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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

#111

Post by erenyeager »

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…

It’s a bit anthropocentric to talk about not making sense from an engineering point of view. One example is the recurrent laryngeal nerve which always appears to take unnecessary detours to people because of what is thought to be historical evolution. But there is deep wisdom and insight we have gleaned in this, but I think it’s not for us to say well we could engineer this better, we don’t have the total knowledge of tools yet & it is dismissive and say disrespectful of the wondrous biological systems that have been made to sustain life.

Hubris and attempts to alter inherent nature are often tied up ironically. But we can benefit a lot more from biological humility, realizing there are many unknown unknowns.

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

#112

Post by erenyeager »

dahfizz wrote: post #93
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".

There is a why and reasons we find and insights we glean. The denial of a why is itself an anthropocentric take on biology, influenced by Darwinian thought. But any biological system we study we need a why, otherwise the corollary of your statement essentially leads to no learning or understanding, because everything becomes “arbitrary” and explained away by randomness.

Ironic to say it’s not optimal, really we don’t have the full knowledge. Often when we learn more we learn how little we really know about biology.

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

#113

Post by amateurCoder5 »

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…

Repetitive DNA sequences do occur and do cause problems.

https://en.m.wikipedia.org/wiki/Trinucleotide_repeat_expansi...

TLDR: DNA triplet repeat expansions cause diseases like Huntington's disease.

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

#114

Post by inciampati »

pcrh wrote: post #39
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…

Encode wikipedia into DNA, then insert it into a horseshoe crab. In a few million years it may still be around to be decoded. >The fossil record of Xiphosura goes back over 440 million years to the Ordovician period, with the oldest representatives of the modern family Limulidae dating to approximately 250 million years ago during the Early Triassic. As such, the extant forms have been described as "living fossils".[…

And yet, in those 250 million years, it's very likely that the genome was completely rewritten. The phenotype of the organism is more stable than its genome. Not a shred of Wikipedia would be left after such a time scale.

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

#115

Post by K0balt »

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…

My scenario is based on the idea that someone would write code that generates an “archive” that is biologically active , like a prion or a virus or something else that has dangerous properties outside of its context as a data storage device. Not so much random DNA but very specific, targeted DNA.

I mean, DNA storage means you have an advanced, high performance DNA synthesis, copying, and sequencing machine. That’s fine in general, because most people using such a machine have a concept of the risks and responsibilities.

But imagine what would happen if we had millions of those machines connected to the internet with unpatched vulnerabilities. It seems like that could have some negative outcomes.

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

#116

Post by usrbinbash »

sterlind wrote: post #89
usrbinbash wrote: post #83

Earlier quoted context omitted.

> 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 rea…

> are you sure about that?

Yes, I am sure about that, because I used to study Biology before going into IT. And we had a lovely lecture in which we used to discuss theoretical setups for lifeforms at a molecular level.

2 nucleotide DNA isn't necessarily less stable. AT-rich domains have less bindings, but if stablity is the issue, use CG instead (3 bindings)...although that is also a compromise, because then opening DNA for transcription gets more difficult.

> your answer is just a hypothesis, not a proof.

My answer is what we observe in evolutionary biology.

I have given an example outside of the molecular world for a reason. There is no real advantage to the inversion of the neural architecture in Chordata, it just didn't matter when the neural tube formation mechanisms came to be. Now, with mammals having huge brains and complex sensory organs, the warts in that design show.

The proof for that is easy to come by, (also a reason btw. why the neural inversion is my favorite example for this): Look an any Protostomia. Their neural system isn't inverted. Consequently, Squids don't have a visual blind spot.

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

#117

Post by throwawaymaths »

K0balt wrote: post #115
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…

My scenario is based on the idea that someone would write code that generates an “archive” that is biologically active , like a prion or a virus or something else that has dangerous properties outside of its context as a data storage device. Not so much random DNA but very specific, targeted DNA. I mean, DNA storage means you have an advanced, high performance DNA synthesis, copying, and sequencing machine. That’s fi…

Unlikely those sequences would pass checksum

Padme meme with checksum

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

#118

Post by j33zusjuice »

sterlind wrote: post #89
usrbinbash wrote: post #83

Earlier quoted context omitted.

> 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 rea…

Idk enough about this discussion to argue it, but his hypothesis does not imply your second point couldn't be true.

> 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.

His hypothesis is, at least in part, “4- won for some reasons for which we have no explanation, and it stayed that way for some reason [that we may or may not know].” I suppose the reason would be that 4- was somehow better suited for the particular use-case at the time.

Of course there’s a ton of interesting details to discuss to discover, and whether if multiple systems coexisted is one of many fascinating things to discuss, and his response never said otherwise.

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

#119

Post by snitty »

asdff wrote: post #97
snitty wrote: post #33

Earlier quoted context omitted.

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.

And like 90% of E. coli genome is protein coding. I intentionally wasn't limiting it to humans because humans make up a very small portion of total DNA in the world.

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

#120

Post by htss2013 »

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…

Maybe it has something to do with protein folding, since apparently scientists do not understand the physical mechanisms that translate a given DNA sequence into a given 3D shape. They best they can do is infer probabilistic patterns using ML to proxy a mechanistic of action. Maybe there's something quantum at work that means it will never be fully deterministic.
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