Genes, proteins and DNA made very simple. A mnemonic.
Ever struggled with the inter-play of DNA,RNA, genes, amino-acids, proteins and wondered how they all fit together? I’ve created a simple aide-memoire. It is called City of Robots.
The City of Robots
There is a City where almost all critical functions are performed by robots. There are robots that carry stuff, build stuff, take messages from one place to another; they make sure the City’s industry is performed with speed and efficiency; they root out and attack enemies entering the city and they are themselves used as structural components for the various structures within the City.
There are billions of these individual robots, but there are only about 100,000 types of robot.
Robot Types
Type I Robot is a robot that has wheels (so it can move) and a funny shaped bolt (shaped like an octagon) upon which it can attach a transport crate that has an octagon shaped dock that can only fit onto an octagon shaped bolt. Robot I’s wheels are stuck to a track that allows it only move from one side of a yard, through a factory wall (yes through) and then back out into the yard.
Type 2 Robot is a door robot that is sometimes open and sometimes shut. When it is open it stretches out into a very particular shape, when it is closed, the shape disappears. Now, let’s say the shape that Robot 2 makes when it is open is the shape of a Type I Robot carrying its Transport Crate — a very particular shape indeed. The reason why it is so particular is that the only thing that the Type 2 Robot lets through is a Type I Robot carrying a Transport Crate. And lets say that there are 1000 Type 2 Robots allowing only 1000 Type 1 Robots carrying transport crates in and out of the factory.
So you can see how there are many more individual robots (there are two-thousand in this factory alone) yet only two types.
And you can also see that each robot’s function is defined by its shape.
Raw Materials
In the City there is a very special factory. A factory that makes the robots themselves. But there is a problem. In the City there are very few raw materials to work with, in fact there are only twenty materials (say Material 1, Material 2, Material 3… etc) and from these twenty materials all 100,000 robots have to be made. How can that be done?
Well, the City’s strategic geniuses noticed something. They noticed that if they put a material into a special water-based solution it would deform — and that each material deformed in a different way — and that deformity would also depend on the nature of the solution itself — it’s temperature and acidity level etc
So they stacked some of the materials on top of each other to form a ‘stack’ and then put the stack into the special water-based solution. Now, because each material reacted in a different way — some would bend left, some right, some would stay rigid — this would cause the stack to form into a shape. More to the point, if they put the right sequence together the stack would deform into a useful shape for a robot.
For example, they noticed that stacking Material 4 onto Material 5 onto Material 5 again and then onto Material 20 onto Material 2 — and then putting that stack into water, it would deform into Robot 1 — woohoo!
They also worked out that stacking Material 14 to Material 8 to Material 18 to Material 18 to Material 18 to Material 14 to Material 1 — and then putting that stack into water, it would deform into Robot 2 — woohoo again!
Workable Stacks
So they could remember, they now called a stack that made a Robot a ‘Workable Stack’. And they eventually worked out a Workable Stack for each of the 100,000+ robots required to run the City.
What’s more, although the sequence of materials in the Workable Stack required for Robot 1 was only five, for some Robots — like, say, Robot 56,789 the sequence ran for many thousands.
A code
But now they had a problem. They soon realized that the information that they had worked out was both incredibly valuable and incredibly huge. Imagine how much time it would have taken to write down Material 14 to Material 9 to Material 3 to Material 17 to Material 2 and on and on for many thousands. Also, now that they had it all written down, they didn’t want it damaged or altered — because get the wrong material wrong in a sequence and you get a faulty robot.
So they came up with a clever solution.
Firstly they created a simple code. Instead of saying ‘Material x’ they gave it a code name of just three letters. eg ‘Material 5’ became ACT
They also realised that they only needed to use four letters to give each of the twenty Raw Materials a three letter code. And, because their President was called Ebeneezer Gact, they decided to use the president’s surname as the four letters (GACT). So, suddenly they were able to create the code like this:
Material 1 — AAA
Material 2 — AAG
Material 3 — AAT
Material 4 — AGA
Material 5 — ACT
Etc etc
Material 20 — TCT
So, suddenly they could write a very quick short hand code to create the Workable Stack for Robot I of
AGA/ACT/ACT/TCT/AAG
(Which is the same as Material 4 onto Material 5 onto Material 5 onto Material 20 onto Material 2)
That is, a code sequence of five.
Eventually they had code sequences for all 100,000+ Workable Stacks. Where each Workable Stack, once it was put into the water-based solution, became a Robot.
The book of code
As we have already seen, although the code sequence for Robot I was only five, some code sequences ran into the hundreds and thousands. And, soon, the book of codes for all 100k+ of Workable Stacks ran for many many many pages.
Since the City Strategists wanted to protect their code from prying eyes they then threw in a lot of extra — redundant or ‘junk’ — sequences into the book. And the book became very huge indeed.
So they broke it down into 23 different chapters and they put each chapter into a box. However, so they generally knew which code was where, they made each box a different size.
And because the code was the most important thing in the City, the boxes were kept in a bank vault right in the middle of the city — where the code could not be removed, altered or damaged.
Protecting the code
Protecting the code from damage was of paramount importance. Access to the code would be limited only to a very special unit called ‘copiers’. When a robot was required to be made, the particular code for the Workable Stack that made the robot would have to be copied down by ‘copiers’ in the bank vault and the copy taken to a robot making factory where it could be used to make the robot.
The City’s imperial ambitions
The City realized that on its own it wasn’t very powerful, and could easily be invaded and destroyed by invading forces. But, in its vault it had an entire blueprint to build other cities. In fact, the blueprint was so flexible that it allowed for the creation of different robots in different quantities so as to create entirely different cities. It realized that if it surrounded itself with cities — some similar, some different — then the empire, as a whole, would be much stronger: to the benefit of all the individual cities. They could share resources, food, defenses and all manner of things.
A duplicate code
But there was a final problem. If the code was to be used as a blueprint for another city, the code in its entirely would be required. However, the code was too important to take out of the vault and it was simply too huge for copiers to copy it all. So they came up with a simple solution.
The book would be ready-copied — a second duplicate version of the code would exist “zipped’ to the original, so, when a new city was to be formed, the duplicate could be unzipped, removed in its entirety then both the original and the new copy could be re-zipped with new duplicates at leisure — with the original version staying in the vault and the new version eventually ending up in the vault of the new city.
And finally, copies of the are not always accurate…
Sometimes, when the copies are made there are little errors made. The code is mis-read (easy to do given the massive volume of code that is required to be copied) so a material is put in the wrong sequence. Much of the time the impact is immaterial, but sometimes this one little change affords the new city an advantage — a stronger type of robot for making walls or for making more efficient factories. Eventually these cities — and eventually the empires that they form part — become more successful than others. As they are more successful then their code will more likely to be used, copied, replicated than even the original code of the City.
Summary
1. The City is run by millions of robots of only 100,000 types.
2. A robot is only useful if it is in a shape fit for its job. Its shape determines its function, and vice versa.
3. A robot is made up of raw materials stacked on top of each other, where that stack is then placed in a water-based solution so that it deforms into the useful shape it is required to be.
4. The sequence of raw materials that allows for a properly formed robot is called a Workable Stack.
5. To make reading sequences easier to read and copy, each raw material is given a three-letter code using any three of the following four letters: GACT
6. And so a code for workable stack would be a sequence of these three-letter codes. Eg AGA/ACT/ACT/TCT/AAG
7. The book of all these codes — plus a whole load of seemingly random (junk) letters to try to protect against prying eyes — is massive, so is divided into 23 different shaped boxes.
8. It is also so valuable that the book is locked away in a bank vault and cannot be removed.
9. Only certain individuals have access to the code — these are ‘copiers’. These guys copy sections of code relating to a Workable Stack and deliver it to robot-making factories to provide the instruction to make the robots.
10. Cities want to make empires but neither do they want to remove their code. So they ‘zip’ the code with a ready made duplicate. This duplicate can be removed in its entirety to make up the code for a second city.
11. Sometimes the duplicates are mis-copies or are mis-read. That will mean subsequent cities may be slightly different — sometimes even slightly better suited to the environment, and, in general their code will more likely be replicated than even the code for the first City.
Glossary
The City = a cell
A robot = protein
Raw material = amino acid
Workable Stack = gene
The sequence of three letter codes = genetic code
The book of all code = DNA
The zipped duplicate of the code = the double helix
The copiers = RNA
The boxes w/in which the DNA is stored = chromosomes
The robot-making factories = ribosomes
Random code vrs prying eyes = Junk DNA
Bank Vault = nucleus
Second city = daughter cell
Empires = multi-cellular bodies (such as humans)
‘Little errors in copying code’ = mutations
‘Better suited to their environment’ = evolution by natural selection
Note:
I hope you enjoyed the City of Robots. A couple of things you should know.
I am an enthusiastic amateur — not a scientist– the City of Robots is a primarily a bit of fun: a very coarse-grained allegory to assist the amateur learn and/or recall, in general terms, the broad mechanisms it describes. In that, it is neither wholly accurate and misses many finer-grained and nuanced processes. Feel free, in the comments, to correct, direct or expand.
Further, the piece contains a fair bit of artistic license. For example, in the real cell there is no such thing as an executive of strategic geniuses. To repeat, the piece is for fun: it makes no religious, political, social or any other point at all.
