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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

#51

Post by usrbinbash »

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 natural selection are the only mechanisms available. Things get selected if they outcompete existing alternatives, they don't need to be the best solutions.

b) All solutions have to be built by modifying what already exists. Evolution doesn't get to do greenfield projects, because anything that has to start from scratch is so disadvantaged in natural selection compared to already evolved complex life, it will fail.

This leads to systems that, from an engineering point of view, don't always make a lot of sense.

Eg. the architecture of the vertebrate neural system creates a lot of issues (eg. our light sensitive cells point in the wrong direction). The only way this makes any sense if when one looks at how the neural tube (the precursor to the backbone) is formed by the endodermis folding in on itself. This process is so deeply at the root of the Chordata, and so many other things depend on it, that it simply cannot change any more.

Many many biological systems are "legacy systems" in the truest sense of the word: Solutions produced a long time ago that may have many problems, but are simply too deeply enmeshed with everything that came after, that they are now impossible to change.

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

#53

Post by jszymborski »

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…

There's a lot of interesting things to consider.

One, is that base 4 makes a lot of sense for the stability of DNA structures. You have two purines, two pyrimadines.

Another is that partly because codons are degenerate, the distribution is way off a uniform distribution. For chemistry and mol bio reasons, the distribution of AGTC is very skewed.

When i fully wake up, this might be a fun blog post to draft.

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

#54

Post by Llamamoe »

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…

Radix is important for digit-efficiency, but in a biological system that's not necessarily related to molecule size efficiency.

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

#55

Post by throwawaymaths »

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…

It's probably not base four because you have to stretch out more pairs to match up four pairs and that's entropically disfavored. However ribosomes can accomodate a four pair matching, though at a very reduced yield (unless you think Schultz's postdoc fabricated those data)

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

#56

Post by Aardwolf »

usrbinbash wrote: post #43
Aardwolf wrote: post #35

Earlier quoted context omitted.

Some 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. "18…

> 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 fa…

I of course wouldn't want to store my data in there today, I wouldn't even trust that I get it back reliably because DNA reading comes with a relatively big error rate for storage purposes (of course error correction can mitigate that). But it would be cool if the technology progresses. All technology, including disks, magnetic tapes, and new alternatives. Whether DNA is viable in the end or not, I don't know. I do know that tech always has been progressing and new alternatives are sometimes found, and that I do see a use for more storage.

But an argument whether DNA is a viable option in the future or not would have to say technically what the issue of DNA is with future tech.

Whether it's more expensive today, or that there's no need for more data today, are not really arguments against it.

I do not intend to be arguing for snake oil or anything here though. If "DNA storage" is in a similar category of "perpetual motion machines" and "cars that run on tap water" then count me out.

I don't even know how our comments ended up being like arguing against each other. The only thing really I didn't agree with in the original comment was "Because, storage isn't something we lack", because I do find it lacking, both at home and in the cloud.

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

#57

Post by throwawaymaths »

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 your image pool library.

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

#58

Post by sparrowInHand »

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…

Short answer: Likelihood of noise (brownian motion) producing the element and keeping it interacting. Then once it gets going, likelihood of keeping state, while interacting.

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

#59

Post by PaulHoule »

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 entirely

https://en.wikipedia.org/wiki/8b/10b_encoding

DNA coding for real proteins is unlikely to be too terribly repetitive but I image a long α helix could have a repetitive amino acid sequence. Many amino acids can be coded with variant codons, I guess if repetition were a problem in a particular gene natural selection could step in.

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

#60

Post by PaulHoule »

throwawaymaths wrote: post #57

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.
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