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A biological camera that captures and stores images directly into DNA
- HlessClaudesman 3y agoMan, I have a hard enough time trying to keep track of a micro SD card, imagine misplacing your DNA based files? Seriously tho, using DNA as an information storage medium is a pretty neat concept.
- Borrible 3y ago>using DNA as an information storage medium is a pretty neat concept And billions of years old.
- Daub 3y agoIts not often that HN makes me laugh.
- DeathArrow 3y ago> And billions of years old. With not quite good backup strategies.
- Borrible 3y agoDNA/RNA looks to be more like storing heuristics, landmarks and clues, not data.
- snitty 3y agoCan 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.
- Scarblac 3y agoIf you create your data right, the actual data can make backups of itself. There's even builtin ways for it to improve itself over time using genetic algorithms.
- TeMPOraL 3y agoA kind of implied meaning of the term "data", especially in context of storage and archiving, is that we do not want it to "improve itself".
- urfullofsht 3y ago[dead]
- dylan604 3y agoCould make for some interesting decoding errors as your original data mutates
- asdff 3y agoHaving an error rate means a small chance of gaining an edge that makes up for having it.
- candiodari 3y agoJust so we're clear, this is ONE pixel per, I don't know, 10000 cells or so. So one bit per DNA chain, with that bit repeated thousands of times to get redundancy. Still and incredible achievement.
- fxtentacle 3y agoThe super neat thing is that they tag each DNA chain with the pixel coordinates, so you can afterwards mix those 10,000 DNA strands each for all 96 pixels into one 1-mio-DNA-strand-soup and still recover the image successfully.
- gsam 3y agoAnyone else think that there is already primitive image data encoded in biological data? Essentially basic shapes and patterns which are passed down semi-generationally.
- f6v 3y agoI think it would have very high energy requirements. For this trait to survive over generations there would need to be a tremendous evolutionary benefit. What would that be for a “primitive image data”?
- yetihehe 3y agoMaybe things like "long green shape" (cats' fear of cucumbers because they resemble snakes), or "a series of black and yellow stripes", or even "a black blob with many appendages" to watch out for spiders? Encoding some primitive image data so that further generations know what to avoid or pursue seems like a very tremendous evolutionary benefit.
- f6v 3y agoYou need to compare that with an alternative solution where this information is learned by each generation and then asses the survival advantage of having it encoded in DNA. This is outside my field and I don’t have a strong opinion.
- techdragon 3y agoYeah, 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’t on average confer a lot of reproductive advantages, so it’s statistically more likely to get optimised out by the random mistakes of evolution, hence entropically “uphill”) … Yet while this fictional form is unlikely we have quite a lot of good examples and evidence for “inherited information”. You have to be careful with it since it’s too easy to accidentally include side channels for organisms to learn the information and thus break the test. Such as insects being genetically driven towards food by smell at a molecular chemical interaction level, and the smell becoming associated with the information you wish to test. A bee colony can’t be reliably tested unless you raise it from a new queen in an odourless environment if you wish to see if bees genetically know that the shape of a flower is associated with food. It’s tough to subtract the potential that a colony will have learned and “programmed” later generations of bees with things like the classic waggle dancing in order to more efficiently gather food. We do have good ones though like cats and snake shaped objects, it’s surprisingly consistent, and pops up in some other animal species. It’s wired into our brains a bit to watch out for such threats. There’s a significant bias towards pareidolia in human brains and it’s telling how deeply wired we have some of these things, but it is there and study shows it seems to form well before our cognitive abilities do… these all have some obvious reproductive advantages however so it makes sense that the “instinct” would be preserved over generations as it confers an advantage. 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.
- JumpCrisscross 3y agoSomething like this was posited in Banks’ Excession, and I remember thinking how advanced passing messages via DNA embedded in bacterial seemed.
- stevenwoo 3y agoIt’s also a key plot point in Tchaikovsky’s recent Children of … trilogy.
- jvanderbot 3y agoCan't wait until they do a worldwide investigation to find patient zero from the selfie encoded in the next pandemic.
- codetrotter 3y ago> Can't wait until they do a worldwide investigation to find patient zero from the selfie encoded in the next pandemic. Then they realise the picture is this dude: https://blogs.loc.gov/loc/2022/07/robert-cornelius-and-the-first-selfie/ https://blogs.loc.gov/loc/2022/07/robert-cornelius-and-the-f...
- ryanjamurphy 3y agoRelated: The Verge's DNA time capsule [0]. [0]: https://www.theverge.com/c/22173998/dna-time-capsule https://www.theverge.com/c/22173998/dna-time-capsule
- xk_id 3y agoOnce upon a time, the Wikipedia article about Hacking provided the following as sort of “canonical” example of hacking: using an optical mouse as barcode scanner. In some ways, this incredible paper feels like an iteration of that example.
- boffinAudio 3y ago[flagged]
- muzani 3y ago[flagged]
- p0w3n3d 3y agoExploit idea: create an image, which, when taken a shot of, would be written to DNA as a virus. (I know viruses are RNA)
- luckystarr 3y agoAnd create a never to be deleted record of images across the infected population?
- pyinstallwoes 3y agoDo a Quine now!
- dillydogg 3y agoThere are plenty of DNA viruses. They aren't limited to RNA at all
- hallihax 3y agoThis is great and all, but the merge process is still messy as hell
- LearningToWalk 3y agoI've been up close to one project working in this space. The obstacles are obviously many, but fascinating to see that progress is made nontheless. Clearly a piece of the-future-puzzle.
- usrbinbash 3y ago> 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 45 TiB of data compressed, with denser capacities planned: https://en.wikipedia.org/wiki/Linear_Tape-Open https://en.wikipedia.org/wiki/Linear_Tape-Open
- Aardwolf 3y agoSome number I found online, while trying to multiply the 30 trillion human cells with the data storage of DNA per cell: "one gram of dried DNA can store 455 exabytes of data" Seems like a pretty sweet use case to me! I definitely do lack storage by the way. Say I want to download the common crawl data set, 380 TiB. And for redundancy I'd need multiple copies of the data too. That's a lot of disks for in the home. "18TiB ought to be enough for everyone" really doensn't cut it.
- usrbinbash 3y ago> one gram of dried DNA can store 455 exabytes of data Yes, and half a gram of Hydrogen could produce ~500 Megawatts of power in a fusion reactor. However, that theoretical value will remain irrelevant, as long as we cannot build a practically useful fusion reactor. And even if we could build one, it still has to compete with all other forms of producing power for scalability, reliability, efficiency and cost. The fact that there is a very high theoretical number that seems really impressive, isn't a use case. So, with that being said: how long does it take to write these 455EiB? How long does it take to read them? How error prone are both processes? And how much does it cost to write/read them? > "18TiB ought to be enough for everyone" really doensn't cut it. Pretty sure I never said that. Also pretty sure common crawl can be compressed. Even assuming only a 2:1 compression rate, that means it fits comfortably on 11 LTO-9's. Now, a quick google-search churned out tape prices of about 110-140 $ per LTO-9. Let's say ~150$ per tape, that means the whole thing fit's on 1650 $ worth of storage. About 5000 bucks with 2 backups included. Double that for uncompressed storage. Alright, so how does that compare to DNA storage? https://www.nanalyze.com/2023/03/dna-data-storage-solution/ https://www.nanalyze.com/2023/03/dna-data-storage-solution/ quote: These days, it costs $600 to sequence a complete genome which contains around 200 gigabytes of data or about $3 per gig. Today, magnetic tape technology offers the lowest purchase price of raw storage capacity at around two cents per gigabyte end quote. So just reading the 380 TiB back from uncompressed storage ONCE, would cost ~1,140,000 dollars. And that's just for reading. At a price differential that is measured in multiple orders of magnitude, a technology better offer some REALLY good, REALLY tangible advantages to compete.
- asimpletune 3y agoSomething 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 purposes, the order base 3, base 4, then base 2. This present a lot of interesting questions to me. Like, why didn't DNA end up as base 3? (probably because 4 naturally lends itself to pairs of 2). Also, this idea of radix economy goes beyond just the encoding of information and is represented in logical economy as well. So for example, ternary logic is (much) more efficient than binary logic. Having that 3rd state just makes problem solving much more elegant. To that end, I have always wondered how nature has exploited this 4-state number system logically. Like, are there all sorts of exotic logic gates that come from a 4 state system?
- go_elmo 3y agoMight error-correction play a role? Having a lightly inefficient base 4 system might provide capacity for the surplus error correcting code information capacity?
- Faaak 3y agoOne mutation in a base pair can lead a totally different amino acid (c.f the genetic code), so I doubt it ?
- go_elmo 3y agoTrue, iff the error persists correction cycles which are present, how exactly they work / if theyre comparable with eccs I dont know.
- toufka 3y agoBUT, 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).
- K0balt 3y agoAm 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.
- fartsucker69 3y agoimagine downloading a tv show and it turns out its shit
- throwawaymaths 3y ago> 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 robotic tape handlers, with WAY MORE expensive robots, and way more expensive cost to read -- you're bulk polluting rivers in china to make the reagents). The only use case I can think of is deep generational archival (like the svalbard seed bank, but for information). Where cost to store by volume is at a premium, and where you'd like to have many many many copies, and you don't mind the cost to read because you won't be reading it but for every 10 or so years, if even. Store your logs in DNA. You're never going to read them anyways.
- asdff 3y agoHaving 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.
- js8 3y agoIt reminds me of children story https://en.m.wikipedia.org/wiki/The_Mystery_of_the_Third_Planet https://en.m.wikipedia.org/wiki/The_Mystery_of_the_Third_Pla..., which had flowers that captured the surroundings in layers, like a film camera.
- throwawaymaths 3y agoMan 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 your image pool library.
- PaulHoule 3y agoWould 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.
- throwawaymaths 3y agoyes, I was very impressed by the title, but once I dug into this it was sort of like "well we could probably have accomplished this ~10 years ago when optogenetics first came out". Definitely a situation where branding the title got something "so silly that no one did it before" got it to be noticed.
- aclatuts 3y agoAssassins Creed is becoming reality soon.
- deleted 3y ago[deleted]
- justsocrateasin 3y agoReminiscent of a very interesting company I interviewed for last year called Cache DNA https://www.cache-dna.com/ 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.
- ray__ 3y agoEven 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?
- stainablesteel 3y agothis is like spy technology, super cool
- swamp40 3y agoI'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.