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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

#101

Post by function_seven »

usrbinbash wrote: post #51
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…

> Like, why didn't DNA end up as base 3? Why did we end up with only 20 proteinogenic amino acids? Why are vertebrate neural architectures inverted (cell bodies on the inside, connections on the outside, even though the other way round way (eg. like a squids brain is organised) is easier and less inhibitive to growth? 2 Reasons: a) Because nature and evolution cannot engineer. Random mutation, recombination and natur…

> (eg. our light sensitive cells point in the wrong direction)

Can you expand on that? Are you talking about front-facing eyes vs. birds' eyes? Or something else like retinal structure?

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

#102

Post by throwawaymaths »

asdff wrote: post #99
throwawaymaths wrote: post #79

Earlier quoted context omitted.

> that would make your storage medium a potential biohazard generally no. If you're worried about random DNA being a biohazard there are way worse things to worry about, like how your immune system uses random stretches of biologically primed dna to create antibody diversity. The real reasons why it's terrible is that write speed is atrocious and read speed is bad (on the order of 2-3x that of amazon glacier's roboti…

Having DNA as a storage medium is the best way to store actual biological data. Currently, we do things like having seedbanks, which need periodic replacing as seeds grow to be nonviable. A library of genomes is a much smaller physical footprint than a seedbank. It doesn't need periodic replacing, provided its not getting bombarded by radiation or anything unusual like that. DNA doesn't even have to be stored frozen;…

> Having DNA as a storage medium is the best way to store actual biological data

100% agreed. I thought that was obvious, was mostly sniping at "DNA based digitalstorage startups", thanks for clarifying for me

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

#103

Post by ray__ »

justsocrateasin wrote: post #86

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 red…

Even just storing family photos would require DNA sequences that are orders of magnitude larger than the human genome, so you're going to be looking at very expensive or very time consuming read/write (and certainly no instant read write at any cost–the turn around time can't be less than hours, even for small files, even with high-end HTS or nanopore approaches afaik). What is the plan for getting around this?

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

#104

Post by dtgriscom »

function_seven wrote: post #101
usrbinbash wrote: post #51

Earlier quoted context omitted.

> Like, why didn't DNA end up as base 3? Why did we end up with only 20 proteinogenic amino acids? Why are vertebrate neural architectures inverted (cell bodies on the inside, connections on the outside, even though the other way round way (eg. like a squids brain is organised) is easier and less inhibitive to growth? 2 Reasons: a) Because nature and evolution cannot engineer. Random mutation, recombination and natur…

> (eg. our light sensitive cells point in the wrong direction) Can you expand on that? Are you talking about front-facing eyes vs. birds' eyes? Or something else like retinal structure?

Retinal structure:

https://en.wikipedia.org/wiki/Retina#Inverted_versus_non-inv...

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

#105

Post by metabagel »

function_seven wrote: post #101
usrbinbash wrote: post #51

Earlier quoted context omitted.

> Like, why didn't DNA end up as base 3? Why did we end up with only 20 proteinogenic amino acids? Why are vertebrate neural architectures inverted (cell bodies on the inside, connections on the outside, even though the other way round way (eg. like a squids brain is organised) is easier and less inhibitive to growth? 2 Reasons: a) Because nature and evolution cannot engineer. Random mutation, recombination and natur…

> (eg. our light sensitive cells point in the wrong direction) Can you expand on that? Are you talking about front-facing eyes vs. birds' eyes? Or something else like retinal structure?

I had to look this up, and I guess what usrbinbash was referring to was the layout of the retina, which places the rods and cones behind layers of transparent neurons.

https://en.wikipedia.org/wiki/Retina#/media/File:Retina-diag...

Edit: ninja'd

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

#106

Post by lurknot »

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…

https://en.wikipedia.org/wiki/Chargaff%27s_rules

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

#107

Post by dekhn »

metabagel wrote: post #105
function_seven wrote: post #101

Earlier quoted context omitted.

> (eg. our light sensitive cells point in the wrong direction) Can you expand on that? Are you talking about front-facing eyes vs. birds' eyes? Or something else like retinal structure?

I had to look this up, and I guess what usrbinbash was referring to was the layout of the retina, which places the rods and cones behind layers of transparent neurons. https://en.wikipedia.org/wiki/Retina#/media/File:Retina-diag... Edit: ninja'd

Yet, it doesn't really have a strong impact as it's been determined that humans can see individual photons and we aren't dependant on night vision for hunting.

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

#108

Post by asimpletune »

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

The efficiency comes from the ratio of the alphabet to the number of character places needed to express them. Otherwise why not base a million? Or a billion?

This ratio is what leads to base e being the theoretical maximum.

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

#109

Post by dekhn »

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.

I do not know of any true "image" data. Most complex patterns in nature are created by generative processes rather than direct encoding.

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

#110

Post by stevenwoo »

JumpCrisscross wrote: post #5

Something like this was posited in Banks’ Excession , and I remember thinking how advanced passing messages via DNA embedded in bacterial seemed.

It’s also a key plot point in Tchaikovsky’s recent Children of … trilogy.
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