Endy:Writing:CCfGDScript
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Chapter 1 - Programming DNA
- Panel 0. Programming DNA
- graphics, title, and credits as appropriate?
- Panel 1. River of Life
- Setting -- little amorphous, faceless, bacterial cells burbling along replicating and racing from the distant past into the distant future (let's call this the River of Life?). The first half of Hardy's poem Heredity about the "family face" sets the mood. Sally and Dude stand overlooking the burbling river of replicating cells. Dude wants to get the cells to do something. Sally does too, but she's feeling more circumspect about taking responsibility for the consequences of success.
- Dialog (all dialog is very drafty/primitive at this point, please just use a placeholder?)
- Dude: Check out those bacteria, they're not doing anything useful. Let's get them to do something for us!
- Sally: How do we know what we want them to do? That what we want will really be useful?
- Dude: We'll only find out by trying! Let's grab one!
- Panel 2. Opening the Hood
- Setting -- Dude has grabbed hold of a squirmy bacteria (buddy). Buddy doesn't really care at this point what's going on, just moving on through the river of life. Sally and Dude need to discuss how Buddy works and how they can program buddy (this might best play out over the next two panels?).
- Dialog
- Dude: How do these things work anyway?
- Sally: All living things run on programs made of DNA. Each of these cells has their own program, called the genome. Check it out!
- (At this point Dude and Sally need some mechanism to "enter" into the cell, or at least change perspective so that they can visualize what's going on in the cell, we'll need to use this change of perspective later)
- Panel 3. Kicking the Tires
- Setting -- Dude and Sally are now inside, or looking inside the cell, they're considering this long snake object, a double helix string of A, T, C, G.
- Dialog
- Sally: That's the master program running the cell.
- Dude: So, that's what we change if we want to reprogram this critter? Looks easy!
- Sally: Change or add to it, but it's not so easy, because nobody completely understands how the program works exactly in the first place
- Dude: I don't have a perfect understanding for anything.
- Sally: No matter. What do you want to try?
- Dude: (Thinking)
- Panel 4. Drawing Board
- Setting -- Back outside cell, Dude is scheming and sketching out lots of ideas (at a board?). Sally is observing thoughtfully. Possible sketches on the board include bacteria blasting off into space, a bacteria chorus line, bacteria toothpaste (Buddy Brand!), etc. Buddy is bouncing quietly off the walls in the background.
- Dialog
- Sally: I'm not sure bacteria can do that?
- Dude: Wanna bet? I'm gonna make bacteria balloons!
- Sally: Uh huh? (skeptical)
- Dude: All I need to do is make them form a closed film, then start producing hydrogen gas, then... (working on sketch at board).
- Dude: OK, got it. So, uh, how do I program this thing (points at Buddy, Buddy stops bouncing)?
- Panel 5. Rubber Meet Road
- Setting -- Still in workspace. Dude is ready to get to work, but needs advice from Sally. Buddy is still bouncing around.
- Dialog
- Sally: (somewhat patronizing) Get the DNA that encodes your program and put it inside Buddy here (Buddy may exhibit a minor look of concern at this point)
- Dude: OK, I need one Balloon-o-Genesis and a Gas-o-Matic module.
- Sally: Get them from the catalog (Sally hand's Dude the Registry of Parts book)
- Dude: (pages through book) OK, got 'em. Now what?
- Panel 6. Biological Speculation
- Setting -- Still in workspace. Dude's got his genetic program and is gonna load it into Buddy. Buddy is bouncing around again?
- Dialog
- Sally: Load your DNA into Buddy and let 'er rip! (Sally hands Dude some sort of DNA loader device)
- Dude: Help me catch this thing (finally catches Buddy, loads in DNA, might zoom into cell here, showing DNA going inside?)
- Buddy: Meep!
- Sally: You might want to stand back.
- Panel 7. Let 'er Rip!
- Setting -- Still in workspace. Dude and Sally are watching Buddy with great interst, waiting to see what happens.
- Dialog
- Buddy: (Looking a little different that before, maybe a bit squeamish)
- Dude: check it out, it's changing!
- Buddy: (starts dividing a lot, making a balloon made up of many Buddy's on the floor, or wherever Buddy is at that point)
- Panel 8. Icarus
- Setting -- Buddy balloon has taken flight, goes up towards ceiling, but then POP!
- Dialog
- Dude: Check it out! It's working!!! Sweet (does a little dance?)
- Buddy Balloon: (looking a little greenish)
- Sally: Hmm. That doesn't look right
- Buddy Balloon: (BANG!)
- Dude: Whaaat? What was that?
- Sally: You forgot to tell your program to stop! It kept going until it was too late.
- Dude: Hmm. I better learn more about what I'm doing before I try anything else
- Sally: Good idea!
Chapter 2 - A Genetic Device
- Panel 0. A Genetic Device
- graphics, title, and credits as appropriate?
- Panel 1. Pondering
- Setting -- Dude is somewhere (hilltop, overlooking River of Life?) trying to figure out what went wrong with Buddy. Sally is nearby.
- Dialog
- Dude: If only I'd some way to stop my Balloon program from growing too much!
- Sally: You know, if you'd included an INVERTER device, hooked up to balloon size, that'd do the trick!?
- Dude: What the heck is an inverter?!
- Sally: (grins knowingly)
- Panel 2. Back to School
- Setting -- Back at the drawing board. This time Sally is schooling Dude. There's a sketch of a genetic inverter on the board. picture of inverter and accompanying text.
- Dialog
- Sally: OK, pay attention! An INVERTER is a combination of basic genetic parts that, working together, turn something upside down. ON becomes OFF, Low becomes High, and so on.
- Dude: Uhm...
- Sally: We call an inverter a DEVICE in order to hide all the details of how it works.
- Dude: OK.
- Sally: TAATACGACTCACTATAGGGAGA. What's that do?
- Dude: (blank look) Dunno (sheepish)
- Sally: That's the point. You shouldn't have to memorize every last piece of DNA. We're going to hide all these details inside the DEVICE.
- Dude: Phew (relief). But how do we do that?
- Panel 3. Black Box
- Setting -- Sally is still schooling Dude. Maybe there's some Buddy residue that at this point has started to recover and is growing into a normal, single Buddy cell. There's still a sketch of a genetic inverter on the board.
- Dialog
- Sally: This is how you make an INVERTER DEVICE. First a RBS, then a ORF, then a Terminator followed by a break. Finally grab another piece of DNA and put an Operator there. Wrap it all in a Black Box and VOILA! We've got ourselves an genetic inverter! High Input, Low Output and vice versa! (Sally's looking pretty kickass at this point) [do we need an explanatory box at top of this panel?]
- Dude: (looking not so kickass, slowly says...) ....OK, but, uh, how does the, uh, inverter(?) work?
- Panel 4. The Man Who Knew Too Much
- Setting -- Sally is still schooling Dude. Buddy's back on his feet, err, flagella.
- Dialog
- Sally: (lecture mode) ...when the input signal is high, the repressor protein is kicked up, and that turns off the output signal. OK?
- Dude: (earnest student mode) Got it!
- Sally: but, the entire point of all this is that we are gonna hide all these details inside a black box, so that you don't have to remember all this stuff (Sally gives Dude a Black Box with some DNA dangling in one side and out the other)
- Dude: Sweet. Genetic Devices. I'm gonna make a whole bunch of 'em!
- Sally: Good luck!
Chapter 3 - Common Signal Carrier
- Panel 0. A Common Signal Carrier for Genetic Devices
- graphics, title, and credits as appropriate?
- Panel 1. Practice Makes Perfect
- Setting -- Dude is in his workshop, making genetic devices (inverters). He's got a ton of black boxes laying all over the place. Sally is sauntering in. Buddy is dancing about (or absent if no room).
- Dialog
- Sally: Dude! What are you doing?
- Dude: Making genetically encoded inverters! (grinning)
- [Panel Break?]
- Sally: Cool! I've been wanting to make a ring oscillator, all I need are three of your inverters!
- Dude: No problem! Here are my best inverters! (pridefully hands Sallys three boxes, but with different "wires" sticking out of each box: A->B, C->D, E->F or whatever works, could be color, shape, or some other property of the "wires" sticking out of each box).
- Sallys: Thanks! I think... (looks at Dude's inverters kinda funny... walks out, or not)
- Panel 2. Reckoning
- Setting -- Dude is still in his workshop, looking proudly at his myriad genetic devices (they can have all sorts of labels on them).
- Dialog
- Sally: Dude! What were you doing?
- Dude: Huh? What's wrong? (gulp)
- Sally: Your genetic devices, I can't hook them up to each other. (pissed)
- Dude: Aye! Why not?
- Sally: They send and receive signals using different proteins!
- Sally: Your genetic devices are no good (sweeps hand across all of Dude's workshop?)
- Dude: Hmm. I never thought of that (sigh).
- Panel 3. Resurrection
- Setting -- Dude is looking down. Sally is about to give him a boost of encouragement, or open fire depending on how things go...
- Dialog
- Sally: Dude. Why not make some better devices, that can be re-used in combination?
- Dude: How?
- Sally: The problem with your old devices is that the Input and Ouput signals are carried by different proteins.
- Dude: But we can measure protein concentrations (points at Buddy, Buddy looks happy).
- Sally: So? (still patient)
- Dude:But I get a prize for discovering an important protein (looks important, Buddy mirrors importance)
- Sally: So? (getting cross)
- Dude: (less sure) But... the state of a cell is best defined by the number of molecules that make up the cell?
- Sally: Maybe not! (Buddy meeps!) Why don't you try something different?
- Panel 4. Itch Scratching
- Setting -- Dude is buring the midnight oil... sketches of inverters back on board in the workshop...
- Dialog
- Dude: (to himself) Hmm...
- Dude: (to himself) What about? (works out something at the board, re-draws correct inverter schema)
- Dude: Check this out!
- Sally: What? (smug)
- Dude: Now my inverters send and receive signal via the rates of gene expression into and out of the device!
- Sally: Nice! (congratulatory)
- Panel 5. Explanation
- Setting -- In the board, or on the DNA itself. This is the panel where the reader might get to ride through the workings of the inverter as per thoughts at the bottom of this page
- Dialog
- Dude: (to himself) When the input rate is HIGH, the Repressor protein gets made, it shoots up and lands on the operator site, and thus the output rate is LOW. When the input rate is low, no Repressor gets made, so the output is LOW!
- Sally: Very good! But what exactly is the rate? (cautiously optimistic)
- Dude: Rate of gene expression!
- Sally: What's that exactly?!
- Panel 6. Current for Gene Expression
- Setting -- On the DNA itself. This is the panel where the reader should experience PoPS (polymerase per second) first hand. Dialog is via disembodied voices?
- Dialog
- Dude: Pretend you are standing on the DNA where the input signal arrives.
- Sally: OK. Now what (patient)
- Dude: Rate of gene expression is the number of RNA polymerase molecules that trundle past you each second.
- Sally: (starts to smile)
- Dude: Let's call this Polymerase Per Second or PoPS!
- Sally: Cool!
- Dude: PoPS is the "flow" of RNA polymerase along my DNA wire
- Sally: Kinda like electrical current!
- Dude: Yes!!
- Panel 7. Home Stretch
- Setting -- Back in the workshop, Sally and Dude are talking over the new devices. Buddy is bouncing boundlessly.
- Dialog
- Sally: Finally, I can connect your PoPS-based devices in combination to make whatever I want (all sorts of crazy system drawings on the board again, Sally is jubilent)
- Dude: (amazed) And all I had to do was change how I organized my device's DNA.
- Sally: (sudden concern) Wait a minute, how do we measure PoPS?
- Dude: (grinning) I don't know, but if you figure it out, we'll rename PoPS after you!
- Sally (thinking of immortality via naming rights) Nice! I'm on it!
- Dude: I wonder if natural biological systems use PoPS?
- Sally: Who cares? We're building stuff!
- Panel 8. References
- Setting -- Need to give some shout outs. What images/scene would work well here? Workshop or River of Life or whatever makes the most sense?
- Reference Elowitz & Leibler paper
- Reference Che et al. manuscript
- Reference WIRED article
- Reference Cartoon Guide to Genetics
- Reference Image & Meaning 2 Conference
- Credits
- Acknowledgements
- Provide contact information
- Setting -- Need to give some shout outs. What images/scene would work well here? Workshop or River of Life or whatever makes the most sense?
