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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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    October 31, 2007

    Spontaneous human combustion and the chemistry of ghosts

    Category: Chemistry & Biochemistry

    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...

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    October 30, 2007

    Tales from the lab: the finale

    Category: Halloween

    What strange things happen in the lab on Halloween? Read part I and part II to find out what's going on. (Reposted in honor of Halloween) "All those beauties in solid motion All those beauties, gonna swallow you up Hi hi hi hi hi hi One time too many Too far to go I - we come to take you...

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    Win fabulous prizes! (by helping schools)

    Category: Science education

    I missed my chance to get my own DonorsChoose challenge together, but that doesn't mean that you have to miss your chance to contribute and, of course:   WIN FABULOUS PRIZES!!!!   WIN FABULOUS PRIZES!!!! WIN FABULOUS PRIZES!!!! It's easy.  Just head on over to one of these pages On Being a Scientist and a Woman   (Her teachers still...

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    October 29, 2007

    Tales from the lab, part II

    Category: Halloween

    Strange things happen when it's Halloween week in the lab. (reposted in honor of Halloween) Catch up on the story by reading part I....

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    Cultural confusion: white papers vs. peer review

    Category: Science culture

    What's the difference?

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    October 28, 2007

    Digging up the dirt on campus bacteria: how do we know if we have good data?

    Category: Bioinformatics

    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...

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    Tales from the lab

    Category: Halloween

    What happens when it's Halloween in the laboratory?

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    October 27, 2007

    Metagenomics, biomes, and dirt: separating good data from bad

    Category: Bioinformatics

    Sequencing the dirt: see how it's done

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    October 26, 2007

    Playing in the dirt: metagenomics on the JHU campus

    Category: Bioinformatics

    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....

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    October 25, 2007

    Metagenomics and the mystery of the dying bees

    Category: Microbiology

    Dying bees and DNA sequencing

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    October 24, 2007

    Making discoveries in the open: doing digital biology with the class

    Category: Bioinformatics

    Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?...

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    October 23, 2007

    California Burning!

    Category: web resources

    The NASA Earth observatory has some amazing photos of the wildfires in California. I've put a small version of one image here, but you should go to the NASA site and see the high resolution images. The fires are horrible but the images are fantastic....

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    Computers vs. the science class: IT 1, Instructor 0

    Category: teaching

    It's hard to teach bioinformatics when schools work so hard to keep us from using computers....

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    October 21, 2007

    Fall bioinformatics class: welcome students!

    Category: Bioinformatics

    Welcome Bio256 students! This quarter, we're going to do some very cool things. We are going to use bioinformatics resources and tools to investigate some biological questions. My goal, is for you to remember that these resources exist and hopefully, be able to use them when you're out working in the biotech world. I don't believe that bioinformatics is a...

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    October 17, 2007

    Help for educators with exploring new worlds

    Category: teaching

    If like me, you were a little disoriented and confused when you visited Second Life and traveled through orientation island, then you may like this....

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    October 16, 2007

    The real cost of J. C. Venter's genome

    Category: Bioinformatics

    A few weeks ago, I did some "back-of-the-envelope" calculations to explain to a reader why genome sequencing costs so much. I estimated that, if JCV's genome were sequenced at the cost advertised by university core laboratories, his genome would cost about $128 million. That was an estimate, of course. But what did it really cost?...

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    October 15, 2007

    ScienceBloggers in Second Life

    Category: Science education

    Our adventures with presenting posters in Second Life.

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    October 14, 2007

    How to attend a poster session in Second Life

    Category: Science education

    Bora and I are giving posters in Second Life. Here's how you can attend.

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    Mendel's Garden: Halloween Edition

    Category: Genetics & Molecular Biology

    October is a month of darkness, mystery, and dread. Only one holiday brings joy in October and even then, October joy is distilled through fear and apprehension. In the early evenings the sun hurries home and once familiar objects loom ominously in the dark. Giant spiders appear out the fog, lurking on webs that span our walkways and doors. Even...

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