I have created a document on HOW TO CREATE AND PUBLISH A BLOG POST on the KABT website for teaching those needing a little guidance.  I hope it helps.  If you have any questions, etc… please feel free to contact me.  I’d be glad to offer advice and encouragement.

Happy Blogging!

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 leafsnap.com 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!

Addendum:

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!

Recently, I have been following Ed Yong on Twitter and was intrigued by his post, Research into reprogrammed stem cells at his blog, Not Exactly Rocket Science, housed on the Discover Magazine website. 

What intrigued me? 

Well, the “timeline” that he created for this post using the online generator at Dipity. 

I assumed that this online tool was pretty user friendly and I took a short time tonight to create a sample timeline containing one-event (Ed’s contains 25 with links to his history of blog posts on the topic), and a 3-page document with directions and screen shots for Creating a Timeline using Dipity.  For those that have used the Dolan DNA Learning Center’s DNAi website timeline to support student understanding of the history of molecular biology, Dipity will allow your students to demonstrate higher level learning through creating their own understanding of such history.

I don’t know what I am going to have my students create yet but this is definitely a tool worth exploring, and I am certain that students will have an enjoyable time being creative with Dipity. 

Enjoy!

American Scientist Pizza Lunches are informal lectures where scientists present new research to an audience of non-scientists.  The talks are hosted in Research Triangle Park, North Carolina, at the headquarters of Sigma Xi, the Scientific Research Society, the publisher of American Scientist magazine.  Originally intended to help inform local science communicators about current and controversial topics, the Pizza Lunch talks are now available to anyone online, and new talks are posted periodically during the academic year.

Download individual talks through following the links below (clicking on the image above will take you to the general Pizza Lunch Podcast website).

1. Whole Genome Analysis in the Clinic
   James Evans, clinical researcher in genetics at the University of North Carolina
   Evans urges us to support genomics medicine research but asks us to temper our enthusiasm until it becomes a proven tool. (April 20, 2010)
2. Genomic and Personalized Medicine
   Geoffrey Ginsburg, director of the Center for Genomic Medicine, Duke University
   Ginsburg presents advances and ongoing research in personalized medicine, from prescribing cancer drugs to predicting flu symptoms. (March 30, 2010)
3. Metapopulation Dynamics of Oyster Restoration in Pamlico Sound, NC
   David Eggleston, director of the Center for Marine Science and Technology, North Carolina State University
   Eggleston discusses the challenges of conserving and restoring North Carolina coastal ecosystems, particularly oyster reefs. (January 26, 2010) 
4. An Empire Lacking Food: The Astonishing Existence of Life on the Deep Seafloor
   Craig McClain, assistant director of science, National Evolutionary Synthesis Center
   McClain explores how the meager availability of food on the deep seafloor shapes the ecology and evolution of the animals that live there. (December 15, 2009)
5. The Evolution of the Human Capacity for Killing at a Distance
   Steven Churchill, professor of evolutionary anthropology, Duke University
   Churchill presents his research on the evolutionary origins of projectile weaponry, and how weapon use changed interactions between humans and other species—including, perhaps, the Neandertals. (October 20, 2009)
6. Our Energy Future: Science and Technology Challenges for the 21st Century
   Thomas Meyer, director, Solar Energy Research Center, University of North Carolina, Chapel Hill
   Meyer discusses the status of the world’s energy supply. In particular, he presents the idea that the sun’s energy could be used to make fuels from water and carbon dioxide for heating, transportation and energy storage. (September 24, 2009)
7. Everything Is Dangerous: A Controversy
   S. Stanley Young, director of bioinformatics, National Institute of Statistical Sciences
   Young critiques statistical analysis by some epidemiologists, especially their multiple testing of data sets obtained from observational studies. (April 22, 2009)
8. From Cloning to Stem Cells: How Can Pigs Help Us Solve Problems in Human Medicine?
   Jorge Piedrahita, professor of genomics, North Carolina State University College of Veterinary Medicine
   Piedrahita describes his research with cloned swine and how their abnormal growth provides insight into human placental defects, the ways transgenic pigs may help grow human tissue and how pigs could help advance stem cell therapies. (March 25, 2009)

I discovered this site via a twitter link today and thought it might provide another means of bringing scientists, although virtually, into the classroom.  Otherwise, if you don’t have a subscription to the American Scientist, it is one of my favorite periodicals.

Click on the image above to access this unique NPR Resources containing

• 4 Interactives on Brewing a Human, An Upright Primer, Lost Cousins and Fossil Forensics (the last two are a small portion of the Smithsonian Human Origins Initiative)
• A collection of 20 NPR audio stories previously broadcast on Morning Edition or All Things Considered that provide an eclectic and pretty comprehensive prespective on human evolution.  Topics include, skin color, walking and running, tools and weapons, diet, brain development, talking and language, culuture and belief systems.

I have not used this resource in class having just noticed it while preparing my previous post on the NPR Science site.  If you have used it before and have particular suggestions on its integration please share your experiences with a comment.

This morning, while browsing through science related twitter posts, I became aware of Google Lab’s new Body Browser, at http://bodybrowser.googlelabs.com/. 

After downloading the Google Chrome browser, which appears to be required for the use of this website, I played around a bit, and took a few screen shots so that you could see what is available. 

The format is similar to Google Maps or Google Earth with regards to the clickable tool allowing one to zoom in and out, and to rotate left, right, up, and down.  Underneath this tool, is a sliding bar with icons for the different systems of the  human body.  As one slides the bar vertically through the icons, the human body progressively displays each system with the current system becoming more transparent as you pass into the next.  The systems are not identified but correspond to the external body, muscular system, skeletal system, internal organs, circulatory system, and nervous system (see the screen shot images that follow).

External Body

Muscular System

Skeletal System

Internal Organs

Circulatory System

Nervous System

As you can see in the next two images, you can zoom, turn on labels at the bottom of the sliding bar, and select a particular labeled item of interest.  Once selected that item will be highlighted relative to the surrounding tissue.  At the moment there aren’t links to information about the particular body parts you select, but I imagine that that will be in a future version.  Click here if you want to give Google Labs feedback and suggest features that would be useful to you.

Nervous System zoomed in on the Brain with Labels On

Image of the Obicularis Oculi muscle selected

Beside viewing the human body in the manner described above, one can selectively adjust the relative transparency of each layer at the same time as well.  To select this second option, click on the oval icon having three vertical lines, just above the labels selection.  Once completed, this displays a sliding bar for each system.  The following image is a screen shot showing such an image.

Viewing Multiple System Layers

While preparing this blog post, my 1st grade son said, ”We could see all this better if we cut open a person”. 

At first, I hestitated acknowledging the comment wondering if he had been exposed to too much violence on television.  But after a pause, he added, “The person could be dead already.” 

I asked, “Where could we get a dead person?”

He suggested, “A junk yard.” 

Having been to a funeral recently, I reminded him that most humans bury their dead, and that it would be against the law for one to dig up a grave.

I added though that Andreas Vesalius did just that in the 1500′s!

I imagine he might be proud of Google’s new Body Browser, as well as my son’s insight.

“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!

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…

Apps for Keeping Abreast of Biology

 NPR News (free)

NPR is a wonderful resource for science related news.  This handy app catalogs the most recent science related broadcasts from the diversity of shows that contain such content, from Morning Edition to Science Friday.   So, if you, like me, often hear an interesting segment that could be used as a nice springboard for student discussion, but rarely have time to find the show on the NPR website, this app is for you.  View the youtube video produced by NPR to introduce the functionality of this app, or read about it at this NPR website.  

I have found the “playlist” most helpful in setting aside links to the audio segments that I may share with my students days or months later.  So that your playlist doesn’t become to too cumbersome over time, I would suggest searching the NPR website for the show and downloading its audio file for future reference.

Science Friday by Ira Flatow also has its own stand alone app as well if you want to be able to more easily manage

 TED Talks (free)

As stated on their website:

TED is a small nonprofit devoted to “Ideas Worth Spreading”.  It started in 1984 as a conference bringing together people from the three worlds of Technology, Entertainment, and Design (TED).  We believe passionately in the power of ideas to change attitudes, lives and ultimately, the world.  So we’re building a clearinghouse that offers free knowledge and inspiration from the world’s most inspired thinkers, and also a community of curious souls to engage with ideas and each other. 

This app gives one easy access to their clearinghouse of free knowledge and inspiration, in other words, videos and audios  of their famed TED Talks.  Although you have to scroll your way through a plethora of non-biological content the content that you will find is worth it.  As an example, I recently listened to an 18 minute talk given by Janine Benyus titled Biomimicry in Action where she discussed the new perspective of engineering which is using biology as it starting reference for design and a web portal for examples using this process (even more recently I listened to Craig Venter’s press briefing about his institutes most recent publication – your students would love to take part in this ground-breaking step in synthetic biology).   The app convieniently allows you to place interesting content within a “favorites”.  To learn more about TED visit their website.

 Amazon (free)

I like to read books, and now with this iPhone app I can easily cut and paste suggetsions from my monthly book review e-mail from the American Scientist into Amazon and save them to my “wish list” or purchase them out right with a few thumb clicks.  This app displays a trimmed down version of the website (it is actually less distracting) with a search window and a few recommendations.   Once you have found your book of choice, you can view a product description, professional reviews, and customer reviews and ratings as at the Amazon website.

 Microbe World ($4.99)

As stated on their website:

MicrobeWorld brings you the latest audio, video, and news content in microbiology, biotechnology, and life sciences from the American Society for Microbiology.  This multimedia application delivers content and news items from the following sources.

“Meet the Scientist” podcast with the renowned author Carl Zimmer
“This Week in Virology (TWiV)” podcast from Columbia Universiy
“This Week in Parasitism (TWiP)” podcast
“MicrobeWorld” video podcasts
“Microbe”, the ASM’s News Magazine in pdf format

This app is a more recent acquisition of mine, but being a fan of Carl Zimmer and familiar with the multitude of resources available via the ASM website, I figured that I would forgoe the cost and support the society with my purchase.  As an example of the content you can find, I recently listened to the most recent podcast of Carl Zimmer’s Meet the Scientist where he interviewed of John Wooley, Associate Vice Chancellor of Research and Professor of Chemistry-Biochemistry and of Pharmacology at UC San Diego, about the emerging field of Metagenomics.

I have more recently begun to listen to TWiP and TWiV in the evening or on a lazy Sunday morning.  These podcasts by Vincent Rancaniello and Dick Despommier from Columbia University are excellent for personal professional development.  Listen yourself and you’ll see why.

 YouTube (with the phone)

I mention this because it could be a useful way for you to by-pass your school’s restrictions.  I guess you would need a phone projector to share with your students though.

Teaching Resources Apps for in the Field

 Google Earth (free)

The Google Earth app is an iPhone version of the software that one can download to view the geography, etc… of the Earth.  View the YouTube video produced by Google to introduce the functionality of this app.  I often introduce my Field Biology and Zoology students to field sites that we plan on visiting via Google Earth on my computer.  Using the sofware gives them a frame of reference and feel for the topography and type of biological communities (whether prairie, forest, or aquatic) at the site.  Now, I can imagine supporting their initial visual introducting to a site through use of this app when we arrive at our destintations as well.

You could even teach your students about cases in which Google Earth images have helped scientists to discover new biological phenomena.

 Weather Bug (free)

Weather Bug is a standard weather app that, once configured for a particular location(s), provides a user with information on the “Current Conditions”, a seven-day “Forecast”, a “Map”, “Video” forecast, and “Camera” image of the weather.  If the National Weather Service has given any warnings, etc… the warning and associated details are posted through the app.  In preparation for this comment, I have just realized that one can view the map as radar, visiable satellite, or infrared satellite as well.  You can even e-mail information to someone else via the app.

I have found this app helpful when trying to make decisions regarding a pending field trips.  Being able to view the radar map as a video over the past hour has helped me to figure out the speed at which weather is approaching, the relative severity of cells in the vicinity, and even predict if there is an expected break in the weather between cells. 

 National Geographic Handled Birds ($14.99)

National Geographics Handheld Birds is the most expensive app that I purchased but I figured that it might help me to become more competent identifying calls.  I have always felt sad for my students, who unlike myself, haven’t had access to a teacher that can impress and inspire students with knowledge of calls.   This app can’t replace a knowledgeable birder for sure but it should help me out.

The app contains content on 867 species of North American birds that is downloaded onto the iPhone so your are not at the mersy of having a network connection at the time of use.  The list of birds can be organized by first name, last name, taxonomically like many current field guides, or by family alphabetically.  There is also a search function but I must add that this is not always useful unless you know the first name in a multi-word name of bird.  For example if one searches ‘cardinal’ or ‘mockingbird’, the search will come back with no results but if you know that they are both ‘northern’ species you would find the entry quite quickly.  In general, I also find all the scrolling one has to do a bit cumbersome.

Once you have choosen a particular species of bird to view the page displays images like those found in the paper copy of their field guide, below which is found a button to play their call.  Beneath the image are Media links that include ‘images’ and ‘audio’, and Description links that include ‘overview’, ‘appearance’, ‘range’, ‘sounds’, and ‘behavior’.  These links contain much information including lists of similar looking and sounding species.  Within the audio link, one can increase the volume of the call playback beyond the range of the iPhone volume controls.  I could easily see that this could be useful in helping students learn the calls of birds, to quiz them in the classroom or in the field, and possibly for even attracting birds for closer identification.

For National Geographic’s description of their product download the following pdf: http://www.handheldbirds.com/HandheldBirds_iPhoneGuide.pdf

 Encyclopedia of Life (free)

The Encylopedia of Life is a website that EO Wilson inspired with the statement “Imagine an electronic page for each species of organism on Earth…” made in at a TED conference lecture a number of years ago.  This EOL app allows one to upload images of organisms that were observed in the field, taken with one’s phone, and to associate your specific location, using the phones internal GPS, with that observation.  In this manner, teachers and students can become citizen scientists helping to develop a database of the specific locations of species throughout the world.  To make the app functional, one has to setup yahoo and flicker accounts (flicker is owned by yahoo), and when opening the app for the first time, one must associate the EOL app with those accounts.  It is a pretty user friendly process.

For an example of its use, I think that once someone identifies Brad’s photos of mammal tracks in the snow, his images, however crude would make a nice addition to the page for that species.  I have already spent time online search for images that would he me in the identification and have realized that I am going to have to pick up a book to find the answer.  If Brad uploads those images, and other like minded individuals did the same, someday the EOL site could use those images in developing a nice key for identification of mammal tracks in snow.  In fact, I could imagine a nice class project where students collect images with such a future goal in mind.

 Pano ($1.99)

The Pano app allow one to easily generate panorama images through providing an easy means of taking multiple overlapping images that the software will stitch together into a single image.  After opening the app one takes a picture using the built in iPhone camera.  Then, after accepting the image the app creates a tranparent sliver of that image on the left hand side of the screen that you can use to align the next image that you take.  Once you have taken all the images for the panorama scene, you can select to merge the images into a single image.  Being a camera phone these images are not of high resolution but it could help you document an entire scene in a simple manner.  I was only disappointed by the fact that it can’t stitch full 360 degree panoramas.

Teaching Resource Apps for the Classroom and Lab

 The Chemical Touch: Lite Edition (free)

The Chemical Touch (TCT) is one of a number of Periodic Table apps available.  I haven’t taken the time to download all of them to compare them and proabably chose this one because is was recommended on some website and is free.  This app provides information on the standard information found on basic period tables inlcuding the name, symbol, and atomic number and mass of each element.  It also contains information on the density, melting point, boiling point, electronegativity for each in a color coded manner that allows one to easily see patterns among the elements.  Similarly, one can view information on the specific heat, heat of fusion and vaporization, and atomic and covalent radii. 

For the designer’s description of the app visit: http://openscience.org/~chrisfen/Pages/Programs/theChemicalTouch.html

 Molecules (free)

Molecules is a simple app for viewing three-dimensional renderings of molecules and manipulating them using your fingers.   The app comes pre-loaded with a DNA model, Acetylcholinesterase, insulin, and the Phenylalanine tRNA.  The app also provides a simple means of downloading other molecules (pdb files) from the  RCSB Protein Data Bank or some other database of your choosing.  Besides allowing one to rotate and zoom in and out of the rendering, one can also change the visualization mode (spacefilling, cylinders, and ball-and-stick) after double tapping on the molecule.  Sadly, it doesn’t have the functionality of freeware like RasMol but it could provide a nice means for those iPhone and iTouch users to become introduced to the protein data bank and molecular visualization.

 Convert ($1.99)

The Convert app is a wonderfully, easy to use, app for making conversions of all types.  Besides the more common convertions in length, temperature, volume, and time, this app also allows conversions in angle, area, computer (bytes, etc…), currency, energy, force, power, pressure, speed, typography (pixels, etc…), and weight.  It also contains a calculator.  Within any choosen convertions one scrolls two column to chose the unit one is converting from and to.  Once, you have chosen your units of conversion, you type in the value for the given unit and the app instentaeously converts and displays the needed conversion.

 Solutions (free)

I currently happen to be one of those biology teachers that infrequently prepares solutions (this will change next year).  When I do, I always check and double check my calculations, and often triple check myself by asking a local chemistry teacher if my logic is correct.  Well, this app from mekentosj.com allows one to quickly calculate the mass, molarity, or volume of a solution from values for the molecular weight, and mass, molarity, or volume that you type in.  The app also provides access to an online database of chemical information and allows you to save information on chemicals that you commonly use.  Learn more at the Solutions website.

 Genetic Code (free) and Genetic Code Pro ($0.99)

The Genetic Code app is a simple app that contains both a traditional table of the genetic code as well as the circular shaped code in the app icon above.  It also contains a picker for you to choose from the 20 amino acids.  Once chosen the app displays the structure of the amino acid which, when tapped, gives you more information on the amino acid including its name, three letter and single letter abbreviations, codons, polarity, side chain formula, side chain charge, type of compound, whether it is essential or not, its relative size, molecular weight, hydropathy, isoelectric point, and pK values.  From the descriptions on iTunes, it is difficult to determine any difference between the free and the pro versions of this app.

 3D Brain

The 3D Brain is a companion app to a portion of the Genes to Cognition website created by the Dolan DNA Learning Center at Cold Springs Harbor Laboratories.  As stated on the app:

The 3D Brain consists of 29 interactive structures that can be rotated in 3D space.  Each structure contains information on associated functions, disorders, brain damage, case studies, and links to contemporary modern research.

This app could be handy visual supplement for student self-review of brain structure and function in the diversity of courses the introduce students to such topics. 

Apps for Keeping in Touch with Students

 Facebook (free)

Besides the more traditional use of Facebook as a means of connecting ‘friends”, Facebook provides a means of maintaining social networks that you have developed in the course of your teaching.  As a rule, I don’t befriend any of my current students or previous students but Facebook provides a means of creating Groups that can facilitate communication without having to become ”friends”. 

Thus, instead of befriending students, I have created a couple of distinct groups that my students or previous students can request to join.  One is for my ex-AP Biology students and the other is for my current Environmental Club.  In either case, groups help to maintain an appropriate virtual distance between the facebook worlds of student and teacher, while taking advantage of the commucations revolution that is social networking.   Specifically, I have used my Environmental Club group to arrange student community service, and have polled previous AP-Biology students to gain important feedback.

It is a bit cumbersome to communicate the initial launching of a group without becoming friends but it can be done (if you choose to do this – contact me for some more tips – since I got blocked from facebook messaging for a while), and once it is up and running your students will actually help spread the word to those that haven’t joined.

 If you have any app suggestions of your own, please take the time to share them too!

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!

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!