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Ask HN: Can we think of DNA as Infrastructure as Code

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Re: Ask HN: Can we think of DNA as Infrastructure as Code

#31

Post by dekhn »

pacificmaelstrm wrote: post #17

DNA is a form of code, but it doesn't encode programs. Instead, like an STL or STEP file it encodes HARDWARE designs. While you could think of it as encoding infrastructure AND code (as in IaS) you'd need to go beyond that to include the hardware for computing AND physical function (like a whole car + computer) in that conception, which is not what IaS means. The hardware side of DNA is easy to overlook since we don'…

This looks like it was written by generative AI but I can't really say for sure.

BTW: protein structure prediction didn't need supercomputers (in the traditional sense) and the PSP problem wasn't solved using supercomputers applying a high quality physics function to simulate folding- instead, it was solved using a combination of ML supercomputers, a really good algorithm (transformers), and a couple of really good data sets- the known structures of proteins, and the known relationship of proteins.

Instead of simulation on a huge supercomputer so they could predict a single strucfture, they trained a model which approximates structure well enough to beat every competitor. From what I can tell, most of the resulting quality doesn't come from their force field but from the distance constraints that are mostly derived from historical relationships between proteins, and the coevolution of their sequences.

Re: Ask HN: Can we think of DNA as Infrastructure as Code

#32

Post by fl0ki »

obrien1984ae wrote: post #24

A better analogy for DNA in computer science would be LLMs. Each organism's DNA represents an experiment being performed in service of training a model. If that experiment manages to procreate, its successful mutations graduate into another round of experiments. This has gone on for several billion years, resulting in a largely stable model within which experiment are continuing to be run. As with LLMs, DNA doesn't k…

I apologize in advance for criticism you only half deserve. I know this is HN, but not every single topic needs to be compared to LLMs or Blockchain. Concepts like fitness functions, selective pressures, feedback mechanisms, etc. -- as applied to both embodied organisms and constructs like cultures and ideologies -- predate not just the last two hype cycles but artificial computation altogether.

Referring to such deeply established foundation is normal -- I'm sure many of us remember when novel AI approaches like perceptrons and evolutionary algorithms were described by analogy to biology -- but skipping over the established literature to talk about nascent concepts makes you sound less like you're contributing to an educated discussion and more like you're courting angel investors with buzzwords.

At the very least it could be "here's the analogy to , and to help round out the concept, is also analogous to with ". That makes both a stronger argument and a more educational essay than skipping straight to the new thing with no foundation.

For example, one very important difference is that DNA can be edited and lose history, unlike blockchain, but an intact fossil record could be used to infer how those edits came in over time and space, kind of like an incomplete distributed ledger.

Re: Ask HN: Can we think of DNA as Infrastructure as Code

#33

Post by plokiju »

skydhash wrote: post #29
plokiju wrote: post #28

Earlier quoted context omitted.

how would you do pattern matching without computations? I think anything that could be described through logic gates or turning machines would be a "computation". And any object or organ that processes information would be a "computer "

Because things are just are. An analogy I can come with is a graph like irrigation canals. You fill them with water and they just are. Or something like an adder circuits. You "input" the numbers and the result is just there. There isn't an algorithmic process with loops, conditions and recursions. We don't store information, we store its patterns and link it to other patterns. We don't process information as much as…

I'm not seeing the distinction. All computation "just is". computation happens through the physical world. adder circuits are performing a computation. an x86 CPU is nothing but a bunch of dumb circuits. water canals can do computations just like electrical circuits. as can biological neurons.

This is a computer with all the abstractions stripped away [1]. It's hard to see the loops and conditionals from the falling marbles, but it is processing information. And electrical computers are essentially the same thing, just scaled up to an unimaginable degree

[1] https://www.youtube.com/watch?v=8BOvLL8ok8I

Re: Ask HN: Can we think of DNA as Infrastructure as Code

#34

Post by plokiju »

aristofun wrote: post #27
plokiju wrote: post #18

Earlier quoted context omitted.

I think that very much depends on how you define "computer". the brain is doing computations, so I think it's safe to think of it as a computer. it's just a completely alien computer to what we build ourselves

> the brain is doing computations Nope. We don't really know yet what exactly the brain is "doing". But again, in _some_ contexts it is better than nothing. Unfortunately good metaphors stick, regardless of their relevance and accuracy :(

there are a lot of mysteries around the brain, but at a high level, I think you'd have a hard time finding a neuroscientist who doesn't believe the brain processes information. what's the alternative?

Re: Ask HN: Can we think of DNA as Infrastructure as Code

#35

Post by obrien1984ae »

fl0ki wrote: post #32
obrien1984ae wrote: post #24

A better analogy for DNA in computer science would be LLMs. Each organism's DNA represents an experiment being performed in service of training a model. If that experiment manages to procreate, its successful mutations graduate into another round of experiments. This has gone on for several billion years, resulting in a largely stable model within which experiment are continuing to be run. As with LLMs, DNA doesn't k…

I apologize in advance for criticism you only half deserve. I know this is HN, but not every single topic needs to be compared to LLMs or Blockchain. Concepts like fitness functions, selective pressures, feedback mechanisms, etc. -- as applied to both embodied organisms and constructs like cultures and ideologies -- predate not just the last two hype cycles but artificial computation altogether. Referring to such dee…

> For example, one very important difference is that DNA can be edited and lose history, unlike blockchain, but an intact fossil record could be used to infer how those edits came in over time and space, kind of like an incomplete distributed ledger.

That is a very good point.

It is true that editing blockchain completely destroys the chain, and editing DNA in very specific ways does not. I was thinking (when I wrote it) that because of the way the genes interact it can be completely destructive to take only a single piece of DNA. But, as you correctly point out, we do that all the time. So, yes, the blockchain analogy only partially fits.

Thank you.

Re: Ask HN: Can we think of DNA as Infrastructure as Code

#36

Post by danwee »

What always surprised me is not DNA, but how other non-living things can exist at all without DNA. It makes sense to me that I have green eyes since that's what my DNA says... but where is defined that a rock has a particular color or weight or texture?

Whenever I think of how planets move around a star, I always think "Ok. So, I imagine that at some point the universe should know the distance between planet X and star Y, and also, probably, maybe, it should know their masses... but that data is nowhere defined (that we know). So, is the data computed 'on the fly' every $minimal-unit-of-time?). Perhaps the universe doesn't need to know distances nor masses, though.

Re: Ask HN: Can we think of DNA as Infrastructure as Code

#37

Post by aristofun »

plokiju wrote: post #34
aristofun wrote: post #27

Earlier quoted context omitted.

> the brain is doing computations Nope. We don't really know yet what exactly the brain is "doing". But again, in _some_ contexts it is better than nothing. Unfortunately good metaphors stick, regardless of their relevance and accuracy :(

there are a lot of mysteries around the brain, but at a high level, I think you'd have a hard time finding a neuroscientist who doesn't believe the brain processes information. what's the alternative?

Processing information is pretty vague and generic idea. You can label virtually anything as “processing information” and be more or less true.

But I doubt i find any neuroscientist worth anything who say “brain is doing computations almost like a computer”.

Re: Ask HN: Can we think of DNA as Infrastructure as Code

#38

Post by sohex »

danwee wrote: post #36

What always surprised me is not DNA, but how other non-living things can exist at all without DNA. It makes sense to me that I have green eyes since that's what my DNA says... but where is defined that a rock has a particular color or weight or texture? Whenever I think of how planets move around a star, I always think "Ok. So, I imagine that at some point the universe should know the distance between planet X and st…

I think you might be trying to form a model based on false premises here. The universe doesn't know anything. Or to put it another way, the universe doesn't know anything because it is everything. You seem to be assuming a sort of director and actor based model wherein the universe (the director) needs to be telling the planets and stars (the actors) what to do, but that's not the case. The planets and stars interact with each other via the various forces that they're subject to and their state may or may not change as a result.

I guess, to generalize, my point is that things are as they are as a consequence of the physics that they're subject to. A rock has its particular color, weight, and texture due to its elemental composition. A molecule doesn't need to know what it is in order to reflect or absorb certain wavelengths of light, that's what naturally occurs when those wavelengths interact with particles that have a certain composition and state. There's no conscious direction happening at any point, nor is there any data being computed.

The universe is essentially a medium that exists with certain properties and everything in it is stuff that also exists with certain properties. We call the manner in which these properties interact physics. So in summation I'd say that there are intrinsic properties and emergent phenomena based on those properties, that's where a rock gets its color, weight, and texture.

Re: Ask HN: Can we think of DNA as Infrastructure as Code

#39

Post by moralestapia »

markus_zhang wrote: post #30
moralestapia wrote: post #9

Not as Infra as Code but you could think of it as another stack with its own architechture and programming language. Also runs on jelly instead of electronics.

Have we figured out how to program it?

Nope :'(.

Re: Ask HN: Can we think of DNA as Infrastructure as Code

#40

Post by plokiju »

aristofun wrote: post #37
plokiju wrote: post #34

Earlier quoted context omitted.

there are a lot of mysteries around the brain, but at a high level, I think you'd have a hard time finding a neuroscientist who doesn't believe the brain processes information. what's the alternative?

Processing information is pretty vague and generic idea. You can label virtually anything as “processing information” and be more or less true. But I doubt i find any neuroscientist worth anything who say “brain is doing computations almost like a computer”.

Like I said, it depends very much on how you define computer. To me "processing information" == "computation". And a physical system that performs "computations" is a computer. Therefore, a brain is just one type of biological computer.

In a computer science class, the first thing they should teach is that the word "computer" in the course name is abstract, and not just about the metal slab on your desk. There are fundamental laws that apply to all information processing systems, whether electrical, mechanical, or biological. So it makes sense to put them in the same category at times.

But obviously words mean different things in different contexts, and "computer" might mean something entirely different to a neuroscientist than a computer scientist. But I don't think a neuroscientist would disagree that a brain is a computer using the loose definition I described above

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