KABT BioBlog

MapFinder: A USGS Topographic Map Index

“MapFinder for Google Earth is a “.kmz” application that loads into Google Earth and shows the 7.5 minute quad USGS topographic map boundaries for the lower 48 states.  Each boundary has an identification point that givse you information about the USGS topo map.  This information includes the map name, scale, year, projection, and contour interval.  The most exciting feature of this application is that there is a download link that enables you to download the topographic map for free.”

Here are the steps:

1. Download Google Earth at http://earth.google.com/download-earth.html.
2. Download the MapFinder file at http://www.usgsquads.com/mapfinder.html.
3. Browse to and open the “.kmz” file from within Google Earth.  When it opens, you will notice a menu within Google Earth that allows you to choose a state of interest.
4. Once you have chosen a state, zoom in on that state and you will see the topographic map boundaries, each with a clickable blue information symbol.  Hover over a particular information symbol, and you will see the name of that topo map.  Upon clicking, a web page will open, where you will see a link to download a tiff file of that map.
5. The tiff file is your free digital copy of the topographic map.

Have fun exploring the US digitally, but I hope these maps give you the knowledge to explore in the real world as well!

A few months ago, I spent quite a bit of time searching for science related apps that could potentially be useful for my life as a biology teacher.  I have downloaded a number and have had the opportunity to discover those that I have found most useful (or potentially useful) in that role.

The main post contains a list of 16 iPhone apps.  Each app icon is followed by a brief description and links that may be helpful for you in making a decision on acquiring the app.   For those that I have found especially useful, I discuss specific manner(s) it has been used.  Furthermore, if you don’t have an iPhone some of the producers of these apps have websites that may be useful as well.

For those unfamiliar with iPhones, these apps must be acquired through the apps store in iTunes so in many cases there are not internet links to pages with further information on these apps.  To learn more, download iTunes, and search the app names in the iTunes store, or google search and read what you can find.

Happy app hunting…

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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.

Enjoy!

Facebook
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.

Frameshift

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!

While learning about those involved in developing the Synthetic Biology survey that some of you may have taken (June 8th post), I serendipitously navigated to a page at Davidson College that made me aware of the Microarrays MediaBook educational website.  Here is what I read, including the link that I chose to follow…

Another of Malcolm Campbell’s efforts, a multimedia presentation entitled “MicroArrays MediaBook,” has received the international Pirelli Award as the “Best Work for Educational Institutions.” Created with collaborators at UNC Chapel Hill, the MicroArrays MediaBook shows students how microarrays are created and analyzed, and applications of the technology. Its graphic sophistication commands attention, and students can test their understanding of the material with questions for each section.

Here is a shot of the homepage with their extensive internal links.  I agree that the “graphic sophistication commands attention”.  I’m still checking it all out and already know that if you touch upon Microarrays in your classroom you should spend sometime this summer checking it out as well…

http://gcat.davidson.edu/Pirelli/index.htm

Here is an paper activity that I have used to teach about Microarrays, a link to the article that I use with the activity, although I think I will be modifying things so that students can use the MediaBook resources instead.  For those beyond a paper activity, Fotodyne has microarray kits for exploring smoking and plant photobiology, and the Genome Consortium for Active Teaching (GCAT) has a wealth of information and resources for developing authentic microarrays (also developed by Malcolm Campbell).

As my father always says, enjoy!

eBird Home Page

Saturday morning, I got up early and headed over to a program presented by Chris Wood, sponsored by the Topeka Audobon folks and hosted by Janeen Walters at Washburn Rural Middle School.   Now I am a geek but the topic had to have a lot of promise for me to give up my Saturday morning cinnamon roll and the promise was more than fulfilled.  Chris Wood works with the eBird program at the Cornell Laboratory of Ornithology.  I’ve got to say from years and years of working in the field of citizen science I was not expecting to be wowed but I was.  My expectations were tempered by the years of struggles trying to figure out how to encourage volunteers to submit, good quality data in a way that benefited the citizen scientist as well as the professional scientist–all the while trying to keep things inviting and exciting for recruiting new folks to participate.   Steve Case and Tom Baker put together a good web based infrastructure to support the Pathfinder science project but today’s Web 2.0 tools take collaboration to an entire new level, creating an environment that can promote and support powerful web-based efforts in conservation science.  eBird provides an exemplary example.

If you are a biology teacher that provides any instruction in or encourages birdwatching or if you are a bird watcher yourself eBird is something to really consider.  I’m not a lister but I think I’m about to start–only because my effort can significantly contribute to a larger effort.  I’m really more of a nature observer–birds just happen to be a convenient focal point.  I have participated in Christmas bird counts and have made a number of reports to the Kansas Bird List about observations and sightings but in general I’m not a hard-core birder.  That is the beauty of eBird.  A more casual birder like myself with just a bit of extra effort to record my sightings can make really significant contributions to a data  base of bird observations while a more intense birder can have a huge impact.  eBird makes it easy to record your sightings and their locations.  eBird simply works for all kinds of birders.

Data input

In fact, I learned from Chris that researchers accessing the data have developed very sophisticated algorithms to take into account your personal bird watching habits.  For instance, I might be hesitant to participate because when I bird in the spring, I’m primarily looking for warblers.  I’ll note the sparrows and such now, but my effort is going to be focused on the warblers.  Well guess what,  the filtering tools will note this correct for this.  That is good because I wouldn’t want my lack of focus on sparrows to indicate that they weren’t there when they probably were.  (That could create conservation issues.)  This is powerful.

Here’s the deal, though.  One of the reasons that Chris came to KS is that we have only a few folks signed up and participating in eBird.  Notice if you go to the site we are not in the top 30 states for observations reported this year, in fact as of this morning there were only 117 observations turned in this year.  The key to this overall effort is large numbers of observers.  For instance here’s part of a bar chart of bird occurrence in Johnson County.

eBird Chart

Because of the numbers involved and the data base is a very rich resource for professional researchers.  The professionals are benefiting and we are learning more and more about our birds.  More importantly, as an educator think of the advantages eBird can offer you and your students to collect and help make sense of observations made from year to year, season to season–all the while contributing to the larger research community.  Think about it, create an account and start to contribute–I am.

 
This post is meant to inform those unable to attend the Dolan DNA Learning Center workshop Inside Cancer at the Stowers Institute today, which unfortunately I can now count myself among since I woke up under the weather the morning of the workshop and didn’t attend.  So, if there is anything that needs to be added to this post, those in attendance feel free to make extensive comments.

Through brief communications with Larry Hare, I learned that besides learning about the Inside Cancer website, they were introduced to the Inside Cancer Teacher Center, where, after registration and login, a teacher can build a classroom presentation selecting from the multitude of resources contained at the Inside Cancer website, develop and share lesson plans that one has developed in association with teaching about cancer with a broad community, and digitally align the lessons that one has developed with national standards.

Inside Cancer Website

Inside Cancer Teacher Center

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This post is meant to inform those unable to attend the Dolan DNA Learning Center workshop at the Stowers Institute on Genes to Cognition.  This is a site that you will want to delve into when you have a bit of time on your hands.  Well, that is if you are interested in learning and teaching about the connect between genes, cognitive behaviors, and their related brain disorders. 

The student-friendly essential question that this site helps students and teachers to explore is, “What good is a brain?” 

In all honesty, the site reminds me of Thomas Huxley’s book The Crayfish through which he demonstrates that the subject of zoology could be taught via a single model organism. 

In a similar manner, Genes to Cognition facilitates the teaching of biology at all levels of complexity, from the molecular communication networks of our cells to the behaviors that emerge from their collective actions.  At the same time, students will realize that there are numerous unanswered scientific questions awaiting research.

Having had little time to digest the material presented, I currently don’t know where I will integrate Genes to Cognition into my courses but “What good is a brain?” it is quite an appropriate question for students to ask and begin to explore.  The site is presented from a perspective that, on one hand acknowledges the importance of the reductionist approach, while fostering the burgeoning systems based perspective.

Genes to Cognition Website

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Here’s the google map to the Fall KABT meeting. I dropped the pin in the parking lot. If you click on larger map and zoom out, you’ll be able to “ask for directions” from your address to KU up at the top of the map. See you Saturday.

BW

View Larger Map

From Charlie Drewes Website (click to go there)

Here’s my favorite lab for the beginning of the year: Blackworm Lab

I modified information and labs from the iconic Charlie Drewes, formerly of Iowa State University, and Randy Dix of Olathe North High School and gave it a special twist I learned from Sandy Collins of West Junior High in Lawrence. For further information on Lumbriculus variegatus you can visit Charlie Drewes’ website which is still being maintained at the university and is a treasure trove of labs and activities with invertebrates.

Charlie Drewes’ Website

From Charlie's web site (click to go there)

Sandy’s idea that I love has students creating labs and experimenting with organisms they believe are being exposed to stimulants and depressants. After they have all completed the lab you tell them that although the water containers were labeled differently, there was no actual difference in the water. I find we can then launch into rich discussions of the reasons for blind and double blind studies AND how some of the greatest discoveries have come about when scientists got unexpected results and strove to understand and uncover what had really happened.

I also find that during the lab some students get data they believe to be wrong (no difference in pulse rates between the groups). They come to me and ask what is wrong – I use the opportunity to ask them if they were very careful in their technique, if they assure me they were I tell them they should trust their data and try to understand it. It’s fun to have students who think they’re getting poor data get rewarded in the long run with praise for having the most accurate results. (I also give a 5 pt bonus for getting good results and recognizing them.)