A little over a year ago, Brad posted a link to a survey on Synthetic Biology.  Although it appears that little has fundamentally changed since then, this burgeoning field, along side nanotechnology, has become front page news, and will hopefully become a topic of conversation in your biology class in the near future.

I don’t pretend to be an expert on Synthetic Biology but I thought a few resources may provide you with enough background knowledge to approach the topic with your students this year.  Maybe they could use this post itself as a springboard for discussion or more research.  The post is in three parts, each accompanied by some thought provoking quotes from Mary Shelley’s Frankenstein…

Early Years and Standford’s Drew Endy

In these links you will will find a reference to one of the first papers in the field, a few comic responses to the field, and links to two YouTube videos (originally TED Talks) of Drew Endy explaining the difference between Synthetic Biology and the more standard and familiar recombinant DNA and genetic engineering technologies.

“The world was to him a secret which he desired to divine. Curiosity, earnest research to learn the hidden laws of nature, gladness akin to rapture, as they were unfolded to him, are among the earliest sensations he can remember . . . It was the secrets of heaven and earth that he desired to learn; and whether it was the outward substance of things or the inner spirit of nature and the mysterious soul of man that occupied him, still his inquiries were directed to the metaphysical, or in it highest sense, the physical secrets of the world.”

1. Synthetic Biology: Engineering Escherichia coli to see light (November 2005)
2. Nature’s comic on Synthetic Biology (November 2005)
3. The Story of Synthia - another comic look at synthetic biology
4. Synthetic Biology Organization with a press link to numerous popular critiques of synthetic biology
5. SEED’s Cribsheet on Synthetic Biology (July 2010)

(June 2007)

(December 2008)

Venter creates the News & President Obama’s Responds

“There was none among the myriads of men that existed who would pity or assist me; and should I feel kindness towards my enemies? No: from that moment I declared everlasting war against the species, and, more than all, against him who had formed me and sent me forth to this insupportable misery.”

(May 2010)

1. The President’s Emerging Technologies Interagency Policy Coordination Committee’s Inaugural Meeting (May 2010)
2. NPR Story, Presidential Panel Scrutinizes Synthetic Biology (July 2010)

Resources for those interested in Doing some Synthetic Biology

The following resources are for entering the field of Synthetic Biology.  The first link will introduce you to an annual competition used to motivate undergraduate teams of students to design and engineer novel pathways in E. coli.  If you search around, I think that you’ll find that there has been a single high school team involved in the competition before.  Some of university sponsors are quite interested in developing a kit to introduce students to the methods synthetic biology.

1. iGEM 2010
2. Authentic Teaching and Learning through Synthetic Biology based the E. coli engineered to sense light
3. The BioBricks Foundation
4. Registry of Standard Biological Parts
5. BioBrick Assembly Kit from New England BioLabs

“‘The labours of men of genius, however erroneously directed, scarcely ever fail in ultimately turning to the solid advantage of mankind.”

While on holiday in Oklahoma this weekend, I happened by this volleyball court on the way to the pool.   My attention was immediately drawn to movements that I observed in my periphery.  Here is what I observed from sand level…

and close-up from above…

The species may be territorial.  While individuals came close to each other it appeared like there were brief chases and overall there was an emergent spatial pattern (I think you can see it in the first video) suggestive of territoriality.   I tried to follow the movement of a single individual but it was too difficult for me.

After spending more time, continuing to ignore my children swimming and doing flips of the side of the pool, I made these more detailed observations suggestive of territoriality as well.  In the first video, you will see interactions between numerous live individuals with a single dead individual of the same species…

Here is a close-up image of an instance of this behavior…

In the second video, you will see interactions of these hymenoptera with a mottled leaf…

Here is a close-up image of an instance of this behavior…

The fact that the colors of the leaf are similar to some of those found in the wasps themselves made me wonder if I could elicit the behavior with another leaf.  The leaf I chose to use, unlike the one I found them naturally interacting with, was entirely yellow.  What do you hypothesize will happen?

Around the periphery of the volleyball court, I noticed holes in the sand that were approximately the same diameter as the cylinder shape of the insect themselves (see below), although maybe a bit weathered.  I should have dug them up but didn’t think of it at the time.

I had noticed similar behavior in a much smaller number of cicada killers in a children’s sandbox, but had no idea what type of hymenoptera this species was.  Similar, I wondered, was this a mating swarm?  Where they recently emerged individuals?  What was the ratio of genders?  How long does this behavior persist?  What resources might they use to maintain their energy?

A few curious individuals did happen to come by while I was making my observations, and I received seemingly conflicting reports on their longevity.  One adult mentioned that they are there all the time, while a couple of kids arriving to play volleyball hadn’t noticed them there the day before.  In fact, later that night I saw, from afar, four people playing volleyball.  I might add, that to get some of the images and video, I walked in amongst the swarm.  I did so slowly but felt that they may have ignored me even if I had walked in at a normal pace.

So, here’s the challenge…

• What is the genus and/or species of this hymenoptera?  and
• What the heck are they doing?

As mentioned in response to Brad’s post on aphids, I think a collection of such videos and images could make an interesting series of ecological activities for students, and possibly a series of models for them to produce their own reports, blogs, etc… on interesting outdoor observations that can motivate learning of particular ecological principles.

For anyone that responds with the answers, unknown to me with any certainty, it would be nice, and potentially helpful in the future, for you to provide links to websites that helped in your identification.

Simply, the method is a ”thought experiment” in which students graphically hypothesize the arrangement of a collection of molecules unknown to them (phospholipids) in three sequential situations, in order to personally discover the self-assembly of phospholipids in generating a simplified cell membrane.

Once students have discovered this basic image of a cell for themselves it becomes easier for them to supplement it generating a more complex conception of the cell.

In fact, I usually draw an analogy between the cellular container and the test tubes and beakers used in chemistry.  Student readily understand that cells, “as places where chemical reactions occur” require:

• a container (the goal of this series of thought experiments),
• reactants,
• points of entry and exit (the membrane and supplemental proteins),
• a solvent (the water inside this simple cell),
• catalysts as biological enzymes,
• energy,
• and a controlling region or some means of regulation.

A summary of the “thought experiment” follows but for those that want more details, including images, or would rather read offline, I have created a document explaining this Cell Membrane Thought Experiment.

Background

Prior to conducting this thought experiment students have a good understanding of the chemical structure and biological importance of water, and have previously introduced to the importance of carbon and the basic structure of organic molecules.

I begin the series of “thought experiments” by drawing a simple representative phospholipid on the board, consisting of a circular head and two lines or tails extending from head.  I inform the students that this is a large organic molecule.  Large enough that one rarely sees it represented in an chemical diagram.  Furthermore, I label the head and tail of the molecule hydrophilic and hydrophobic, respectively.  We discuss the roots words and then begin…

Experiment 1

• I have the students take out a piece of paper and draw a beaker that is 2/3 full of water.
• Next, I walk around the room and give them a number of imaginary phospholipids.
• Finally, I challenge them to graphically represent how these molecules will arrange themselves if dropped into their beaker.

This thought experiment is rather easy for the majority of students.  I walk around the room checking their progress and have a student share their answer and logic on the board.  At this point all the students feel confident, and I have one share their logic verbally for all to hear.

Experiment 2

• I have the students draw a second beaker filled with water, and I give them more imaginary phospholipids.
• In this situation, I tell the students that they again have to represent the arrangement of the molecules after being dropped into the beaker, but with the added stipulation that the molecules have to be  submerged entirely below the surface of the water and are not allow to touch the sides of the beaker.  I remind them of the properties of the molecules and tell them that if the tails of their molecules are touching water they aren’t happy, and that that such arrangements are incorrect.

In contrast to the previous situation, the majority of students are now dumbfounded.  I let them struggle, giving them plenty of wait time.   A few students generally arrive at an answer though, and when I notice their correct answers I immediately turn their paper over so that others can’t copy.   There are actually two distinct graphic answers for this situation.  Some students draw a sphere of heads while others cut their sphere showing a cross-section of their arrangement showing the tails inside.

So that more students feel the joy of success, I often hint that the molecules must “work together” to solve the problem, and for even better results I may later add that “they protect each other”.  Finally, I elect an excited student to draw and share their logic from the board.

Experiment 3

• I have student draw one final beaker of water, and give them their last pile of phospholipids.
• Like the previous situation,  I tell the students that the arrangement of molecules they draw has to be entirely submerged but with the added stipulation that the structure has to be a container for water as well.

Students easily see that they have to modify the previous structure since the tails don’t like water, but some need time to think about it.  Some will quickly come to an answer through, applying the logic from the previous situation.  For this situation I again walk around the room turning over correct answers.  At some point I will have a different student share their drawing and logic.

Finale

After we finish this series of “thought experiments”, I remind the students that we don’t know identity of the molecules that we have been playing with, and that I never even shared an biological objective for the activity.  So, for closure I tell them that I will give extra credit to the first person who identifies the molecule that we have been representing and/or names the three dimensional structure that we graphically represented in the third experiment.  The students happily compete to discover “phospholipids” and the “cell” or “cell membrane” (sometimes they find the “lipid bilayer” but I usually direct them to find a more common name for the structure).

Extentions

Other cellularly important topics that such a simple model helps to elucidate include:

• Origins of Life – Self-assembly is a concept that is important …  The Discover article The First Cell …
• Cell Size – this model helps to focus students on the relationship between the membrane surface area and the cytoplasmic volume.
• Cellular Evolution – this model helps students to appreciate the hypothesized origin of the eukaryotic nucleus and associated cytomembrane system from infolding of the phospholipid bilayer, eukaryotic cells grow larger in size than prokaryotic cells.
• Protein Folding – the model helps students in their application of the concepts of hydrophilic and hydrophobic to their understanding of the nature of some amino acid sidechains, protein folding, and the structure of globular and membrane proteins that result from these characteristics.

I have also created a Chime tutorial covering this same information.  Chime is a little bit dated, since you will have to acquire and install a plug in as directed on the site (if you can’t anymore let me know), before being able to observe and interact with the imagery on the website.

Let me know if your student enjoy this “thought experiment” as much as mine!

I am not sure what KABT’s goal for the field trip were but for me they were two-fold.  I wanted to provide an inspirational outdoor experience for four of my senior students, and two of my children, who eagerly participated in the trip, while learning myself about the wonderful short-grass prairie from our very own sage, the Yoda-like natural history master, Stan Roth. 

In both regards the trip was a resounding success, even though I failed to continue to follow Noah’s driving lead into better pastures where he was finally able to witness the character of our pursuit, the endangered a recently re-established Black-Footed Ferret (see Noah’s posts). 

If you are sad that you missed the trip, continue on since I did my best to record it all for you…

More specifically, follow along to see what I saw, learn what I learned, listen while I contemplate what KABT may have learned, and educate yourself on the prairie dog wars of Logan County, Kansas in hopes of a return trip to this wonderful county… 

I apologize up front for the lack of quality audio in some of the following videos…  I was just using a flip mino, and as you will see, it can get quite windy out west. 

Also, two the videos I am sharing are too large for YouTube standards (more than 10 minutes), so I have provided a link to the files being stored elsewhere.  They should open and play in windows media player but if not (which has happened to me already), just right-click, save to your local machine, and view using Quick Time.  I will continue to work on having them display in a more user friendly manner…

What did I see?

I know I won’t be all inclusive since I didn’t record all the plants and birds that we observed, but here goes…

yucca, indian blanket, prince’s plume, little bluestem, buffalo grass, western salsify, prickey pear and button cactus, sage, larkspur, stinkhorn mushroom, green sunfish (in the Smoky Valley River that had flowing water), great plains toad, woodhouse’s toad, plains spadefooted toad, ornate box turtle, prairie lizard, six-linned racerunner, earless lizard, coachwhip, plains garter snake, common kingsnake, bullsnake, prairie rattlesnake, racer, western hognose snake, eastern and western kingbirds, mocking bird, blue jay (two words), orchard oriole, barn owl, red-headed woodpecker, grasshopper sparrow, horned lark, barn swallow, cliff swallow, night hawk, turkey vulture, red-tailed hawk, burrowing owl, ferruginous hawk, unidentified rodents, kangaroo rat, cotton tail rabbit, black-tailed jack rabbit, raccoon, white-tailed deer, mule deer, pronghorn, and swift fox. 

It sounds like a short-grass prairie doesn’t it?

Well, we also saw humans, yellow sweat clover, corn, wheat, a dog, some cats, lambs, chickens, and quite a number of cows.  No herds of bison, at least out west…

• View my pdf slideshow of images from KABT Spring 2010 Field Trip to Logan County, Kansas

What did I learn?

1. From Stan, How to capture a Kangaroo Rat… at least theoretically…

and the empirical results…

more on Kangaroo Rats from David Attenbourgh at YouTube…

2. Stinkhorns really do attract flies! 

Maybe these videos (or pictures from the slide show) could be used in conjunction with Brad’s recent images of aphids to begin to produce a class set of such “interaction” images that students could use as a springboard for learning about interesting and complex ecological relationships…

3. about the Cretaceous Seas of Kansas from Chuck Bonner (~15 minute video).

4. Cochineal scale insects, found on prickly pear cacti, produce a cool pigment called Carmine!

more on Cochineal insects at wikipedia…

5. From rancher Larry Haverfield, How to manage your land for Prairie Dogs (~50 minutes video)

6. How to spotlight for Black-Footed Ferrets!

listen for  Owen’s prophetic response to my saying “but we haven’t seen a ferret yet”…

What may KABT have learned?

Well, I don’t want this to come across wrong but it turned out to be a blessing that so many KABTers were unable to make the field trip this spring.  In an effort to boost participant numbers, Brain Coon approached Stan to consider opening up the trip to a few of our students, and he agreed.  Thanks Stan!  Thus, six lucky high school students were able to be moved by the western scenery of our state.

The trip proved to be a mutualistic group learning experience where besides the tradiational teachers-learning-from-teachers situation, students learned from teachers, teachers learned from students, and students learn from each other. 

My experiences with taking students on the Kansas Herpetological Society spring and fall field trips for over 10 years has taught me that such outdoor opportunities can change the trajectory of a student.  I know that KABT has been open to the children of participants in the past, and I certainly wouldn’t want student particpation to keep a teacher from participating or from overshadow learning by the members themselves, but I think the society should consider killing two birds with one stone and continue to open up appropriate spring field trips to student participation. 

Prairie Dog Wars History & Noah’s Ferret Sighting from My Perspective.

Larry Haverfield, on June 5, 2o1o discussing his ranching approach with KABT Field Trip participants

December 5, 2006, Outlaw Prairie Dogs Find Refuge with Rancher - NPR’s All Things Considered by Jeff Brady

December 6, 2006, In Kansas, a Line Is Drawn Around a Prairie Dog Town- New York Times by Felicity Barringer

August 5, 2007, Landowners, commisioners split over prairie dog control-  The Topeka Capital Journal by Jan Biles

December 20, 2007, Black-Footed Ferret’s Return to Kansas- Audobon of Kansas Website

December, 2007, Black-Footed Ferret’s Return to Kansas! – Defenders of Wildlife website

January 21, 2008, Poison talk not kaput – The Hays Daily News by Mike Corn (here is a link to an entire series of articles on the “Prairie Dog Divide” by Mike Corn)

December 20, 2008 – New war being waged against prairie dogs in Logan County by Mike Corn

November/December 2009, Doggone!- Audubon Magazine by Ted Williams

November 8, 2009, Prairie Dog Wars images - Mat Slaby images for Audubon article

April 2, 2010, Palco students help survey ferrets – The Hays Daily News by Richard Robinson

June 5, 2010, Larry Haverfield in his own words - video taped by Eric Kessler on the KABT Field Trip (same as the 50 minute video above) 

June 21, 2010, When some ranchers use poison – just like the old days – High Country News by Ted Williams

Noah Busch overlooking the prairie dog hole where he last observed the ferret just before sunrise!

Noah Busch and Stan Roth talking to Larry Haverfield about the mornings observations,
and here is the actual conversation…

If this post made you jealous, please consider joining us next year!

Looking for a new outdoor ecology investigation to conduct with your students?  … something that will require them to get their hands dirty?  … and aid in their learning and appreaciation for our native fauna? 

Then look no further than the new citizens science project, Earthworms Across Kansas organized by Dr. Bruce Snyder at Kansas State University.  As stated on their website and in an introductory letter I recieved a few weeks ago…

Earthworms Across Kansas is a free program that engages middle and high school students throughout the state in answering some basic, yet unanswered questions about Kansas earthworms, such as “Which species are here?” and “What are the ranges of these species?”

The project aims to educate Kansas’ middle and high school students about earthworm biology and invasive species issues by engaging them as citizen scientists.  One-third of the approximately 170 species of earthworms known to reside in the United States have arrived here from another continent.  We expect that most every earthworm your students collect will be an exotic species.

We are currently recruiting teachers to participate (online registration form), although only until we run out of kits.  Once registered, you can prepare for your participation by viewing curricula and lesson plans associated with earthworm biology that will be posted online through May.  In July or August your kit will be mailed, and your students can complete their collecting anytime during the 2010-2011 academic year.  The data from across the state will be uploaded on their interactive google map, and thus facilitate your students answering the basic questions posed by the project.

If you’d like more information about the program before registering certainly visit their website, and if you have further questions, please email the project at earthworm@k-state.edu.

I haven’t read through the protocols for this project yet but thought you may interested in learning from the active worm collectors and the research associated with their methods.  Check out Worm Grunting, Fiddling, and Charming—Humans Unknowingly Mimic a Predator to Harvest Bait published in PLOS.  Besides the article there are a number of interesting quicktime video links demonstrating the research.

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!

During the holiday break, I have come across a number of valuable resources (video, audio, and paper) for demonstrating to students that the processes of natural selection and speciation, that Darwin made us aware of 150 years ago this past year, are actually occuring before our very eyes.  

Instead of hypothetical just-so-stories, these resources are user friendly and thought provoking real world examples with organisms and adaptations that students can relate to.  These examples also highlight the work of the people, and the personalities, behind the acquisition of new scientific knowledge.  I commend these scientists and numerous others who understand the importance of communicating science to a sometimes skeptical public and whose efforts have provided us with these wonderful resources and springboards for learning.

Read on to find out about these 7 resources…

• What Darwin Never Knew
  This is a new 2-hour Nova video that was broadcast on December 29th.  I must admit that I didn’t know of the broadcast but once I happened upon this new resource while flipping channels, I stopped and was mesmorized by the show.  The segments I saw appeared to be a video compliation of Sean Carroll’s Making of the Fittest and other similar recent research.
• The Aquatic Hypothesis for our Hairlessness
  This is a 17 minute TED Conference lecture by Elaine Morgan an avid supporter, as you will see and hear, of the aquatic hypothesis for the evolution of our hairlessness.  I had heard of this hypothesis but never knew much about its supporting evidence.  This is a good introductory lecture on the topic of our nakeness.
• Bird Feeders Speed Up Evoltion, May Split Species
  This is a 12 minute audio segment on the “Reporting in Current Biology, researchers write of a warbler that has quickly evolved an unorthodox migration path to England to take advantage of backyard bird feeders. Study author Martin Schaefer explains how the clever migrants could become a distinct warbler species.”
• Of Fish and Flies: The Evolutionary Role of Genes
  This is a 4 minute audio segment of the on genes involved in the divergence phenotypes of stream and pond sticklebacks and fruit fly wing pigmentation discovered by David Kingsley at Stanford and Sean Carroll at the University of Wisconsin, respectively.  I believe that this radio segment may have been inspired by the NOVA video mentioned above.
• Kinkiness Beyong Kinky
  This is a blog post on Discover’s website by Carl Zimmer who reports on the interesting coevolution of male and female reproductive anatomy in ducks.  Videos are included.
• Radiations & Extinctions: Biodiversity through the Ages
  This is a full chapter excerpt from the latest book by Carl Zimmer, The Tangled Bank provided by the National Center for Science Education.  If you end up enjoying the read, use the this link to surf to amazon to make the purchase.
• Convergent Evolution and Divergent Selection: Lizards at the White Sands Ecotone
  While reading the year end review in the most recent issue of the journal Science, I came across this example of natural selection in three species of lizards at White Sands National Park in New Mexico (see this blog posts accompanying image).  This research conducted by Erica Bree Rosenblum at UC Berkeley helps to bring the ecosystems, organismal, molecular, and genetic prespectives in an easy to relate to manner.  The title link will take you to a pdf copy of the original paper published in the American Naturalist (2006 isn’t really that recent), while the two links that follow are to a more student friendly magazine article and blog post on the research.
  http://www.nps.gov/whsa/naturescience/upload/Rosenblum%20-%20lizards.pdf
  http://scienceblogs.com/notrocketscience/2009/12/three_desert_lizards_evolve_white_skins_through_different_mu.php

Happy New Year!  I hope you enjoy the links, and look for a post on iPhone apps for Biology Teachers in the near future.

Where: Linda Hall Library
When: October 1, 2009 through March 27, 2010

• Monday: 9:00 am – 8:30 pm
•  Tuesday-Friday: 9:00 am – 5:00 pm
• Saturday: 10:00 am – 4:00 pm

A little over a week ago, on the evening of October 1, I had the pleasure of attending the opening of this wonderful exhibition.  My words would put the exhibit to shame so read the introductory words that the library has published in a brochure for the exhibit.

Charles Darwin was born on February 12, 1809.  When he was fifty years old, in 1859, he published On the Origin of Species, a book destined to radically change our view of the living world.  In 2009, we celebrate both the bicentennial of Darwin’s birth and the 150th anniversary of the publication of his great work.

Darwin began his scientific career as a naturalist, as someone who collected plant and animal specimens, studied and recorded the details of their structures, and attempted to identify and classify them.  He thus worked within the framework that was known as natural history.  Natural history had a vernerable pedigree, with its roots in Aristotle, but it especially flourished and matured in the four centuries before the Origin of Species.  Darwin was the direct heir of naturalists like Konrad Gesner, who published the first illustrated encyclopedia of zoology (1551-58), Carl Linnaeus, who successfully sorted out the plant and animal kingdoms with his influential taxonmic Systems of Nature (1735), Joseph Banks, who sought new species in the south seas on the first voyage of Captain Cook (1768-71), and Jean Lamarck, who made the study of invertebrates a respectable branch of zoology (1801).

We choose to honor Darwin, therefore, by showcasing the tradition out of which he himself evolved.  Fortunately, for exhibition purposes, the works we have chosen to display are not only important intellectually, but are also some of the most beautiful books ever published.  “There is gradeur in this view of life,” Darwin remarked in the last sentence of the Origin of Species.  We hope our exhibition captures some of the grandeur, and of Darwin’s great achievement.

I also had the pleasure of listening to Lyanda Haupt’s lecture on “Darwin’s Evolution as Naturalist: A Bird’s-eye View”, and have subsequently purchased and have begun to read her book, Pilgrim on the Great Bird Continent, that the lecture was based on.  It has been a good read so far…   Luckily for you there are two remaining lectures in the series honoring Darwin, on October 29th and December 3rd.  To learn more about these lectures visit Linda Hall’s Darwin Lecture Series site.

So, as we draw near to the anniversary of the publication of our Origins, take a few minutes and tour the grand exhibit at Linda Hall and please inspire your students to do the same.

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!