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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

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 https://arxiv.org/pdf/q-bio/0605036.pdf for interesting thoughts. Remember, evolutionary biology is a field and people think about these questions!

idiotsecant 3y ago
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.
- hotstickyballs 3y ago
  If you iron man the argument then it’s an error correction argument in that this simple ecc method can be what favours a base-4 encoding instead
- t_serpico 3y ago
  How have I missed the point? The answer that nature cannot engineer and can't start de novo are trivially true statements that provide no actual insight into the question. I fully agree the original question itself is a deep one. A quick literature search is more productive than pontificating with weak analogies. See https://www.math.unl.edu/~bdeng1/Papers/DengDNAreplication.pdf https://www.math.unl.edu/~bdeng1/Papers/DengDNAreplication.p... for what seems to be an interesting analysis regarding base number and DNA replication rate.
  - usrbinbash 3y ago
    > that provide no actual insight into the question Mind elaborating on that? Because there is no biochemical reason why DNA could not have incorporated, say, a third pairing pair, so while base-3 (which I don't specifically mention in my post btw.) wouldn't work, base 6 or 8 would have been possible. "Unnatural Base Pairs" are even known to work in laboratory settings. There is also no biochemical reason why base2 life wouldn't work. Expand the reading frame of the translation machinery to 5 instead of three, and you have enough coding space for polypeptides. My answer adresses the question completely, because the only reason behind these "decisions" is an ancient system that simply got "frozen", and now cannot change any more.
    - sterlind 3y ago
      > 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 reason behind these "decisions" is an ancient system that simply got "frozen", and now cannot change any more. your answer is just a hypothesis, not a proof. these things can be studied (by studying abiogenesis in-vitro), and it's not certain these decisions were "flash frozen" like you describe. 2-, 4-, and 6- nucleotide coding systems might have coexisted in the RNA world, and 4- could have won out for some reason.
      - usrbinbash 3y ago
        > 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 DNA for transcription gets more difficult. > your answer is just a hypothesis, not a proof. My answer is what we observe in evolutionary biology. I have given an example outside of the molecular world for a reason. There is no real advantage to the inversion of the neural architecture in Chordata, it just didn't matter when the neural tube formation mechanisms came to be. Now, with mammals having huge brains and complex sensory organs, the warts in that design show. The proof for that is easy to come by, (also a reason btw. why the neural inversion is my favorite example for this): Look an any Protostomia. Their neural system isn't inverted. Consequently, Squids don't have a visual blind spot.
        sterlind 3y ago
        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.
usrbinbash 3y ago
> Base 3 wouldn’t work in that sense. 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.

idiotsecant 3y ago

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.

hotstickyballs 3y ago
If you iron man the argument then it’s an error correction argument in that this simple ecc method can be what favours a base-4 encoding instead
t_serpico 3y ago
How have I missed the point? The answer that nature cannot engineer and can't start de novo are trivially true statements that provide no actual insight into the question. I fully agree the original question itself is a deep one. A quick literature search is more productive than pontificating with weak analogies. See https://www.math.unl.edu/~bdeng1/Papers/DengDNAreplication.pdf https://www.math.unl.edu/~bdeng1/Papers/DengDNAreplication.p... for what seems to be an interesting analysis regarding base number and DNA replication rate.
- usrbinbash 3y ago
  > that provide no actual insight into the question Mind elaborating on that? Because there is no biochemical reason why DNA could not have incorporated, say, a third pairing pair, so while base-3 (which I don't specifically mention in my post btw.) wouldn't work, base 6 or 8 would have been possible. "Unnatural Base Pairs" are even known to work in laboratory settings. There is also no biochemical reason why base2 life wouldn't work. Expand the reading frame of the translation machinery to 5 instead of three, and you have enough coding space for polypeptides. My answer adresses the question completely, because the only reason behind these "decisions" is an ancient system that simply got "frozen", and now cannot change any more.
  - sterlind 3y ago
    > 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 reason behind these "decisions" is an ancient system that simply got "frozen", and now cannot change any more. your answer is just a hypothesis, not a proof. these things can be studied (by studying abiogenesis in-vitro), and it's not certain these decisions were "flash frozen" like you describe. 2-, 4-, and 6- nucleotide coding systems might have coexisted in the RNA world, and 4- could have won out for some reason.
    - usrbinbash 3y ago
      > 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 DNA for transcription gets more difficult. > your answer is just a hypothesis, not a proof. My answer is what we observe in evolutionary biology. I have given an example outside of the molecular world for a reason. There is no real advantage to the inversion of the neural architecture in Chordata, it just didn't matter when the neural tube formation mechanisms came to be. Now, with mammals having huge brains and complex sensory organs, the warts in that design show. The proof for that is easy to come by, (also a reason btw. why the neural inversion is my favorite example for this): Look an any Protostomia. Their neural system isn't inverted. Consequently, Squids don't have a visual blind spot.
      - sterlind 3y ago
        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.

usrbinbash 3y ago

> Base 3 wouldn’t work in that sense. 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.