71–80 of 125 posts
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…
>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.
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DNA mostly relies on the fact that there's 2 strands that are (logically speaking) a mirror copy of each other (a C is paired with a G and vice versa, an A to a T and vice versa), it's like RAID 3 with only 2 disks (one being parity). Apart from repairing structural damage such as missing bonds, the cell can even repair missing bases or non-straight breaks without loss. This mechanism is also used for replication: th…
Im aware of that, but was rather thinking about ECCs like hamming-code, that are able to correct single sequences of info based on surplus info in that same string.
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A classic armchair response. DNA has complementary nucleotides (AT,GC) that facilitates its pairing. Base 3 wouldn’t work in that sense. Also, you can’t forget about the genetic code. See https://arxiv.org/pdf/q-bio/0605036.pdf for interesting thoughts. Remember, evolutionary biology is a field and people think about these questions!
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.
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A classic armchair response. DNA has complementary nucleotides (AT,GC) that facilitates its pairing. Base 3 wouldn’t work in that sense. Also, you can’t forget about the genetic code. See https://arxiv.org/pdf/q-bio/0605036.pdf for interesting thoughts. Remember, evolutionary biology is a field and people think about these questions!
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.
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If 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.
A 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".
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.
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.
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.
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> 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…
A classic armchair response. DNA has complementary nucleotides (AT,GC) that facilitates its pairing. Base 3 wouldn’t work in that sense. Also, you can’t forget about the genetic code. See https://arxiv.org/pdf/q-bio/0605036.pdf for interesting thoughts. Remember, evolutionary biology is a field and people think about these questions!
That's true, but a) not the point I am making, and b) I am pretty sure it says nowhere in my post that it would.