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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 •
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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- Sandra Porter on Workforce shortages in biotechnology, part I. Why is this a problem?
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Digital Biology Fridays:
Digital Biology Friday: Who were those molecules anyway?
Two molecules are locked in a tight embrace. Who are they?Posted on December 28, 2007 10:12 AM • 0 Comments •
Digital Biology Friday: Free to evolve? - the answer
Last week I posted an image with two molecules (below the fold), one protein and one nucleic acid, and asked you about the probability of finding similar molecules in different species. You gave me some interesting answers....Posted on December 14, 2007 10:33 AM • 4 Comments •
Digital Biology Friday: Free to evolve?
This is a fun puzzle. The pink molecule is a protein and the other molecule is a nucleic acid....Posted on December 7, 2007 9:30 AM • 17 Comments •
Digital Biology Friday: Animal Mitochondria and Evolution, part II
You too, can compare chimp and human DNA.Posted on November 16, 2007 8:51 AM • 0 Comments •
Digital Biology Friday: Animal Mitochondria and Evolution Revisited
An evolution activity for the classroom.Posted on November 9, 2007 3:47 PM • 0 Comments •
Digital Biology Friday: What sequences do you believe?
During the past few Fridays (or least here and here), we've been looking at a paper that was published from China with some Β-lactamase sequences that were supposedly from Streptococcus pneumoniae. The amazing thing about these particular sequences is that Β-lactamase has never been seen in S. pneumoniae before, making this a rather significant (and possibly scary) discovery. If it's...Posted on September 7, 2007 8:43 AM • 5 Comments •
Digital Biology Friday: A helpful hint
I began this series last week with a question about a DNA sequence that was published and reported to be one the first beta-lactamases to be found in Streptococcus pneumoniae. Mike has a great post about one of problems with this paper. I think the data themselves are awfully suspicious....Posted on August 24, 2007 6:44 PM • 4 Comments •
Digital Biology Friday: the answer to last week's puzzle
Last Friday, we had another in the series of weird DNA structures. (You can see the first here). I asked the audience to identify the unusual feature in this molecule. Here's the first picture: tags: DNA structure, DNA , molecular structure, biochemistry Here's the answer:...Posted on August 3, 2007 10:19 AM • 4 Comments •
Digital Biology Friday: More puzzling structures
I've had some requests for some more molecular puzzles since the last one that I posted (see A DNA puzzle ). One person liked it so much he even blogged about it. So, here's one for you to chew on over the weekend. This puzzle is a variation of an activity in Exploring DNA Structure, a CD/lab book that I...Posted on July 27, 2007 4:17 PM • 3 Comments •
Digital Biology Friday: hot plants and viruses, the finale
Could a protein from a virus help plants handle global warming?Posted on June 1, 2007 9:15 AM • 0 Comments •
Digital Biology Friday: hot plants and viruses V
Through the Related Structures tab and what I found there.Posted on May 25, 2007 9:00 AM • 2 Comments •
MeSH part I. Where can you find the meaning of "life"?
The best place for biology words.Posted on February 9, 2007 11:58 AM • 3 Comments •
Digital Biology Friday: Searching for synonyms
In last week's episode, your assignment was to think of an interesting plant trait and find a description about a gene, related to that trait, by searching PubMed....Posted on October 13, 2006 12:00 PM • 0 Comments •
Digital Biology Friday: Finding genes with PubMed
Many of you might take this for granted, and I know it seems amazing today, but I when first started teaching, our access to scientific literature was pretty limited. I could go to the UW and use Grateful Med to search Medline, but we didn't have anything like it at my college and web browsers, like Mosaic, had yet to...Posted on October 6, 2006 2:00 AM • 1 Comments •
What is the direction of the rainbow?
and what is the volume of the sea? This sounds a bit like the beginning of a poem but it's really the answer to the question we posed last week on a Digital Biology Friday....Posted on September 22, 2006 2:50 PM • 1 Comments •
Digital Biology Friday: Rainbows, Models, and DNA
Today, we're going to look for rainbows in double-stranded DNA and see what they can tell us about DNA structure....Posted on September 15, 2006 2:18 PM • 0 Comments •
Digital Biology Friday: Seeing in 3D with Cn3D
Why do I love Cn3D? Let me count the ways. What does Cn3D do? (Hint: say "Cn3D" out loud). Seriously, Cn3D is a program that draws lovely pictures of molecular structures by using experimental data from techniques like X-ray crystallography and nuclear magnetic resonance spectroscopy. Surprisingly (to some), and in contrast to many bioinformatics programs, Cn3D is really easy and...Posted on September 8, 2006 11:38 AM • 0 Comments •
Digital Biology Friday: The importance of being aerobic
If we compare sections 1, 2, and 3, we see that section 2 matches very well in a number of different samples, and that there are differences between the sequences in sections 1 and 3. We also learn something about the people who did the experiment....Posted on September 1, 2006 11:37 AM • 0 Comments •
Digital Biology Friday: All mutations are not alike
Like biology, all bioinformatics is based on the idea that living things shared a common ancestor. I have posted, and will post other articles that test that notion, but for the moment, we're going to use that idea as a starting point in today's quest. If we agree that we have a common ancestor, then we can use that idea...Posted on August 25, 2006 8:10 AM • 2 Comments •
Digital Biology Friday: Monkeying around with mitochondrial DNA
The past few Fridays, we've been comparing human mitochondrial DNA with the mitochondrial DNA of different apes. We started doing this here, where you can find directions for getting started. And, we've found some interesting things....Posted on August 18, 2006 3:43 PM • 2 Comments •
Digital Biology Friday: How similar are apes and humans?
During these past couple of weeks, we've been comparing mitochondrial DNA sequences from humans and great apes, in order to see how similar the sequences are. Last week, I got distracted by finding a copy of a human mitochondrial genome, that somehow got out of a mitochondria, and got stuck right inside of chromosome 17! The existence of this extra...Posted on August 11, 2006 1:14 PM • 5 Comments •
Digital Biology Friday: Hey, who moved my DNA?
Last week, we decided to compare a human mitochondrial DNA sequence with the mitochondrial sequences of our cousins, the apes, and find out how similar these sequences really are. The answer is: really, really, similar. And you can see that, in the BLAST graph, below the fold. A quick glance shows that the ape with the most similar mitochondrial sequence...Posted on August 4, 2006 1:39 PM • 3 Comments •
Digital Biology Friday: That was no ape, that was my brother!
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 on July 28, 2006 8:00 AM • 0 Comments •
Digital Biology Friday: It's still Friday!
"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 on July 21, 2006 7:26 PM • 1 Comments •
Digital Biology Friday: What was that gene anyway?
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 on July 21, 2006 4:19 PM • 3 Comments •
Digital Biology Friday: Those BLASTed results!
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 on July 14, 2006 11:35 AM • 3 Comments •
Digital Biology Fridays: It begins with a BLAST
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 on July 7, 2006 9:00 AM • 2 Comments •
