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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

#21

Post by wespiser_2018 »

I've both worked with infrastructure as code, Pulumi, and was a grad student researcher in bioinformatics for several years, and I've developed the following take:

Biology is messy, tangled, and sloppy system built over a billion years under evolutionary pressure. There's no clear analogy to intelligently designed software, and anytime you make an analogy, like DNA == Source code, there's a mechanism which would destroy it's predictive power to explain biological phenomena. Like with DNA, computer software doesn't create the machine it's executed on, code is 1d, while DNA is definitely multi-dimensional, where it's folding, epigentic modifications, and other modifications matter a lot.

All the interesting biology for complex animals happens during the first few stages of development. There's no computational equivalent to this recursively constructive process. Additionally, biology has a single guiding principle through which we understand everything: evolution, and using computer analogies really diminish that.

Therefore, biology is biology. It's not analogous to a Von Neuman architecture machine, or any other computing device we've created. The first principles are simple different.

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

#22

Post by Noneofya »

blurbleblurble wrote: post #3

We can if we'd like to but remember that it's an analogy, no matter how useful, inspiring or beautiful the connections might be. I don't like this analogy too much because it collapses "DNA" into a singular thing that's somehow related to classical computing, even though there's no indication that DNA and the multiple layers of systems interacting with it are limited in the same ways as classical computers. I prefer…

>Memory is everywhere, whether or not anyone or anything remembers it.

That one is beautiful.

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

#23

Post by skydhash »

wespiser_2018 wrote: post #21

I've both worked with infrastructure as code, Pulumi, and was a grad student researcher in bioinformatics for several years, and I've developed the following take: Biology is messy, tangled, and sloppy system built over a billion years under evolutionary pressure. There's no clear analogy to intelligently designed software, and anytime you make an analogy, like DNA == Source code, there's a mechanism which would dest…

I was reading "The Origin of Knowledge and Imagination" and the author was reflecting on the same thing. The mind is not a computer, you do not think like a computer. In fact, there is no separate concept called "the mind". The whole body is part of our perception and action ecosystem. It makes sense as software, while imperfect, is too orderly and simplistic.

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

#24

Post by obrien1984ae »

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 know anything about the data it is being trained on ("Nature"). And that model continues to change even as the experiments are run.

So DNA is a "blockchain" record of previous and current hypotheses on which traits enable an organism to live to viability. Some of these hypotheses are "dead code," as the environment no longer contains the pressure which made them critical. Some of them are essential to viability. Some of them are experiments whose value has not yet been determined.

Assuming your question is whether IaC could learn from patterns in DNA, I think that's a very interesting idea. Certainly we desire that every loadbalancer, database, and iam policy be capable of self-defense, and be the hardiest, most fit version of itself possible.

Where the analogy struggles is that people writing IaC are more in the business of designing "natures" than they are designing individual organisms which would survive a chaotic and hostile "nature" being enforced on them. And people who write IaC might be unhappy to hear that getting to a "viable" database would require launching several thousand databases in an environment and, after some period of changes, seeing which one is performing best so they can clone that "best" database configuration when new databases are needed.

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

#25

Post by skydhash »

plokiju wrote: post #18
aristofun wrote: post #8

There is no direct parallels. And guess what - the brain is not even a computer. Everything this was just metaphors for non experts, irrelevant contexts and making money on pseudo science books.

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

By computation, do you mean problem solving? The most simplistic model I have of the brain (not a psychologist, just from thing I read) is that the brain is an advanced pattern matcher. I don't think we even do linear "computation", just because of the quantity of data we are ingesting, storing and retrieving.

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

#26

Post by adayanti »

wespiser_2018 wrote: post #21

I've both worked with infrastructure as code, Pulumi, and was a grad student researcher in bioinformatics for several years, and I've developed the following take: Biology is messy, tangled, and sloppy system built over a billion years under evolutionary pressure. There's no clear analogy to intelligently designed software, and anytime you make an analogy, like DNA == Source code, there's a mechanism which would dest…

Thank you @wespiser_2018, spot on.

My career is in both fields + PhD in one. Tortured analogies of biology as computers make me cringe, they're misleading at best. Sure the ribosome superficially looks like a FSM, but that gets you basically nowhere.

Comp-sci people: If you're curious about biology, spend some quality time at Kahn or edX, watch some university intro-bio lectures on youtube, read an intro-level undergrad biol textbook, etc.

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

#27

Post by aristofun »

plokiju wrote: post #18
aristofun wrote: post #8

There is no direct parallels. And guess what - the brain is not even a computer. Everything this was just metaphors for non experts, irrelevant contexts and making money on pseudo science books.

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 :(

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

#28

Post by plokiju »

skydhash wrote: post #25
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

By computation, do you mean problem solving? The most simplistic model I have of the brain (not a psychologist, just from thing I read) is that the brain is an advanced pattern matcher. I don't think we even do linear "computation", just because of the quantity of data we are ingesting, storing and retrieving.

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 "

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

#29

Post by skydhash »

plokiju wrote: post #28
skydhash wrote: post #25

Earlier quoted context omitted.

By computation, do you mean problem solving? The most simplistic model I have of the brain (not a psychologist, just from thing I read) is that the brain is an advanced pattern matcher. I don't think we even do linear "computation", just because of the quantity of data we are ingesting, storing and retrieving.

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 we filter it through patterns we've stored. Like logic gates do not process electricity, our brain do not process information.

(This is very much armchair psychology theory)

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