2020(S10) Lecture:week 4

= Week 4 Tuesday =

The envelope please...
The final groups are

Starting a 4 part challenge
"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 over 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."

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

 * Strawberries (frozen or fresh)
 * 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 or to run on the Lego-Phoresis gel if it's ready.

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

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

Design


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: 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
 * 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?

= 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
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.
 * 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)

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) [[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. 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
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.
 * 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?

= Week 4 Thursday =

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

Homework for Tuesday's challenge session
There are two short parts to this assignment and you should spend no more than 1 hour reading the first two pages of [[Media:Bdg final.pdf| this essay,]] and the chapter by Charles Weiner that was photocopied from the "Encyclopedia of Ethical, Legal, and Policy Issues in Biotechnology." Our guest speaker next week, Mark Ptashne, has offered to talk about his life in science and on the widely applicable lessons learned from a simple system like the phage lambda. He has been quoted as saying, A few simple principles underlie gene regulation across the board, from bacteria to yeast, plants, fruit flies and humans. As part 1 of your homework today you'll show your understanding of these "simple principles." Please download [[Media:Phagelambda review.pdf| the following image]] and label as indicated. You can hand in a hard copy of your work on Tuesday of next week, or you can scan it and upload the finished version to the Stellar website. A generation ago, there were many key events that established our current practices for the regulation of experiments involving recombinant DNA. Among these were: All of these are described in Charles Weiner's chapter that you were given and you can familiarize yourself with the details there. 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 filed with Maxine Singer's papers at the National Library of Medicine 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."
 * Part 1: Do the lambda switch
 * Part 2: Public scrutiny of research decisions
 * the 1973 Gordon Conference
 * the 1974 Berg letters in Nature and Science
 * the 1975 Conference in Asilomar
 * the establishment of the Recombinant DNA Advisory Committee
 * Then choose ONE of the three quotes shown below and:
 * 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

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 1976 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 two part assignment, please upload what you can of 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