Junk DNA

Is anything truly random, or is there always structure and cause? These were his thoughts as he stared at the diagram he had assembled on his computer.

The diagram showed the various chemical pathways that had been discovered surrounding “junk” DNA. Junk DNA is made up of the bits of DNA that are non-functional. This means that they don’t code for proteins, but it also means they aren’t non-coding genes for tRNA or ribosomal RNA. Defining what exactly functional means had always been a subject of heated debate, he had voiced his own strong opinions on this subject, but there was no doubt that some portion of one’s DNA was seemingly decoupled from use by biology. And full of randomness.

The diagram he had assembled was the result of many careers of biochemistry graduate students. Each edge in his graph was a Ph.D., and each edge was filled with hopes, dreams, and tiny bits of the delusion that their edge would lead to fame and fortune. Or at least a coveted tenure track professorship. That their work, their edge, would be a functional part of the biochemical cannon.

It was only recently that enough graduate student fuel had been burned to show a nearly complete picture of the mechanisms surrounding junk DNA. Yes, this DNA was non-functional, in that it didn’t have a part to play in life, but each time DNA was copied junk DNA was there. At the beginning and at the end. So there was mechanism in going from before to after. He strained his eyes at the diagram, trying to comprehend.

Random is hard, but complex is not. Take a number. There are many things you can do to it. Multiply it by another number, add a number to it. Square the number or take the remainder of a number divided by some other number. If the formula you come up with for changing a number to another number is complex, it may be very hard to figure out how to get back your input number out from the output of your formula. Of course some functions make this impossible, they have the same outputs that come from multiple inputs. But even when the formula is guaranteed to have a unique input for every output, it could be hard to find this input. You might be mistaken for thinking that the output was random, how on earth could it be related to your input?

A similar sort of idea was found in fingerprints. Humans are giant complex beasts, but there is a small part of your body, the skin folds on your finger tips, which are unique to you (or at least two people having the same fingerprint is rare.) There is some mechanism that goes from you as a fertilized egg to you and your fingerprint. But looking at just your fingerprint we cannot rebuild the fertilized egg, and we cannot rebuild you. Fingerprints are seemingly random, but they were created via a mechanism, and reverse engineering this is seemingly impossible.

But he thought, this concept of a fingerprint was a lie. Of course fingerprints aren’t just genetic. They also depend on the environment that you developed in. So this formula for going from fertilized cell to you involves not just you, but every bit of the world you interacted with as you grew from w to organism.

In the days of social media excess, back when the riots inspired by vast waves of fossilized thought decoupled people from reality and led to the overthrow of governments, one particular band of crazy ideas had arisen called digital money. He recalled how these systems burned vast sums of energy but also how they used fingerprints.

Money is keeping track of what you spend and receive, you need some way to keep track of these pluses and minuses. Mistaking trust as a problem, the long dead citizens of this era worked to see if they could reproduce trust via mathematical and game theoretic guarantees. To do this they created a list of the pluses and minuses of their money, but to keep it from being mutated, they made each part of this ledger include a fingerprint of the last part of the ledger. This meant that the whole chain of transactions could be verified: statting with the most recent entry you could read the fingerprint of that entry and verify that it was the fingerprint for the previous entry.

And so, as he sat there, looking at the diagram of junk DNA, it occurred to him this Junk, this stuff of non-functional form was really a cryptographic hash, i.e a fingerprint. Your stands of Junk DNA were a fingerprint of your parents DNA. By looking at your junk DNA, and the DNA of your parents, one could run a short computer program to verify that those were indeed your parents.

He sat there, stunned, upon reaching this conclusion. How on earth. Or more directly how on evolution, he wondered. And then there was another flash of insight, and he remembered mice and dolphins and whales and petunias, and he wondered, who, exactly is using us as a digital currency?