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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

#91

Post by toufka »

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…

You (at least) have 3 systems that are optimized in concert in a (our) DNA/Protein world.

DNA base set, Amino acid set, Translation layer between DNA/Proteins.

Currently, we've got: 4 DNA bases, 3 bases/AA, 20 AAs; 4^3 => 20

If you change one of those numbers, you'll need to rejigger the rest, and you'd need to reoptimize. And there are competing goals which at least include: - maximize access to biophysical/chemical diversity - minimize energy expenditure to produce each component, chemically - minimize energy expenditure to both copy instructions & produce products - maximize information fidelity - minimize or at least degrade gracefully in the context of errors

In the context of a 3-base system, you very well could throw off those optimizations given the consequences for the other 2 parameters (#AA & nt/AA). 3^3 = 27, which is very close to the maximum of 20 amino acids. Which means you'd probably need a 4nt->AA translation layer to keep the same number of AAs, and that alone would add 30% more energy expenditure. If you kept the 3nt->AA system you'd BOTH need to reduce the number of accessible amino acids AND you'd lose some of the error correction mechanisms of having degenerate codons code for the same amino acid.

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

#92

Post by ohwellhere »

nicoburns wrote: post #73
dylan604 wrote: post #70

Earlier quoted context omitted.

>So for example, ternary logic is (much) more efficient than binary logic. Having that 3rd state just makes problem solving much more elegant. Binary for electronics is obvious because there are 2 states in electric components: on or off. There is no 3rd option.

I believe "on" and "off" in electronics typically correspond to different voltage levels. So you absolutely could have a third intermediate state if you wanted to. Flash memory does this (and even sometimes has 4 states). I guess designing switches (transistors) that could take advantage of and propagate these extra states could be tricky though.

https://en.wikipedia.org/wiki/Ternary_computer

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

#93

Post by dahfizz »

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…

Why do my eyelashes, meant to protect my eyes, fall into my eyes? Why do my cheeks/tongue sometimes get in the way of my teeth so that I bite them? And why do they then get inflamed so that I continually byte them for the next few days?

We are all a bunch of biological goop resulting from random processes. Don't expect optimal solutions from evolution. There is no "why".

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

#94

Post by guerrilla »

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…

> (probably because 4 naturally lends itself to pairs of 2).

Why would pairs of two be favorable?

> So for example, ternary logic is (much) more efficient than binary logic. Having that 3rd state just makes problem solving much more elegant.

What do you have in mind here?

> Like, are there all sorts of exotic logic gates that come from a 4 state system?

I don't know but you may be interested in this [1].

1. https://en.wikipedia.org/wiki/Catu%E1%B9%A3ko%E1%B9%ADi

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

#95

Post by swamp40 »

I've always wondered if the plant/animal shapes and sizes were represented literally in a 3D mapping of the DNA. Like we could already have a picture of what it will become, if we could just decode the DNA sequences properly.

Like we have the sequence of numbers for a jpg, but we've never seen the picture.

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

#96

Post by asdff »

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…

On paper this might be an interesting game, but you have to think of things in terms of crystal structure, what is able to form hydrogen bonds, what ends up being sterically hindered and what that means for the molecule. This is why watson and crick and franklin's work was so seminal, it showed how genetic information was inherited through mechanical logic of these molecules alone. Before the structure of DNA was solved, there were a lot of competing theories over what molecule was the source of heritable information, and how this information was exactly passed down between generations.

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

#97

Post by asdff »

snitty wrote: post #33
Borrible wrote: post #31

Earlier quoted context omitted.

DNA/RNA looks to be more like storing heuristics, landmarks and clues, not data.

Can you elaborate on that? A significant portion of DNA in organisms literally encodes for protein sequences. It also has functional parts (binding sites for proteins, promoter sequences). Some RNAs are not translated because the RNA itself has function, but I don't see that same argument for DNA.

Only like 1.5% of the human genome is protein coding.

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

#98

Post by asdff »

DeathArrow wrote: post #30
Borrible wrote: post #8

Earlier quoted context omitted.

>using DNA as an information storage medium is a pretty neat concept And billions of years old.

> And billions of years old. With not quite good backup strategies.

Having an error rate means a small chance of gaining an edge that makes up for having it.

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

#99

Post by asdff »

throwawaymaths wrote: post #79
K0balt wrote: post #41

Am I alone in thinking that using regular DNA is a terrible idea for data storage? I mean, that would make your storage medium a potential biohazard. Although it probably would all be cool until someone put smallpox.bin on a major torrent tracker. If it’s really that good, we should come up with a variant using slightly different chemistry so that biocontamination is not a factor.

> 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; you can freeze dry it and store it at room temp for a very long time before any significant degradation. You can also just have the sequence stored digitally, and synthetically build out the dna molecule as you need it (I think this is still pretty costly though and not that efficient). With the right molecular biological tooling, one could conceivably introduce these genomes into a plant cell line and grow them up in tissue culture, you don't have to for example grow a tree and let it mature and go to seed since plant cells are pluripotent, everything can be done in a lab much faster.

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

#100

Post by techdragon »

TeMPOraL wrote: post #64
techdragon wrote: post #24

Earlier quoted context omitted.

Yeah, I expect this isn’t going to be how that sort of mechanism works, but it’s always been an interesting concept for me, that while “genetic memory” as presented in much fiction is extremely unlikely just from the sheer entropic hill such mechanisms would have to evolutionarily climb to be able to pass on so much information (on top of the baseline necessary information for reproduction, the majority of memory won…

> But it’s still impressive that it can encode moderately complex information like “looks like the face of my species” or “cylindrical looking objects on the ground might be dangerous”… even if it’s encoded in a lossy subconscious instinctual level. I think it helps that the encoding does not have to be transferable in any way. This kind of "memory" has no need for portability between individuals or species - it does…

Oh absolutely... and that's a great analogy for the more computer oriented, "Reflections on Trusting Trust" highlights how it can be the supporting infrastructure of replication that passes on the relevant information... a compiler attack like that is equivalent to things like epigenetic information transfer... and for fun bonus measure since it came to mind... the short story Coding Machines goes well for really helping to never forget the idea behind "Reflections on Trusting Trust" https://www.teamten.com/lawrence/writings/coding-machines/

It definitely would be minimised data transfer, be it via an epigenetic nudge that just happens to work by sheer dumb luck because of some other existing mechanism or a sophisticated DNA driven growth of some very specific part of the mammalian connectome that we do not yet understand because we've barely got the full connectome maps of worms and insects, mammals are a mile away at the moment... no matter the mechanism evolution will have optimised it pretty heavily for simply information robustness reasons, fragile genetic/reproductive information transfer mistakes that work, break and get optimised out in favour of the more robust ones that don't break and more reliably pass on their advantage.

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