2020(S09) Lecture:week 4

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(New page: {{Template:20.20(S09)}} <div style="padding: 10px; width: 670px; border: 5px solid #99FF99;"> =<center>Week 4 Tuesday</center>= ==Challenge: <font color = blue>[http://batman-versus-super...)
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=<center>Week 4 Tuesday</center>=
=<center>Week 4 Tuesday</center>=
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==Challenge: <font color = blue>[http://batman-versus-superman.com/Statistics.html Superman vs Batman] </font color>==
 
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'''Instructions:''' If you're looking to start an argument on a playground, ask a few different elementary school kids who would win if Superman fought Batman. Superman has a number of innate "super" abilities, while Batman comes prepared with a handy utility belt plus plenty of training.  It would be a close fight, for sure, but there's little agreement about which character would remain standing after a head-to-head battle. At your tables you should decide the winner and what powers or properties of the victor tipped the balance for your group. Start by considering each hero's
 
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* mobility,
 
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* fighting abilities,
 
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* fighting style and,
 
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* vulnerabilities. <br>
 
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To support your discussion, you might want to list the strengths and weaknesses of each character or you might want to read up on the histories of the heroes and their battles. '''After 15 minutes''' we will reconvene as a class to list the attributes that each table has considered and to tally the Superman vs Batman votes. May the best superhero win!<br>
 
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<br>
 
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'''Framing comment:''' The Batman vs Superman battle can help to illustrate the relationships of science to engineering.  This coupling is particularly apt in Biological Engineering because so much of the natural living world remains to be discovered and understood (does Biology = Superman?), while at the same time engineers are already working evermore to make new tools and products (does Biotechnology = Batman?).<br>
 
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<br>
 
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'''From Science to Engineering, and Back Again:''' To further examine the coupling between science and engineering, we'll consider the history of humans and flight. Our conversation in class will consider both natural flying systems (e.g., birds) as well a man-made flying objects (e.g., planes, paper or otherwise)!<br>
 
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<br>
 
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First, consider this [http://www.youtube.com/watch?v=EqGY3uNR4ko movie] of birds flying. How many different, independent features or functions can you observe and define about flight by watching these natural flying machines?  As a group, compile a list of all the features or functions that you can observe, including whether or not any particular feature is essential for flight.  Can you define each function or feature such that one is independent from the next?<br>
 
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<br>
 
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Now check out these two movies of damselflies in flight: [http://www.youtube.com/watch?v=gkFOBgl1P3Y Movie 1], [http://www.youtube.com/watch?v=DGkZLvung_o Movie 2].  Can you add any new functions or features to your list of what's important for flight?  Again, try to have each feature or function be independent from all the others.<br>
 
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<br>
 
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Next, consider this [http://www.youtube.com/watch?v=iMhdksPFhCM video] of early flying machines.  Again, working as a group, spend a few minutes to decide if there are any new features or functions that you didn't find by watching birds or insects in flight.  Write these new features down so that we can discuss them as a class.  Also, see if you can list any essential features of flight that you identified by considering birds and insects, but which these early inventors left out.<br>
 
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<br>
 
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Jumping ahead ~100 years, note that we (i.e., humans) are now pretty good at building "first-order" flying machines (e.g., the [http://www.youtube.com/watch?v=dd9NM9vsGD8 Boeing 777]).  How come?  Well, one reason might be that the engineering community has developed powerful tools to help with the design and testing of flying machines.  Check out this [http://www.youtube.com/watch?v=ER8qjvdHEyQ video] of simulated airflow around a model for a plane.  Next, consider this [http://www.youtube.com/watch?v=b4qROcBXs6Y simulation] of airflow past an unmanned aerial vehicle.  Also, consider this [http://www.youtube.com/watch?v=pe9PVaFGl3o movie] showing a wing loading test for a 777.  Discuss at your table both (a) what each movie is showing, (b) how such tools or methods would help with the design of flying machines, (c) why Boeing conducted an expensive wing loading test if their design tools are so great?<br>
 
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<br>
 
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Can the same tools that are used to help design synthetic flying machines also be used to understand how natural flying machines work?  Check out two videos before discussing and answering this question: [http://www.youtube.com/watch?v=u6Xrhdkuqr0 Movie 1], [http://www.youtube.com/watch?v=x3th_3BZVHQ Movie 2]. Now, have a quick discussion to make sure that everybody understands what these movies depict.  Once settled, do you think that these simulators are good enough to help us understand how natural flying machines really work?  Why or why not?<br>
 
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<br>
 
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Finally, check out these videos:<br>
 
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#[http://www.youtube.com/watch?v=ttz5oPpF1Js Wingsuits]
 
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#[http://www.youtube.com/watch?v=SHYXrqoS08o Jetdude]
 
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#[http://harvardmagazine.com/web/extras/robotic-fly Robotic Fly]
 
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#[http://www.youtube.com/watch?v=l131fSveof8 MIT Daedalus]
 
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Discuss with your table-mates what you think flight will be like 100 years from today.  Also, consider what lessons you might draw from the last 100 years of humans studying and building flying machines that could be relevant to the next 100 years of humans studying and building biological machines.
 
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<br>
 
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'''Before leaving lecture''' today, complete your response log entry. In your response, you should note:
 
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* what the activity was
 
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* why you think it might have been included in this class
 
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* if the activity helped you think about:
 
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** ways to make biology easier to engineer
 
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** consequences of successfully engineering biology
 
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** clever ways nature solves physical challenges
 
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** ways nature innovates
 
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*if the activity has given you any new tools/considerations that could be useful for your project.
 
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Upload these responses to the lecture response log in the homework dropbox that's [https://stellar.mit.edu/S/course/20/sp08/20.020/homework/index.html?toolset=hidden here]<br>
 
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==Follow-up homework==
 
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Spend 20 minutes watching Janine Benyus present [http://www.ted.com/index.php/talks/view/id/18 "12 sustainable design ideas from nature."] You'll notice that she is '''not''' lobbying for biology to do our bidding, but rather for our technology developers to learn more from nature's ingenious solutions. You'll also notice that she doesn't actually get through 12 ideas but here is a partial list of natural adaptations that designers might mimic:
 
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# '''Self-assembly,''' e.g. the work of [http://www.unm.edu/~solgel/ Jeff Brinker] and that at the [http://www.sandia.gov/ Sandia Nat'l Labs]
 
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# '''Biomineralization,''' e.g. the work of [http://www.alcatel-lucent.com/wps/portal/!ut/p/kcxml/04_Sj9SPykssy0xPLMnMz0vM0Y_QjzKLd4y3cDcFSYGZzgH6kShiBvGOCJEgfW99X4_83FT9AP2C3NCIckdHRQBnvc7J/delta/base64xml/L3dJdyEvd0ZNQUFzQUMvNElVRS82X0FfN01U?LMSG_CABINET=Bell_Labs&LMSG_CONTENT_FILE=News_Features/News_Feature_Detail_000013&lu_lang_code=en_WW  Joanna Aizenberg at Lucent]
 
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#''' CO2 as feedstock,''' e.g. the work of [http://www.sciencedaily.com/releases/2003/03/030324063233.htm Geoff Coates at Cornell]
 
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# '''Solar transformations,''' e.g. using purple bacteria as they do at [http://photoscience.la.asu.edu/photosyn/ ASU]
 
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# '''The power of shape,''' e.g. the whale's fin as studied by [http://bio.wcupa.edu/biology/content/view/125/2/ Frank Fish]
 
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# '''Water harvesting,''' e.g. the way the [http://database.biomimicry.org/item.php?table=organism&id=1010 Stenocara beetle does,] as described by the [http://www.biomimicryguild.com/ Biomimicry Guild]
 
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# '''Separation techniques,''' e.g. metals without mining at [http://www.mr3systems.com/ MR3]
 
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#''' Green chemistry,''' e.g. as described in the [http://www.epa.gov/greenchemistry/pubs/pgcc/presgcc.html Presidential Green Chemistry Challenge]
 
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# '''Timed degradation,''' e.g. as applied to [http://www.in-pharmatechnologist.com/news/ng.asp?id=55575-vaccines-without-refrigeration vaccine stability] <br>
 
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After watching the video, consider which kind of natural adaptation is the most interesting to you and follow the associated link to read more about it. Then spend '''20 minutes writing an email job request''' to a person associated with that effort. In your email you should introduce yourself, talk about your MIT education and if/how it has helped you explore this area of interest, say what precisely intrigues you about this approach and what you are asking for (e.g. a summer job/a phone conversation/a newspaper interview/a preprint of an article...). Upload your email to the homework drop box that's [https://stellar.mit.edu/S/course/20/sp08/20.020/homework/index.html?toolset=hidden here]<br>
 
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'''Total time''' to spend on this assignment '''<1 hour.'''
 
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=<center>Week 4 Studio</center>=
 
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==<font color = blue>Nip and Tuck</font color>==
 
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In today's studio, project teams will be assigned. These teams are loosely grouped around common interests, be they project areas or project approaches. Once you have assembled into your groups, be sure to introduce yourselves, exchange contact information and figure out which interests landed you on the same team. Then you can use the rest of the studio time to work on your team's "facebook" page. The required content for this page is:
 
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* a name for your team
 
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* the names of your team members
 
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* the names of your team mentors (20.902/947 students who will be the go-to folks for questions and guidance on your project)
 
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* what challenge your team will address
 
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* what ideas you have agreed to work on (at least 3, no more than 5)
 
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As you develop your ideas, you might also want to keep in mind the requirements for your [http://openwetware.org/wiki/20.020:_3_ideas_presentation "3 ideas presentations"] that will take place in two weeks. Think about what you will have to present, and how you would like to present it. Maybe the work could/should be divided up or maybe you need to hash out ideas on the spot together. You will use the remaining time today and all of next week studio time to make real progress on these high level questions about your project. At a minimum, today's work should allow your team's Facebook page to be uploaded to the Team Project section of the homework dropbox that's [https://stellar.mit.edu/S/course/20/sp08/20.020/homework/ here.] Make sure one of your team makes this his/her responsibility.
 
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=<center>Week 4 Thursday</center>=
 
''"The new techniques, which permit combination of genetic information from very different organisms, place us in an area of biology with many unknowns."''  <br>
''"The new techniques, which permit combination of genetic information from very different organisms, place us in an area of biology with many unknowns."''  <br>
Summary Statement of the Asilomar Conference on Recombinant DNA Molecules<br>
Summary Statement of the Asilomar Conference on Recombinant DNA Molecules<br>
Berg et al PNAS 1975 72:1981.  
Berg et al PNAS 1975 72:1981.  
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Starting today and continuing into the next two weeks, we'll consider intentional manipulation of DNA. During this time we'll consider some of the scientific advances that have enabled genetic engineering. For instance, almost any string of genetic material can now be reliably re-ordered. Additionally, the cross-species barriers to DNA transfer have been reduced to a point that its now commonplace to get a gene of interest expressed in an organism even when that gene came from a wholly different critter. These feats would have seemed like science fiction just 50 years ago when Watson and Crick published the double helical structure for DNA. And just as a replication mechanism did not escape Watson and Crick's attention when they described DNA's structure, the potential for positive and negative outcomes from recombinant DNA techniques did not escape anyone's notice when these techniques were developing. Everyone took notice: the scientists involved, the government oversight groups,t he media and the public. As a class, we will consider some of the ethical, legal and policy issues that arose with the advent of recombinant DNA technology. But today we'll step back and consider the DNA material itself.  
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Starting today and continuing into the next two weeks, we'll consider intentional manipulation of DNA. During this time we'll consider some of the scientific advances that have enabled genetic engineering. For instance, almost any string of genetic material can now be reliably re-ordered. Additionally, the cross-species barriers to DNA transfer have been reduced to a point that its now commonplace to get a gene of interest expressed in an organism even when that gene came from a wholly different critter. These feats would have seemed like science fiction just 50 years ago when Watson and Crick published the double helical structure for DNA. And just as a replication mechanism did not escape Watson and Crick's attention when they described DNA's structure, the potential for positive and negative outcomes from recombinant DNA techniques did not escape anyone's notice when these techniques were developing. Everyone took notice: the scientists involved, the government oversight groups, the media and the public. As a class, we will consider some of the ethical, legal and policy issues that arose with the advent of recombinant DNA technology. But today we'll step back and consider the DNA material itself. <center>
*Is DNA (the physical material) inherently dangerous?  
*Is DNA (the physical material) inherently dangerous?  
*What makes it (or could make it) dangerous?  
*What makes it (or could make it) dangerous?  
*How can you tell if it’s dangerous?
*How can you tell if it’s dangerous?
*Are there special places that DNA (the physical material) should be kept?  
*Are there special places that DNA (the physical material) should be kept?  
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*Are there rules that can be enforced about its manipulation?  
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*Are there rules that can be enforced about its manipulation? </center>
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If you've spent time in a research lab, there's a good chance you've worked with DNA there. Is that the only place DNA can be manipulated? What if the techniques and facilities for manipulating DNA were available to everyone? What if they already are? If you've never spent time working with DNA, then you're in for a treat. Today you'll isolate and purify some DNA using materials found in most any kitchen or garage.  
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{| cellspacing="2"
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<div style="padding: .4em .9em .9em">
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<center>'''Why are we doing this??'''</center>
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If you've spent time in a research lab, there's a good chance you've worked with DNA there. But is that the only place DNA can be manipulated? What if the techniques and facilities for manipulating DNA were available to everyone? What if they already are? If you've never spent time working with DNA, then you're in for a treat. Today you'll isolate and purify some DNA using materials found in most any kitchen or garage. And from this challenge, you'll be better able to judge the capabilities and possibilities of "amateur bioengineering." 
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</div>
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|}
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==Challenge: <font color = blue>Backyard Biology</font color>==
==Challenge: <font color = blue>Backyard Biology</font color>==
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===Cookin' up some DNA in your kitchen===
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===Part 1: Cookin' up some DNA in your kitchen===
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#Pour ~50 ml of water into a small white cup
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This protocol is from [http://www.exploratorium.edu/ti/who_we_are/staff_bios.html| Karen Kalumuck] at San Franscisco's [http://www.exploratorium.edu/index.html| Exploratorium]<br>Another variation can be found on the University of Utah's [http://learn.genetics.utah.edu/content/labs/extraction/howto/ Learn.Genetics] site.
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#Add 1 tsp wheat germ and mix with a coffee stirrer for 3 minutes
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=====Materials=====
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#Add one glop of liquid soap
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*Frozen Strawberries
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#Mix a little bit every 1 minute for 5 minutes
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*Seal-able plastic "baggies" (sandwich and gallon)
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#Add 1/4 tsp meat tenderizer and mix
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*No 2 Coffee Filters
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#Add 1/2 tsp baking soda and mix
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*6% solution of NaCl (dissolve 1/2 tablespoon salt in 1/2 cup water) 
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#Allow the slurry to settle and pour some of the top liquid into a clear cup
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*25% strength liquid dish soap (1 part liquid soap into 3 parts water)
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#Dribble some rubbing alcohol down the side of the cup so it sits on top of but does not mix with the wheat germ liquid
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*Eye droppers
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#Over the next 5 minutes watch to see what happens at the interface between the wheat germ liquid and the rubbing alcohol
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*70% Isopropanol
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#Try to spool or scoop out some of the goop with a paper clip hook or eyedropper
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*Toothpicks or coffee stirrer
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=====Steps=====
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#Obtain 2 small to medium sized strawberries
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#Place them in a sandwich-sized seal-able plastic baggie.
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# Add about 1/2 a cup of the 6% NaCl solution, and seal the bag.
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#Squash the strawberry in the salt solution thoroughly, while it's in the baggie.  Try to break up large pieces of berry into mush.
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#Add about 2 tablespoons of the detergent solution.  Seal the baggie and gently mix the berry mush with the detergent.  Avoid producing bubbles/foam.
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#Optional clean up step: Put the entire extraction (strawberry goo, salt, detergent) through a filter -- coffee filter over a cup is just fine.  This gets rid of a lot of the stringy strawberry goo, and the extraction is cleaner. Place the cleaned up material that passes through the filter into a new baggie. 
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#Hold the baggie by one of the upper corners so that the mush accumulates in a corner of the baggie.  Use a pipette or dropper to gently trickle down about 10 - 20 ml of alcohol down a side crease of the baggie.  The alcohol should layer onto the surface of the mush. Hold the bag still (or VERY gently rock back and forth) for 1 minute.
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#Observe what's happening at the interface.  You should use a coffee stirrer to "spool" up the material at the interface, to save for next time.
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===Lego™phoresis===
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===Part 2: Lego™phoresis===
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This design is a variations of the one shown in [http://makezine.com/07/ MAKE magazine, volume 07]  
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====Cast your gel====
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====Part 1: Cast your gel====
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This design is a variation of the one shown in [http://makezine.com/07/ MAKE magazine, volume 07] <br>
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Materials
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=====Materials=====
*small plastic container
*small plastic container
*scissors
*scissors
Line 108: Line 60:
**adjust with more water or baking soda as needed
**adjust with more water or baking soda as needed
*microwave
*microwave
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Design
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Note: you'll cast your gel this time and run the DNA through it next time.
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=====Design=====
[[Image:Lego1.png|300px|left|thumb|Cut ends off small container and tape closed]]
[[Image:Lego1.png|300px|left|thumb|Cut ends off small container and tape closed]]
[[Image:lego2.png|300px|right|thumb|Arrange Lego™s for casting wells]]
[[Image:lego2.png|300px|right|thumb|Arrange Lego™s for casting wells]]
[[Image:lego3.png|300px|left|thumb||Melt 1/2 tablespoon agar-agar with 1/2 cup running buffer in a paper cup and pour gel ~1cm thick. Lego™ casting wells should be embedded in agar-agar while liquid but not touch bottom of container. You might consider resting the casting tray in a larger container in case the tape leaks.]]
[[Image:lego3.png|300px|left|thumb||Melt 1/2 tablespoon agar-agar with 1/2 cup running buffer in a paper cup and pour gel ~1cm thick. Lego™ casting wells should be embedded in agar-agar while liquid but not touch bottom of container. You might consider resting the casting tray in a larger container in case the tape leaks.]]
[[Image:lego4.png|300px|right|thumb|Once gel has solidified, remove Lego™s, tape and add DNA with glycerin/red food coloring]]
[[Image:lego4.png|300px|right|thumb|Once gel has solidified, remove Lego™s, tape and add DNA with glycerin/red food coloring]]
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<br style="clear:both" />
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====Part 2: Run your gel====
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=='''Homework''' before tomorrow's studio session==
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You can find the term "biohacking" and "DIYbio" (for "Do It Yourself Biology) increasingly tossed into conversations and presentations. There are examples ranging from [http://www.aboutus.org/BioHackery.com "how to" websites] to an [http://web.mit.edu/newsoffice/2007/comm-vestspeech-0608.html MIT commencement address.] Begin your follow-up work from today's lecture by '''reading Freeman Dyson's 2007 New York Times article''' in which he writes about [http://www.nybooks.com/articles/20370 "our biotech future."]  He foresees a domestication of biotechnology that will dominate our lives for the next 50 years. He foresees an "era of Open Source biology (in which) the magic of genes will be available to anyone with the skill and imagination to use it."
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Based on your backyard biology experience today, what do you think of the present and future possibilities of biohacking? As a point of comparison you might consider the [http://www.builderau.com.au/blogs/byteclub/viewblogpost.htm?p=339270810 hacking of the iPhone]. Here are some other questions you might consider as you think about this topic:
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*Who can hack computers and who can hack biology?
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*Are there speed, safety, and training considerations?
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*Do you expect to see garage biotechnologists in your lifetime? Do they already exist? Should they?
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Decide for yourself if biohacking is '''confirmed, plausible or busted''' and write-up your reflections. You might include thoughts on today's challenge, on Freemon Dyson's vision, on what you imagine the DIYbio movement will look like in 2 years or in 20. Your paragraph can be added to your "Personal Design Portfolio" in the [https://stellar.mit.edu/S/course/20/sp09/20.020/homework/index.html homework dropbox] before tomorrow's studio session, calling your assignment: FirstInitial_LastName_PDP_7.doc, for example: <font color = red>J_Watson_PDP_7.doc</font color> <br>
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=<center>Week 4 Studio</center>=
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==Part 1: <font color = blue>Nip and Tuck</font color>==
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In today's studio, project teams will be assigned. These teams are loosely grouped around common interests, be they project areas or project approaches. Once you have assembled into your groups, be sure to introduce yourselves, exchange contact information and figure out which interests landed you on the same team. Then you can use the rest of the studio time to work on your team's "facebook" page and your "team contract." The required content for each is:
 +
===Team Facebook Page===
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* a name for your team
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* the names of your team members
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* the names of your team mentors (20.902 students who will be the go-to folks for questions and guidance on your project)
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* what challenge your team will address
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* what ideas you have agreed to work on (at least 3, no more than 5)
 +
As you develop your ideas, you might also want to keep in mind the requirements for your [http://openwetware.org/wiki/20.020:_3_ideas_presentation "3 ideas presentations"] that will take place in two weeks. Think about what you will have to present, and how you would like to present it. Maybe the work could/should be divided up or maybe you need to hash out ideas on the spot together. You will use the time today and all of next week studio time to make real progress on these high level questions about your project.
 +
===Team Contract===
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These team building tools have been developed by [http://engineering.mit.edu/education/special_programs/gordon.php| MIT's Gordon Engineering Leadership Program,] appreciating that teamwork and leadership underlie nearly all successful engineering projects. 
 +
<br>
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Start by reading (independently) [[Media:PhilipsArticlemember of a team.pdf| this short article]] by Patricia Philips that describes the different kinds of teams that exist and some common stages that teams go through. Once everyone has finished reading, discuss the article as a group, paying particular attention to team and individual roles and responsibilities as they may relate to your particular project and team.<br>
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Then as a team, work through the following questions in order to form your team contract. You can work through the questions fast or slow, all of them or just a few. After considering these questions, write a team contract that you can all agree to work with for the rest of this term.
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====Questions To Consider To Create a Team Contract====
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These questions have been adapted from Lori Breslow's work at MIT for the subject, 15.279.
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=====Part 1: Goals=====
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*What are the goals of the team?
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*What are your personal goals for this assignment?
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*What kind of obstacles might you encounter in reaching your goals?
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*What happens if all of you decide you want to get an “A,” but because of time constraints, one person decides that a “B” will be acceptable?
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*Is it acceptable for two or three team members to do more work in order to get an “A” ?
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=====Part 2: Meeting Norms=====
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*Do you have a preference for when meetings will be held? Did you have a preference for where they should be held?
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*How often do you think the team will need to meet outside of class? How long do you anticipate meetings will be?
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*Will it be O.K. for team members to eat during meetings?
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=====Part 3: Work Norms=====
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*How much time per week do you anticipate it will take to make the project successful?
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*How will work be distributed?
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*How will deadlines be set?
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*How will you decide who should do which tasks?
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*What will happen if someone does not follow through on a commitment (e.g., missing a deadline, not showing up to meetings)?
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*How will the work be reviewed?
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*What happens if people have different opinions on the quality of the work?
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*What will you do if one or more team members are not doing their share of the work?
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*How will you deal with different work habits of individual team members (e.g., some people like to get assignments done as early as possible; others like to work under the pressure of a deadline)?
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=====Part 4: Decision Making=====
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*Do you need 100% approval of each team member before making a decision?
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*What will you do if one of you fixates on a particular idea? <br>
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Before you leave today, upload your Team Facebook Page and your Team Contract to the "Project Development Notebook" in the [https://stellar.mit.edu/S/course/20/sp09/20.020/homework/index.html homework dropbox], calling your assignments: TeamName_PDN_1.doc and TeamName_PDN_2.doc, for example: <font color = red>EauDcoli_PDN_1.doc</font color>
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'''Please make sure that every member of your team has a copy of the Facebook Page and the Team Contract.'''
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=<center>Week 4 Thursday</center>=
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==Challenge:<font color = blue> Making Biology Easier to Engineer</font color>==
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===FooCamper's Guide===
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===Optional Challenge: Lego™phoresis (con't)===
Materials
Materials
*steel wire
*steel wire
Line 121: Line 129:
**1/4 tsp glycerine/glycerol
**1/4 tsp glycerine/glycerol
**a few drops red food coloring
**a few drops red food coloring
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**DNA you isolated from wheatgerm
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**DNA you isolated from strawberries
*remaining running buffer from part 1
*remaining running buffer from part 1
*9V batteries
*9V batteries
*Aquarium antimicrobial (ideally 2.3% methylene blue diluted 1:100 in bottled water) to stain DNA in gel after run
*Aquarium antimicrobial (ideally 2.3% methylene blue diluted 1:100 in bottled water) to stain DNA in gel after run
[[Image:Legophoresis.png|300px|thumb|center| 9V batteries in series to power DNA through the gel]]
[[Image:Legophoresis.png|300px|thumb|center| 9V batteries in series to power DNA through the gel]]
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=='''Homework''' for Tuesday's challenge session==
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==Follow-up homework==
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There are three short parts to this assignment and you should '''spend no more than 1 hour''' reading the chapter by Charles Weiner that was photocopied from the "Encyclopedia of Ethical, Legal, and Policy Issues in Biotechnology," and then answering these questions.
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There are 2 parts to today's follow-up!
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*'''Part 1: What is recombinant DNA?'''<br>
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*First, real quick: The "Backyard Biology" project involved four independent tasks
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To illustrate your understanding of genetic engineering techniques, describe how you might make the DNA that programs the GloFish shown [http://en.wikipedia.org/wiki/Recombinant_DNA here][[Image:250px-GloFish.jpg|thumb| image of GloFish from Wikipedia entry about Recombinant DNA]]. Call the gene for glowing "GFG" and the fish plasmid "pFP."
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**1: isolating DNA  
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*'''Part 2: Key events for regulation of experiments involving recombinant DNA'''<br>
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**2: building a gel casting apparatus
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Concisely describe the relevance/importance of
-
**3. casting a gel
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**1973 Gordon Conference
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**4: building an electrophoresis rig
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**1974 Berg letters in Nature and Science
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Was your team able to completw all four tasks in the time alloted? If not, how could you have organized your team differently at the start of the challenge so that you might have had a better chance of finishing.
+
**1975 Conference in Asilomar
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*Second: You can find the term "biohacking" increasingly tossed into conversations and presentations. There are examples ranging from [http://biohackery.com/taxonomy/term/3 "how to" websites] to an [http://web.mit.edu/newsoffice/2007/comm-vestspeech-0608.html MIT commencement address.] Begin your follow-up work from today's lecture by '''reading Freeman Dyson's 2007 New York Times article''' in which he writes about [http://www.nybooks.com/articles/20370 "our biotech future."] He foresees a domestication of biotechnology that will dominate our lives for the next 50 years. He foresees an "era of Open Source biology (in which) the magic of genes will be available to anyone with the skill and imagination to use it."
+
**Recombinant DNA Advisory Committee
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Based on your backyard biology experience today, what do you think of the present and future possibilities of biohacking? As a point of comparison you might consider the [http://www.builderau.com.au/blogs/byteclub/viewblogpost.htm?p=339270810 hacking of the iPhone]. Here are some other questions you might consider as you think about this topic:
+
All of these are described in Charles Weiner's chapter that you were given.
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*Who can hack computers and who can hack biology?
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*'''Part 3: Public scrutiny of and say in research decisions'''
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*Are there speed, safety, and training considerations?
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Consider these three quotes and then
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*Do you expect to see garage biotechnologists in your lifetime? Do they already exist? Should they?
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**give your idea(s) about how to best engage the public in the scientific enterprise
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'''Decide for yourself if biohacking is confirmed, plausible or busted''' <br>
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**comment on '''one''' author's viewpoint or agenda, as best you can glean from the short quote
 +
**and finally say if you think the publication was an appropriate places to express that author's viewpoint
 +
'''Quote 1:''' from pg 910 of Encyclopedia chapter (above) "The motive from the start was to avoid public interference and to demonstrate that the scientists on their own could protect laboratory workers, the public and the environment."<br>
 +
'''Quote 2:''' from [http://profiles.nlm.nih.gov/DJ/B/B/H/F/ Open Letter to the Asilomar Conference] written by Science for the People "There is little evidence that the technologies being discussed at this meeting arise from social or medical needs of large segments of the population. Rather, they represent specialized interests including those of the scientific community itself."<br>
 +
'''Quote 3:''' from [http://www.pnas.org/cgi/reprint/72/6/1981?ck=nck Summary Statement of the Asilomar Conference] written by Paul Berg et al and published in Proceedings of the National Academy of Science "In the longer term, serious problems may arise in the large scale application of this methodology in industry, medicine and agriculture. But it was also recognized that further research and experience may show that many of the potential biohazards are less serious and/or less probable than we now suspect."  
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{| cellspacing="2"
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|width="670px" class="MainPageBG" style="border: 1px solid #336600; color: #000; background-color: #FFFFFF"|
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<div style="padding: .4em .9em .9em">
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<center>'''Why are we doing this??'''</center>
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This homework assignment serves three important purposes for our class. First, it provides some context for the upcoming video presentation of the 1974 Cambridge City Council Hearings. These hearings enabled the citizens of Cambridge to directly address the scientists themselves and question the intent and efficacy of national safety guidelines for recombinant DNA work. The video was made available to us by Charles Weiner and it will be shown on Tuesday in class. Second, this chapter will give some timeline for the development of recombinant DNA technology itself as well as for the meetings and hearings that addressed its hazards. Finally, this chapter gives some insight into the polarizing viewpoints and biases inherent in many of the discussions associated with these issues.
 +
</div>
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|}
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When you have completed this three part assignment, please upload your response to your "Personal Design Portfolio" in the [https://stellar.mit.edu/S/course/20/sp09/20.020/homework/index.html homework dropbox], calling your assignment: FirstInitial_LastName_PDP_8.doc, for example: <font color = red>D_Baltimore_PDP_8.doc</font color> <br>

Current revision

Contents

Week 4 Tuesday

"The new techniques, which permit combination of genetic information from very different organisms, place us in an area of biology with many unknowns."
Summary Statement of the Asilomar Conference on Recombinant DNA Molecules
Berg et al PNAS 1975 72:1981.

Starting today and continuing into the next two weeks, we'll consider intentional manipulation of DNA. During this time we'll consider some of the scientific advances that have enabled genetic engineering. For instance, almost any string of genetic material can now be reliably re-ordered. Additionally, the cross-species barriers to DNA transfer have been reduced to a point that its now commonplace to get a gene of interest expressed in an organism even when that gene came from a wholly different critter. These feats would have seemed like science fiction just 50 years ago when Watson and Crick published the double helical structure for DNA. And just as a replication mechanism did not escape Watson and Crick's attention when they described DNA's structure, the potential for positive and negative outcomes from recombinant DNA techniques did not escape anyone's notice when these techniques were developing. Everyone took notice: the scientists involved, the government oversight groups, the media and the public. As a class, we will consider some of the ethical, legal and policy issues that arose with the advent of recombinant DNA technology. But today we'll step back and consider the DNA material itself.
  • Is DNA (the physical material) inherently dangerous?
  • What makes it (or could make it) dangerous?
  • How can you tell if it’s dangerous?
  • Are there special places that DNA (the physical material) should be kept?
  • Are there rules that can be enforced about its manipulation?
Why are we doing this??

If you've spent time in a research lab, there's a good chance you've worked with DNA there. But is that the only place DNA can be manipulated? What if the techniques and facilities for manipulating DNA were available to everyone? What if they already are? If you've never spent time working with DNA, then you're in for a treat. Today you'll isolate and purify some DNA using materials found in most any kitchen or garage. And from this challenge, you'll be better able to judge the capabilities and possibilities of "amateur bioengineering."

Challenge: Backyard Biology

Part 1: Cookin' up some DNA in your kitchen

This protocol is from Karen Kalumuck at San Franscisco's Exploratorium
Another variation can be found on the University of Utah's Learn.Genetics site.

Materials
  • Frozen Strawberries
  • Seal-able plastic "baggies" (sandwich and gallon)
  • No 2 Coffee Filters
  • 6% solution of NaCl (dissolve 1/2 tablespoon salt in 1/2 cup water)
  • 25% strength liquid dish soap (1 part liquid soap into 3 parts water)
  • Eye droppers
  • 70% Isopropanol
  • Toothpicks or coffee stirrer
Steps
  1. Obtain 2 small to medium sized strawberries
  2. Place them in a sandwich-sized seal-able plastic baggie.
  3. Add about 1/2 a cup of the 6% NaCl solution, and seal the bag.
  4. Squash the strawberry in the salt solution thoroughly, while it's in the baggie. Try to break up large pieces of berry into mush.
  5. Add about 2 tablespoons of the detergent solution. Seal the baggie and gently mix the berry mush with the detergent. Avoid producing bubbles/foam.
  6. Optional clean up step: Put the entire extraction (strawberry goo, salt, detergent) through a filter -- coffee filter over a cup is just fine. This gets rid of a lot of the stringy strawberry goo, and the extraction is cleaner. Place the cleaned up material that passes through the filter into a new baggie.
  7. Hold the baggie by one of the upper corners so that the mush accumulates in a corner of the baggie. Use a pipette or dropper to gently trickle down about 10 - 20 ml of alcohol down a side crease of the baggie. The alcohol should layer onto the surface of the mush. Hold the bag still (or VERY gently rock back and forth) for 1 minute.
  8. Observe what's happening at the interface. You should use a coffee stirrer to "spool" up the material at the interface, to save for next time.

Part 2: Lego™phoresis

Cast your gel

This design is a variation of the one shown in MAKE magazine, volume 07

Materials
  • small plastic container
  • scissors
  • masking tape
  • legos
  • agar-agar
  • running buffer
    • 500 ml bottled water
    • pinch of table salt
    • 1/4 tsp baking soda
    • Aquarium pH kit to check pH ~7.5
    • adjust with more water or baking soda as needed
  • microwave

Note: you'll cast your gel this time and run the DNA through it next time.

Design
Cut ends off small container and tape closed
Cut ends off small container and tape closed
Arrange Lego™s for casting wells
Arrange Lego™s for casting wells
Melt 1/2 tablespoon agar-agar with 1/2 cup running buffer in a paper cup and pour gel ~1cm thick. Lego™ casting wells should be embedded in agar-agar while liquid but not touch bottom of container. You might consider resting the casting tray in a larger container in case the tape leaks.
Melt 1/2 tablespoon agar-agar with 1/2 cup running buffer in a paper cup and pour gel ~1cm thick. Lego™ casting wells should be embedded in agar-agar while liquid but not touch bottom of container. You might consider resting the casting tray in a larger container in case the tape leaks.
Once gel has solidified, remove Lego™s, tape and add DNA with glycerin/red food coloring
Once gel has solidified, remove Lego™s, tape and add DNA with glycerin/red food coloring


Homework before tomorrow's studio session

You can find the term "biohacking" and "DIYbio" (for "Do It Yourself Biology) increasingly tossed into conversations and presentations. There are examples ranging from "how to" websites to an MIT commencement address. Begin your follow-up work from today's lecture by reading Freeman Dyson's 2007 New York Times article in which he writes about "our biotech future." He foresees a domestication of biotechnology that will dominate our lives for the next 50 years. He foresees an "era of Open Source biology (in which) the magic of genes will be available to anyone with the skill and imagination to use it." Based on your backyard biology experience today, what do you think of the present and future possibilities of biohacking? As a point of comparison you might consider the hacking of the iPhone. Here are some other questions you might consider as you think about this topic:

  • Who can hack computers and who can hack biology?
  • Are there speed, safety, and training considerations?
  • Do you expect to see garage biotechnologists in your lifetime? Do they already exist? Should they?

Decide for yourself if biohacking is confirmed, plausible or busted and write-up your reflections. You might include thoughts on today's challenge, on Freemon Dyson's vision, on what you imagine the DIYbio movement will look like in 2 years or in 20. Your paragraph can be added to your "Personal Design Portfolio" in the homework dropbox before tomorrow's studio session, calling your assignment: FirstInitial_LastName_PDP_7.doc, for example: J_Watson_PDP_7.doc

Week 4 Studio

Part 1: Nip and Tuck

In today's studio, project teams will be assigned. These teams are loosely grouped around common interests, be they project areas or project approaches. Once you have assembled into your groups, be sure to introduce yourselves, exchange contact information and figure out which interests landed you on the same team. Then you can use the rest of the studio time to work on your team's "facebook" page and your "team contract." The required content for each is:

Team Facebook Page

  • a name for your team
  • the names of your team members
  • the names of your team mentors (20.902 students who will be the go-to folks for questions and guidance on your project)
  • what challenge your team will address
  • what ideas you have agreed to work on (at least 3, no more than 5)

As you develop your ideas, you might also want to keep in mind the requirements for your "3 ideas presentations" that will take place in two weeks. Think about what you will have to present, and how you would like to present it. Maybe the work could/should be divided up or maybe you need to hash out ideas on the spot together. You will use the time today and all of next week studio time to make real progress on these high level questions about your project.

Team Contract

These team building tools have been developed by MIT's Gordon Engineering Leadership Program, appreciating that teamwork and leadership underlie nearly all successful engineering projects.
Start by reading (independently) this short article by Patricia Philips that describes the different kinds of teams that exist and some common stages that teams go through. Once everyone has finished reading, discuss the article as a group, paying particular attention to team and individual roles and responsibilities as they may relate to your particular project and team.
Then as a team, work through the following questions in order to form your team contract. You can work through the questions fast or slow, all of them or just a few. After considering these questions, write a team contract that you can all agree to work with for the rest of this term.

Questions To Consider To Create a Team Contract

These questions have been adapted from Lori Breslow's work at MIT for the subject, 15.279.

Part 1: Goals
  • What are the goals of the team?
  • What are your personal goals for this assignment?
  • What kind of obstacles might you encounter in reaching your goals?
  • What happens if all of you decide you want to get an “A,” but because of time constraints, one person decides that a “B” will be acceptable?
  • Is it acceptable for two or three team members to do more work in order to get an “A” ?
Part 2: Meeting Norms
  • Do you have a preference for when meetings will be held? Did you have a preference for where they should be held?
  • How often do you think the team will need to meet outside of class? How long do you anticipate meetings will be?
  • Will it be O.K. for team members to eat during meetings?
Part 3: Work Norms
  • How much time per week do you anticipate it will take to make the project successful?
  • How will work be distributed?
  • How will deadlines be set?
  • How will you decide who should do which tasks?
  • What will happen if someone does not follow through on a commitment (e.g., missing a deadline, not showing up to meetings)?
  • How will the work be reviewed?
  • What happens if people have different opinions on the quality of the work?
  • What will you do if one or more team members are not doing their share of the work?
  • How will you deal with different work habits of individual team members (e.g., some people like to get assignments done as early as possible; others like to work under the pressure of a deadline)?
Part 4: Decision Making
  • Do you need 100% approval of each team member before making a decision?
  • What will you do if one of you fixates on a particular idea?

Before you leave today, upload your Team Facebook Page and your Team Contract to the "Project Development Notebook" in the homework dropbox, calling your assignments: TeamName_PDN_1.doc and TeamName_PDN_2.doc, for example: EauDcoli_PDN_1.doc Please make sure that every member of your team has a copy of the Facebook Page and the Team Contract.

Week 4 Thursday

Challenge: Making Biology Easier to Engineer

FooCamper's Guide

Optional Challenge: Lego™phoresis (con't)

Materials

  • steel wire
  • large plastic container
  • loading buffer
    • 1/4 tsp glycerine/glycerol
    • a few drops red food coloring
    • DNA you isolated from strawberries
  • remaining running buffer from part 1
  • 9V batteries
  • Aquarium antimicrobial (ideally 2.3% methylene blue diluted 1:100 in bottled water) to stain DNA in gel after run
9V batteries in series to power DNA through the gel
9V batteries in series to power DNA through the gel

Homework for Tuesday's challenge session

There are three short parts to this assignment and you should spend no more than 1 hour reading the chapter by Charles Weiner that was photocopied from the "Encyclopedia of Ethical, Legal, and Policy Issues in Biotechnology," and then answering these questions.

  • Part 1: What is recombinant DNA?
To illustrate your understanding of genetic engineering techniques, describe how you might make the DNA that programs the GloFish shown here
image of GloFish from Wikipedia entry about Recombinant DNA
image of GloFish from Wikipedia entry about Recombinant DNA
. Call the gene for glowing "GFG" and the fish plasmid "pFP."
  • Part 2: Key events for regulation of experiments involving recombinant DNA

Concisely describe the relevance/importance of

    • 1973 Gordon Conference
    • 1974 Berg letters in Nature and Science
    • 1975 Conference in Asilomar
    • Recombinant DNA Advisory Committee

All of these are described in Charles Weiner's chapter that you were given.

  • Part 3: Public scrutiny of and say in research decisions

Consider these three quotes and then

    • give your idea(s) about how to best engage the public in the scientific enterprise
    • comment on one author's viewpoint or agenda, as best you can glean from the short quote
    • and finally say if you think the publication was an appropriate places to express that author's viewpoint

Quote 1: from pg 910 of Encyclopedia chapter (above) "The motive from the start was to avoid public interference and to demonstrate that the scientists on their own could protect laboratory workers, the public and the environment."
Quote 2: from Open Letter to the Asilomar Conference written by Science for the People "There is little evidence that the technologies being discussed at this meeting arise from social or medical needs of large segments of the population. Rather, they represent specialized interests including those of the scientific community itself."
Quote 3: from Summary Statement of the Asilomar Conference written by Paul Berg et al and published in Proceedings of the National Academy of Science "In the longer term, serious problems may arise in the large scale application of this methodology in industry, medicine and agriculture. But it was also recognized that further research and experience may show that many of the potential biohazards are less serious and/or less probable than we now suspect."

Why are we doing this??

This homework assignment serves three important purposes for our class. First, it provides some context for the upcoming video presentation of the 1974 Cambridge City Council Hearings. These hearings enabled the citizens of Cambridge to directly address the scientists themselves and question the intent and efficacy of national safety guidelines for recombinant DNA work. The video was made available to us by Charles Weiner and it will be shown on Tuesday in class. Second, this chapter will give some timeline for the development of recombinant DNA technology itself as well as for the meetings and hearings that addressed its hazards. Finally, this chapter gives some insight into the polarizing viewpoints and biases inherent in many of the discussions associated with these issues.

When you have completed this three part assignment, please upload your response to your "Personal Design Portfolio" in the homework dropbox, calling your assignment: FirstInitial_LastName_PDP_8.doc, for example: D_Baltimore_PDP_8.doc
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