2020(S08) Lecture:week 4

= Week 4 Tuesday =

Challenge: Superman vs Batman
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 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! 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?). 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)! First, consider this 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? Now check out these two movies of damselflies in flight: Movie 1, 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. Next, consider this 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. Jumping ahead ~100 years, note that we (i.e., humans) are now pretty good at building "first-order" flying machines (e.g., the 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 video of simulated airflow around a model for a plane. Next, consider this simulation of airflow past an unmanned aerial vehicle. Also, consider this 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? 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: Movie 1, 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? Finally, check out these videos: 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. Before leaving lecture today, complete your response log entry. In your response, you should note: Upload these responses to the lecture response log in the homework dropbox that's here
 * mobility,
 * fighting abilities,
 * fighting style and,
 * vulnerabilities.
 * 1) Wingsuits
 * 2) Jetdude
 * 3) Robotic Fly
 * 4) MIT Daedalus
 * what the activity was
 * why you think it might have been included in this class
 * if the activity helped you think about:
 * ways to make biology easier to engineer
 * consequences of successfully engineering biology
 * clever ways nature solves physical challenges
 * ways nature innovates
 * if the activity has given you any new tools/considerations that could be useful for your project.

Follow-up homework
Spend 20 minutes watching Janine Benyus present "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: 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 here Total time to spend on this assignment <1 hour. = Week 4 Studio =
 * 1) Self-assembly, e.g. the work of Jeff Brinker and that at the Sandia Nat'l Labs
 * 2) Biomineralization, e.g. the work of Joanna Aizenberg at Lucent
 * 3)  CO2 as feedstock, e.g. the work of Geoff Coates at Cornell
 * 4) Solar transformations, e.g. using purple bacteria as they do at ASU
 * 5) The power of shape, e.g. the whale's fin as studied by Frank Fish
 * 6) Water harvesting, e.g. the way the Stenocara beetle does, as described by the Biomimicry Guild
 * 7) Separation techniques, e.g. metals without mining at MR3
 * 8)  Green chemistry, e.g. as described in the Presidential Green Chemistry Challenge
 * 9) Timed degradation, e.g. as applied to vaccine stability

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. The required content for this page is: 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 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 here. Make sure one of your team makes this his/her responsibility.
 * a name for your team
 * the names of your team members
 * the names of your team mentors (20.902/947 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)

= Week 4 Thursday = "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,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. 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.
 * 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?

Cookin' up some DNA in your kitchen

 * 1) Pour ~50 ml of water into a small white cup
 * 2) Add 1 tsp wheat germ and mix with a coffee stirrer for 3 minutes
 * 3) Add one glop of liquid soap
 * 4) Mix a little bit every 1 minute for 5 minutes
 * 5) Add 1/4 tsp meat tenderizer and mix
 * 6) Add 1/2 tsp baking soda and mix
 * 7) Allow the slurry to settle and pour some of the top liquid into a clear cup
 * 8) 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
 * 9) Over the next 5 minutes watch to see what happens at the interface between the wheat germ liquid and the rubbing alcohol
 * 10) Try to spool or scoop out some of the goop with a paper clip hook or eyedropper

Lego™phoresis
This design is a variations of the one shown in MAKE magazine, volume 07

Part 1: Cast your gel
Materials Design
 * 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

Part 2: Run your gel
Materials
 * steel wire
 * large plastic container
 * loading buffer
 * 1/4 tsp glycerine/glycerol
 * a few drops red food coloring
 * DNA you isolated from wheatgerm
 * 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

Follow-up homework
There are 2 parts to today's follow-up! Was your team able to complet all four tasks in teh tie 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. 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: Decide for yourself if biohacking is confirmed, plausible or busted and then post your ideas, examples and opinions to the homework drop box that's here
 * First, real quick: The "Backyard Biology" project involved four independent tasks
 * 1: isolating DNA
 * 2: building a gel casting apparatus
 * 3. casting a gel
 * 4: building an electrophoresis rig
 * Second: You can find the term "biohacking" 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."
 * 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?