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Is life a form of computation?

(thereader.mitpress.mit.edu)
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matheusmoreira ◴[] No.45353829[source]
I love thinking about life as computation. Cells are computers, enzymes are functions, ribosomes are compilers, nucleic acids are source code...

Enzymes in particular are a lot like unix pipelines. An enzyme catalyzes its substrate's conversion into its product which is the substrate of another enzyme. When cells ingest glucose, it flows through the glycolysis metabolic pathway until it becomes pyruvate, and may be reduced even further depending on available resources. It's a huge pipeline of enzymes. They just kinda float around within the cell and randomly perform their tasks when their substrates chemically interact with them. No explicit program exists, it emerges from the system within the cell.

  Cell              - Computer
  Enzyme            - Function / Process / Filter
  Substrate         - Data
  Product           - Data
  Metabolic pathway - Program / Script
I've been playing in my mind with an idea for an esoteric programming language modeled around enzymes. The program defines a set of enzymes which are functions that match on the structure of data, automatically apply themselves to them and produce a modified version of the input which may in turn match against other enzymes. The resulting program metabolizes input by looping over the set of enzymes and continuously matching and applying them until the data is reduced to its final form. If no enzymes match, the output is the unmodified input.
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heavyset_go ◴[] No.45354002[source]
I think the issue with this way of thinking is that humans think in abstractions.

Abstractions don't really exist, they're a product of the human mind, but then we apply them to nature. Calling DNA code, comparing NNs and the brain, etc. But those abstractions fall apart when you look a little too deeply at what actually happens in nature.

Is DNA code? Or is it more like a machine? Is it neither, or is it something embedded in such a complex space that our simple abstractions can't capture the full nature of its being?

When you look at the nature of DNA, it does more than simply act as code. It can edit and self-modify, self-assemble, self-replicate, it can turn genes on and off, it can perform what can be argued as computations itself. If you limit yourself to thinking of it as code, you might miss crucial ways it exists/performs in real life.

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1. matheusmoreira ◴[] No.45354144[source]
> When you look at the nature of DNA, it does more than simply act as code.

> It can edit and self-modify, self-assemble, self-replicate, it can turn genes on and off

Unless my knowledge of biology is very outdated or incomplete, all of those things you cited are done to DNA. They don't happen spontaneously.

DNA doesn't self-replicate, a whole bunch of enzymes come and actively copy it. Genes don't spontaneously turn on and off, some enzyme comes and attaches or removes a methyl group. DNA doesn't self-assemble, it is actively coiled around histones to form nucleosomes. Bacteria have a huge variety of enzymes for manipulating native and foreign DNA, they have their own CRISPR mechanisms.

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2. zmgsabst ◴[] No.45354728[source]
I think RNA (in particular, ribozymes) does those things.

But DNA is effectively separation of concerns: RNA systems evolved to RNA mediated systems with DNA as more inert and reliable storage and enzymes as more effective catalysts. Or so the RNA world hypothesis goes.

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3. matheusmoreira ◴[] No.45354854[source]
> ribozymes

I learned something new today! Thank you.

It's impressive that RNA of all things can be folded in such a way that it also acts like an enzyme.

4. heavyset_go ◴[] No.45355116[source]
I'm thinking more of early RNA and DNA life, where ideas like the RNA-world might have happened and applied. RNA can assemble, replicate, and catalyze to form deoxynucleosides in a proto-DNA, without "outside" work needing to happen from enzymes/proteins/etc.

Similarly, RNA and DNA "machines" could have existed before cellular life, in which genetic material self-assembled, transferred genes horizontally/vertically, etc, blurring the lines between genes as "code" and something else.

5. dillydogg ◴[] No.45360288[source]
There are deoxyribozymes though are far less common than ribozymes. DNA aptamers may also meet your definition of reactions involving DNA but not acting upon DNA.