Halobacterium sp. NRC-1 “How To” document

Hello all,

Thanks for the fun yesterday!  This link will take you to a word doc with everything I could think of to help you with Halobacterium in your classroom:  KABT handout post online

If you do use Halobact, pop me a note or post a comment so I can update the list of possible activities.



Avida-Ed: Exploring Evolution in Silico

At the NABT Conference in Atlanta in the fall of 2007, Brad Williamson talked me and a few others who were loitering around to come to a workshop presentation on Avida-Ed software as a means of fostering inquiry of evolutionary processes.  After the presentation, Brad suggested that I write a post about the experience.  At the time, I didn’t have much to say.

Having had time to play around with Avid-Ed and to make my way through most of the unedited model lessons downloadable from the Avida-Ed website, I have decided to make the post.  The best place to start is to download the software developed by Robert T. Pennock from the Avida-Ed website at Michigan State University, and to read the Discover magazine article written by Carl Zimmer highlighting Robert Pennock’s development and use of the research version of the software to study the process of evolution (The first activity below has pre-activity questions that require students to read this article).  The links below will get you that far.

  1. Avida-Ed Website
  2. Testing Darwin by Carl Zimmer in February 2005 edition of Discover magazine.

If you are a self learner, after downloading the Avida-Ed, open it, drag the @ancestor into the black area of the Petri Dish window to the right, select the play button, and have fun.  Otherwise, keep reading…

Well, as I said, I have had the time to make my way through the unedited model lessons posted on the Avida-Ed website.  In effort to prepare to introduce my freshman honors biology and AP Biology student for the software, I have cut and pasted, edited, and created (in some cases) more detailed step-by-step instructions for the activities presented in their models lesson.  In a few cases, I have even collected and attached data in a teachers section at the end of the student friendly documents that help you understand what the students will be doing prior to your own exploration of the software.

Explorations in Evolution Series

  1. I – Introduction to Avida-Ed
  2. II – Observing an Instance of Evolution in Avida-Ed
  3. III – How do Resource Availability & Mutation Rate influence Avidian Fitness?
  4. IV – Observing Mutations in the Genomes of Evolving Avidians
  5. V – Common Misconceptions of Evolution

I look forward to your comments and criticism of the activities but realize that I am just beginning to use these activities in my class for a second time.

As a justification for activities such as these, if you take the time to read the Bio2010 published by the National Academies as well as the most recent bulletin from HHMI (read Thinking like an Engineer and Add 56), you will quickly learn that we should be doing more to motivate our keen biology students to appreciate the importance of other scientific perspectives (mathematics, computer science, physic and engineering).  Similarly, we should be reaching out equally to those that are already bent toward study in these other fields and show them that they can fulfill there interests while helping to make new discoveries in the biological sciences.

Download the non-education version of Avida.


Facebook and Frameshift

I don’t know about you, but I timidly joined facebook last fall to begin my journey in learning how this social networking resource might be of use both personally and professionally.  

Happily, I have discovered that there are educational relevant uses for facebook!  I will write a extended blog post on how I use it with students in the near future but today I read something on my facebook home page that I thought I should pass along.

As a member of facebook, one can join groups and follow updates on other people’s pages.  Some of these people happen to be practicing scientists or others on the periphery of the science community.  One individual I happen to follow is Carl Zimmer.  Most of you are familiar with Carl’s collection of quality books.   If you aren’t a member of facebook, you can follow his blog via his website (which links to the Discover’s blogsite – my how connected things are – if you have your own website you can add it with an RSS feed – maybe KABT should consider this).  

Well, the cool thing about reading Carl’s blog is that you are kept up-to-date on his insights into the active world of science, and don’t have to wait a year or two for such insights to be integrated into his next book.


In one of his posts from yesterday, Losing Teeth, but Keeping Genes, he reviews a recently published article Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals from the online journal PLOS Genetics.    Here is the gist of the story from Carl:

Their results were pretty much what they expected, but they’re still pretty amazing. There were no frameshift mutations in ENAM among the mammals with teeth. But 17 out of 20 species without teeth or enamel had at least one. In all 20 enamel-free species, a stop command (known as a stop codon) was present. These genes are shot.

I am certain that you all teach about “frameshift” mutations.  The two resources above could become additions to your bag of supplemental tricks that make such concepts come alive for your students.  They can also help in your integration of evolutionary biology throughout the curriculum, and to supplement topics like “adaptation, pseudogenes, purifying and neutral selection, molecular clocks, and radiation and convergent evolution”. 

Enjoy reading, and maybe I’ll see meet you in facebook someday soon!