TBT: Synthetic Biology (July 2010)

Editors note: This post on Synthetic Biology was originally published on the BioBlog 18 July 2010. While he at one point mentions that he doesn’t “pretend to be an expert” on SynBio, author Eric Kessler has gone on to do some amazing work with his students in the field. Somethings have changed in six years (here is a story by Ed Yong from March 2016), but please enjoy this look back into our archives. 


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.”

CALL FOR PROPOSALS- KABT Fall Conference 2016

Colleagues!  It is my pleasure to invite you to fill out a proposal to share your experiences with the KABT membership at our Fall Conference. This year’s conference will take place 9/10/2016 on the campus of Emporia State University. Our conference theme is the use of organisms in the classroom, and biohazard safety, storage, and disposal. Please fill out the proposal form below. If you have any questions, contact Drew Ising at andrewising@gmail.com. Thank you for your time, and we look forward to receiving your presentation proposals!


Time for a little “Service to the Profession”…

Hey everybody! There are some new Teacher Education Program Standards that would have an effect on licensure in the future. The standards are open for comments now until May 8th, 2016. So if you are looking for some light reading, or you just want to do your part to ensure that we are putting out high-quality educators, please use the link below and give them some feedback– positive, negative, or otherwise. As we know, more data leads to stronger conclusions, and more voices will lead to better standards.

KS Licensure Standards for Biology Educators

Leave comments with KSDE, then let us know what you think about what you read. Like them? Love them? Loathe them? Can’t wait to hear!

Get Ready and Sign up for DNA Day

ks_DNADay_logo_goldLast year, the biology folks at the University of Kansas adapted a successful program from the University of North Carolina:  DNA Day.  The teachers I talked to loved the program and so did their students.  Don’t miss out.

Sign-ups for Kansas DNA Day 2016 are now open! Kansas DNA Day features graduate and advanced undergrad students in the biological sciences traveling to local high schools to give interactive lessons on the applications of genetics and genomic sequencing. The event will be held the week of April 21st. We currently have ambassadors ready for the greater Kansas City, Lawrence, Manhattan and Wichita areas so if you are a high school science teacher in one of these areas, sign up to have ambassadors come visit your classroom! More info and a link get involved can be found at http://ksdnaday.odst.dept.ku.edu/Welcome.html, or e-mailkansasdnaday@gmail.com for more info.

Environmental Education Workshop at Baker Wetlands

KACEEWorkshop

Anyone else ready to start thinking about getting students outside to explore their local environment with all this nice weather? Need an excuse to get out to the amazing new Baker Wetlands Discovery Center? This workshop might be for you! February 12th and 13th, the Kansas Association for Conservation and Environmental Education (KACEE) is putting on a short course for teachers of students Pre-K through grade 12. The course consists of 8 hours at Baker Wetlands and 8 hours online, and graduate credit is available through Baker University.  Questions can be directed to Ashlyn Kite-Hartwich from KACEE at 785-889-4384 or akite@kacee.org.

Hope to see a lot of you out there!

A Mentoring Program for New AP Biology Educators

From the Editor: I received this message from David Knuffke, moderator of the AP Biology teacher community, and all-around Rock Star-level educator. As someone who was new to AP Biology in the not-so-distant past, I will vouch for the benefit of such a program. I, luckily, kept my head above water long enough to produce/modify the resources I needed reach the high expectations from the College Board, my administrators, and students. However, many do not, and are miserable. We absolutely do NOT need to be losing  good teacher to stress. If you have any questions about this program, teaching AP Biology, or anything at all, please reach out to us here at askKABT@gmail.com. Happy Holidays, and have a great Finals Week!   -Drew Ising 

Hi friends,

One of the major issues that I hear about (from new AP teachers and veterans) is that some of the structure that the CB has in place (e.g. the Teacher Community) can be a bit overwhelming.

One initiative we are interested in working towards is the establishment of a mentor network for new AP Bio teachers. Robin Groch has volunteered to serve as the point person for this project. We envision a pretty casual mentoring relationship between a new teacher and a veteran mentor. At the same time, we aren’t clear if this is something that is tenable, and won’t know for sure until we see what kind of interest there is in serving as a mentor among our veterans. In that vein, we have created a form for anyone who is interested in serving as a mentor to fill out. Once we have a handle on the number of veteran teachers who are willing to do this, we hope that we will have a great pool of people to connect to new AP Bio teachers. This is very much an interest assessment form. By filling it out, you are NOT committing to actually becoming a mentor, should the project move forward.

As far as I’m concerned, outside of a certain weekly conversation that I have, my role as a district mentor is incredibly rewarding and helpful for my own practice. I hope many of the talented AP Bio teachers on this listserv might consider signing up to serve in a mentoring capacity. I think we have a pretty great opportunity to help new AP Bio teachers get more comfortable.

Here is a link to the mentoring interest form:http://goo.gl/forms/QRmVDVPiWi

David Knuffke
Deer Park, NY

http://www.mrknuffke.net
@DavidKnuffke

Notes from NABT 2015

Writing from a hotel room in beautiful Rhode Island, I am here to bring you two things:

  1. Here is a Google Doc with collaborative notes from this year’s NABT conference. A couple notes about it:
    • While some of my notes are there, it really is due to the large collective effort of my peers in the Knowles Science Teaching Foundation (next summer, please consider asking new teachers to apply who are currently in, or about to be entering, their first year of teaching) who helped create and contribute to this document. Note-taking styles may be unique but still very well done.
    • It is not exhaustive, we went to sessions that interested us most, if it’s not on there, we didn’t see it and therefore have no notes.
    • I appreciated ANY FEEDBACK about this document and process. I think it could be cool for others to consider using similar notes for NSTA, KABT, KATS, etc.
  2. For a bonus I’ve included an ID Challenge all the way from the Atlantic Ocean.

IMG_8951

Enjoy!

In My Classroom #10: Protein Folding

Welcome to the KABT blog segment, “In My Classroom”. This is a segment that will post about every two weeks from a different member. In 250 words or less, share one thing that you are currently doing in your classroom. That’s it.

The idea is that we all do cool stuff in our rooms and to some people there have been cool things so long that it feels like they are old news. However, there are new teachers that may be hearing things for the first time and veterans that benefit from reminders. So let’s share things, new and old alike. When you’re tagged you have two weeks to post the next entry. Your established staple of a lab or idea might be just what someone needs. So be brief, be timely and share it out! Here we go:

 

Last week I used a very simple, very low-tech but highly effective way to teach protein folding.  After teaching my students how to read the genetic code, I gave them a strand of DNA for which they would transcribe and translate to find the amino acid sequence.  Students then used those little marshmallows and strung them on a strand of thread, much the way many of us strung popcorn garland for the holidays.

 

FullSizeRender (1)

 

They wrote on each marshmallow (with sharpies) the name of the amino acid.  I provided each student a chart which gave them a basic chemical description of each amino acid (polar, non-polar, etc..)  We then walked through how the primary structure of their protein would fold.  With each fold they would use toothpicks to hold their marshmallows in place – representing whichever type of bond formed.  When we were done – volla!  A 3D protein!  (My students have not had chemistry yet, so we needed to cover basic chemical bonding….but they generally got the idea.)

 

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I just finished grading their assessments late last week, and the majority of students have a decent understanding of tertiary structure of proteins.  I like taking an abstract concept and turning it into something concrete!  Now….its Drew Ising’s turn……..tag!

The Great Gradeless Experiment #2

Well, after 5 weeks of using the gradeless system, I figured it’s time for an update. If you’re just now joining me, my first post can be found here: http://www.kabt.org/2015/06/26/the-great-gradeless-experiment-1/

We’ve just finished our first unit (Structure and Function), which means we’ve had our first summative assessment. We’ve also submitted our first progress report grades of the year. I’ll be using this update to talk about both of these things.

Summative assessment:

In early August, Steve Young at Olathe East held a workshop over how students learn (if you have a chance to attend in the future, I highly recommend it!). My big “a-ha” learning moment of the workshop also solved a major problem I was having with setting up my gradeless system – How will assess my students?

If you’re following along at home, I’m using a 0-4 scale to assess student learning. This means I need a way to assess students at all levels. I originally thought of including test questions of varying difficulty. Steve Young taught me to differentiate.

I offered my students 3 different exams to choose from. The level 2 exam tested basic skills and vocabulary, the level 3 exam tested application, and the level 4 exam was an open-ended writing assignment. Link to the exams: DNA and Protein Synthesis Test 2015

My students were able to choose which exam they were comfortable taking based on how well they thought they understood the information. Students were encouraged to come in after school to retake the exam at higher difficulties to demonstrate mastery of the content. Exams could be retaken an unlimited number of times.

Most students tested at the level 2 and level 3 level. A handful of students were comfortable (and successful) at level 4. This is about what I expected. Most students were honest about how much they knew and where they were in their learning. Since taking the test, I’ve had a number of students come to me to take the exam at a different level.

Progress report:

A gradeless system doesn’t play very nicely with a more traditional A-F grading system. We’re not bothering with percentages in my class (because honestly, can you tell the difference between student work if one student earned an 88% and another that earned a 92%? I know I can’t.). This means I had to figure out how to translate my 0-4 scales into letter grades. The obvious way would to make an A=4, B=3, C=2, etc., but what happens if you have a student that scores across the board, depending on the content?

I chose to hold individual conferences with each student. During these conferences, I asked each student what letter grade they thought they deserved and why. When students received reviewed work from me, they kept it in a folder in my room. This became their evidence during their conferences. If a student earned mostly 3s and 4s on assignments and wanted an A, they were able to argue for it. Together we decided on the letter that would represent their learning for the first grading period.

Overall, my letter grade recommendation and the students’ matched almost every time. If anything, students tended to underestimate their learning.

These conferences were enjoyable to do – I got to talk to each student one-on-one about their learning and I think it helped students learn to trust me more in regards to this new grading system.

Final thoughts:

This grading system is not perfect yet and I’m still trying to work out a few kinks (like eligibility for athletes), but so far I am pleased with how things are going. It’s still early into the school year, but I feel like the students are starting to worry less about their percentage and letter grade and are focusing more on learning the content.

I gave a presentation over this gradeless system during the Fall KABT conference last Saturday. If you weren’t in attendance, we have the videos linked in the post below. You can also find my PowerPoint at: Going Gradeless PPT

In My Classroom #8 – Get At the Engineering

Welcome to the KABT blog segment, “In My Classroom”. This is a segment that will post about every two weeks from a different member. In 250 words or less, share one thing that you are currently doing in your classroom. That’s it.

 

The idea is that we all do cool stuff in our rooms and to some people there have been cool things so long that it feels like they are old news. However, there are new teachers that may be hearing things for the first time and veterans that benefit from reminders. So let’s share things, new and old alike. When you’re tagged you have two weeks to post the next entry. Your established staple of a lab or idea might be just what someone needs. So be brief, be timely and share it out! Here we go:

 

My student teacher and I made a decision to try to do a better job of addressing the engineering aspects of the NGSS expectations this year. I wanted to take a new look at the end of my Scientific Method unit to insert some engineering considerations. Vivian Choong had the idea to discuss water quality and use the 2016 Olympic Games in Rio as a context for a PBL.

 

It's in the standards, seriously.

It’s in the standards, seriously.

 

We decided to retool my blackworm lab to use them as bioindicators of water quality and take measurements of the worms’ homeostasis before and after different remediation attempts on some “polluted” water. Students designed ecological water filters (soil, sawdust… that kind of thing, not chemical filtration) and considered the economic costs and ecological benefits of their interventions.

We thought the students would measure blackworm pulse rate or other behavior indicators, but they gravitated much more to measurements of water turbidity and coloration. It’s super cool and they’re really engaged with the topical nature of the problem. This is a keeper that I hope to formalize after some debrief and further revision.

Here is our anchor video for the activity. Don’t ask me for submission tiers, because we’re not there yet!

https://www.youtube.com/watch?v=z_w16PjoNVE

IMG_20150902_090823 IMG_20150902_090839

That’s it for me. Tag Andrew Davis, you’re it.