# 2020(S08) Lecture:week 8

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Week 8 Tuesday
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Week 8 Tuesday
= - ==Challenge: Flip Books== + This week you will spend nearly all of our lecture and studio time specifying these aspects of your project: - *Warm up: flip book + *a system overview - *Melbourne 2007 project timing diagram [http://parts.mit.edu/igem07/jam07media/Jam07_Melbourne.mp4 presentation] + *a device list + *a timing diagram + *a parts list + It's unlikely you'll be "done" with any of them by the time the week ends, especially since you may need to revise what seemed like completed aspects of your project as you learn more about what's available and how things work. Design/revise/design/revise/design/revise.... + ==Challenge: System Overview: Flip Books or Phase Wheel== + *Here's a warm up challenge to show what is meant by a system overview + **Option 1: Working independently, you should take 10 minutes to sketch a process into a flip book (materials to be provided). The process you choose to illustrate is up to you. It can be a plant growing, a house of cards being built, or a happy message appearing letter by letter on a computer screen. What you choose is limited only by the number of pages in your book, your ability to draw, and the limited amount of time we've given you to complete this challenge. '''10 minutes only!''' + **Option 2: The moon and the sun move through the earth's sky in a predictable pattern. Working independently, you can assemble a lunar phase wheel that illustrates this pattern. The phase wheel (materials to be provided) is a device that was developed by Dr. Mary Urquhart at the University of Texas at Dallas. It represents our view of the sky, the different appearances the moon can take in our sky, and the movement of each lunar phase relative to the sun. '''In 10 minutes''' you should be able to assemble the lunar phase wheel and use it to answer the following questions in your project design notebook: + ***At sunrise, where is the sun relative to the horizon? + ***At sunrise, where is a full moon relative to the horizon? + ***Moving the sun from sunrise to sunset, is the full moon visible during the day? + ***What kinds of moon(s) are visible for the greatest number of daylight hours? + **Before we move on to the next part of today's class we'll hear from some of the flip-book drawers and some of the lunar phase wheelers to learn '''what worked well and what didn't about each device in terms of providing an overview of the system''' to be illustrated. + *Next you and your project team will generate a system overview for the Melbourne 2007 iGEM "coliform" project + **The Melbourne team wanted to build a 3D, floating mass of bacteria that adhered to one another when the cells detected both blue and red light. In other words: at the intersection of an incoming red light beam and blue light beam, a solution of bacteria would clump and remain suspended in its growth media. + [[Image:Coliform.png|thumb| coliformers from Melbourne's iGEM 2007 team]] + **As a class we'll watch the first 5 minutes of the Melbourne team's [http://parts.mit.edu/igem07/jam07media/Jam07_Melbourne.mp4 iGEM presentation] + **Next your project team should work out a system overview for the coliform project. You can either get an unused flip book (or use the back of one from the warmup exercise), turn the lunar phase wheel over, or come up with some other mechanism of illustrating how the Melbourne team's system would work. '''You should not spend more than 10 minutes''' on this activity.  When you are done, give the overview to one of the team mentors to hand in or explain to Drew and Natalie. You and your team can get right to work on the last thing planned for today's lecture. + *Finally, take the rest of today's lecture time to illustrate or specify the system overview of your team's project. You do not need to make either flip books or phase wheels unless you find these useful ways to brainstorm and define the outstanding issues. Ideally the system overview you generate today will be shown in your [http://openwetware.org/wiki/20.020:_Technical_Specification_Review Tech Spec Review,] that is happening one week from tomorrow (eek!). ==Before tomorrow's studio time== ==Before tomorrow's studio time== - If there are outstanding issues related to the timing diagram for your project be sure everyone on your team knows how you'll solve the issue(s) and make a plan to come to studio tomorrow with materials for finishing the timing diagram. + If there are outstanding issues related to the system overview for your project be sure everyone on your team knows how you'll solve the issue(s) and make a plan to come to studio tomorrow with materials for finishing the system overview and getting good work done on the device list and the timing diagram. =
Week 8 Studio
= =
Week 8 Studio
= - ==Part 1: Wrap-up Timing Diagram== + ==Part 1: Wrap-up System Overview== + You will have time to polish up any leftover work on this aspect of your project once we have introduced device lists and timing diagrams. - ==Part 2: Generate Device and Parts list == + ==Part 2: Generate Device list and Timing Diagram== + Consider again the coliform project from the Melbourne 2007 iGEM team. The team listed six devices they needed to realize their idea: + # a red light sensor + # a blue light sensor + # an AND gate to trigger a cellular behavior when both lights are present + # a GFP reporter to monitor easily/quantifiably the AND gate's function + # expression of adhesive proteins under the control of the AND gate + # a gas vesicle expression cassette to produce neutrally buoyant bacteria + Working with your project team at the white boards, + # draw a '''wiring diagram''' for the six devices listed here. A sample wiring diagram from the IAP 2004 [http://parts.mit.edu/wiki/index.php/IAP2004:Polkadorks Polkadork's] ''Ecoli''-brator project is shown below. Note how some of the entry and exit wires are given names as well. + # list the six devices (or the named connections between these devices) on a y-axis and time on an x-axis and then indicate the '''timing for operation''' of each device or wire, including the persistence of each device's signal through time--shown in PS (protein synthesis) and PD (protein degradation) below. You can keep a running list of any uncertainties.
+ '''After 15 minutes of work''', we'll have each team report back to the group, and then you can spend the rest of today's studio time working on a device list and timing diagram for your own project. + + [[Image:Intro21-SystemDiagram.png|center|650 pxl| wiring for the Polkadork's Ecolibrator project]] [[Image:Ecolibrator TimingDiagram.png|center|650pxl| timing diagram for the Polkadork's Ecolibrator project]]

- ==For next time== =
Week 8 Thursday
= =
Week 8 Thursday
= ==Challenge: Time is \$\$ == ==Challenge: Time is \$\$ == - ==Mapping these ideas to your project== + As much as we'd all like to have unlimited amounts of time and funding, few of us do. Let's warm up for today's lecture-time work with two quick conversion challenges. + ===Part 1: take me away!=== + Spring Break has just passed but who wouldn't mind another getaway. Maybe even for just a day--skip classes on Friday and come back late Saturday. All of Sunday to catch up. Hmm. Delta has a direct flight to Bermuda. Kayak.com.... + *Flight 508 departs Logan Friday at 8:53 AM and arrives at Bermuda International at noon then + *Flight 507 leaves BDA Saturday at 4:35 PM, back at Logan at 5:50...in time for Saturday dinner. + Airfare alone is \$371. '''Should I take the T or a cab to Logan?''' + '''Take 10 minutes to decide as a group if you'd travel by T or taxi to the airport.''' Be sure to keep track of your reasons that favor one or make you disinclined to the other. After 10 minutes of work on this challenge, we'll hear the choice and the top 2 reasons from each group. + ===Part 2: better to be lucky than good?=== + [[Image:1101540329 400.jpg|thumb|left| Jonas Salk/Time magazine cover]]Some people seem destined to be in the right place at the right time. There are businessmen, military heroes, and celebrities whose good personal outcomes seem best explained as lucky alignments of stars and planets. Critically good timing was a strength of Jonas Salk, who is commonly credited as ''the'' scientist responsible for the polio vaccine. As profiled in [http://www.time.com/time/time100/scientist/profile/salk.html Time Magazine], Jonas Salk was "strictly a kitchen chemist (who) never had an original idea in his life," according to Albert Sabin one of "the other" men credited for conquering polio. How can timing be related to cost of launching a project? In Salk's case, his ability to offer a killed-virus as a polio vaccine was wholly enabled by John Ender's discovery of effective culturing techniques for the polio virus itself.
+ Consider once more the Melbourne 2007 iGEM project. In a series of questions at the end of [http://parts.mit.edu/igem07/jam07media/Jam07_Melbourne.mp4 their presentation], the team gets asked about any changes to the gas vesicles device that might allow gas-filled cells to become even more buoyant. Their answer speaks to some scientific work others have done to understand the vesicle-encoding operon , research that has shown at least one gene in the operon is a negative regulator. By deleting that gene, the Melbourne team thinks they might make their cells even more buoyant. '''If you and your team were the Melbourne team, what would you do with this information?'''
+ Here are some options. You can consider these or others, but weigh them in terms of their associated cost (both time and money). + *Use the entire gas vesicle operon to get the basic Coliform system working then tweak the system later to improve it. + *Wait to assemble your system until you can perform experiments to know more about each gene in the operon. + *Divide the team in half, with some launching into the project with the DNA as is, and others studying it and refining it. + *Spend one week in the library to read all you can about these vesicles and then decide. + *Place a DNA synthesis order for the full operon (6 kilobases) as well as every single gene knockout and double gene knockout. + '''After 10 minutes''' we will hear back from each group about their preferred strategy for optimizing time and money. + + ===Mapping these ideas to your project=== + Now it's time to look at the list of devices you have identified as part of your project (some of you may have a full list of needed devices and some of you will have only a partial list, in which case you'll have to consider these ideas now and then revisit them when your device list is complete). What might factor into the cost and time of assembling the devices into your working system? Do you know all you need to know about how they work? Are there easy ways to find out more? Do the devices already exist or will you have to make them yourself? You might want to make a chart that lists your degree of confidence in each device, where confidence is tempered by its cost/time/source/description and perhaps safety/security concerns...something we will return to next week.
+ Generate a list or table that might be useful as part of your [http://openwetware.org/wiki/20.020:_Technical_Specification_Review Tech Spec Review] next week.

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# Week 8 Tuesday

This week you will spend nearly all of our lecture and studio time specifying these aspects of your project:

• a system overview
• a device list
• a timing diagram
• a parts list

It's unlikely you'll be "done" with any of them by the time the week ends, especially since you may need to revise what seemed like completed aspects of your project as you learn more about what's available and how things work. Design/revise/design/revise/design/revise....

## Challenge: System Overview: Flip Books or Phase Wheel

• Here's a warm up challenge to show what is meant by a system overview
• Option 1: Working independently, you should take 10 minutes to sketch a process into a flip book (materials to be provided). The process you choose to illustrate is up to you. It can be a plant growing, a house of cards being built, or a happy message appearing letter by letter on a computer screen. What you choose is limited only by the number of pages in your book, your ability to draw, and the limited amount of time we've given you to complete this challenge. 10 minutes only!
• Option 2: The moon and the sun move through the earth's sky in a predictable pattern. Working independently, you can assemble a lunar phase wheel that illustrates this pattern. The phase wheel (materials to be provided) is a device that was developed by Dr. Mary Urquhart at the University of Texas at Dallas. It represents our view of the sky, the different appearances the moon can take in our sky, and the movement of each lunar phase relative to the sun. In 10 minutes you should be able to assemble the lunar phase wheel and use it to answer the following questions in your project design notebook:
• At sunrise, where is the sun relative to the horizon?
• At sunrise, where is a full moon relative to the horizon?
• Moving the sun from sunrise to sunset, is the full moon visible during the day?
• What kinds of moon(s) are visible for the greatest number of daylight hours?
• Before we move on to the next part of today's class we'll hear from some of the flip-book drawers and some of the lunar phase wheelers to learn what worked well and what didn't about each device in terms of providing an overview of the system to be illustrated.
• Next you and your project team will generate a system overview for the Melbourne 2007 iGEM "coliform" project
• The Melbourne team wanted to build a 3D, floating mass of bacteria that adhered to one another when the cells detected both blue and red light. In other words: at the intersection of an incoming red light beam and blue light beam, a solution of bacteria would clump and remain suspended in its growth media.
coliformers from Melbourne's iGEM 2007 team
• As a class we'll watch the first 5 minutes of the Melbourne team's iGEM presentation
• Next your project team should work out a system overview for the coliform project. You can either get an unused flip book (or use the back of one from the warmup exercise), turn the lunar phase wheel over, or come up with some other mechanism of illustrating how the Melbourne team's system would work. You should not spend more than 10 minutes on this activity. When you are done, give the overview to one of the team mentors to hand in or explain to Drew and Natalie. You and your team can get right to work on the last thing planned for today's lecture.
• Finally, take the rest of today's lecture time to illustrate or specify the system overview of your team's project. You do not need to make either flip books or phase wheels unless you find these useful ways to brainstorm and define the outstanding issues. Ideally the system overview you generate today will be shown in your Tech Spec Review, that is happening one week from tomorrow (eek!).

## Before tomorrow's studio time

If there are outstanding issues related to the system overview for your project be sure everyone on your team knows how you'll solve the issue(s) and make a plan to come to studio tomorrow with materials for finishing the system overview and getting good work done on the device list and the timing diagram.

# Week 8 Studio

## Part 1: Wrap-up System Overview

You will have time to polish up any leftover work on this aspect of your project once we have introduced device lists and timing diagrams.

## Part 2: Generate Device list and Timing Diagram

Consider again the coliform project from the Melbourne 2007 iGEM team. The team listed six devices they needed to realize their idea:

1. a red light sensor
2. a blue light sensor
3. an AND gate to trigger a cellular behavior when both lights are present
4. a GFP reporter to monitor easily/quantifiably the AND gate's function
5. expression of adhesive proteins under the control of the AND gate
6. a gas vesicle expression cassette to produce neutrally buoyant bacteria

Working with your project team at the white boards,

1. draw a wiring diagram for the six devices listed here. A sample wiring diagram from the IAP 2004 Polkadork's Ecoli-brator project is shown below. Note how some of the entry and exit wires are given names as well.
2. list the six devices (or the named connections between these devices) on a y-axis and time on an x-axis and then indicate the timing for operation of each device or wire, including the persistence of each device's signal through time--shown in PS (protein synthesis) and PD (protein degradation) below. You can keep a running list of any uncertainties.

After 15 minutes of work, we'll have each team report back to the group, and then you can spend the rest of today's studio time working on a device list and timing diagram for your own project.

# Week 8 Thursday

## Challenge: Time is \$\$

As much as we'd all like to have unlimited amounts of time and funding, few of us do. Let's warm up for today's lecture-time work with two quick conversion challenges.

### Part 1: take me away!

Spring Break has just passed but who wouldn't mind another getaway. Maybe even for just a day--skip classes on Friday and come back late Saturday. All of Sunday to catch up. Hmm. Delta has a direct flight to Bermuda. Kayak.com....

• Flight 508 departs Logan Friday at 8:53 AM and arrives at Bermuda International at noon then
• Flight 507 leaves BDA Saturday at 4:35 PM, back at Logan at 5:50...in time for Saturday dinner.

Airfare alone is \$371. Should I take the T or a cab to Logan? Take 10 minutes to decide as a group if you'd travel by T or taxi to the airport. Be sure to keep track of your reasons that favor one or make you disinclined to the other. After 10 minutes of work on this challenge, we'll hear the choice and the top 2 reasons from each group.

### Part 2: better to be lucky than good?

Jonas Salk/Time magazine cover
Some people seem destined to be in the right place at the right time. There are businessmen, military heroes, and celebrities whose good personal outcomes seem best explained as lucky alignments of stars and planets. Critically good timing was a strength of Jonas Salk, who is commonly credited as the scientist responsible for the polio vaccine. As profiled in Time Magazine, Jonas Salk was "strictly a kitchen chemist (who) never had an original idea in his life," according to Albert Sabin one of "the other" men credited for conquering polio. How can timing be related to cost of launching a project? In Salk's case, his ability to offer a killed-virus as a polio vaccine was wholly enabled by John Ender's discovery of effective culturing techniques for the polio virus itself.

Consider once more the Melbourne 2007 iGEM project. In a series of questions at the end of their presentation, the team gets asked about any changes to the gas vesicles device that might allow gas-filled cells to become even more buoyant. Their answer speaks to some scientific work others have done to understand the vesicle-encoding operon , research that has shown at least one gene in the operon is a negative regulator. By deleting that gene, the Melbourne team thinks they might make their cells even more buoyant. If you and your team were the Melbourne team, what would you do with this information?
Here are some options. You can consider these or others, but weigh them in terms of their associated cost (both time and money).

• Use the entire gas vesicle operon to get the basic Coliform system working then tweak the system later to improve it.
• Wait to assemble your system until you can perform experiments to know more about each gene in the operon.
• Divide the team in half, with some launching into the project with the DNA as is, and others studying it and refining it.
• Spend one week in the library to read all you can about these vesicles and then decide.
• Place a DNA synthesis order for the full operon (6 kilobases) as well as every single gene knockout and double gene knockout.

After 10 minutes we will hear back from each group about their preferred strategy for optimizing time and money.

### Mapping these ideas to your project

Now it's time to look at the list of devices you have identified as part of your project (some of you may have a full list of needed devices and some of you will have only a partial list, in which case you'll have to consider these ideas now and then revisit them when your device list is complete). What might factor into the cost and time of assembling the devices into your working system? Do you know all you need to know about how they work? Are there easy ways to find out more? Do the devices already exist or will you have to make them yourself? You might want to make a chart that lists your degree of confidence in each device, where confidence is tempered by its cost/time/source/description and perhaps safety/security concerns...something we will return to next week.

Generate a list or table that might be useful as part of your Tech Spec Review next week.