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.
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).
e-mail digitalbio at gmail.com
July 31, 2006
Category: Miscellany
I've been fortunate, living in Seattle, to hear talks from many people that my colleagues and co-bloggers might consider to be rock stars - people like Mary-Claire King, Nancy Wexler, Francis Collins, Leroy Hood, Eugenie Scott, David Haussler, Harold Varmus, and Elaine Ostrander. But, if I think about who the public might see as a rock star, the list gets...
Posted by Sandra Porter at 6:00 PM • 2 Comments •
July 28, 2006
Category: Digital Biology Fridays
We've had a good time in the past few last weeks, identifying unknown sequences and learning our way around a GenBank nucleotide record. To some people, it seems that this is all there is to doing digital biology. They would, of course, be wrong. We can do much, much more than identifying DNA sequences and obtaining crucial information, like who...
Posted by Sandra Porter at 8:00 AM • 0 Comments •
July 26, 2006
Category: Classic Digital Bio
Trade publications; such as catalogs, technical bulletins, and web sites; are a valuable source of information for students in biotechnology-related courses. Not only do catalogs and technical publications provide current information, but they also contain a wealth of useful facts and physical constants that biologists need on-the-job. Further, using catalogs in the classroom mimics the way that science is carried...
Posted by Sandra Porter at 8:33 PM • 3 Comments •
July 25, 2006
Category: Science education
One of my favorite experiments, in our biotech program at Seattle Central Community College, was when my students sequenced promoters that they had cloned from E. coli . I liked this activity because it pulled lots of pieces together and allowed the students to connect the dots between the DNA sequences that regulate gene expression, the DNA sequences that code...
Posted by Sandra Porter at 8:00 AM • 0 Comments •
July 24, 2006
Category: Classic Digital Bio
A few years ago, the General Biology students at the Johns Hopkins University began to interrogate the unseen world. During this semester-long project, they study the ecosystems of the Homewood campus, and engage in novel research by exploring the microbial ecosystems in different sections of the campus. Biology lab students gather environmental samples from different campus ecosystems, isolate DNA, amplify...
Posted by Sandra Porter at 9:20 PM • 0 Comments •
July 21, 2006
Category: Digital Biology Fridays
"Hey Rocky, watch me pull a rabbit out of my hat!" I realized that I should add just a bit more information to last answer on gene identification, so here it is. After the last installment, Diego commented: but still you do not know exactly what part of your DNA sequence is matching to the annotated protein....
Posted by Sandra Porter at 7:26 PM • 1 Comments •
Category: Digital Biology Fridays
Welcome back! If you've just joined us, we're in the middle of a quest to find the identity of an unknown nucleotide sequence. To summarize our results so far, we used this sequence to do a blastn search of GenBank, using all the default settings at the NCBI. You can see the beginning of the project here. And we had...
Posted by Sandra Porter at 4:19 PM • 3 Comments •
July 14, 2006
Category: Digital Biology Fridays
Last week, we embarked on an adventure with BLAST. BLAST, short for Basic Alignment Search Tool, is a collection of programs, written by scientists at the NCBI (1) that are used to compare sequences of proteins or nucleic acids. BLAST is used in multiple ways, but last week my challenge to you, dear readers, was to a pick a sequence,...
Posted by Sandra Porter at 11:35 AM • 3 Comments •
July 12, 2006
Category: Science education
Many regions in the United States, and the world for that matter, are seeking to entice biotech companies to relocate. As Lorraine Ruff and David Gabrilska describe in their Genetic Engineering News Article, "Metrics for Economic Development," the exhibitors at meetings like BIO work hard to: ".. entice founders and CEOs with a wide spectrum of inducements: institutional and technological...
Posted by Sandra Porter at 11:40 AM • 0 Comments •
July 10, 2006
Category: molecular structures
Although, I certainly didn't believe it. Truly in nature, it can be described as nonpareil. With all the years that I've heard (or taught) that all DNA is antiparallel, it was hard to believe my own eyes when I saw this structure. Yet here is, on the screen, parallel DNA....
Posted by Sandra Porter at 10:50 PM • 0 Comments •
Category: Bioinformatics
How did the human genome ever get finished if every one of the three billion bases had to be reviewed by human eyes? In the early days of the human genome project, laboratory personnel routinely scanned printed copies of chromatograms, editing and reviewing all DNA sequences by eye. For more background, see the post on qualitative measures of DNA quality....
Posted by Sandra Porter at 3:00 PM • 0 Comments •
July 8, 2006
Category: Ask a Science Blogger
I mean phone call. Because, if I thought he remembered me, I would call and say "thank you." Because of the time I spent in his lab, I know that cloning started long before Dolly. The first vertebrate animal was cloned over 50 years ago. And it wasn't a sheep....
Posted by Sandra Porter at 9:09 PM • 3 Comments •
July 7, 2006
Category: Digital Biology Fridays
My colleagues have come up will all kinds of interesting bloggy things to use as an excuse for Friday celebrations. Adventures in Ethics and Science has Friday Sprog Blogging for cute stories about her kids. A Blog Around the Clock considers Friday's the perfect day to write about weird sex. Pharyngula salutes the spineless with Friday Cephalopods. Good Math, Bad...
Posted by Sandra Porter at 9:00 AM • 2 Comments •
July 6, 2006
Category: Science education
Our official challenge period has ended, but that doesn't mean that our drive to support science education has to stop. I'm keeping a Donors Choose button up in the side menu, just in case anybody feels the need to give back to society and help with science education. Now, I just need to study up on subliminal messaging see the...
Posted by Sandra Porter at 12:49 PM • 0 Comments •
July 5, 2006
Category: Bioinformatics
What do genetic testing and genealogy have in common? The easy answer is that they're both used by people who are trying to find out who they are, in more ways than one. Another answer is that both tests can involve DNA sequence data. And that leads us to another question. If the sequence of my mitochondrial DNA is only...
Posted by Sandra Porter at 7:00 AM • 2 Comments •
July 3, 2006
Category: Humor
Past Favorites for the holidays: Now that the dog genome is done, maybe we need a new project in genetic variation. What genotypes make people look like their dogs? technorati tags: dogs, humor dog genome...
Posted by Sandra Porter at 9:58 AM • 0 Comments •
July 2, 2006
Category: Genetics & Molecular Biology
Mendel's Garden, that is. Enjoy a quiet mental stroll among the shady trees where Hsien Hsien Lei from Genetics and Health has compiled perennial favorites and annual suprises. Even though the season is young, Mendel's Garden is clearly growing. This edition of Mendel's Garden is great spot to branch out and explore the natural world. Check out the garden tour...
Posted by Sandra Porter at 1:17 PM • 1 Comments •
Category: viruses
If you're going to create a new life form (even if it's only digital), Sunday seems like the best day to give it a try....
Posted by Sandra Porter at 7:00 AM • 0 Comments •
July 1, 2006
Category: Announcements
Pedro Beltao, of Public Rambling, has started a bioinformatics blogs carnival named Bio::Blogs. The first edition is up and ready to be read. This looks like a promising collection. technorati tags: carnival, bioinformatics...
Posted by Sandra Porter at 5:12 PM • 0 Comments •
Category: Science education
This summer I have a high school teacher working with me as an intern, because of an RET (Research Experience for Teachers) grant from the National Science Foundation. Yesterday, he told me a story about the science activity that really lit a fire in his class. His 75 students used PCR to amplify DNA from their cheek cells. The Dolan...
Posted by Sandra Porter at 1:24 PM • 0 Comments •
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