2020(S09) Lecture:week 4

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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, 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.  
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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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<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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==Challenge: <font color = blue>Backyard Biology</font color>==
==Challenge: <font color = blue>Backyard Biology</font color>==

Revision as of 21:19, 2 January 2009

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

  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

Part 2: Lego™phoresis

Cast your gel

This design is a variations 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

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

Run your gel (if there's time!)

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
9V batteries in series to power DNA through the gel
9V batteries in series to power DNA through the gel

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 on the today's challenge, Freemon Dyson's vision and 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 the homework dropbox. before tomorrow's studio session, calling your assignment: FirstInitial_LastName_PDP_6.doc, for example: J_Watson_PDP_6.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. The required content for this page is:

  • 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)

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.

Part 2: GEL team roles

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Week 4 Thursday
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