4 ms·

My favorite thing about mtDNA is that two separate genes overlap using separate reading frames. The end of one gene is the same as the start of another, and t

My favorite thing about mtDNA is that two separate genes overlap using separate reading frames. The end of one gene is the same as the start of another, and they are laid out in the circular mitochondrial genome to take advantage of this fact. I've also read that DNA chromosomes can under go conformal changes in response to the environment it's in, making certain reading frames more or less likely to be transcribed, which makes DNA something like an environmentally sensitive memory subsystem for RNA. Which I've always wondered if this mechanism is involved in how the homeobox genes work to alter genetic express across the "floor plan" of the body. Anyways, I guess all this means, to whatever extent you might be able to identify programming "constructs" within the system, the overall effects are going to be dominated by noise and emergent behaviors, and the overall mode of the system is one of "feedback control loops."

pyinstallwoes 3y ago
That reminds me of how the Vedas Sanskrit flows and also forms error-correction from verse to verse. The beginning is the end is the beginning.
6177c40f 3y ago
I think you'll find some of the tricks that (mostly) viruses use to be interesting. Take a look at ribosomal frameshifting [1], where the viral RNA has a special structure such that at a certain point during translation in the ribosome it will skip back 1 nucleotide (a -1 frameshift; -2 and +1 frameshifts have been observed as well, more rarely), thus changing the whole reading frame. Viruses use this to encode multiple protein products in a single strand of RNA, a sort of compression. But that's not all. Say that the amount of "0-frame" protein to "-1-frame" protein needs to be at a ratio of 20:1; then if the frameshift occurs with a probability of about 5% (i.e. 5% of the time that the viral RNA is translated), these protein products will then be produced in just the right ratio (this isn't a made up example either, see [2]). So not only does this trick allow for the RNA to be compressed, it also regulates protein expression. All with just one strand of RNA. [1] https://en.wikipedia.org/wiki/Ribosomal_frameshift https://en.wikipedia.org/wiki/Ribosomal_frameshift [2] https://en.wikipedia.org/wiki/HIV_ribosomal_frameshift_signal https://en.wikipedia.org/wiki/HIV_ribosomal_frameshift_signa...
- bglazer 3y ago
  Fuck that’s crazy. For the CS people who don’t understand what this means, a rough analogy is that HIV does something like steganography to encode two proteins in one gene.
  - dekhn 3y ago
    Evolution was done by Mel: http://www.catb.org/jargon/html/story-of-mel.html http://www.catb.org/jargon/html/story-of-mel.html
- pyinstallwoes 3y ago
  Quine based attack vectors on DNA platforms as a way to use the substrate as a reconfigurable bootloader through changing expected address. Virus.
dekhn 3y ago
overlapping genes show up all over the place and I think they contribute to lots of errors in papers. During my postdoc I analyzed the results from a yeast gene survey where the authors ignored genes overlapping and misannotated genes, imputing their function when really it was the overlapping gene. This is where I started to learn that "if it's in Nature, it's probably wrong"
moring 3y ago
You might find the coding for selenocysteine interesting: https://en.wikipedia.org/wiki/SECIS_element https://en.wikipedia.org/wiki/SECIS_element tl;dr: selenocysteine doesn't have a normal coding as a base triple, but as re-interpretation of a stop codon due to the information stored _after_ that stop codon that makes an RNA stick to itself during translation.
speps 3y ago
> The end of one gene is the same as the start of another Kind of like "de Bruijn sequences" which can be used to reduce the total length of brute force attacks on pins.
collyw 3y ago
Is that specific to mtDNA? From what I remember it isn't that uncommon. There are a lot of bits of DNA that work in both directions for different genes.Been a a couple of decades since I studied that though.

pyinstallwoes 3y ago

That reminds me of how the Vedas Sanskrit flows and also forms error-correction from verse to verse. The beginning is the end is the beginning.

6177c40f 3y ago

I think you'll find some of the tricks that (mostly) viruses use to be interesting. Take a look at ribosomal frameshifting [1], where the viral RNA has a special structure such that at a certain point during translation in the ribosome it will skip back 1 nucleotide (a -1 frameshift; -2 and +1 frameshifts have been observed as well, more rarely), thus changing the whole reading frame. Viruses use this to encode multiple protein products in a single strand of RNA, a sort of compression. But that's not all. Say that the amount of "0-frame" protein to "-1-frame" protein needs to be at a ratio of 20:1; then if the frameshift occurs with a probability of about 5% (i.e. 5% of the time that the viral RNA is translated), these protein products will then be produced in just the right ratio (this isn't a made up example either, see [2]). So not only does this trick allow for the RNA to be compressed, it also regulates protein expression. All with just one strand of RNA. [1] https://en.wikipedia.org/wiki/Ribosomal_frameshift https://en.wikipedia.org/wiki/Ribosomal_frameshift [2] https://en.wikipedia.org/wiki/HIV_ribosomal_frameshift_signal https://en.wikipedia.org/wiki/HIV_ribosomal_frameshift_signa...

bglazer 3y ago
Fuck that’s crazy. For the CS people who don’t understand what this means, a rough analogy is that HIV does something like steganography to encode two proteins in one gene.
- dekhn 3y ago
  Evolution was done by Mel: http://www.catb.org/jargon/html/story-of-mel.html http://www.catb.org/jargon/html/story-of-mel.html
pyinstallwoes 3y ago
Quine based attack vectors on DNA platforms as a way to use the substrate as a reconfigurable bootloader through changing expected address. Virus.

dekhn 3y ago

overlapping genes show up all over the place and I think they contribute to lots of errors in papers. During my postdoc I analyzed the results from a yeast gene survey where the authors ignored genes overlapping and misannotated genes, imputing their function when really it was the overlapping gene. This is where I started to learn that "if it's in Nature, it's probably wrong"

moring 3y ago

You might find the coding for selenocysteine interesting: https://en.wikipedia.org/wiki/SECIS_element https://en.wikipedia.org/wiki/SECIS_element tl;dr: selenocysteine doesn't have a normal coding as a base triple, but as re-interpretation of a stop codon due to the information stored _after_ that stop codon that makes an RNA stick to itself during translation.

speps 3y ago

> The end of one gene is the same as the start of another Kind of like "de Bruijn sequences" which can be used to reduce the total length of brute force attacks on pins.

collyw 3y ago

Is that specific to mtDNA? From what I remember it isn't that uncommon. There are a lot of bits of DNA that work in both directions for different genes.Been a a couple of decades since I studied that though.