mrcreek: Rana palustris, the pickerel frog (Default)
[personal profile] mrcreek
Polymer Monopoly is a fantasy. The setting does not really exist, the characters are fictional, and according to basic physics it would actually be impossible for the miraculous technology that fills the story to work as described.

And yet, it all seems kind of familiar, especially if you've ever studied any molecular biology or spent time in Washington State. Sure, you could read and enjoy the story without any knowledge of these things, but if you're curious, here's some of the background behind the various plot elements (contains spoilers).

First, some terminology. Living things are built of proteins. There's also some other stuff there like sugars and fats, but basically all of the sugars and fats and whatnot are put together by enzymes, which are proteins, so it all comes down to proteins in the end. Protein molecules are polymers, which means they are long chains build of many smaller molecules. These smaller molecules are called amino acids, which are a type of zwitterion. In the story, I called them zwitters. "Zwitter" is German for hermaphrodite, referring to the "male" and "female" ends of the molecule which have opposite charges. The sequence of amino acids determines the structure of the protein in roughly the way it is described in the story: charged amino acids attract each other, oily (hydrophobic) amino acids bury themselves inside the clump to get away from water, etc.

The main energy source for proteins is a molecule called adenosine triphosphate. Scientists usually abbreviate it to "ATP," but I called it triph in the story because I thought a name is more memorable than an acronym. ATP is "charged" in living cells by a protein complex which is very similar to the triph synthesizers in the story. The protein compelx is inserted through a membrane that separates two compartments, one of which has a higher concentration of protons than the other. As protons flow through the little molecular motor, ATP is produced. These proton-dense compartments include the intermembrane space of mitochondria and the thylakoid lumen of plant chloroplasts (guess which term contributed to the name of the volcano).

DNA is a fairly passive molecule that mostly just stores instructions on how to build proteins, which then do all of the actual work of the cell. The locomotive was broadly based on polymerase enzymes which travel along the DNA molecule.

That's the essential biochemistry on which the world of the story is built. Some of the machines, like the antibodies, the triph synthesizers, and the locomotive are modeled on specific real proteins. Others, like the Locust, the rotorcraft, and the cephalases, are designer proteins unlike anything seen in nature. Others are somewhere in the middle. For example, the knot that locks Montgomery's iron gate isn't anything in particular, but many proteins are activated by transmitters which are modified amino acids, just like the key in the story. Likewise, there are proteins that "walk" in a manner similar to Wilkins' moped. The proportions of all the molecular technologies are roughly consistent with each other. If proteins were are big as cars, protons would still be too small to see, and if dissolved in a liquid would appear to be part of the fluid. An organelle like a chloroplast would be the size of a mountain.

So are the characters inside a cell? Despite Wilkins' pun in Chapter 8, I don't think they are. I mean, they're in freaking Seattle. There's a sky, and trees, and seafood, and top hats. Inside a cell you couldn't stand on solid ground and breathe the air; you'd be floating around in a fluid medium. Besides, in no real cell would you find both an antibody and a thylakoid membrane. I prefer to believe that they live in an alternate universe where they have these objects which happen to share a lot in common with biomolecules, and the people have developed them into machines in place of the technologies we developed here on Earth, such as steel, steam engines, or guns. I didn't want to tell a story about life inside a cell, I wanted to highlight the bizarre juxtaposition between molecular machines and the mundane objects of wood and glass we encounter at our own normal scale.

Thus, the Pacific Northwest seemed like a perfect setting for this story. I know it doesn't really rain all the time, but it it damp and cloudy a lot, which makes it more plausible to have technology that has to stay wet. Then all the various elements just fit together, from totem poles to volcanoes. Besides, Seattle has an interesting history that played an important role in global industrialization, but it's mostly been overlooked in the steampunk genre. As I discussed in a previous post, the official nickname of Seattle, Washington was "Queen City" for over one hundred years, before it was dropped in 1982 due to its homosexual connotations. In its early days, Seattle was relatively lawless and rife with gambling, liquor, prostitution, riots, and general exploitation of the poor (including many Chinese and Native Americans) by the wealthy. For some reason, it didn't occur to anyone that building a city on muddy tidal flats might be foolish. After putting up with with filth and floods for a while, they decided to raise the city up a story. At first, just the streets were elevated above the storefronts, but eventually the entire ground level was covered by downtown Seattle, under which it still lies abandoned to this day.

From the vantage point of Seattle, Mt. Rainier (also know as Mt. Tacoma) looks a bit like Chekhov's volcano - it's always looming on the horizon, and why would it be there if it's not going to go off some day? It seemed only natural that if I were going to incorporate the mountain into my story, that it would have to eventually erupt. The magma pressure inside a volcano and the proton pressure inside a thylakoid are superficially similar, but of course the metaphor does not extend much beyond the way it was used in the story.

Wilhelm Boeing, who later anglicized his first name to "William," was born in Michigan in 1881. After seeing his first flying machine in Seattle, he remained in that city and there founded his eponymous company which has continued to lead the world in airplane manufacturing for almost a century. My character of Wilhelm probably does not reflect the exact personality of the real historical Wilhelm, but I can only imagine that they were both equally excited by large transportation machines.

Perhaps I need to talk a bit about intelligent design. The metaphor that biological structures are machines goes back at least as far as Descartes. Unfortunately, some people have a hard time remembering that it's just a metaphor, and believe that biomolecules are literal machines that were created to do a particular job by some sort of sentient agent. Yes, that's true in my story, but no, it's not true in real life. Again, I hope it is obvious that the world of the story is not the same as our world. In the real world, proteins aren't created from scratch, they evolve from other proteins, and we can see their relatedness in their sequence similarity, something that wouldn't be possible if each protein were just designed separately on (theological) paper.

While the story is not intended to be some kind of politico-economic allegory, certain themes are worth taking to heart. As I finished up the story, I was appalled to hear the news of the gushing oil well in the Gulf of Mexico, a spooky parallel to the eruption of Mt. Thylacoma. We make enormous messes trying to get our energy. We need accountability and responsibility from the people who run energy companies, and we need to have diverse and sustainable energy sources. And, although this is thankfully not such a pressing issue in the real world, decapitating people who oppose your business practices is just wrong.

This story has kept me entertained for many months, and I learned a lot while writing it. I can't really explain where the idea for it came from, other than that I wanted to merge the modern-day tinkering that is happening in the field of synthetic biology with the mechanical tinkering that was happening during the industrial revolution. The main point of the story is to illustrate how the world that I have imagined works, so I just thought about the important parts I wanted to show and went from there. If there's anything you don't understand that I failed to explain here, or if you have any other comments, please let me know.


mrcreek: Rana palustris, the pickerel frog (Default)

October 2015

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