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!

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

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

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

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

As my father always says, enjoy!

eBird Home Page

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

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

Data input

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

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

eBird Chart

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

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

Inside Cancer Website

Inside Cancer Teacher Center

As you can see below the Inside Cancer website is separated into four categories, Hallmarks of Cancer, Causes and Prevention, Diagnosis and Treatment, and Pathways to Cancer, each of which contain a number of sub-headings that link to interviews and other multimedia resources, that have become the hallmark of Dolan DNA Learning Center resources.

The Inside Cancer Teacher Center appears as shown below.

Supplemental Resources

Below are resources that I was prepared to mention during the workshop but did not get the chance.  These are mentioned because I had noticed that the cancer biologist Robert Weinberg is one of the main scientists participating in the Inside Cancer website.

Books

• One Renegade Cell: The Quest for the Origin of Cancer by Robert Weinberg

Other

• Via iTunes, iTune Store, find the navigate the following sequential links iTunesU, Universities and Colleges, MIT, Biology, and finally MIT 7.012 Introduction to Biology, Fall 2004.  This course was taught by Professor Eric Lander, Professor Robert Weinberg, and Dr. Claudette Gardel.  You can download the entire course or individual course lectures as either audo files or video files.  One of the course lectures is a 49 minute lecture on Cancer by Dr. Weinberg.  Here is the link to this course on MIT’s OpenCourseWare.  At this site, you can find the course syllabus, calendar, readings, recitations, assignments, exams, study material, and the video lecture (by-passing iTunes).  Here is a sample recitation from their studies on cancer and the answers.

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

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

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

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

Genes to Cognition Website

The site is divided into three sections including Disorders, Cognitive Processes, and Research Approaches.  Like the DNAi website, it uses flash to provide a number of resources.  There are texts, interactive animations, and one-on-one videos with important researchers in the field.  Some of the animated interactive activities are experimental in nature. 

Once you choose a particular section on the website, there are two main means of navigation.  One is the subway line navigation along the top (like bread crumbs) that follows a more chronological traditional story line through genes, biochemicals, cells, brain anatomy, cognition, and the environment.  The other means of navigation is through a more open ended network (concept map) approach in the main window ot the screen.  If you get lost you can always click on the Genes to Cognition icon in the upper lefthand corner to return to the home page.

For a good example of their interactive experimental animations, click Sap102 and simulate the experiments on memory in swimming mice that have had the Sap102 gene knocked out, or click Fly School and try to train fruit flies to remember an association between a particular odor and shock.

Interestingly, the site also incorporates links to external research websites like PubMed, NCBI, etc… so there is a seemless connection between the Genes to Cognition content and the world of active biological research.  There is also a teacher feature area where one can access pdf files for lessons, and a 3D brain that helps with underlying brain anatomy.

The site is still under construction and their target for full functionality is January 2008.  If you don’t want to waste time navigating an unfinished site you can take a sneak peek of two resources through the home page of the Dolan DNA Learning Center.

Supplemental Resources

Below are resources that participants mentioned during the workshop.

Websites

• Scientific American Frontiers – The Gene Hunters 
  This is a TV Show that contains resources that connect, in a number of ways, to the Fly School activity on Model Organisms and Tim Tully’s research on the CREB gene.  In fact, it contains a video segment where Dr. Tully describes his research with this gene.  If you want to watch that segment, click here and then scroll down to find the Gene You Won’t Forget sement.  As discussed, Dr. Tully has recently started a private company, Helicon Therapeutics, to develop and apply his finding to humans.
• Nobel Website
  I hope that you are already aware of this website.  You can find more information about the Nobel Laureate Eric Kandel including an autobiography, CV, a video tape and text document of his Nobel Lecture, etc…  If you have used any of the Nobel interactive activities or games, the Dolan DNA Learning Center has beat them to the punch in offering materials that allow one to explore Dr. Kandel’s novel research. 
• Nova Science Now
  Here is the link that was brought up regarding a 14 minute video on Mirror Neurons.
• NCBI’s Online Textbooks
  An online Neuroscience textbook.
• American Association for the Advancement of Science
  The Project 2061 is their initiative to advance literacy in science, mathematics, and technology.  One of their products is an Atlas of Maps (some online) that relate important concepts.
• Institute for Human and Machine Cognition
  This site provides a concept mapping tool that is described and can be downloaded for free.  It is quite user friendly software that allows students to create concept maps similar to the one’s on the g2c website.  In fact, the Dolan Center is currently creating their own mapping software that can be used in conjunction with the site.  For example, it may keep track of a students particular navigation history of the site (this is already being done at the bottom of the screen)and potentially provide an intial list of appropriate concepts for them to map based on that history.  Thus, providing a tool for formative assessment.

Papers

• Theory Underlying Concept Maps by Joseph Novak
• The Quest for a Smart Pill Pill by Stephen Hall regarding Tim Tully’s venture with Helicon Therapeutics from Scientific American, Sept. 2003

Books

• Time, Love, and Memory: A Great Biologist and His Quest for the Origins of Behavior by Jonathan Weiner about the fruit fly, etc… research of Seymour Benzer.  It is a wonderful read.
• In Search of Memory: The Emergence of a New Science of Mind by Eric Kandel.  The book is more than an autobiography of Dr. Kandel’s research with Aplysia.  It is a widow into the life of an individual, plagued by memories of the Nazi’s rise, whose motive and persistence has helped to discover the psychological basis for memory through experimental studies of small systems of neurons and their molecular components.

BW

View Larger Map

From Charlie Drewes Website (click to go there)

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

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

Charlie Drewes’ Website

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

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

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

]]> http://www.kabt.org/2008/09/09/blackworm-lab-for-beginning-the-year/feed/ 2 http://www.kabt.org/2008/05/08/hardy-weinberg-spreadsheet-model/ http://www.kabt.org/2008/05/08/hardy-weinberg-spreadsheet-model/#comments Thu, 08 May 2008 16:51:36 +0000 Brad Williamson http://www.kabt.org/2008/05/08/hardy-weinberg-spreadsheet-model/ As part of the KABT thread at the recent KATS KAMP, I argued that we should be asking our students to use spreadsheets to model the concepts of population genetics–in particular Hardy-Weinberg equilibria. I tried to make the case that most of the efforts to model H-W equilibrium in classroom activities such as the AP Biology H-W lab, the M & M’s labs or with beans suffer from too small of sample size (population) or are tedious for the students to explore. On the other hand, working up your own models or having students create their own can be a challenge. The benefits to learning are worth the challenge. In this post, I’ll present the essential parts of an EXCEL spreadsheet that can be used to explore some of the first principles of the effects of population size on drift. This is not presented as the definitive spreadsheet model but rather a rather simplistic model accessible and modifiable by your students. BTW, it takes longer to read this post than it takes to make this relatively simple spreadsheet. I suggest that you bring up EXCEL or some other spreadsheet in a different window and try to create this worksheet as you follow these instructions. Once you’ve mastered this and can creat or modify it at will, then try it out with your students–they can handle this level of difficulty. And when do, they will have an effective tool to explore the basic principles of H-W equilibrium–one that they created.

Here’s what we are shooting for; the basic spreadsheet model for a 2 allele model:

(I’ve recently reviewed this and found that I didn’t mind my p’s and q’s–sorry for the error but the technique is the same.)

Like other simulations, this first spreadsheet assumes a sexually reproducing species with an infinite gene pool, limited zygotes, random mating, no selection, no mutation, and no migration. The green zone on this spreadsheet represents the gene pool. Note that the value for p is entered in cell”B1″and the value for q is calculated by a formula in cell “C1″.

Enter the label, “gametes” in cell “C4″, the label “zygote” in cell “D4″, the label “AA” in cell “E4, the label “Aa” in cell “F4″, and the label “aa” in cell “H4″

The gene pool is assumed to be infinite and the selection for gametes for the next generation is assumed to be random. To accomplish this in the spreadsheet we call on the RANDOM function. If you were to pick an empty cell on the spreadsheet and enter the following function: =RAND() you’d get a random number returned that was somewhere between 0 and 1. Try it out and see. Our entire model is based on this RANDOM function and unfortunately I’m not sure how random it really is but for our purposes it will work.

In cell “C5″ we will generate a random number, compare it to the value of p, and then place either an “A” gamete or an “a” gamete in the cell.

Note that the function that is entered in cell “C5″ is: =IF(RAND()<=B$1,”A”,”a”)

Which basically says, if a random number between 0 and 1 is less than or equal to the value of p then put an “A” gamete in this cell or if it is not less than or equal to the value of p put an “a” gamete in this cell. “IF” functions and “RAND” functions are very powerful tools when you try to build models for biology. Now create the same formula in cell “D5″. When you have this completed then press the “F9″ key on your windows keyboard to force a recalculation of your spreadsheet. If you have entered the functions correctly in the two cells you should see changing values in the two cells.

We’ll put the zygotes in cell “E5″ . The zygote is a combination of the two randomly selected gametes. In spreadsheet vernacular you want to concantenate the values in the two cells: In cell “E5″ enter the function: =CONCANTENATE(C5,D5)

The next columns on the sheet, “F”, “G” and “H” are used for bookkeeping–keeping track of the numbers of each zygote’s genotype. They are rather complex functions that use nested “IF” functions and also the “EXACT” function. The”EXACT” function is required to determine the difference between “A” and “a”. Here goes:

The function in cell “F5″ is: =IF(EXACT(E5,$F$4),1,0)

which basically states: if the value in cell “E5″ is exactly “AA” then put a 1 in this cell, if not then put a 0.

Enter a very similar function in cell “H5″.

=IF(EXACT(E5,$H$4),1,0)

which basically states: if the value in cell “E5″ is exactly “aa” then put a 1 in this cell, if not then put a 0. (Note that the value “aa” is stored in cell “H5″

Now let’s tackle the nested “IF” function. This is needed to test for either “Aa” or “aA”

In cell “G5″ enter the nested function: =IF(EXACT(E5,$G$4),1,IF(EXACT(E5,”aA”),1,0))

The example in the image has an extra set of parentheses–something that sometimes happens when I’m trying to nest functions. At any rate this function basically says: if the value in cell “”E5″ is exactly equal to “Aa” then put a 1; if not then if the value in cell “E5″ is exactly “aA” then put a one; if it is neither then put a 0 in this cell….

There you have it. Copy the cells “C5″ through “H5″ down for as many zygotes as you’d like in the first generation. Sum up the values in the “F”, “G”, and “H” columns to summarize the genotype frequencies in the next generation, make a histogram and you end up with something like this:

With a model like this you can vary the number of offspring by inserting or deleting rows to investigate the effect the size of the population has on the gene frequencies in the next generation. Those of you with the AP Biology Lab manual can use this spreadsheet to answer the first few questions in the simulation part of the exercise and it should be pretty easy to modify it to answer others. That’s your challenge. Let me know how it works out.

BW