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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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Sandra Porter 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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    Chemistry & Biochemistry:

    A molecule for May

    APRIL was so much fun, that I thought I should find a molecule for May. I searched both the Gene database, the structure database, everywhere, without any luck. Finally, I decided to change the search and use the date instead of the name of the month. And here we have it, straight from PubChem. A molecule for May. 05012008 is...

    Comparing mutant and wild type structures

    How to compare mutant and normal protein structures.

    Open Access and using molecular structures in education

    I love using molecular structures as teaching tools. They're beautiful, they're easy to obtain, and working with them is fun. But working with molecular structures as an educators can present some challenges. The biggest problem is that many of the articles describing the structures are not accessible, particularly those published by the ACS (American Chemical Society). I'm hoping that the...

    I eat genomes for breakfast

    And so do you.

    Hunting for huntingtin, part I

    How do you go about researching a genetic disease? This multi-part series explores how digital resources can be used to learn about Huntingtin's disease. Reposted and updated from the original DigitalBio. A bit of background Alice's Restaurant is a movie with an unforgettable song that mostly revolves around Arlo Guthrie hanging out with his friends. Somewhere in the movie, the...

    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....

    Physical chemistry in the kitchen

    How do you use science outside of the lab? People say that transferring knowledge and skills from one subject to another represents one of the highest levels of learning. They also say that it hardly ever happens. Perhaps this explains some of the more astounding things that we hear from Nobel Prize winners, like when Francis Crick proposed that Earth...

    Make a merry molecule mug!

    The perfect science gift.

    Irony in RNA: a puzzle

    RNA by any other name would smell as sweet. Or would it?

    Spontaneous human combustion and the chemistry of ghosts

    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 too, are the stories about it's...

    How does a single nucleotide change make influenza virus resistant to a drug?

    Fun with molecular models!

    When your water starts tasting like dirt...

    It could be geosmin....

    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:...

    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...

    Antibiotic resistance: taking the bypass

    The wind storms and heavy rains that hit Seattle recently, demonstrated why a bypass mechanism can be a helpful thing - for both bacteria and motorists. Under the bridge on Mercer, from the Seattle Times...

    Antibiotics au naturale?

    What's the difference between a synthetic drug and an antibiotic? Sometimes there's no difference at all. Let's take a look at chloramphenicol and couple of pencillins....

    Bored on Thanksgiving?

    Here's an experiment you can do at home.

    Plants that make crystals that look like plants

    It's a crystalline botanical fashion show.

    Every Structure has a Story

    Molecular structures are wonderful for science and enjoyable, in their own respect, as works of art. Here are some of my favorite DNA structures.

    "I hear the cottonwoods whispering above.."

    Remember that scene in "The Wizard of Oz" when the trees get ticked off and start hurling apples at poor Dorothy? How do you think real plants defend themselves?

    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...

    Dangerous chemistry: explosive experiments with junk food

    Ole and Lena's hot dish on a stick probably is explosive if you like to ride on a tilt-a-whirl afterwards. But what do you do if you're far from St. Paul? Never fear. There is more to life than hot dish....

    What's that stuff?

    Have you ever wondered about Cheeze Whiz? why new cars have a distinctive smell? or what makes golf balls so springy?...

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