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A biological camera that captures and stores images directly into DNA

nature.com

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Re: A biological camera that captures and stores images directly into DNA

#81

Post by [deleted] »

PaulHoule wrote: post #59
asimpletune wrote: post #36

Something that I always found fascinating is how DNA is a base 4 information format. There's this thing called radix economy, which is basically an expression of how efficient a number system is. Base e is the theoretical maximum, and so base 3 is the closest integer. Obviously if you have a special use case, then that may dominate your radix economy (like hex, b64, etc...), but for general purpose information purpos…

DNA has the same limitation that many serial protocols have: if you repeat the same base pairs (e.g. "AAAAAAAAAAAAAAAAAAAAAA") you will have trouble w/ the DNA not spiraling correctly. Some sequences of 2-6 repeated base pairs seem to "deliberately" cause variant behavior in DNA and RNA, see https://en.wikipedia.org/wiki/Repeated_sequence_(DNA) Many real wire protocols have mechanisms to prevent repeated sequences en…

[deleted]

Re: A biological camera that captures and stores images directly into DNA

#82

Post by JumpCrisscross »

pythonguython wrote: post #61
Llamamoe wrote: post #54

Earlier quoted context omitted.

Radix is important for digit-efficiency, but in a biological system that's not necessarily related to molecule size efficiency.

I’m also failing to see how digit efficiency would be important in DNA. In fact, it seems that a high base system would be more efficient. If you had 80 nucleobases instead of 4, each base pair would contain far more information

> If you had 80 nucleobases instead of 4, each base pair would contain far more information

Which is a problem given DNA is a lossy format.

Re: A biological camera that captures and stores images directly into DNA

#83

Post by usrbinbash »

t_serpico wrote: post #76
idiotsecant wrote: post #65

Earlier quoted context omitted.

This is pretty smug for someone who seems to have managed to miss the point entirely. Yes, DNA has certain features that require a base 4 system. That is not necessarily true of all possible systems with DNA-equivalent function, which is the point this whole thread is making.

How have I missed the point? The answer that nature cannot engineer and can't start de novo are trivially true statements that provide no actual insight into the question. I fully agree the original question itself is a deep one. A quick literature search is more productive than pontificating with weak analogies. See https://www.math.unl.edu/~bdeng1/Papers/DengDNAreplication.p... for what seems to be an interesting a…

> that provide no actual insight into the question

Mind elaborating on that?

Because there is no biochemical reason why DNA could not have incorporated, say, a third pairing pair, so while base-3 (which I don't specifically mention in my post btw.) wouldn't work, base 6 or 8 would have been possible. "Unnatural Base Pairs" are even known to work in laboratory settings.

There is also no biochemical reason why base2 life wouldn't work. Expand the reading frame of the translation machinery to 5 instead of three, and you have enough coding space for polypeptides.

My answer adresses the question completely, because the only reason behind these "decisions" is an ancient system that simply got "frozen", and now cannot change any more.

Re: A biological camera that captures and stores images directly into DNA

#84

Post by aclatuts »

PaulHoule wrote: post #60
throwawaymaths wrote: post #57

Man what a confusing title. It's not a single strand of DNA that gets the image information. You get a pool of DNA, which collectively hold the images information. This is done in a pretty obvious way, each "pixel" is a well in a 96-well e.g. plate and you expose the bacteria in these wells to different light and then the DNA transformation is triggered by the light, then you harvest the DNA from the bacteria and get…

Would be neat if you could somehow splice them into a sequence but I think you'd have some alternating sequences that determine position and sequences that really code information.

Assassins Creed is becoming reality soon.

Re: A biological camera that captures and stores images directly into DNA

#85

Post by nico »

dghughes wrote: post #18
gsam wrote: post #4

Anyone else think that there is already primitive image data encoded in biological data? Essentially basic shapes and patterns which are passed down semi-generationally.

Anton Petrov has a recent video on YouTube I never watched it yet but it's title is "Could Life Be Transmitted Via Radio Waves? Information Panspermia". Just a bit of fun I'm sure Anton isn't too wild he puts out some interesting videos but not in a way to push quackery. https://www.youtube.com/watch?v=K4Zghdqvxt4

Fascinating, thank you

Recently here on HN someone posted a quote saying something like “if you shine light at something for a long enough time, don’t be surprised if you end up getting a plant”

It was about how the environment seems to reorganize in certain ways to use up energy (the latest Veritasium video about entropy also talks about this)

Re: A biological camera that captures and stores images directly into DNA

#86

Post by justsocrateasin »

Reminiscent of a very interesting company I interviewed for last year called Cache DNA

https://www.cache-dna.com/

This is the future. I don't think it will look exactly like this, and I don't think it will be here any time soon, but I'm excited to see these advancements.

What Cache is doing presently is trying to do archival storage in DNA - it has a lot of potential to be cheaper, more energy efficient, and more redundant. But some of the processes still aren't there yet.

Re: A biological camera that captures and stores images directly into DNA

#88

Post by piyh »

usrbinbash wrote: post #32

> DNA synthesis remains a bottleneck in the adoption of DNA as a data storage medium. Yes, one of many. Another one is a simple question: What exactly is the use case again? Because, storage isn't something we lack. Especially when talking about storage where, obviously, fast random access isn't a requirement, aka. data archiving. We have good solutions for that; an LTO-9 tape can hold 18TiB of data native and up to…

Can your tapes self replicate? /s

The goal of replacing memory cards is dumb, the tech that enables the storage is a foundational step forward in bio engineering.

Re: A biological camera that captures and stores images directly into DNA

#89

Post by sterlind »

usrbinbash wrote: post #83
t_serpico wrote: post #76

Earlier quoted context omitted.

How have I missed the point? The answer that nature cannot engineer and can't start de novo are trivially true statements that provide no actual insight into the question. I fully agree the original question itself is a deep one. A quick literature search is more productive than pontificating with weak analogies. See https://www.math.unl.edu/~bdeng1/Papers/DengDNAreplication.p... for what seems to be an interesting a…

> that provide no actual insight into the question Mind elaborating on that? Because there is no biochemical reason why DNA could not have incorporated, say, a third pairing pair, so while base-3 (which I don't specifically mention in my post btw.) wouldn't work, base 6 or 8 would have been possible. "Unnatural Base Pairs" are even known to work in laboratory settings. There is also no biochemical reason why base2 li…

> There is also no biochemical reason why base2 life wouldn't work.

are you sure about that? are you sure there's no weird effects that might destabilize very long sequences of 2-nucleotide DNA? or on how wide DNA-binding domains have to be to cope with reduced information density, and how that might sterically hinder smaller arrangements of proteins?

> My answer adresses the question completely, because the only reason behind these "decisions" is an ancient system that simply got "frozen", and now cannot change any more.

your answer is just a hypothesis, not a proof. these things can be studied (by studying abiogenesis in-vitro), and it's not certain these decisions were "flash frozen" like you describe. 2-, 4-, and 6- nucleotide coding systems might have coexisted in the RNA world, and 4- could have won out for some reason.

Re: A biological camera that captures and stores images directly into DNA

#90

Post by toufka »

Faaak wrote: post #45
go_elmo wrote: post #38

Earlier quoted context omitted.

Might error-correction play a role? Having a lightly inefficient base 4 system might provide capacity for the surplus error correcting code information capacity?

One mutation in a base pair can lead a totally different amino acid (c.f the genetic code), so I doubt it ?

BUT, if you look at the codon table, precisely because it's base-4 and not base-3, many base flips are silent when coded.

By using base-4, there's enough space to permit lossiness of the coding itself - given the number of amino acids and the 3-NT encoding.

So you really aren't optimizing JUST for nucleotide encoding, but you're also optimizing in concert with 3-nt/AA, and 20AA codes.

So if you have to optimize for information density and fidelity, given X-nucleotides, Y nucleotides/AA, and Z AAs, and sample as much chemical and physical diversity in those AAs life has settled upon: X=4, Y=3, Z=20.

If we went with X=3, you might need Y=4 to get the same kind of fidelity, but that cranks up your energy costs by 30% (from 3 to 4 NT per AA).

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