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

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=<center>Week 11 Studio</center>=
=<center>Week 11 Studio</center>=
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After the challenge, consider the following questions:
After the challenge, consider the following questions:
#Was it easy or hard to license parts?
#Was it easy or difficult to license parts?
#What determined the value of a part? Did inventors tend to overvalue parts? Did investors tend to undervalue parts?
#What determined the value of a part? Did inventors tend to overvalue parts? Did investors tend to undervalue parts?
#The challenge system contained 12 parts.  What would happen if you needed to assemble a system that contained 100 parts?  Or, 1000 parts?
#Were any parts licensed for free?  Why?
#The challenge system in today's class contained 12 parts.  Would it be easier or more difficult to license the parts for a system that contained fewer parts (e.g., 3 parts)?  What about more parts (e.g., 100 parts)?


==Part 2: <font color = blue>Project Redesign Day 2 </font color>==
==Part 2: <font color = blue>Project Redesign Day 2 </font color>==
The rest of Wednesday's class is for working on projects.  There's today, tomorrow and next week left to work!


=<center>Week 11 Thursday</center>=
=<center>Week 11 Thursday</center>=
==Challenge: <font color = blue> Parts</font color>==
==Challenge: <font color = blue> Parts</font color>==
===Poetry by Numbers===
==Part 1: <font color = blue>Poetic Parts</font color>==
Inspired by This American Life #354: Mistakes Were Made
This challenge was inspired by This American Life [http://www.thisamericanlife.org/Radio_Episode.aspx?episode=354 #354: Mistakes Were Made]<br>
 
Consider the content of [http://www.poets.org/viewmedia.php/prmMID/15535  ‘This is Just to Say”] a poem by William Carlos Williams
 
====Poem 1====
====Poem 1====
Consider the content of [http://www.poets.org/viewmedia.php/prmMID/15535  ‘This is Just to Say”] a poem by William Carlos Williams


I have eaten<br>
I have eaten<br>
Line 53: Line 56:
so sweet<br>
so sweet<br>
and so cold<br>
and so cold<br>
The poem is often taught in poetry classes and often spoofed. Consider, for instance, these 2 spoofs by [http://www.radio-sweethearts.com/2008/04/21/public-radio-poetry-vol-3-william-carlos-williams-on-this-american-life/ Kenneth Koch]:<br>


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


Last evening<br>
Last evening<br>
Line 71: Line 75:
I am sorry, but it was morning, and I had nothing to do<br>
I am sorry, but it was morning, and I had nothing to do<br>
and its wooden beams were so inviting.<br>
and its wooden beams were so inviting.<br>
And one more spoof from the blog [http://somewhereinthesuburbs.wordpress.com/2008/04/21/this-is-just-to-say/ somewhere in the suburbs]<br>


====Poem 4====
====Poem 4====
And one more spoof from the blog [http://somewhereinthesuburbs.wordpress.com/2008/04/21/this-is-just-to-say/ somewhere in the suburbs]<br>


I have dried<br>
I have dried<br>
Line 89: Line 95:
so short<br>
so short<br>
and so small<br>
and so small<br>
===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  
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  
Line 163: Line 167:
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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."  
Well shoot, that's horrible. For one thing: It doesn't say anything understandable---this can be broadly described as a problem of '''functional compostion'''. For another thing: the connection between the different elements is, well, "awkward" at best---this can be broadly described as a problem of '''physical composition'''. If physical and functional composition of poems were working perfectly then every part would grammatically connect to the ones that flank it, and the meaning of the connected pieces would be interpretable at worst and clear at best.  
 
==Part 2: <font color = blue>Genetic Parts</font color>==
 
The physical and functional assembly of the poetic parts can be mapped to biological engineering once we define what a genetic "part" is. Let's start by extending what we did with the William Carlos Williams poem, namely let's consider a few natural genetic compositions, see what common elements compose them, and then try to bin these so we might compose new genetic elements by mixing and matching parts.
 
The bacterial lac operon is one we're already familiar with from our conversation with Jon Beckwith earlier in the term.
[[Image:Lac operon1.png|600 px]]
 
There are several genes encoded by this composition. LacI is made and we can see it's flanked by a promoter and a terminator. Lac Z, Y, and A are also made and they are flanked by a promoter + an operator on one end and a terminator on the other. So some genetic parts we might consider naming are:
*promoter
*operator
*protein-coding gene
*transcriptional terminator
 
Recombinant DNA technology gives us great power to move pieces of DNA around but it doesn't answer all the questions we might have about the resulting composition. For instance, are promoters/operators/genes and terminators all the parts we need to write a genetic program. Would the promoter that's in front of LacI make sense in front of LacZ, Y, and A? Is there something important about the junction of the parts?
An introduction to systematic examination and nomenclature of genetic parts, watch Device dude and Systems Sally's introduction to [http://biobuilder.org/part.html Parts]
 


These problems in assembly of the poetic parts are discussed in the realm of biological engineering as problems of  
==Part 3: <font color = blue> The Registry of Standard Biological Parts</font color>==
#"functional composition" (put the parts together in the right pattern but the outcome doesn't make sense) and
The animation ends with a screen shot from the [http://bbf.openwetware.org/ BioBricks Foundation] a not-for-profit organization that "encourages the development and responsible use of technologies based on BioBrick™ standard DNA parts that encode basic biological functions." BioBricks™ represent one kind of standard biological parts, standardized to enable reliable physical composition.
#physical composition (enabled by a common junction between parts so you don't get gibberish like, "I chopped down the house and which...")
Just as we mixed and matched poetic elements, here are some mixed and matched genetic elements made from BioBrick™ parts.  
<center>
[[Image:BBa_I13603.png]]<br>
[[Image:BBA-I13521.png]]<br>
[[Image:Be109BBa M30010.jpg]]<br>
[[Image:BBa_J44011.png]]<br>
</center>


As introduction to genetic parts, watch Device dude and Systems Sally's introduction to [http://biobuilder.org/part.html Parts]
Just as we could identify "forgive me"-ish elements in the "this is just to say poems" we can see common elements in these genetic compositions: the green arrow element which is = a promoter, but which comes in different flavors (I13452, R0040 or R0011), the red stop signs = transcriptional terminators (B0010, B0012).  


The part numbers as well as the DNA itself are collected at the [http://parts.mit.edu/registry/index.php/Main_Page Registry of Standard Biological Parts].


==Challenge: <font color = blue> Registry</font color>==
For your final project in this class, you will enter a part into the registry. We'll show you some good parts and some good documentation in class so you can model your work on those examples.

Latest revision as of 13:37, 6 June 2008

<html> <style>#en2020 a {color:black;}</style> </html>

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, perhaps, great profits!

After the challenge, consider the following questions:

  1. Was it easy or difficult to license parts?
  2. What determined the value of a part? Did inventors tend to overvalue parts? Did investors tend to undervalue parts?
  3. Were any parts licensed for free? Why?
  4. The challenge system in today's class contained 12 parts. Would it be easier or more difficult to license the parts for a system that contained fewer parts (e.g., 3 parts)? What about more parts (e.g., 100 parts)?

Part 2: Project Redesign Day 2

The rest of Wednesday's class is for working on projects. There's today, tomorrow and next week left to work!

Week 11 Thursday

Challenge: Parts

Part 1: Poetic Parts

This challenge was inspired by This American Life #354: Mistakes Were Made

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

Poem 1

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

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

Poem 2

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.


And one more spoof from the blog somewhere in the suburbs

Poem 4

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

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---this can be broadly described as a problem of functional compostion. For another thing: the connection between the different elements is, well, "awkward" at best---this can be broadly described as a problem of physical composition. If physical and functional composition of poems were working perfectly then every part would grammatically connect to the ones that flank it, and the meaning of the connected pieces would be interpretable at worst and clear at best.

Part 2: Genetic Parts

The physical and functional assembly of the poetic parts can be mapped to biological engineering once we define what a genetic "part" is. Let's start by extending what we did with the William Carlos Williams poem, namely let's consider a few natural genetic compositions, see what common elements compose them, and then try to bin these so we might compose new genetic elements by mixing and matching parts.

The bacterial lac operon is one we're already familiar with from our conversation with Jon Beckwith earlier in the term.

There are several genes encoded by this composition. LacI is made and we can see it's flanked by a promoter and a terminator. Lac Z, Y, and A are also made and they are flanked by a promoter + an operator on one end and a terminator on the other. So some genetic parts we might consider naming are:

  • promoter
  • operator
  • protein-coding gene
  • transcriptional terminator

Recombinant DNA technology gives us great power to move pieces of DNA around but it doesn't answer all the questions we might have about the resulting composition. For instance, are promoters/operators/genes and terminators all the parts we need to write a genetic program. Would the promoter that's in front of LacI make sense in front of LacZ, Y, and A? Is there something important about the junction of the parts? An introduction to systematic examination and nomenclature of genetic parts, watch Device dude and Systems Sally's introduction to Parts


Part 3: The Registry of Standard Biological Parts

The animation ends with a screen shot from the BioBricks Foundation a not-for-profit organization that "encourages the development and responsible use of technologies based on BioBrick™ standard DNA parts that encode basic biological functions." BioBricks™ represent one kind of standard biological parts, standardized to enable reliable physical composition.

Just as we mixed and matched poetic elements, here are some mixed and matched genetic elements made from BioBrick™ parts.





Just as we could identify "forgive me"-ish elements in the "this is just to say poems" we can see common elements in these genetic compositions: the green arrow element which is = a promoter, but which comes in different flavors (I13452, R0040 or R0011), the red stop signs = transcriptional terminators (B0010, B0012).

The part numbers as well as the DNA itself are collected at the Registry of Standard Biological Parts.

For your final project in this class, you will enter a part into the registry. We'll show you some good parts and some good documentation in class so you can model your work on those examples.

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