Save Our Schools March

This is not directly biology related, but it affects all of us. I encourage everyone to try and make it to the rally listed below. Details will be forthcoming, but all of our classrooms are being affected by state and national policy, often to the detriment of our students. This rally is nation-wide. Kansas’ will probably be in Topeka. Will post again when I know specifics. Put this on your calendar and spread the word to others.

Kansas Families for Eduction is participating in the Kansas observance of the Save Our Schools March & National Call to Action on July 30. Across the country, people will march in Washington and in state capitals to demonstrate their support for our public schools and the vital role they play in our economy, our democracy and our future. More details on the Kansas effort will be coming soon, but in the meantime, save the date, and more importantly, SPREAD THE WORD: Post this on your social networks and use good old-fashioned word-of-mouth to make sure everyone knows about this important event. We need a BIG turnout to this non-partisan event to show the politicians that we want strong public schools and an end to the severe, short-sighted budget cuts that are threatening our ability to compete. Click on the link below for more information about the national effort.

More on “Spring Swarm”

Earlier today, I heard a wonderful NPR story by Robert Krulwich that provides a more extended and experimental discussion of bee swarming behavior that I blogged on a few weeks ago.

His story is called “Nature’s Secret: Why Honey Bees are Better Politicians than Humans.”  It’s only 7 minutes in length and really provides interesting insight on this beehavior.

Planet Of Viruses

I just finished reading Carl Zimmer’s newest book, A Planet of Viruses.  When the book arrived and I realized its viral stature (a mere 94 pages containing 4 sections with 12 chapters and images) I was a bit saddened.  Having previously read Microcosm, on the biology gleaned from the science of studying E. coli, I was primed to delve into the practice of virology and didn’t think 94 pages could deliver the fix I desired. 

Well, having read the book, I still can’t say that it did.  But is wasn’t a waste of time either.  Here are a few thoughts…

  • Each chapter informs about a particular virus or group of viruses and is written with an expected passion for the history and science.  The chapters are a bit too succinct though.  You get drawn in to the story that is being told only for it to finish too soon.  In fact, the chapters average just over 6 pages in length (some 76 written pages in total).  Each chapter is a wonderful stand-alone story that shares specific researched insights that could inform any class discussion of the world of viruses, and may make a good introduction for students and lay people alike. 
  • The book has a more general trajectory as well, progressing from our initial awareness of viruses (via Tobacco Mosaic Virus), through old companions (Rhinovirus, Influenza Virus, and Human Papillomavirus) and their ubiquity (Bacteriophages, Marine Phages, and Endogenous Retroviruses), to more recent epidemics and issues of eradication (HIV, West Nile Virus, SARS and Ebola, and Smallpox).  The layout fully supports the title’s claim, and Zimmer presents an apprecaited and new perspective on the viruses as a necessary and integral part of the living world.

I took some time looking around for some more literary reviews of the book to share (NY Times, etc…), but I couldn’t find much more than book sellers and other useless links.  Here the few that I found…

The book was born from a more general project led by the University of Nebraska at Lincoln called the World of Viruses.  This site is still in development but appears to have the goal of supporting some curricular materials on viruses in the future.

In summary, I enjoyed and learned enough from Carl’s new book to make it a worth while read, although I expected much more.


This morning, I saw a twitter post on an interesting new free phone app.  Here is a brief video on the app posted at YouTube:

and here is what the developers say on their website:

Leafsnap is the first in a series of electronic field guides being developed by researchers from Columbia University, the University of Maryland, and the Smithsonian Institution.  These researchers are working on visual recognition software to help identify species from photographs. Leafsnap is the first in a series of electronic field guides being developed to demonstrate this new technology.  This free mobile app helps identify tree species from photographs of their leaves and contains beautiful high-resolution images of their flowers, fruit, petiole, seeds, and bark. Leafsnap currently includes the trees of New York City and Washington, D.C., and will soon grow to cover the trees of the entire continental United States.

Leafsnap turns users into citizen scientists, automatically sharing images, species identifications, and geo-coded stamps of species locations with a community of scientists who will use the stream of data to map and monitor the ebb and flow of flora nationwide.

The genesis of Leafsnap was the realization that many techniques used for face recognition developed by Professor Peter Belhumeur and Professor David Jacobs, of the Computer Science departments of Columbia University and the University of Maryland, respectively, could be applied to automatic species identification.Professors Jacobs and Belhumeur approached Dr. John Kress, Chief Botanist at the Smithsonian, to start a collaborative effort for designing and building such a system for plant species. Columbia and the University of Maryland designed and implemented the visual recognition system used for automatic identification. In addition, Columbia University designed and wrote the iPhone, iPad, and Android apps, the website, and wrote the code that powers the recognition servers. The Smithsonian was instrumental in collecting the datasets of leaf species and supervising the curation efforts throughout the course of the project. As part of this effort, the Smithsonian contracted the not-for-profit nature photography group Finding Species, which collected and photographed the high-quality photos available in the apps and the website.

Once downloaded and opened, one can challenge oneself to one of a number of identification “Games”, “Browse” the current field guide of 184 plants, set particular “Options”, and take a picture using the phone’s built in camera that should automatically upload to the leafsnap database via “Snap It!”.  Once you have uploaded images, I assume you can view your own “Collection”.

Once you are browsing, you can view the species contained in the app using their common or scientific name, in a manner familiar to iPhone users and also used by National Geographic’s bird identification app.  By clicking on the image icon in the upper left-hand corner of this screen, the app toggles between displays of a representative leaf, flower, or fruit associated with each tree specimen, a nice feature that could help to confirm one’s hypothesis of identification.


Once you select a particular species, you can view a collection of detailed images of the trees leaves, flowers, fruits, seeds, and bark, or use the image icon in the upper right-hand corner to toggle to a dispaly basic information on the species being viewed.


The games section includes timed quizzes that test one’s ability to identify tree specimens by leaf, flower, or fruit in the “Leaf Challenge”.  The second image below is a screen shot of this game.  The name of the tree leaf to identify with a finger tap is noted, while the number correct and time left are noted in the upperleft and right-hand corners of the screen, respectively. 

In “Green Sweep” you are given four leaves to identify that are floating around the screen.  You identify each by moving them into their appropriately labeled square, with a touch and a drag.  If correct, it challenges you with another four leaves to identify, and continues in this manner until your time is up.  Each of the game categorizes your exepertise based on your score at the end of the game.


In using “Snap It!” the app uses the phone’s built in camera to take a picture which is then uploaded for identification by the recognition software described previously. 

Sadly, I have not been able to get this function of the app to work completely.   I went out a tried to take a picture of a redbud leave only to realize that your are supposed to take the picture of the leaf on a white background (I hadn’t read the top of the screen).  The app realized this though and informed me which was demonstrates its sophistication. 

After correcting this mistake, I had issues with the app crashing when I took a picture within the app.  So, I exited the app and took the picture within phone’s camera app, and selected to chose that image from within leafsnap.  This time, I experienced crashes while the app attempted to upload the image for identification.  I even changed the image resolution to small in the options setting to no avail.

With the number of people working on this app, I imagine that such problems will be solved in a short time.  I only wish they had a way to report bugs via the app or on their website.  If and when I get this aspect of the app working, I will edit the post and make a comment to report changes.

I look forward to using this app with my students!


Since the time of the orignal post, I e-mailed leafsnap, noticed that an update was posted on twitter, downloaded the update, and tried to upload an image of a Redbud from my back yard again.  This time it worked!


After uploading the image, it loads results to your phone.  The results are ordered, I assume by some probability of it being a match with the outline of the uploaded leaf image (you can see the top three results in the middle image above).  If you click on the “map” button at the top of the page it shows where the leaf was collected (dang, now you know where I live).


To verify a particular result, one finger swipes across the chosen selection to bring up the red label button (first image above), and selects the “label” button by touching it (second image above).  Once this is done, the labelled image now appears in your “Collection.”

Pretty cool! 

Now, I challenge you to be the second to add an image from the Kansas landscape!

Johnson County Science Cafe

Johnson County Science Cafe’

What studying little worms can tell us about human diseases: or why NIH spends your tax dollars to learn about a worm’s sex life

Speaker: Dr. Matthew Buechner, Cell Biologist, Dept. of Molecular Biosciences, Univ. of Kansas

Date: May 17, 2011

Time: 6:30 pm

Location: Coaches Bar and Grill, 14893 Metcalf, in private room

The Human Genome Project is finding out the location of thousands of mutations that cause genetic diseases in people.  But we don’t know what the “disease genes” normally do until we compare them to similar genes in other organisms, including mice, fruit flies, and roundworms, the topic of tonights’ talk.  Some of those diseases include diabetes, muscular dystrophy, and polycystic kidney diseases.

Dr. Buechner uses genetics to study mutations that affect kidney tubules and the nervous system .  He has won several teaching awards, including the HOPE Award for outstanding teaching at KU.

For more information:

Orchid in Flower

Early this morning I checked on one of the showy orchids–the buds were finally open.


Challenge:  What’s that hairy, little thing, on the ground, in the lower right hand corner of the photo above?

Here’s a close up:

Spring Swarm

An Animal Behavior Challenge!

Earlier this week, Jim, a previous neighbor of mine, called to inform me of an interesting “natural event” that was taking place in a shrub next to his driveway. 

Here is a video of that event up close.  He had been out performing yard work in the past days and was sure that these bees had shown up over a short period of time.

I an effort to find out what exactly was happening and what he could do, Jim called his mother, who called her neighbor (who happened to be a master gardener), who then contacted Jarrett Mullenbruch (pictured below) who happens to be a sculpter with an interest in ecology, and who is currently working on an installation that integrates live bees. 

Once Jarrett arrived, he proceeded to talk to us about his Deep Ecology Project and then collected the bees for his installation.   To view a pdf slideshow of the images that I took, click on the image above.  You can view a collection of videos documenting the collection of the bees below.

Thanks for letting me in on the experience Jarrett and Jim!

Now for the Behavioral Challenge…

  1. How many bees would you estimate are in this swarm?
  2. Can you explain why the bees are engaged in this behavior in the first place? 
  3. Why is a bee hanging around the container full of bees in the third video?

I imagine that students could generate numerous questions that would stimulate quality discussions of this interesting animal behavior…

Providing some interesting links to resources or websites that could help students uncover the details of this natural event would be welcome as well.

Teaching Food Safety through Food Science

Professional Development at the International Animal Health and Food Safety Institute
at K-State Olathe Campus

When: June 13-16, 2011, from 8:00 am to 5:00 pm
Who: Middle and High School Teachers
Application Deadline: May 13

Classroom and laboratory instruction focusing on:

  • Food safety and food borne illness prevention
  • Chemistry and microbiology of food
  • Food safety and public health career pathways
  • Field experience in industry & horticultural settings

The lessons will be led by researchers from KSU, and participants will be taking field trips to Sysco, Danisco, and The K-State Research and Extension Horticultural Center at Sunflower as well.

The workshop includes a $1000 scholarship to offset potential expenses, and can be taken from for Graduate Credit.

See the following Flyer or website for more details, and contact Roberta Robinson at or 913.307.7316 with any questions.