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Is life a form of computation?

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Re: Is life a form of computation?

#101

Post by dsign »

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…

> In that sense life is obviously not a computation: it makes some sense to view DNA as symbolic but it is misleading to do the same for the proteins they encode.

Proteins can also be seen as sequence of symbols: one symbol for each aminoacid. But that's beyond the point. Computational theory uses Turing Machines as a conceptual model. The theories employ some human-imposed conceptual translation to encode what happens in a digital processor or a Lego computer, even if those are not made with a tape and a head. Anybody who actually understands these theories could try to make a rigorous argument of why biological systems are Turning Machines, and I give them very high chances of succeeding.

> These proteins are solving physical problems, not expressing symbolic solutions to symbolic problems

This sentence is self-contradictory. If a protein solves a physical problem and it can only do so because of its particular structure, then its particular structure is an encoding of the solution to the physical problem. How can that encoding be "symbolic" is more of a problem for the beholder (us, humans), but as stated before, using the aminoacid sequence gives one such symbolic encoding. Another symbolic encoding could be the local coordinates of each atom of the protein, up to the precision limits allowed by quantum physics.

The article correctly states that biological computation is full of randomness, but it also explains that computational theories are well furnished with revolving doors between randomness and determinism (Pseudo-random numbers and Hopfield networks are good examples of conduits in either direction).

> ... whatever.

Please don't use this word to finish an argument where there are actual scientists who care about the subject.

Re: Is life a form of computation?

#102

Post by moi2388 »

robotresearcher wrote: post #52
nathan_douglas wrote: post #39

Earlier quoted context omitted.

I suppose I fail to see why evolution through natural selection is not optimizing. That was Darwin's big idea, right? That given heredity, selection, and variation you end up with life forms we'd consider optimized for their environments? Or do you mean that optimization by definition must include intent, and evolution as a mindless process has no intentionality? I'm just not sure what you're driving at.

Optimization is by definition with respect to some cost function or goal. Evolution has none. Evolution happens, but has no goal.

That’s the claim. But are we sure about that?

I certainly have a goal when selecting my partner and creating my offspring; at the very least that they’re happy and healthy.

Re: Is life a form of computation?

#103

Post by dluan »

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…

You might be interested in Tinkercell, though at this point it may be somewhat outdated and old. There are lots of other more granular systems biology/chemical reaction network software tools, the most ambitious is probably OpenWorm which is still active.

Just keep in mind though that you have to think of cells as very slow, but massively parallel computers.

Re: Is life a form of computation?

#104

Post by random3 »

measurablefunc wrote: post #20
karmakurtisaani wrote: post #9

I don't see the point of asking this question. Like, sure, all physical systems follow certain rules, so any such process will develop in a way that it look like a computation of an algorithm. Also, evolution itself is constantly optimizing organisms to best adapt to their environment, just like a computation. So asking if life is a computation seems mostly like a semantic musing. Define "life" and define "computatio…

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.

That's a rather strong statement, but incorrect in both result and formulation.

How is mutation and selection entail it's not optimization? Your motivating the lack of a goal for a process by describing it's composition. It seems like a logical (Non sequitur fallacy) and categorical erorr.

For reference

> optimization = the selection of a best element, with regard to some criteria, from some set of available alternatives

What's the selection selecting from, what's evolution evolving towards?

Moreover, you motivate with conservation. Conservation is an optimization criterion.

Re: Is life a form of computation?

#106

Post by [deleted] »

moi2388 wrote: post #102
robotresearcher wrote: post #52

Earlier quoted context omitted.

Optimization is by definition with respect to some cost function or goal. Evolution has none. Evolution happens, but has no goal.

That’s the claim. But are we sure about that? I certainly have a goal when selecting my partner and creating my offspring; at the very least that they’re happy and healthy.

[deleted]

Re: Is life a form of computation?

#107

Post by AIPedant »

ants_everywhere wrote: post #77
AIPedant wrote: post #69

Earlier quoted context omitted.

No, analog computers truly are symbolic. The simplest analog computer - the abacus - is obviously symbolic, and thus is also true for WW2 gun fire control computers, ball-and-shaft integrators, etc. They do not use inscriptions which is maybe where you're getting confused. But the turning of a differential gear to perform an addition is a symbolic operation: we are no more interested in the mechanics of the gear than…

I'm not confused, and an abacus is a digital computer. You keep referring to what we are interested in, but that's not a relevant quantity here. A symbol is a discrete sign that has some sort of symbol table (explicit or not) describing the mapping of the sign to the intended interpretation. An analog computer often directly solves the physical problem (e.g. an ODE) by building a device whose behavior is governed by…

This is where you are confused - in fact just plain wrong:

  A symbol is a discrete sign that has some sort of symbol table (explicit or not) describing the mapping of the sign to the intended interpretation
Symbols do not have to be discrete signs. You are thinking of inscriptions, not symbols. Symbols are impossible for humans to define. For an analog computer, the physical system of gears / etc symbolically represent the physical problem you are trying to solve. X turns of the gear symbolizes Y physical kilometers.

Re: Is life a form of computation?

#108

Post by GoatOfAplomb »

bgwalter wrote: post #11
rck wrote: post #10

This feels like the kind of popsci that's written for people who already agree with the author - there's nothing resembling an argument, or even a definition of "computation." There are nods to Church-Turing, but the leap from "every effectively calculable function is computable" to "life is a computation" is larger than anything you could fit in a book.

I felt reminded of Hofstadter's Goedel/Escher/Bach mysticism that somehow everything is recursion.

In any case, he did fit that into a book! If only barely.

Edit: On further reflection, I suppose he didn't, if we consider the effort to span Gödel Escher Bach and I Am a Strange Loop.

Re: Is life a form of computation?

#109

Post by jampekka »

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…

> I think the issue with this way of thinking is that humans think in abstractions.

Isn't that the entire point of making abstractions? Understanding things "as they are" is impossible, so we need simplifications. Of course it should be appreciated that the abstractions are always "wrong".

"A map is not the territory it represents, but, if correct, it has a similar structure to the territory, which accounts for its usefulness."

https://en.wikipedia.org/wiki/Map%E2%80%93territory_relation

Re: Is life a form of computation?

#110

Post by popalchemist »

I understand that this post is actually about biology and DNA, but the headline asks a broader and more interesting question than what the article itself cares to address --

At the root of this question is whether life is entirely deterministic. Either position - yes it is, or no it isn't - is unfalsifiable.

And in either case, one must live as if life is not deterministic, or else one's sense of agency and meaning dissolve.

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