User:Nkuldell:The grafting parlour

Note that you have two options for this assignment
OPTION 1 is a collaborative science and art project with the League of Imaginary Scientists, a "non-exclusive society for creative scientists, and mechanically-inclined artists." Together you and the LoIS will design and build a playful and informative genetically engineered exhibit. If you choose, you might build your project after 109 is over, and then your work can be shown in one or more of the international exhibits that are described below. OPTION 2 is a more traditional research proposal in which you and your partner can identify a topic of interest and design an experimental approach to investigate some outstanding issue related to that topic. It's worth mentioning that some 20.109 research proposals have led to UROPs in BE labs, enabling students to carry out their proposed work. The topic you choose, however, can be completely unrelated to any ongoing work in our department.

You may need to consider both of these options for a while until you and your partner find one that you're both excited about. Choosing is an important part of the exercise, as you will often be called on to decide how your limited energy and time can best be spent, here at MIT and beyond.

OPTION 1 : Guidelines for "The Grafting Parlour"
The Grafting Parlour will open a dialogue by "grafting" science, technology and art. Your goal for this project is to design and specify a genetically programmed work that the public can interact with and shape. Your collaboration with the League of Imaginary Scientists will help start the dialogue but the goal is to enable anyone (artist, scientist, public) to participate in a conversation with your engineered, artful organism. For this assignment, you are only required to specify a plan for building this object. If you choose to build it, we can try to work that out after the term is done. Some ideas that could drive creative projects are shown below. These are offered by the League's artists as conversation starters. Where you actually go with this opportunity is your call.


 * Inter-species communication
 * One way : how can you talk to bacteria? If you could talk to bacteria, what would you say?
 * Two way: is there a way for people to direct the growth of bacteria by SMS? what is the human-bacteria relationship, and how do we build upon it? OR can we enhance exchanges between or about different kinds of bacteria?
 * A portal to connect MIT and your exhibit to the northernmost forest of Finland, where people can talk to trees and peer at brightly colored bacteria in the arctic ice
 * Going green
 * Can photo-reactive yeast be a light bulb? Perhaps yeast could be adhered to a light bulb and programmed to react in a visible way to changes in planetary health (i.e. CO2), or to population density (more people in the room makes the cells glow brighter)?
 * Can we reverse the energy cycle - bacteria, loose electrons, and electricity (a little poetic license!)?
 * Biology at play
 * If bacteria were play-do, what would you sculpt?
 * If yeast were building blocks, what would you build?

Your project may be included in the following exchange opportunities: ISEA pre-symposium, November 13, 2008: A Citizen’s Call to Synthesize! a creative conversation with science on public participation in the laboratory Lightwave 2009, January 24 – February 21, 2009: Growing Light and Other Conversations, inter-species communication and illumination Greece Biennale at the State Museum of Contemporary Art in Thessaloniki, May, 2009: Presenting with e-MobiLArt Academy of Fine Arts in Poland, Autumn, 2009: Presenting with e-MobiLArt

presenting your project to your classmates
You and your partner should prepare a 10 minute power point presentation that captures the reasoning, planning and endpoints you have for your project. A general outline for the presentation of your playful, informative exhibit is:
 * a description of existing ways the public can interact with science (and/or) how a new model for an interactive laboratory can fit into the history of science and knowledge (and/or) your ideas about citizenship and biological engineering
 * a statement of the exhibit's goal(s) and a summary of your planned exhibit, assuming your work is fully successful
 * a detailed plan for the exhibit, including (1) a high level "system summary" or "timing diagram", and (2) a list of "parts" or "devices," i.e. a list of DNA functions, that you'll need to find/clone/synthesize
 * a detailed plan for the laboratory, including (1) first experimental steps that will be needed and (2) a measurement or control experiment you'll perform to assess how well your exhibit is working. You must include hypothetical data for the measurement or control, explicitly describing what values or outcome you'd expect a working and a non-working system.
 * needed resources to complete the work
 * societal impact if all goes well

On the day you present your team should print out and bring three copies of your powerpoint slides. Black and white is fine and you can print more than one slide per page if you like. You should also write and print out your "talking points" into the comments box of each of the slides you'll present. These are speaking notes for your presentation. They should include the words you'll use to describe each slide and the transitions you've planned between them. For example from last year's presentations, one slide's talking points were: As you can see from this image, taken from a review on hydrocarbon metabolism in marine bacteria, the alcanivorax species is the first to grow in population after an oil spill, and its growth correlates with a decrease in aliphatic hydrcarbons.  The next slide (transition statement) began: To remedy this, we decided to look into other bacteria into which we could move the hydrocarbon metabolic pathways
 * After most alkanes have been degraded, the Cycloclaticus species blooms while aromatic hydrocarbon levels decrease
 * One thing to note is that as soon as they have done their job, both species return to their normal population levels.
 * One problem with using Alcanivorax and Cycloclasticus to clean oil spills, however is that they can only be found in specific locations

You will be graded on the integrated success of your presentation: concepts, slides, talking points, and presentation.

OPTION 2 : Guidelines for your 20.109 research proposal
Writing a research proposal requires that you identify an interesting topic, spend lots of time learning about it, and then design some clever experiments to advance the field. It also requires that you articulate your ideas so any reader is convinced of your expertise, your creativity and the significance of your findings, should you have the opportunity to carry out the experiments you’ve proposed. To begin you must identify your research question. This may be the hardest part and the most fun. You can start by finding a handful of topics to share with your lab partner. Together you should discuss and evaluate the topics you’ve gathered. Consider them based on:
 * your interest in the topic
 * the availability of good background information
 * your likelihood of successfully advancing current understanding
 * the possibility of advancing foundational technologies or finding practical applications
 * if your proposal could be carried out in a reasonable amount of time and with non-infinite resources

It might be that not one of the topics you’ve identified is really suitable, in which case you should find some new ideas. It’s also possible that through discussion with your lab partner, you’ve found something new to consider. Both of these outcomes are fine but relatively quickly you and your partner should settle on a general topic or two so you can begin the next step in your proposal writing, namely background reading and critical thinking about the topic.

A few ground rules that are 20.109 specific:
 * you should not propose any research question that has been the subject of your UROP or research experience outside of 20.109. This proposal must be original.
 * you should keep in mind that this proposal will be presented to the class, so try to limit your scope to an idea that can be convincingly presented in a ten minute oral presentation.

Once you and your partner have decided on a suitable research problem, it’s time to become an expert on the topic. This will mean searching the literature, talking with people, generating some ideas and critically evaluating them. To keep track of your efforts, you should start a wiki catalog on your OpenWetWare user page. How you format the page is up to you but check out the “yeast rebuild” or the “T7.2”  wiki pages on OpenWetWare for examples of research ideas in process.

As you become more expert on your research topic, you'll read a lot about it and you may feel (a) like there's too much to read (b) like you have too many ideas and no way to map or prioritize them (c) like you don't understand what you're reading (d) all of the above.

One of the best ways to help frame the problem for yourself is to discuss it with someone new. You will have an opportunity during lab to talk with a person from another lab group. This person will offer you a fresh ear to consider your proposal. You can rework your proposal based on the conversations you've had.

presenting your project to your classmates
You and your partner should prepare a 10 minute powerpoint talk that describes the research question you have identified, how you propose to study the question and what you hope to learn. A general outline your research proposal presentation is:
 * a brief project overview
 * sufficient background information for everyone to understand your proposal
 * a statement of the research problem and goals
 * project details and methods
 * predicted outcomes if everything goes according to plan and if nothing does
 * needed resources to complete the work
 * societal impact if all goes well

On the day you present your team should print out and bring three copies of your powerpoint slides. Black and white is fine and you can print more than one slide per page if you like. You should also write and print out your "talking points" into the comments box of each of the slides you'll present. These are speaking notes for your presentation. They should include the words you'll use to describe each slide and the transitions you've planned between them. For example from last year's presentations, one slide's talking points were: As you can see from this image, taken from a review on hydrocarbon metabolism in marine bacteria, the alcanivorax species is the first to grow in population after an oil spill, and its growth correlates with a decrease in aliphatic hydrcarbons.  The next slide (transition statement) began: To remedy this, we decided to look into other bacteria into which we could move the hydrocarbon metabolic pathways
 * After most alkanes have been degraded, the Cycloclaticus species blooms while aromatic hydrocarbon levels decrease
 * One thing to note is that as soon as they have done their job, both species return to their normal population levels.
 * One problem with using Alcanivorax and Cycloclasticus to clean oil spills, however is that they can only be found in specific locations

You will be graded on the integrated success of your presentation: concepts, slides, talking points, and presentation.