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Ask HN: if DNA is the code, are proteins the processes?
2 points by niels_olson on Dec 17, 2012 | hide | past | web | favorite | 6 comments
I'm a physician, teaching myself python (hat tips to LPTHW, Codecademy, and Lutz). If DNA is the code. I'm guessing RNA is ... like the front-side bus and proteins are the running processes? Does that sound about right?

I don't really program. I know a little html and css. But I am guessing you mean the folded proteins that the cell creates as tools? I am not sure that most programmers necessarily know the direct connection between genes and "proteins". I would think most people here view "protein" as a nutritious part of their hamburger or building blocks for their own muscles. I only know that "protein" can equal "important cellular process mechanism" because of my genetic disorder, which miscodes a protein which handles traffic of specific molecules into and out of the cell. I think even people with genetic disorders frequently poorly understand that connection, though, as I understand, the malfunction caused by most disorders is rooted in a missing or defective protein. I happen to have thought a lot about the way my miscoded genes impact cell function. That isn't the way most people frame things. So I think relatively few people will see a connection between "protein" and "process".

So I will suggest that you might need to expand a little on the biological half of your metaphor here before you get much useful feedback.

What is the computer? The cell?

Python code is not DNA.

Even to say binary is DNA seems a stretch, and of course it's quaternary.

With cells, there is no single "front-side bus". There is Brownian motion, geometry (e.g. at the level of DNA, A,T,C and G each have their own geometry), collisions and a poorly understood process of geometrical "recognition". We know how to build circuits and registers and construct computers from them, but we don't understand how RNA builds up a cell from scratch. We can only speculate that RNA can do this... the origin of life.

Perhaps Python would be a protein, but certainly not one that is required for the cell to function. Some interesting exogenous protein perhaps. If you want to control the essential "cellular proteins", the basic machinery of the cell, e.g. the enzymes you allude to, then you need to learn assembly. Python, like an exogenous protein, only acts to influence the machinery of the cell, including the proteins within the cell: in the case of the computer, circuits, registers and an assembly language.

Processes could be analagous cellular processes, i.e. what the proteins may take part in, their various roles in the biochemical reactions that drive the cell. Proteins are not the running processes, they are running the processes.

I think, with respect to coding, more important than the accuracy of the metaphor is simply the skill of being able to think abstractly and derive metaphors. So just the exercise of trying to come up with a comparison is something a programmer would instinctually do.

All of our attempted comparisons are likely flawed in numerous ways. But it's the exercise of making them that makes them worthwhile.

Good luck.

Why should there be any direct analog between "things" in the cell and "things" in computing? Perhaps there is no real mapping between the two that either makes sense, or is in any way useful.

Not to stop you from trying to find connections, but you seem to be certain that there must be, and I was wondering why.

Well, the deeper you get into cell bio, it's a huge amount of protein A phosphorylates protein B phosphorylates protein C, cleaves protein D into D1 and D2, D2 phosphorylates ...

And it seems like there are some pretty basic verbs. I'm just playing around with it all in my head, thought I'd ask the question.

The DNA is definitely the code but I think proteins are code,data and the processor itself depending upon what role its playing in the cell. At molecular level protein structures can affect creation or destruction of other protein structures, they also act as logic-gates. So proteins are clearly part of the cell hardware that regulates the cell. They also act as messages and if-else control logic (its also called GNR, Gene Regulatory Network) to read different DNA chunks based on certain conditions, so in that way they are part of the code. So I think DNA is the code on the disk-drive but proteins is "in memory" code,data and the hardware itself.

DNA is the class. Proteins are the instantiations.

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