2020(S08) Lecture:week 11: Difference between revisions

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#The gene encoding the "BAT2" enzyme
#The gene encoding the "BAT2" enzyme
#The gene encoding the "THI3" enzyme
#The gene encoding the "THI3" enzyme
Good luck (and profits)!


==Part 2: <font color = blue>Project Redesign Day 2 </font color>==
==Part 2: <font color = blue>Project Redesign Day 2 </font color>==

Revision as of 08:19, 23 April 2008

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Week 11 Studio

Part 1: Ownership and Sharing Challenge

Many useful genetic parts are currently protected by patents. For example, "uses of green fluorescent protein" is protected by United States Patent #5,491,084. At least 200 more recent patents protect additional uses of various fluorescent proteins. Patents are a legislated form of "intellectual property" by which inventors are granted a limited-time monopoly (~17 years) during which they can control access to the patented technology (e.g., by selling exclusive or non-exclusive licenses). In establishing the U.S. patent system, the founders of our country wanted to balance the sharing of inventions (e.g., via the publishing of patent applications) while also encouraging the investment and profit needed to drive innovation.

For today's challenge, many of your classmates will act as the inventors and patent holders of various genetic parts; each patent holder may license the use of their patents for profit (exclusively or non-exclusively), or give away the rights for free. Other classmates will act as investors who are seeking to license the complete set of genetic parts needed to encode the now familiar Eau d'E.coli system.

The first investor who is able to acquire licenses for all the genetic parts needed to encode the full Eau d'E.coli system will earn $100 in real cash money. This winning investor (if any) will be required to pay all inventors whatever fees might have been negotiated in obtaining the rights to use various genetic parts. If the promised fees are less than $100 then the investor can keep any additional cash. If the promised fees are greater than $100 then the investor must pay all additional licensing fees out of their own cash reserves.

The 12 components needed to produce a full Eau d'E.coli system are:

  1. A genetically encoded "inverter"
  2. A "constitutive PoPS source"
  3. A "stationary phase PoPS source"
  4. A "transcription terminator"
  5. A "weak ribosome binding site"
  6. A "strong ribosome binding site"
  7. The gene encoding the "ATF1" enzyme
  8. The gene encoding the "BSMT" enzyme
  9. The gene encoding the "PCHA" enzyme
  10. The gene encoding the "PCHB" enzyme
  11. The gene encoding the "BAT2" enzyme
  12. The gene encoding the "THI3" enzyme

Good luck (and profits)!

Part 2: Project Redesign Day 2

Week 11 Thursday

Challenge: Parts

Poetry by Numbers

Inspired by This American Life #354: Mistakes Were Made

Poem 1

Consider the content of ‘This is Just to Say” a poem by William Carlos Williams

I have eaten
the plums
that were in
the icebox
and which
you were probably
saving
for breakfast
Forgive me
they were delicious
so sweet
and so cold

Poem 2

The poem is often taught in poetry classes and often spoofed. Consider, for instance, these 2 spoofs by Kenneth Koch:

Last evening
we went dancing
and I broke your leg
Forgive me
I was clumsy and
I wanted you here
in the wards
where I am the doctor

Poem 3

I chopped down the house that you had been saving to live in next summer.
I am sorry, but it was morning, and I had nothing to do
and its wooden beams were so inviting.

Poem 4

And one more spoof from the blog somewhere in the suburbs

I have dried
the shirt
made of 100% cotton
that was on your floor
and which
you were probably
planning
to air dry
Forgive me
if you had sorted
your own laundry
it would not be
so short
and so small

Poetic Parts

If you wanted to write your own spoof of the William Carlos Williams poem, you might begin by comparing the structure of these four poems. As a starting point they can be broken into 5 elements, namely

  • 2 part situation
  • “forgive me,” and
  • 2 part explanation.

For each poem, these elements are:

Situation (part 1) Situation (part 2) Forgive me Explanation (part 1) Explanation (part 2)
I have eaten the plums that were in the icebox and which you were probably saving for breakfast Forgive me they were delicious so sweet and so cold
Last evening we went dancing and I broke your leg Forgive me I was clumsy and I wanted you here in the wards where I am the doctor
I chopped down the house that you had been saving to live in next summer. I am sorry, but it was morning, and I had nothing to do and its wooden beams were so inviting.
I have dried the shirt made of 100% cotton that was on your floor and which you were probably planning to air dry Forgive me if you had sorted your own laundry it would not be so short and so small

Mix & Match Poetry

Now we can try to swap these poetic elements to see what interesting and clever spoofs we write. How about:

Situation (part 1) Situation (part 2) Forgive me Explanation (part 1) Explanation (part 2)
I have eaten the plums that were in the icebox and I broke your leg Forgive me but it was morning, and I had nothing to do and I wanted you here in the wards where I am the doctor

That seems to work but is it better? Let's try again:

Situation (part 1) Situation (part 2) Forgive me Explanation (part 1) Explanation (part 2)
I chopped down the house and which you were probably planning to air dry Forgive me they were delicious it would not be so short and so small

Well shoot, that's horrible. For one thing: It doesn't say anything understandable and for another thing: the connection between the different elements is, well, "awkward."

These problems in assembly of the poetic parts are discussed in the realm of biological engineering as problems of

  1. "functional composition" (put the parts together in the right pattern but the outcome doesn't make sense) and
  2. physical composition (enabled by a common junction between parts so you don't get gibberish like, "I chopped down the house and which...")

As introduction to genetic parts, watch Device dude and Systems Sally's introduction to Parts


Challenge: Registry

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