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A biological camera that captures and stores images directly into DNA

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

#61

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…

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

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

#62

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…

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!

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

#64

Earlier quoted context omitted.

Maybe 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.

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 doesn't even need to be factored out as a thing in any meaningful sense. I.e. we may not be able to isolate where exactly the "snake-shaped object" bit of instinct is stored, and even if we could, copy-pasting it from a cat to a dog wouldn't likely lead the (offspring of the) latter to develop the same instinct. The instinct encoding has to only ever be compatible with one's direct offspring, which is a nearly-identical copy, and so the encoding can be optimized down to some minimum tweaks - instructions that wouldn't work in another species, or even if copy-pasted down couple generations of one's offspring.

(In a way, it's similar to natural language, which rapidly (but not instantly) loses meaning with distance, both spatial/social and temporal.)

In discussing this topic, one has to also remember the insight from "Reflections on Trusting Trust" - the data/behavior you're looking for may not even be in the source code. DNA, after all, isn't universal, abstract descriptor of life. It's code executed by a complex machine that, as part of its function, copies itself along with the code. There is lots of "hidden" information capacity in organisms' reproduction machinery, being silently passed on and subject to evolutionary pressures as much as DNA itself is.

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

#65

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…

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.

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

#66
post #16
post #15

Earlier quoted context omitted.

>successfully Except when it recombines weirdly and gets mixed up as per the article.

Those are just mutations in the image

"Hallucinations" seems to be the modern term.

/s, but only slightly.

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

#67
post #46
post #38

Earlier quoted context omitted.

Might error-correction play a role? Having a lightly inefficient base 4 system might provide capacity for the surplus error correcting code information capacity?

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.

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

#68
post #20

Exploit idea: create an image, which, when taken a shot of, would be written to DNA as a virus. (I know viruses are RNA)

And create a never to be deleted record of images across the infected population?

Cue "tasteless porn in bitcoin blockchain forever".

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

#69
post #45
post #38

Earlier quoted context omitted.

Might error-correction play a role? Having a lightly inefficient base 4 system might provide capacity for the surplus error correcting code information capacity?

One mutation in a base pair can lead a totally different amino acid (c.f the genetic code), so I doubt it ?

True, iff the error persists correction cycles which are present, how exactly they work / if theyre comparable with eccs I dont know.

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

#70

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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