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Is life a form of computation?

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Re: Is life a form of computation?

#41

Post by heavyset_go »

matheusmoreira wrote: post #34

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 r…

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.

Re: Is life a form of computation?

#43

Post by Xcelerate »

AIPedant wrote: post #29

Articles like this indicate we should lock down the definition of "computation" that meaningfully distinguishes computing machines from other physical phenomena - a computation is a process that maps symbols (or strings of symbols) to other symbols, obeying certain simple rules[1]. A computer is a machine that does computations. In that sense life is obviously not a computation: it makes some sense to view DNA as sym…

> a computation is a process that maps symbols (or strings of symbols) to other symbols, obeying certain simple rules[1]

There are quite a number of people who believe this is the universe. Namely, that the universe is the manifestation of all rule sets on all inputs at all points in time. How you extract quantum mechanics out of that... not so sure

Re: Is life a form of computation?

#44

Post by eig »

I'm not too impressed with this article since it doesn't really give a definition for computing, just picks a few similarities between what we see as computing (in the practical sense) and what cells do.

It's a shame because there *has* been a lot of deep work done on what kind of computer life is. People often use the Chomsky Hierarchy (https://en.wikipedia.org/wiki/Chomsky_hierarchy) to define the different types of computer vs automata. Importantly, a classical Turing machine is Type-0 on the Chomsky Hierarchy. Depending on what parts you include from a biological system, you could argue it's anywhere from Type-0 to Type-4.

Interestingly, the PhD thesis of well-known geneticist Aviv Regev was to show that certain combinations of enzymes with chemical concentration states are enough to emulate pi-calculus, and therefore are Turing machines! https://psb.stanford.edu/psb-online/proceedings/psb01/regev....

Re: Is life a form of computation?

#45

Post by measurablefunc »

heavyset_go wrote: post #38
measurablefunc wrote: post #20

Earlier quoted context omitted.

Evolution is not optimizing anything. What's happening in the biosphere is a process of mutation & selection, it's not optimization towards any particular goal or objective. Furthermore & slightly more abstractly, b/c of conservation of mass & energy, what's actually happening is re-organization of existing biomass into different life forms enabled by solar radiation.

> what's actually happening is re-organization of existing biomass into different life forms enabled by solar radiation. And the flux of geothermal and chemical energy

That's true. We wouldn't have fossil fuels w/o geological activity & mass churning.

Re: Is life a form of computation?

#46

Post by matheusmoreira »

heavyset_go wrote: post #41
matheusmoreira wrote: post #34

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 r…

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 e…

> 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.

Re: Is life a form of computation?

#50

Post by ants_everywhere »

AIPedant wrote: post #29

Articles like this indicate we should lock down the definition of "computation" that meaningfully distinguishes computing machines from other physical phenomena - a computation is a process that maps symbols (or strings of symbols) to other symbols, obeying certain simple rules[1]. A computer is a machine that does computations. In that sense life is obviously not a computation: it makes some sense to view DNA as sym…

I think you may be forgetting about analog computers https://en.wikipedia.org/wiki/Analog_computer
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