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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

#121

Post by Llamamoe »

JumpCrisscross wrote: post #82
pythonguython wrote: post #61

Earlier quoted context omitted.

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

> If you had 80 nucleobases instead of 4, each base pair would contain far more information Which is a problem given DNA is a lossy format.

Strictly speaking, you could encode more error-correction bits into a higher nucleobase count but that'd pretty much require intelligent design, and wouldn't necessarily be viable for microorganisms to have that many proteins handling all the metabolic scaffolding.

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

#122

Post by sterlind »

usrbinbash wrote: post #116
sterlind wrote: post #89

Earlier quoted context omitted.

> 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…

your example of the blind spot is quite elegant and convincing. I think it's partly so convincing because there's a large fossil record and diverse phylogenetic tree, with many gaps covered. conversely, we're missing direct evidence for the pre-LUCA era, and what we have is bottlenecked. this makes me more skeptical.

for instance, I've seen arguments that the codon mapping, and even the particular set of protein- coding amino acids, that we ended up with was arbitrary, but I've also read papers arguing that the amino acids include a sort of spanning set of different structural scaffolds with different polarity that happen to mesh well with DNA, and that the particular choices of codons were influenced by how the RNA t-acyl transferases arose, etc.

so, I'm still unconvinced, but I find this area fascinating to read about.

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

#123

Post by usrbinbash »

function_seven wrote: post #101
usrbinbash wrote: post #51

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…

> (eg. our light sensitive cells point in the wrong direction) Can you expand on that? Are you talking about front-facing eyes vs. birds' eyes? Or something else like retinal structure?

https://en.wikipedia.org/wiki/Cephalopod_eye#/media/File:Evo...

Lefthand is a vertebrate eye, righthand is a squids eye.

In Vertebrates (really in all Chordata), the light sensitive "tips" of the sensory cells point inwards, aka. the exact wrong direction. At the base of the cells are the axons (nerve connections) which transmit the information into the brain.

Due to the aforementioned orientation, these axons run along the outer layer of our light sensitive cells, and at some point have to travel "invards" towards the brain. At that point there can be no cell bodies, and that's the "visual blind spot" of our eyes.

A squids eye doesn't have that problem; all the light sensitive cells point outwards, the axons are at the innermost layer, and connectivity can be achieved without a blind spot (also, they don't need a reflective layer).

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

#124

Post by usrbinbash »

dekhn wrote: post #107
metabagel wrote: post #105

Earlier quoted context omitted.

I had to look this up, and I guess what usrbinbash was referring to was the layout of the retina, which places the rods and cones behind layers of transparent neurons. https://en.wikipedia.org/wiki/Retina#/media/File:Retina-diag... Edit: ninja'd

Yet, it doesn't really have a strong impact as it's been determined that humans can see individual photons and we aren't dependant on night vision for hunting.

It doesn't have a strong impact, and the design also doesn't prevent good night vision (the basic structure of a cats eye is similiar, ALL chordata have an inverted neural makeup).

But that doesn't mean the setup makes sense, and that is exactly my point.

And long term, this has an impact. For example, vertebrate brain size is limited by the simple factor, that we have to put all the connections on the outside. The more neuronal bodies we have, the more connections they require.

    N  N
In this clumsy diagram, 2 neurons talk with the connections on the inside. However, vertebrate brains have to do this instead:

    +--------------+
    |              |
    +-> N      N
It's easy to see how the second setup becomes prohibitive when more Neurons are added to it. The brains of Protostomia again don't have that problem...they can have the connections on the inside, and the neuron bodies on the outside, aka. the logical setup.

Now there are ways around that, eg. Reptile and Bird brains grow in bulbs that theoretically allow sustained growth without the connective layer getting in the way. But similar to the reflective layer in our eyes, this is not a setup that's there because it makes a lot of sense...it's a hack, a workaround for some "legacy system", that is now so enmeshed, it's impossible to change.

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

#125

Post by pcrh »

inciampati wrote: post #114
pcrh wrote: post #39

Earlier quoted context omitted.

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.

There's a lot of redundancy and "archaic" DNA in most multicellular organisms. I imagine that over 50% of wikipedia would still be present after a million years.

The inserted wiki-DNA could also conceivably be constructed so as to ensure its own perpetuation.

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