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I eat genomes for breakfast
And so do you.Posted on April 4, 2008 12:45 PM • 21 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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Recent Posts
- 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
- The snake rescuer
- A molecule for May
- A vaccine against lung cancer?
- Comparing mutant and wild type structures
- The Personal Genome discussion
- The wonders of webinars
Recent Comments
- Sandra Porter on Workforce shortages in biotechnology, part I. Why is this a problem?
- Deepak on Workforce shortages in biotechnology, part I. Why is this a problem?
- Jan Miernyk on Would your class like to clone and sequence plant genes?
- Brian M. 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?
- Deepak on Workforce shortages in biotechnology, part I. Why is this a problem?
- Martin Robbins 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?
- Becca on Workforce shortages in biotechnology, part I. Why is this a problem?
- Sigmund on Would your class like to clone and sequence plant genes?
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Basics:
How do I love thee SQL? Let me COUNT the ways. Number 1...
I love the way you show me secret things. All I do is type: Select * from name_of_a_table And you share everything with me. Without you, my vision is obscured, and all I see is the display on the page. In fact, this was the push that finally made me decide to learn SQL....Posted on February 16, 2008 7:42 PM • 3 Comments •
Genetic Variation I: What is a SNP?
If you've read any of the many stories lately about Craig Venter or Jim Watson's genome, you've probably seen a "SNP" appear somewhere. (If you haven't read any of the stories, CNN has one here, and my fellow bloggers have posted several here, here, here, here, here, and here.) You may be wondering, and rightly so: just what is a...Posted on September 5, 2007 10:35 AM • 4 Comments •
Learning styles and science labs
Science labs are not for all people.Posted on March 31, 2007 7:44 PM • 7 Comments •
What made me sick?
How do microbiologists determine which microbe caused a disease? As Tara has eloquently described (I, II), we are covered with bacteria and other microbes. A reasonable question then, is when we get sick, how do we which little devil deserves the blame?...Posted on February 17, 2007 3:29 PM • 7 Comments •
What are hypothetical and putative proteins?
"Beware the Jabberwock, my son! The jaws that bite, the claws that catch! Beware the Jubjub bird, and shun The frumious Bandersnatch!" - from Jabberwocky, by Lewis Carroll I'm certain that if we ever sequenced DNA from the frumious Bandersnatch it would match hypothetical and putative proteins....Posted on February 8, 2007 3:17 PM • 1 Comments •
Sequencing a Genome, part VII: Want to win $10 million dollars?
How to win the X PRIZE in genomics In October, 2006, the X PRIZE foundation announced that second X prize would focus on genomics. The first team to successfully sequence 100 human genomes in 10 days will win $10 million dollars. And I would venture to guess, that the winning team would also win in the IP (intellectual property) game...Posted on February 5, 2007 9:00 AM • 2 Comments •
Biology as a second language: what is a vector?
Defining a biology term for scientists in other disciplines.Posted on February 2, 2007 2:23 PM • 6 Comments •
Sequencing a Genome, part VI: Chimeras are not just funny-looking animals
Chimeras invade the sequencing lab!Posted on February 1, 2007 6:01 PM • 0 Comments •
Sequencing a Genome, part V: checking out the library
Send in the clones, but only the random ones.Posted on January 31, 2007 1:02 PM • 2 Comments •
Basics: How do you sequence a genome? Part IV. How many reads does it take?
"How deep is the ocean? How high is the sky?"Posted on January 30, 2007 4:49 PM • 2 Comments •
Basics: How do you sequence a genome? part III, reads and chromats
In which we define reads, chromatograms, and shotgun sequencing.Posted on January 28, 2007 8:51 PM • 2 Comments •
Basics: How do you sequence a genome, part II
Some background on the strategies: mapping vs. shotgunPosted on January 27, 2007 1:50 PM • 2 Comments •
Basics: How do you sequence a genome?
Ask Dr. Science: yes, I do take requests.Posted on January 22, 2007 8:59 AM • 7 Comments •
What is a gene? My definition is better
In the effort to help us define a few basic concepts, PZ started out by giving us a nice simple definition of a gene, but as he, rightly noted: I tell you right now that if I asked a half dozen different biologists to help me out with this, they'd rip into it and add a thousand qualifiers, and it...Posted on January 21, 2007 3:44 PM • 7 Comments •
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...Posted on January 4, 2007 8:28 AM • 0 Comments •
Five paths to antibiotic resistance: a quick summary
How do I resist thee? Let me count the ways.Posted on January 3, 2007 8:04 AM • 0 Comments •
Are antibiotics really only made by bacteria and fungi?
Is it really safe to pierce your tongue?Posted on January 2, 2007 9:00 AM • 5 Comments •
Antibiotic resistance: How do antibiotics kill bacteria?
Part III in a multipart series on antibiotic resistance.Posted on December 30, 2006 5:30 PM • 5 Comments •
There's no place like "ome"
A quick guide for the omically challenged.Posted on December 1, 2006 1:35 PM • 18 Comments •
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....Posted on November 29, 2006 8:00 AM • 1 Comments •
A primer on antibiotic resistance, part I: what are antibiotics?
Antibiotics are molecules of biological warfare. Produced by bacteria and some fungi, in response to extracellular signals, antibiotics represent a diverse group of compounds that inhibit bacterial growth at different points and different stages of the life cycle. We will get around to antibiotic resistance, but in these few words, I think I already wrote quite a bit. Admittedly, some...Posted on November 28, 2006 10:21 AM • 3 Comments •
