2020(S10) Lecture:week 1

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(Homework for tomorrow's challenge session)
(Homework for tomorrow's challenge session)
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**How does the RNA regulate transcription (i.e., what is the molecular mechanism by which is affects protein output)? <br>
**How does the RNA regulate transcription (i.e., what is the molecular mechanism by which is affects protein output)? <br>
**Their documentation for their project also notes, "(Non-coding RNAs) also offer other advantages over transcriptional regulation such as using fewer cell resources and the ability to turn genes on or off more quickly." Please explain this comment.  
**Their documentation for their project also notes, "(Non-coding RNAs) also offer other advantages over transcriptional regulation such as using fewer cell resources and the ability to turn genes on or off more quickly." Please explain this comment.  
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*The MIT team made some "on the fly" adjustments to their project based on early data collected. For instance they decided to control the banana smell for expression in stationary phase since the smell overwhelmed the wintergreen. **Could they have used a computer simulation of their system to make this decision? Why or why not?  
+
*The MIT team made some "on the fly" adjustments to their project based on early data collected. For instance they decided to control the banana smell for expression in stationary phase since the smell overwhelmed the wintergreen.<br>
 +
**Could they have used a computer simulation of their system to make this decision? Why or why not?  
When you are finished, please upload your assignment to your "Personal Design Portfolio" in the [https://stellar.mit.edu/S/course/20/sp10/20.020/homework/index.html homework dropbox.], calling your assignment: FirstInitial_LastName_PDP_1.doc, for example: <font color = red> B_Obama_PDP_1.doc </font color><br>
When you are finished, please upload your assignment to your "Personal Design Portfolio" in the [https://stellar.mit.edu/S/course/20/sp10/20.020/homework/index.html homework dropbox.], calling your assignment: FirstInitial_LastName_PDP_1.doc, for example: <font color = red> B_Obama_PDP_1.doc </font color><br>
2. You should revise your letter based on any feedback you received from your classmates today. When you are finished, please upload your letter to your "Personal Design Portfolio" in the [https://stellar.mit.edu/S/course/20/sp10/20.020/homework/index.html homework dropbox.], calling your assignment: FirstInitial_LastName_PDP_2.doc, for example: <font color = red>T_Swift_PDP_2.doc</font color> <br><center>
2. You should revise your letter based on any feedback you received from your classmates today. When you are finished, please upload your letter to your "Personal Design Portfolio" in the [https://stellar.mit.edu/S/course/20/sp10/20.020/homework/index.html homework dropbox.], calling your assignment: FirstInitial_LastName_PDP_2.doc, for example: <font color = red>T_Swift_PDP_2.doc</font color> <br><center>

Revision as of 09:47, 31 January 2010

Contents

Week 1 Tuesday

Challenge: Project Runway

Instructions: Today you will design, build (i.e. fold) and launch a paper airplane. Your goal is to make a plane that travels further than anyones (we'll be comparing the resting spots for all the entries). Working in teams of 3, choose one person to be the designer, one to be the builder, and one to be the launcher. You can talk to each other at all stages but be sure each person does the assigned job and that someone takes notes of your work together (decisions, uncertainties, disagreements, expertise etc). Your team may use the internet if you want. The designer has one dollar to spend and your team must keep track of costs. No refunds will be issued for parts you do not use. In the event of a tie, cost and aesthetics will serve as the tie breaker. Relevant materials cost:

  • paper is 30 cents a sheet
  • paper clips are 10 cents each
  • scotch tape is 5 cents per 1 inch strip
  • pennies cost 20 cents each
  • a pencil costs 10 cents
  • scissors are unavailable
  • a test flight before the competition costs 30 cents.

Your team has 20 minutes to design and build a plane for the competition. If you are not ready to launch at this time, you will forfeit.

Why are we doing this??

Once "project runway" has launched and the winning design team has been recognized, we'll work as a class to add more ideas, questions and thoughts to this list.

  • from 2008: "this was as an exercise in engineering. We had to solve a given problem with limited time and resources, while working effectively as a team."
  • from 2008: "We ended up using my design choice because I am more stubborn. This is not a great success story in terms of teamwork, but it did produce the best plane in the class."
  • from 2009: "to give us a problem we might feel is more approachable"
  • from 2009: "the most complicated design isn't always the best. Simple works"
  • from 2009: "how different all the plane designs are, even starting with the same materials."
  • from 2009: " I think it was difficult to decide on rolls"

Homework for tomorrow's studio session

Draft a letter. Address this letter to someone(s) you care about. Your letter should introduce and describe a real world problem or opportunity, one that you have inherited, identified, dreamed about, or otherwise encountered, and that you would like to solve or realize. Your letter should explain why you feel the problem or opportunity is important, and what the consequences of success might be. You can focus on more than one issue, but each issue needs to be explained. Please print and bring your letter to the studio tomorrow. Time to complete this letter: 1 hour MAX.

Why are we doing this??

We're looking ahead to the project you and your team will design this term...the first step is for you to decide what you'd like to work on. This letter should start you thinking about your areas of interest. The letter will also be a way to talk with others about things that interest them. Maybe you'll hear an idea you never considered and want to investigate it further. Maybe you'll find someone with very similar concerns.

Week 1 Studio

Part 1: Wednesday matinee

Instructions: Today you will have the opportunity to watch two videos showcasing completed iGEM projects. "iGEM" stands for the "international Genetically Engineered Machines" competition. It is a summer-long opportunity for teams of students working at colleges and universities around the world to design and build genetically engineered machines, many of which use standard biological parts from the Registry of Standard Biological Parts. The videos will orient you to the kinds of accomplishments realized in a summer by teams of undergraduates and their advisers.

Our first feature presentation

Our first featured presentation will emphasize cellular computation and some of the basic biology that's often present in "synthetic biology." As a class we'll watch:


In watching their project we can focus on

modularity
modularity
control of gene expression
control of gene expression
    • cellular logic functions and the control of gene expression
      • our ppt review of these processes is [[]] here

Note As part of their human practice work, the Heidelberg iGEM team in 2008 developed a tremendously useful website that describes the basic background a person might need to understand the much of synthetic biology--at least as it applies to bacterial cells. If your molecular biology is rusty, you can refresh your memory here

Our second feature presentation

Eau D'coli
Eau D'coli
Our second featured presentation will emphasize some of the "engineering" that can be accomplished in a summer by a talented group of undergrads much like yourselves. We'll listen to

Their project will allow us to focus on

    • programming genetic logic, growth phases of bacterial cultures, ethical questions of human experimentation
      • our ppt review of these processes is here

After each presentation

You will have 10 minutes to gather with your fellow moviegoers and discuss what you saw, using these "iGEM review questions" as a guide for your conversations:

  1. what was the problem this team chose to address and why?
  2. is this an important problem and why or why not?
  3. did they succeed in part or in total?
  4. are there aspects of the work that are unclear to you?
  5. if you could ask this team one question what would it be?

Why are we doing this??

Most of our studio session today was spent considering two projects carried out by undergraduates not unlike yourself. The iGEMers worked in teams (as you will) to figure out what they wanted to build (as you will) and then spent some time in the lab realizing their project (not possible in this class but you could join the iGEM program this summer, as three of the 20.020 students from Spring 2008 and one for 2009 did!). Remember that these are just two projects of many and you should feel motivated by them to work this term on a project that's important to you. The projects also highlight a few of the many widgets in the toolbox for biological engineers. You might want to revisit these projects as the details of your project becomes clearer.

Part 2: Dear John

As homework you were asked to draft a letter describing a real world problem or opportunity you have inherited that could be addressed in the near term. You should discuss these letters at your team tables and make some notes about them on the white boards. For example,

  • who were they addressed to?
  • how many problems/opportunities did each letter address?
  • what areas were tackled?
  • how many also proposed solutions to these problems?

After about an hour of discussion at your tables, you'll have a chance to hear from the other groups. Be sure to take notes on your letter about any new ideas, clarifications, or thoughts you have from the discussion. You will turn in a revised letter before tomorrow. (and note that if you've finished your discussion about the letters early you can get to work on the homework below).

Homework for tomorrow's challenge session

1. To solidify the biology and engineering that's associated with the two projects we studied today, please look at the documentation of their project (here for Illinois 2009 and here for MIT 2006) and answer the following questions:

  • The 2009 Illinois iGEM team wanted to program some logic devices and they chose to use RNA as their mechanism for regulating gene expression.
    • How does the RNA regulate transcription (i.e., what is the molecular mechanism by which is affects protein output)?
    • Their documentation for their project also notes, "(Non-coding RNAs) also offer other advantages over transcriptional regulation such as using fewer cell resources and the ability to turn genes on or off more quickly." Please explain this comment.
  • The MIT team made some "on the fly" adjustments to their project based on early data collected. For instance they decided to control the banana smell for expression in stationary phase since the smell overwhelmed the wintergreen.
    • Could they have used a computer simulation of their system to make this decision? Why or why not?

When you are finished, please upload your assignment to your "Personal Design Portfolio" in the homework dropbox., calling your assignment: FirstInitial_LastName_PDP_1.doc, for example: B_Obama_PDP_1.doc

2. You should revise your letter based on any feedback you received from your classmates today. When you are finished, please upload your letter to your "Personal Design Portfolio" in the homework dropbox., calling your assignment: FirstInitial_LastName_PDP_2.doc, for example: T_Swift_PDP_2.doc
Time to complete this letter revision and answer these questions: 1 hour MAX.

Week 1 Thursday

Challenge: Sexy on the inside 2

  1. Watch this video in which Gever Tulley talks about learning by doing.
  2. Watch this video of a person taking apart a MacBook Air
  3. Working in groups of 3, you will take apart a tape recorder. One person should work the tools, another should record the process (e.g. "began by taking off back panel), another should keep a parts list (e.g. "4 Phillips-screws 3 mm long from back panel") and should record the purpose of each component (e.g. "Phillips screws held back panel in place). Your team's goal is to disassemble the tape recorder into the greatest number of re-usable parts... note of the word "reusable" since next time we meet, the goal will be to reassemble your tape recorder into a working machine. As you work, you may find it helpful to describe what you think each component does and if it's made of sub-components that can be separated further without forever destroying the component's function.
    • "One of the problems of taking things apart and seeing how they work--supposing you're trying to find out how a cat works--you take that cat apart to see how it works, what you've got in your hands is a non-working cat," Douglas Adams
  4. If there's time, watch this video showing the inner life of the cell, an understanding largely achieved by scientific "take apart" techniques.

Why are we doing this??

Taking something apart is one way to understand how it works. Having disassembled a simple machine, you should consider what you've gained from the process. What did you learn? What about this challenge resembled science and what did or didn't feel like engineering? Was the tape player build to enable this sort of work? What (else) has the tape player been built for/ optimized for? What are the chances you'll be able to re-assemble this machine next week? Before leaving class today we'll add ideas/questions/thoughts to this list.

  • from 2008: by taking the tape player apart, we learned in great detail how it worked.
  • from 2008: I think this activity was useful because it showed us that we needed to be really diligent about keeping track of each and everything we did.
  • from 2009: advice: "draw pictures, taking pictures would be even better"
  • from 2009: what would have helped? "more time, not having to reassemble, knowing which parts can be broken, if the tape player was build for human understanding and use"
  • from 2009: thoughts for next time: "I hope not every part is needed""it would have been easier if we could re-assemble it right away rather than wait until Tuesday"
  • from 2009: what were these built for: "these are battery eaters, optimized for disposable, cheap economy"
  • from 2009: woulda-shoulda-coulda: "we should have tested it before we took it apart"
  • from 2009: If the tape player had been built to take apart, thered probably be..."fewer parts esp if not all parts are needed" "easier open/close, no hidden clips" "documentation" "higher quality parts"

Homework for next week's challenge session

  1. Over the next week we'll be turning the letter you wrote into a script and then a story board. The script should be fun to write and doesn't have to win you a Pulitzer Prize since you'll be turning it into a comic book. For inspiration, look through Adventures in SB. Then, using the problem or opportunity you described in your letter, draft a two chapter script for a comic book using characters from your imagination. In chapter 1, have the characters talk about the problem or opportunity. In chapter 2, have the characters brainstorm a way to solve the issue. Before next Tuesday's challenge session, please upload your letter to your "Personal Design Portfolio" in the homework dropbox., calling your assignment: FirstInitial_LastName_PDP_3.doc, for example: H_Clinton_PDP_3.doc
    You should also print out a copy to bring to the 20.020 studio time next Wednesday.
    Time to complete this script: 1 hour MAX.
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