmental Microbiology
Hot springs, salty lakes, arid soil and good science.Posted on January 29, 2007 11:39 AM • 1 Comments •
A Sunday with the Tardigrades
Cute little tardigrades are great research subjects.Posted on November 13, 2006 11:46 AM • 2 Comments •
Seattle cabs are naturally gassed
As they say, there's nothing like travel to learn new and unexpected things. Especially from cab drivers. One of my ScienceBlog Sibs, Shelly, spends time talking with cabbies about earwax, but I seem to invite other kinds of lectures....Posted on September 22, 2006 9:53 PM • 4 Comments •
TV for teachers
"And it's a hard, and it's a hard, it's a hard, and it's a hard, And it's a hard rain's a-gonna fall. " - BoB Dylan Tired of Simpson reruns and the exploits of Friends? [From the WSTA] NOVA is broadcasting an entire series of shows on hurricanes, Katrina, and what the experts predicted would happen should a hurricane ever...Posted on September 9, 2006 5:25 PM • 0 Comments •
Just a Box of Rain
We heard quite a bit about rainforest destruction in the 80's and 90's. Even the Grateful Dead joined the efforts to raise awareness and gather support for rain forest preservation. In the past, the Dead stayed away from political activism because (quoting Jerry Garcia): Power is a scary thing. When you feel that you are close to it, you want...Posted on August 23, 2006 12:52 PM • 2 Comments •
