KABT BioBlog

The 21st Century Prometheans?

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.”

Observations at a Volleyball Court, accompanied by an ID & Behavioral Challenge

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.

Observations of tadpoles in a local pond

Two days ago, while driving my eldest daughter and a friend to morning swim practice, we ran across, but not over, a rather large snapping turtle crossing the road.  This happened just east of Mission Road on 71st Street in Shawnee Misson, Kansas (it appears that he may have grown up in Indian Hills County Club).  Although the turtle appears to have lived quite a productive live to that moment, we figured that we might increase its life span by moving him somewhere a little bit less populated.

Yesterday, my two younger children and I, released our find in a wetland area adjacent to the Blue River in southern Johnson County.  While there, I treated my kids to one of the ponds I frequent with students when I am teaching about amphibians.  Here is an interesting observation that we made…

A quick google search this morning suggests that field biologist may not fully understand this behavior, and not for lack of thoughtful consideration and experimentation.  I know that school is out and that critical observations and experimentation are dependent on the life cycle of an organism who doesn’t realize that, but I share this observation none-the-less, for its potential…

…and if you want to ID the tadpoles you can do that too…

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.

George Pisani and Bill Busby are looking for help.  You, your students and other interested parties can help expand the knowledge of two Eastern Kansas snakes:  Red-bellied and Smooth Earth Snakes.  Note that these are some of the earliest snakes to show up in the spring (March).  Spread the word to others in your community.  If you want to participate you’ll need to get going. Here are the details:

Smooth Earth Snake and Redbelly Snake Population Survey

Kansas Biological Survey (KBS) is conducting a survey of these two Kansas snakes recognized as Threatened in the State. We are looking for new populations and ask that students and teachers in the eastern counties of Kansas be on the lookout for these species in your area, and report sightings to us using the report form available at http://people.ku.edu/~gpisani/SWGform.html. Sightings must be confirmed by us, either by a live specimen (which may be released at capture point after we confirm identification) and/or high-quality photograph. We also need detailed documentation of habitat in which you may find them! If you find either species, note the area well and contact us ASAP! We especially need people to help us in Linn and Anderson counties; email us as soon as possible if you can help.

Both species are cool-weather snakes, and are among the very earliest to emerge from hibernation. Look for them under cover objects (tin, rocks, wood) from early March on (depending upon temperature). A great way to locate these snakes is to distribute 2ftx4ft pieces of salvaged barn tin (the corrugated kind) in likely habitat, especially edge zones between woods and unmowed grass areas. Part of this effort is to determine just what sorts of habitat both species prefer, so don’t overlook pastures, woods , or whatever habitat is in your area.. Spread some tin [with landowner permission]; see what comes in! And don’t forget to remove the tin when done sampling an area..
For an overview of current Kansas records of these species, visit the Kansas Herpetofaunal Atlas pages from links on our web site (above).

To add incentive, we will award publications to people with the most confirmed sightings in new localities during 2010 as follows:

Most new localities reported: A copy of 2nd printing (1980) Autecology of the Copperhead 1960 by Henry S. Fitch and also a copy of 2nd printing (1991) Reproductive Cycles in Lizards and Snakes 1970 by Henry S. Fitch.
Second place, most new localities reported: CHOICE OF ONE OF THE FOLLOWING- a copy of 2nd printing (1980) Autecology of the Copperhead 1960 by Henry S. Fitch and also a copy of 2nd printing (1991) Reproductive Cycles in Lizards and Snakes 1970 by Henry S. Fitch.
Third place, most new localities reported:  A copy of Biology, status and management of the Timber Rattlesnake (Crotalus horridus): A guide for conservation (1993), by William S. Brown.

George Pisani                                                Bill Busby
gpisani@ku.edu                                            wbusby@ku.edu

A post just came through the KS-Bird list about an interesting Cornell Citizen science program:

The Rusty Blackbird Blitz

Rusty Blackbirds are in decline and Kansas is part of their winter range.  This “blitz”/survey is set up for the first two weeks of Feb.  Check out the link for protocols.  If you decide to get out and count blackbirds don’t just report to eBird;  share your experience here on the KABT BioBlog.

An excerpt from the Cornell eBird website:

January 11, 2010

Singing male Rusty Blackbird, Alaska. Photo by David Shaw (www.wildimagephoto.com).

Populations of Rusty Blackbirds are crashing! Their numbers have plummeted by as much as 88-98% over the last few decades, according to data gathered between 1966 and 2006 for the North American Breeding Bird Survey and Christmas Bird Count. A species that was once considered to be abundant is rapidly disappearing before our eyes. Your observations can help save this species by arming scientists with critical information about its ecology. The Rusty Blackbird Working Group has developed the Rusty Blackbird Blitz, a winter survey whose goal is to count Rusty Blackbirds range-wide just prior to spring migration.  From 30 January – 15 February, search for Rusty Blackbirds in your area and report your observations to eBird.

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!

Before the weekend, I received an e-mail from a colleague asking “Do you know of a good place I can go gather termites… anywhere woody?”

I responded with my suggestions, and because I was intrigued, I replied with a question of my own, “What do you plan to do with them?”

Well, after a making my own way through portions of two decaying logs, and acquiring some special and not-s0-special writing utensils, see what we ended up witnessing by watching the following videos… 

1. Termite and paper (30 sec.)
2. Termite, paper, and pencil drawn Infinity (30 sec.)
3. Termite, paper, and Sanford Uniball Black drawn Infinity (30 sec.)
4. Termite, paper, and Papermate Red drawn Infinity (30 sec.)
5. Termite, paper, and Papermate Red drawn Spiral (30 sec.)

Sorry for the out-of-focus imagery but I hope these 2.5 minutes of observation motivate you as much as they did us before we introduced these creature to our classes today!  Experiment with other colors, other writing utensils, and have fun googling to see what is already known about the behavior you witnessed.

Happy Inquiry!

Those of you who have followed this blog probably know of my long time fascination with antlions.  If you have a ready source of them, they make a great organism to inspire student generated research.  Today, I’ve run across two excellent photo resources on antlions.  Alex Wild’s Mymercos Blog has exceptional images of an antlion in action and in the comments to Alex’s amazing photos you can find a link to Mikko Kolkkala’s images of an antlion parasatoid.  Check them out you’ll be amazed–maybe you’ll even go to the trouble of collecting antlions this summer for the first week of school next year.

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

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

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

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

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

As my father always says, enjoy!